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AB_310_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_3130_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_3130_X_L_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_3730_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_3730_X_L_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_5500_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_5500_XL_GENETIC_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_5500_XL_W_GENETIC_ANALYSIS_SYSTEM - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_SOLID_SYSTEM - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_SOLID_SYSTEM_2_0 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

AB_SOLID_SYSTEM_3_0 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ABI_SOLID - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

absolutePath(VersionedFileFields<Long>) - Method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener

Whenever a VersionedFileFields is loaded from the database, we need to translate it's path from a relative path to an absolute path based on the storage directory for the type.

AbsoluteToRelativePaths - Class in ca.corefacility.bioinformatics.irida.database.changesets

Custom SQL change converting absolute paths to relative in the database

AbsoluteToRelativePaths() - Constructor for class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

AbstractAnalysisSubmission - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Abstract superclass for analysis submissions.

AbstractAnalysisSubmission() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

AbstractExportModel - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models

Parent class of all export model to hold utility functions.

AbstractExportModel() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.AbstractExportModel

acceptsPairedSequenceFiles() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Whether or not this workflow accepts paired sequence files as input.

acceptsParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Determines if this workflow accepts parameters.

acceptsSingleSequenceFiles() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Whether or not this workflow accepts single sequence files as input.

activateAccount(String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetAjaxController

Activate the user account

activateAccount(String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPasswordResetService

Activate the user account

ActivitiesAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.activities

AJAX controller to handle actitivies

ActivitiesAjaxController(UIActivitiesService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.activities.ActivitiesAjaxController

Activity - Class in ca.corefacility.bioinformatics.irida.ria.web.activities.dto

Model for an Activity (Event).

Activity(Long, String, String, Date, List<ActivityItem>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

ActivityItem - Class in ca.corefacility.bioinformatics.irida.ria.web.activities.dto

Used to create either the subject or the predicate of an activity.

ActivityItem(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.ActivityItem

ActivityType - Enum in ca.corefacility.bioinformatics.irida.ria.web.activities

Define specific type activities.

add(SearchCriteria) - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.ProjectSampleJoinSpecification

Add a SearchCriteria

add(Iterable<Link>) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Adds all given Links to the resource.

add(Link) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Adds the given link to the resource.

add(Type) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

Add a new ResourceCollection to this collection.

addArgumentResolvers(List<HandlerMethodArgumentResolver>) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

addAssociatedProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController

Create a new associated project linkage

addAssociatedProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService

Create a new associated project linkage

addBaseDirectory(Class<?>, Path) - Static method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener

Add a base directory to safe files to

addChild(TreeNode<ValueType>) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Add a child to the children list

addId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.SubmissionIds

add an id to the submission ids

addInterceptors(InterceptorRegistry) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

additionalProperties(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the additionalProperties

addMemberToProject(Long, NewMemberRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Add a user to a project

addMemberToProject(Long, NewMemberRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Add a user to a project

addMemberToUserGroup(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Add a new member to the user group

addMemberToUserGroup(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Add a new member to the user group

addNewAssemblyToSample(Long, MultipartFile, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

Upload a new GenomeAssembly and add it to a Sample

addNewFast5FileToSample(Long, MultipartFile, SequenceFileResource, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REST function to add new Fast5 object to a sample

addNewSequenceFilePairToSample(Long, MultipartFile, SequenceFileResource, MultipartFile, SequenceFileResource, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Add a pair of SequenceFiles to a Sample

addNewSequenceFileToSample(Long, MultipartFile, SequenceFileResource, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Add a new SequenceFile to a Sample.

addNotification(Notification) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse

Add a new notification to the response

addOptionalProperty(String, String) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

Add one optional property to the map of properties

addOptionalProperty(String, String) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Add one optional property to the map of properties

addParameter(String, String, String) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy

Adds a new parameter name/value mapping for Galaxy.

addProjectSettings(Project) - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

Enhance the QCEntry with a Project if required.

addProjectSettings(Project) - Method in class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

Enhance the QCEntry with a Project if required.

addProjectSettings(Project) - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

Enhance the QCEntry with a Project if required.

addProjectSubscriptionForProjectAndUser(Project, User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Create a new project subscription associated with a Project and User.

addProjectSubscriptionForProjectAndUser(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService

Create a new project subscription associated with a Project and User.

addProperty(String, Object) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Add a property to the tree node

addProperty(String, Object) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

Add a property to the map

addProperty(String, Object) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

Add an additional map property to be serialized to JSON

addReferenceFileToProject(Project, ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Add a ReferenceFile to a Project.

addReferenceFileToProject(Project, ReferenceFile) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Add a ReferenceFile to a Project.

addReferenceFileToProject(Long, List<MultipartFile>, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController

Add a new reference file to a project.

addReferenceFileToProject(Long, List<MultipartFile>, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService

Add a new reference file to a project.

addRelatedProject(Project, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Add a related Project to the given Project

addRelatedProject(Project, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Add a related Project to the given Project

addResourceHandlers(ResourceHandlerRegistry) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

addSample(Sample, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Add a sample to the cart

addSampleGenomeAssemblyJoin(SampleGenomeAssemblyJoin) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

Add a sample to this assembly

addSampleMetadata(Long, AddSampleMetadataRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Add a metadata field and entry to Sample

addSampleMetadata(Long, AddSampleMetadataRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Add metadata for the sample

addSampleMetadata(Long, Map<String, MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

Add select new metadata fields to the Sample.

AddSampleMetadataRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to handle requests from the UI to add a sample metadata.

AddSampleMetadataRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

AddSampleMetadataRequest(Long, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

AddSampleMetadataResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to handle responses to the UI to add a piece of sample metadata.

AddSampleMetadataResponse(Long, String, String, Long, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

addSamplesToCart(AddToCartRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Add a set of samples to the cart from a particular project

addSamplesToCart(AddToCartRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Add samples from a project to the cart.

addSampleToProject(Project, Sample, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Add the specified Sample to the Project.

addSampleToProject(Project, Sample, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Add the specified Sample to the Project.

addSampleToProject(Long, Sample, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Create a new sample resource and create a relationship between the sample and the project.

addSequenceFilesToSequencingRun(Long, Map<String, String>, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunSequenceFilesController

Add a relationship between a SequencingRun and a SequenceFile.

addSequencingObjectLinks(T, Long) - Static method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Add the links for a SequencingObject to its sample, self, to each individual SequenceFile

addSequencingObjectToSequencingRun(SequencingRun, SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

Create a join between a SequencingObject to a SequencingRun

addSequencingObjectToSequencingRun(SequencingRun, SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingRunService

Create a join between a SequencingObject to a SequencingRun

AddToCartRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

Request sent from the UI to add Samples from a Project to the cart.

AddToCartRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

AddToCartRequest(Long, List<Long>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

addUserGroupToProject(Project, UserGroup, ProjectRole, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Add the specified UserGroup to the Project with a Role .

addUserGroupToProject(Project, UserGroup, ProjectRole, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Add the specified UserGroup to the Project with a Role .

addUserGroupToProject(Long, NewMemberRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Add a user group to the current project

addUserGroupToProject(Long, NewMemberRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Add a UserGroup to the current Project

addUserToGroup(User, UserGroup, UserGroupJoin.UserGroupRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Add a user to the group with the specified role.

addUserToGroup(User, UserGroup, UserGroupJoin.UserGroupRole) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Add a user to the group with the specified role.

addUserToProject(Project, User, ProjectRole, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Add the specified User to the Project with a Role .

addUserToProject(Project, User, ProjectRole, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Add the specified User to the Project with a Role .

addUserToProject(Long, Map<String, String>, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Add a relationship between a Project and a User.

addViewControllers(ViewControllerRegistry) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

adminAccessAllowed(Authentication, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission

Check whether admins should be quick-approved for this permission.

adminAccessAllowed(Authentication, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.RepositoryBackedPermission

Check whether admins should be quick-approved for this permission.

AdminBaseController - Class in ca.corefacility.bioinformatics.irida.ria.web.admin

Admin Panel Page Controller

AdminBaseController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminBaseController

adminNewPasswordReset(Long, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Create a new PasswordReset for the given User

adminNewPasswordReset(Long, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Create a new PasswordReset for the given User

AdminStatisticsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.admin

Controller to handle ajax requests for the Admin Panel statistics page.

AdminStatisticsAjaxController(UIAdminStatisticsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

AdminUsersTableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

This overrides the default TableRequest for the administrators users table to allow for custom handling of setting the sort column since several columns do not directly match up.

AdminUsersTableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.AdminUsersTableRequest

AgGridColumn - Class in ca.corefacility.bioinformatics.irida.ria.web.components.agGrid

AgGrid column is used to represent a generic AgGrid Column

AgGridColumn() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

AgGridColumn(String, String, String, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

Create a column header for a UI Ag Grid instance

AjaxCreateItemSuccessResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

UI Response for successfully creating an item.

AjaxCreateItemSuccessResponse(long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxCreateItemSuccessResponse

AjaxErrorResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

Response returned if there is an error creating a new item in IRIDA.

AjaxErrorResponse(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxErrorResponse

AjaxFormErrorResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

AJAX response to return form errors to the client

AjaxFormErrorResponse(Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxFormErrorResponse

ajaxGetAnalysisInputFiles(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get analysis input files and their sizes

ajaxGetDataForDetailsTab(Long, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get analysis details

ajaxGetJobErrors(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get a dto with list of JobError for an AnalysisSubmission under key `galaxyJobErrors` and the `galaxyUrl` for the galaxy instance

AjaxItemNotFoundException - Error in ca.corefacility.bioinformatics.irida.ria.web.errors

Error thrown if an item is not found on an Ajax Request

AjaxItemNotFoundException(String) - Constructor for error ca.corefacility.bioinformatics.irida.ria.web.errors.AjaxItemNotFoundException

AjaxResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

Generic parent response type for AJAX requests.

AjaxResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse

AjaxSuccessResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

Response returned if an upload of an item is successful.

AjaxSuccessResponse(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxSuccessResponse

ajaxUpdateEmailPipelineResult(AnalysisEmailPipelineResult, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Update an analysis email pipeline completion result

AjaxUpdateItemSuccessResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

UI Response for successfully updating an item.

AjaxUpdateItemSuccessResponse(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxUpdateItemSuccessResponse

ajaxUpdateSubmission(AnalysisSubmissionInfo, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Update an analysis name and/or priority

ALL_METADATA_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

allowRoleChange(UserGroup, UserGroupJoin.UserGroupRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Check to see if changing the role will change the number of group owners to 0.

ALWAYS_CLEANUP - Static variable in interface ca.corefacility.bioinformatics.irida.service.CleanupAnalysisSubmissionCondition

Condition which always cleans up analysis submissions.

AMPLICON - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

AnalysesFilters - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Represents the filters on the Analyses Table.

AnalysesFilters() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

AnalysesListRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used to handle a UI Request for the Analyses Page.

AnalysesListRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesListRequest

AnalysesOutputsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.analyses

Controller for handling all ajax requests for Single Sample Analyses Outputs.

AnalysesOutputsAjaxController(UIAnalysesOutputsService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

AnalysesTableAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis

Controller to handle ajax requests for the Analyses table

AnalysesTableAjaxController(AnalysisSubmissionService, AnalysisTypesService, ProjectService, IridaWorkflowsService, MessageSource, UpdateAnalysisSubmissionPermission, AnalysisAudit, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Analysis - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

An analysis object for storing results of an analysis execution.

Analysis() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

For hibernate

Analysis(String, String, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Builds a new Analysis object with the given information and an empty set of output files.

Analysis(String, Map<String, AnalysisOutputFile>, AnalysisType) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Builds a new Analysis object with the given information.

Analysis(String, Map<String, AnalysisOutputFile>, String, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Builds a new Analysis object with the given information.

ANALYSIS_EXECUTION_ASPECT_ORDER - Static variable in class ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect

Defines the order for the AnalysisExecutionServiceAspect.

ANALYSIS_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

ANALYSIS_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

ANALYSIS_TYPES - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

AnalysisAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis

Controller for individual Analysis ajax requests (details page, analysis outputs, project analysis outputs)

AnalysisAjaxController(AnalysisSubmissionService, IridaWorkflowsService, UserService, SampleService, ProjectService, UpdateAnalysisSubmissionPermission, MetadataTemplateService, SequencingObjectService, AnalysisSubmissionSampleProcessor, MessageSource, ExecutionManagerConfig, AnalysisAudit, AnalysisTypesService, EmailController, UpdateSamplePermission) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

AnalysisAlreadySetException - Exception in ca.corefacility.bioinformatics.irida.exceptions

This exception is thrown when AnalysisSubmission.setAnalysis(Analysis) is called, but the instance of AnalysisSubmission already has a non-null instance of an Analysis assigned to it.

AnalysisAlreadySetException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.AnalysisAlreadySetException

Create a new instance of AnalysisAlreadySetException.

AnalysisAudit - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing

This class component is used for auditing AnalysisSubmission.

AnalysisAudit(AnalysisSubmissionRepository) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit

AnalysisCleanedState - Enum in ca.corefacility.bioinformatics.irida.model.enums

Defines the state for cleaning up intermediate files of an analysis.

analysisCollectionServiceGalaxy() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisCollectionServiceGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

A service for constructing dataset collections of input files for workflows in galaxy.

AnalysisCollectionServiceGalaxy(GalaxyHistoriesService) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisCollectionServiceGalaxy

Builds a new AnalysisCollectionServiceGalaxy with the given information.

AnalysisController - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis

Controller for Analysis.

AnalysisController(AnalysisSubmissionService, IridaWorkflowsService, UserService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

analysisDescription - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

analysisDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets the description of the analysis run

AnalysisDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating analysis details

AnalysisDetails() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

AnalysisDetails(String, String, String, String, Long, Date, AnalysisSubmission.Priority[], boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

AnalysisEmailPipelineResult - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a request to update if a user should receive email an email upon completion or error..

AnalysisEmailPipelineResult() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

AnalysisEmailPipelineResult(Long, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

analysisExecutionScheduledTask() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Creates a new bean with a AnalysisExecutionScheduledTask for performing the analysis tasks.

AnalysisExecutionScheduledTask - Interface in ca.corefacility.bioinformatics.irida.service

A service for executing AnalysisSubmission tasks.

AnalysisExecutionScheduledTaskImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Implementation of analysis execution tasks.

AnalysisExecutionScheduledTaskImpl(AnalysisSubmissionRepository, AnalysisExecutionService, CleanupAnalysisSubmissionCondition, GalaxyJobErrorsService, JobErrorRepository, EmailController, AnalysisWorkspaceService) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Builds a new AnalysisExecutionScheduledTaskImpl with the given service classes.

analysisExecutionService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisExecutionService - Interface in ca.corefacility.bioinformatics.irida.service.analysis.execution

Service for submission of AnalysisSubmissions to an execution manager.

analysisExecutionServiceAspect(AnalysisSubmissionRepository, EmailController) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig

AnalysisExecutionServiceAspect - Class in ca.corefacility.bioinformatics.irida.service.analysis.execution

Switches an AnalysisSubmission to an error state on an exception when being submitted for analysis.

AnalysisExecutionServiceAspect(AnalysisSubmissionRepository, EmailController) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect

AnalysisExecutionServiceConfig - Class in ca.corefacility.bioinformatics.irida.config.analysis

Configuration for an AnalysisExecutionService class.

AnalysisExecutionServiceConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisExecutionServiceGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy

Service for performing analyses within a Galaxy execution manager.

AnalysisExecutionServiceGalaxy(AnalysisSubmissionService, GalaxyHistoriesService, AnalysisExecutionServiceGalaxyAsync, AnalysisExecutionServiceGalaxyCleanupAsync) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Builds a new AnalysisExecutionServiceGalaxy with the given information.

analysisExecutionServiceGalaxyAsync() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisExecutionServiceGalaxyAsync - Class in ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy

Service for executing AnalysisSubmission stages within a Galaxy execution manager asynchronously.

AnalysisExecutionServiceGalaxyAsync(AnalysisSubmissionService, AnalysisService, GalaxyWorkflowService, AnalysisWorkspaceServiceGalaxy, IridaWorkflowsService, AnalysisSubmissionSampleProcessor) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

Builds a new AnalysisExecutionServiceGalaxyAsync with the given information.

analysisExecutionServiceGalaxyCleanupAsync() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisExecutionServiceGalaxyCleanupAsync - Class in ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy

Service for cleaning up an AnalysisSubmission within a Galaxy execution manager asynchronously.

AnalysisExecutionServiceGalaxyCleanupAsync(AnalysisSubmissionService, GalaxyWorkflowService, GalaxyHistoriesService, GalaxyLibrariesService) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyCleanupAsync

Builds a new AnalysisExecutionServiceGalaxyCleanupAsync with the given information.

AnalysisFastQC - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

Specific implementation of Analysis for storing properties created by FastQC.

AnalysisFastQC() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

Required for hibernate, should not be used anywhere else, so private.

AnalysisFastQC(AnalysisFastQC.AnalysisFastQCBuilder) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

AnalysisFastQC.AnalysisFastQCBuilder - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

Builder for creating instances of AnalysisFastQC.

AnalysisFastQCBuilder() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Create an instance of AnalysisFastQCBuilder,

AnalysisInfo - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used by UI to encapsulate analysis information

AnalysisInfo(AnalysisSubmission, String, AnalysisState, String, String, boolean, boolean, AnalysisState, Long, boolean, boolean, boolean, List<AnalysisSampleProject>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

AnalysisInputFiles - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating analysis input files data which includes the samples, reads, and reference file if it was required by workflow

AnalysisInputFiles() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

AnalysisInputFiles(List<AnalysisSamples>, List<AnalysisSingleEndSamples>, ReferenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

AnalysisJobError - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating galaxy job errors, the url of the galaxy instance, and the galaxy history id.

AnalysisJobError() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

AnalysisJobError(List<JobError>, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

AnalysisModel - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used to represent an AnalysisSubmission for consumption by the user interface.

AnalysisModel(AnalysisSubmission, AnalysisStateModel, Long, String, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

AnalysisOutputFile - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

Store file references to files produced by a workflow execution that we otherwise don't want to parse metadata from.

AnalysisOutputFile(Path, String, String, ToolExecution) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

Create a new instance of AnalysisOutputFile.

AnalysisOutputFileDownloadManager - Class in ca.corefacility.bioinformatics.irida.ria.web.components

This Spring Bean stores a temporary selection of ProjectSampleAnalysisOutputInfo and AnalysisOutputFile for batch download of the selected files.

AnalysisOutputFileDownloadManager(AnalysisSubmissionService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager

AnalysisOutputFileInfo - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

DTO for AnalysisOutputFile text contents

AnalysisOutputFileInfo() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

AnalysisOutputFileInfo(Long, Long, Long, String, String, Long, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

AnalysisOutputFileRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis

A custom repository for managing AnalysisOutputFile objects.

AnalysisOutputFileRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.analysis

Custom implementation of FilesystemSupplementedRepositoryImpl for AnalysisOutputFile.

AnalysisOutputFileRepositoryImpl(EntityManager, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepositoryImpl

AnalysisParameterService<WorkflowInputsType extends WorkflowInputsGeneric> - Interface in ca.corefacility.bioinformatics.irida.service.analysis.workspace

A service for setting up parameters for an analysis.

AnalysisParameterServiceGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

A Galaxy implementation for preparing parameters for an analysis.

AnalysisParameterServiceGalaxy() - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisParameterServiceGalaxy

AnalysisProjectShare - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Represents the update for sharing an analysis with a project.

AnalysisProjectShare() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

AnalysisProjectShare(Long, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

AnalysisProvenanceResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating the file provenance

AnalysisProvenanceResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

AnalysisProvenanceResponse(String, AnalysisToolExecution) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

analysisProvenanceService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisProvenanceServiceGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

A class used to collect provenance data from Galaxy that corresponds to a specific output file generated by an analysis submission.

AnalysisProvenanceServiceGalaxy(GalaxyHistoriesService, ToolsClient, JobsClient) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisProvenanceServiceGalaxy

AnalysisRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis

A custom repository for managing Analysis objects.

AnalysisSampleProject - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used to return a sample linked to a project to the UI.

AnalysisSampleProject(Long, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject

AnalysisSamples - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating analysis paired end sample data

AnalysisSamples() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

AnalysisSamples(String, Long, Long, SequenceFile, SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

AnalysisSampleUpdater - Interface in ca.corefacility.bioinformatics.irida.pipeline.results.updater

A service for updating samples with results from a particular Analysis type.

AnalysisScheduledTaskConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Scheduled task configuration for running analysis pipelines

AnalysisScheduledTaskConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

AnalysisService - Interface in ca.corefacility.bioinformatics.irida.service

Service for managing objects of type Analysis.

AnalysisServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Implementation of AnalysisService.

AnalysisServiceImpl(AnalysisRepository, AnalysisOutputFileRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.AnalysisServiceImpl

AnalysisServiceStatus(Long, Long) - Constructor for class ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService.AnalysisServiceStatus

AnalysisSingleEndSamples - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating analysis single end sample data

AnalysisSingleEndSamples() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

AnalysisSingleEndSamples(String, Long, Long, SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

AnalysisSistrResults - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating a SISTR result object as well as the sample name and if there was a parsing error

AnalysisSistrResults() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

AnalysisSistrResults(String, Boolean, SistrResult) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

AnalysisState - Enum in ca.corefacility.bioinformatics.irida.model.enums

Defines a set of states for an AnalysisSubmission.

AnalysisStateModel - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

UI Representation of an Analysis Submission state.

AnalysisStateModel(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisStateModel

AnalysisSubmission - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Defines a submission to an AnalysisService for executing a remote workflow.

AnalysisSubmission() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

AnalysisSubmission(AnalysisSubmission.Builder) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Builds a new AnalysisSubmission with the given AnalysisSubmission.Builder.

AnalysisSubmission.Builder - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Used to build up an AnalysisSubmission.

AnalysisSubmission.Priority - Enum in ca.corefacility.bioinformatics.irida.model.workflow.submission

Enum encoding the priority of analysis submissions

analysisSubmissionCleanupService(AnalysisSubmissionRepository, UserService) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

AnalysisSubmissionCleanupService - Interface in ca.corefacility.bioinformatics.irida.service

A service for cleaning up certain aspects of AnalysisSubmissions.

AnalysisSubmissionCleanupServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.analysis.submission

Implementation for a service to cleanup inconsistencies with AnalysisSubmissions.

AnalysisSubmissionCleanupServiceImpl(AnalysisSubmissionRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionCleanupServiceImpl

Builds a new AnalysisSubmissionCleanupServiceImpl with the given information.

AnalysisSubmissionInfo - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a request to update the analysis name and/or priority.

AnalysisSubmissionInfo() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

AnalysisSubmissionInfo(Long, String, AnalysisSubmission.Priority) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

AnalysisSubmissionRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

A repository for managing AnalysisSubmission objects.

AnalysisSubmissionRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

Interface for methods using native SQL queries to get AnalysisOutputFile info for Project and User

AnalysisSubmissionRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

Implementation of AnalysisSubmissionRepositoryCustom with methods using native SQL queries to get AnalysisOutputFile info for Project and User

AnalysisSubmissionRepositoryImpl(DataSource, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryImpl

analysisSubmissionSampleProcessor() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisSubmissionSampleProcessor - Interface in ca.corefacility.bioinformatics.irida.pipeline.results

Updates samples from an AnalysisSubmission with results from the analysis.

AnalysisSubmissionSampleProcessorImpl - Class in ca.corefacility.bioinformatics.irida.pipeline.results.impl

Updates samples from an AnalysisSubmission with results from the analysis.

AnalysisSubmissionSampleProcessorImpl(SampleRepository, List<AnalysisSampleUpdater>) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl

Builds a new AnalysisSubmissionSampleProcessorImpl.

AnalysisSubmissionService - Interface in ca.corefacility.bioinformatics.irida.service

A service for AnalysisSubmissions.

AnalysisSubmissionService.AnalysisServiceStatus - Class in ca.corefacility.bioinformatics.irida.service

Class to store the number of running and queued analyses

AnalysisSubmissionServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.analysis.submission

Implementation of an AnalysisSubmissionService.

AnalysisSubmissionServiceImpl(AnalysisSubmissionRepository, AnalysisSubmissionTemplateRepository, UserRepository, ReferenceFileRepository, SequencingObjectService, GalaxyHistoriesService, ProjectAnalysisSubmissionJoinRepository, JobErrorRepository, IridaWorkflowsService, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Builds a new AnalysisSubmissionServiceImpl with the given information.

AnalysisSubmissionSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification for searching AnalysisSubmission properties

AnalysisSubmissionSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.AnalysisSubmissionSpecification

AnalysisSubmissionTemplate - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Shell for an analysis template to be submitted automatically when data is uploaded to a project.

AnalysisSubmissionTemplate() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

AnalysisSubmissionTemplate(String, UUID, IridaWorkflowNamedParameters, ReferenceFile, boolean, String, boolean, boolean, Project) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

AnalysisSubmissionTemplate(String, UUID, Map<String, String>, ReferenceFile, boolean, String, boolean, boolean, Project) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

AnalysisSubmissionTemplateRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

Repository for storing and retrieving AnalysisSubmissionTemplates

analysisTaskExecutor(UserService) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

Builds a new Executor for analysis tasks.

AnalysisTemplate - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto

Response class for easily formatting analysis templates for the project settings page

AnalysisTemplate(Long, String, String, boolean, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

AnalysisToolExecution - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating the tools used in the provenance as well as the execution parameters for these tools

AnalysisToolExecution() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

AnalysisToolExecution(String, ArrayList<AnalysisToolExecutionParameters>, ArrayList<AnalysisToolExecution>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

AnalysisToolExecutionParameters - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating tool execution parameters

AnalysisToolExecutionParameters() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

AnalysisToolExecutionParameters(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

AnalysisTreeResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating a newick string and an optional server message.

AnalysisTreeResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

AnalysisTreeResponse(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

AnalysisType - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis.type

Defines a particular type of Analysis available in IRIDA.

AnalysisType() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

AnalysisType(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

Creates a new AnalysisType with the given type.

AnalysisTypeModel - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

UI Representation of an Analysis Type

AnalysisTypeModel(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTypeModel

AnalysisTypeSet - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config

A class wrapping around AnalysisType to contain them in a set for Spring configuration.

AnalysisTypeSet() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config.AnalysisTypeSet

Builds an empty AnalysisTypeSet.

AnalysisTypeSet(Set<AnalysisType>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config.AnalysisTypeSet

Builds a new AnalysisTypeSet of AnalysisTypes.

analysisTypesService() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaAnalysisTypesServiceConfig

Builds a new bean for a AnalysisTypesService to handle registered AnalysisTypes.

AnalysisTypesService - Interface in ca.corefacility.bioinformatics.irida.service

A service for managing registered AnalysisTypes.

AnalysisTypesServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

A service for managing registered AnalysisTypes.

AnalysisTypesServiceImpl() - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Builds a new default AnalysisTypesServiceImpl.

analysisWorkspaceService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

AnalysisWorkspaceService - Interface in ca.corefacility.bioinformatics.irida.service.analysis.workspace

Defines a service used to perform the tasks for execution of a workflow.

AnalysisWorkspaceServiceGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

A service for performing tasks for analysis in Galaxy.

AnalysisWorkspaceServiceGalaxy(GalaxyHistoriesService, GalaxyWorkflowService, GalaxyLibrariesService, IridaWorkflowsService, AnalysisCollectionServiceGalaxy, AnalysisProvenanceServiceGalaxy, AnalysisParameterServiceGalaxy, SequencingObjectService) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy

Builds a new AnalysisWorkspaceServiceGalaxy with the given information.

analyticsHandlerInterceptor() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

AnalyticsHandlerInterceptor - Class in ca.corefacility.bioinformatics.irida.ria.config

Interceptor to add analytics to every page.

AnalyticsHandlerInterceptor(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.AnalyticsHandlerInterceptor

Announcement - Class in ca.corefacility.bioinformatics.irida.model.announcements

An announcement object.

Announcement(String, String, boolean, User) - Constructor for class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

Create a new Announcement object, for display on the front page.

Announcement(String, String, boolean, User, Date) - Constructor for class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

Create a new Announcement object with a created date, for testing purposes.

AnnouncementAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements

Controller for all ajax requests from the UI for announcements.

AnnouncementAjaxController(UIAnnouncementsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

AnnouncementRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for managing Announcements

AnnouncementRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements.dto

Data transfer object for requesting information about an announcement.

AnnouncementRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

AnnouncementsController - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements

Controller for handling Announcement views

AnnouncementsController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementsController

AnnouncementService - Interface in ca.corefacility.bioinformatics.irida.service

AnnouncementServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service for managing @{link Announcements}

AnnouncementServiceImpl(AnnouncementRepository, AnnouncementUserJoinRepository, UserRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

AnnouncementSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

A specification for searching for Announcements

AnnouncementSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.AnnouncementSpecification

AnnouncementTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements.dto

User interface model for administration of Announcement

AnnouncementTableModel(Announcement) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel

AnnouncementUserJoin - Class in ca.corefacility.bioinformatics.irida.model.announcements

AnnouncementUserJoin object This is created whenever a User has confirmed that they have read an Announcement

AnnouncementUserJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

AnnouncementUserJoin(Announcement, User) - Constructor for class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

AnnouncementUserJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.announcement

Repository for managing AnnouncementUserJoins

AnnouncementUserReadDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements.dto

Data transfer object for retrieving announcement details from a sql query.

AnnouncementUserReadDetails(Long, String, boolean, Date, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

AnnouncementUserTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.announcements.dto

User interface model for viewing Announcement

AnnouncementUserTableModel(User, AnnouncementUserJoin) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserTableModel

AntPagination - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Class to represent a page request in a AntD Table Request.

AntPagination(int, int) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntPagination

AntSearch - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Class to represent a single column search in a AntD Table Request.

AntSearch() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSearch

AntSort - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Class to represent a single column sort in a AntD Table Request.

AntSort(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSort

AntTableItem - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Base class to be used to represent a row in a AntD table.

AntTableItem(Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableItem

AntTableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Table request for an Ant Design UI Table

AntTableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

AntTableResponse<T extends AntTableItem> - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Base class to be used to represent a single page in a AntD table.

AntTableResponse(List<T>, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse

apiViewResolver(ContentNegotiationManager) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

appendToFile(Path, SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenator

Append a SequenceFile to a Path on the filesystem

ApplicationContextAwareSpringLiquibase(ApplicationContext) - Constructor for class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase

ApplicationContextSpringResourceOpener(ResourceLoader) - Constructor for class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase.ApplicationContextSpringResourceOpener

ASSEMBLY_ANNOTATION - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

ASSEMBLY_ANNOTATION_COLLECTION - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

assemblyFileBaseDirectory() - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

AssemblySampleUpdater - Class in ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl

Updates a sample with the results from a genome assembly.

AssemblySampleUpdater(SampleGenomeAssemblyJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.AssemblySampleUpdater

AssociatedProject - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto

Representation of an Associated Project for the project associated projects page.

AssociatedProject(Project, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

ASYNC_ORDER - Static variable in class ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

The order for asynchronous tasks.

ATTACHMENT_FILENAME - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

attributes - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

Attributes on the Sample

auditReader(EntityManagerFactory) - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig

authenticate(HttpSession, RemoteAPI, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

Begin authentication procedure by redirecting to remote authorization location

authenticate(Authentication) - Method in class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationProvider

authenticationManager() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

authenticationProvider() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

authorizationConsentService(JdbcTemplate, RegisteredClientRepository) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

AuthorizationServerConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

authorizationServerSecurityFilterChain(HttpSecurity) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

authorizationService(JdbcTemplate, RegisteredClientRepository) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

automated(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets whether this pipeline is being run as part of an automated process

AutomatedAnalysisFileProcessor - Class in ca.corefacility.bioinformatics.irida.processing.impl

File processor used to launch an automated analysis for uploaded data.

AutomatedAnalysisFileProcessor(SampleSequencingObjectJoinRepository, ProjectSampleJoinRepository, AnalysisSubmissionRepository, AnalysisSubmissionTemplateRepository, ProjectAnalysisSubmissionJoinRepository, IridaWorkflowsService, SequencingObjectRepository, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.AutomatedAnalysisFileProcessor

AutomatedAnalysisToTemplate - Class in ca.corefacility.bioinformatics.irida.database.changesets

Liquibase update to convert the project settings for automated Assembly and SISTR checkboxes to analysis templates.

AutomatedAnalysisToTemplate() - Constructor for class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

AutomatedSISTRUpdate - Class in ca.corefacility.bioinformatics.irida.database.changesets

Class to translate automated SISTR analyses into metadata entries for associated samples.

AutomatedSISTRUpdate() - Constructor for class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

B

BASE_URL - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.PipelineController

BaseController - Class in ca.corefacility.bioinformatics.irida.ria.web

Base class for controllers so that they all can have access to common functionality.

BaseController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.BaseController

BaseModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models

Base for UI models

BaseModel(Long, String, Date, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

BasePermission<DomainObjectType> - Interface in ca.corefacility.bioinformatics.irida.security.permissions

Root interface for any permissions being built within IRIDA.

BasicStatsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics

UI Response to to encapsulate basic usage statistics.

BasicStatsResponse(Long, List<GenericStatModel>, List<GenericStatModel>, List<GenericStatModel>, List<GenericStatModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

BGISEQ - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

BGISEQ_500 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

BIO_HANSEL - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

BioHanselSampleUpdater - Class in ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl

AnalysisSampleUpdater for bio_hansel results to be written to metadata of Samples.

BioHanselSampleUpdater(MetadataTemplateService, SampleService) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.BioHanselSampleUpdater

BioJavaSequenceFileUtilitiesImpl - Class in ca.corefacility.bioinformatics.irida.service.util.impl

Sequence file utilities class using BioJava for calculation

BioJavaSequenceFileUtilitiesImpl() - Constructor for class ca.corefacility.bioinformatics.irida.service.util.impl.BioJavaSequenceFileUtilitiesImpl

bioSample(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

BioSample identifier for these files

BISULFITE_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

BLOCKLIST - Static variable in class ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName.ValidProjectNameBlocklist

BLOCKLIST - Static variable in class ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName.ValidSampleNameBlocklist

breadCrumbInterceptor() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

BreadCrumbInterceptor - Class in ca.corefacility.bioinformatics.irida.ria.config

Interceptor for handling UI BreadCrumbs

BreadCrumbInterceptor() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.BreadCrumbInterceptor

Constructor

BreadCrumbInterceptor(ProjectService, SampleService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.BreadCrumbInterceptor

build() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Build an instance of NcbiBioSampleFiles

build() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Build an AnalysisFastQC with the currently set parameters

build() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder

Builds a new GalaxyWorkflowStatus from the underlying history details.

build() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Build the analysis submission from the set parameters

buildEmptyLibrary(GalaxyProjectName) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

Builds a new empty library with the given name.

builder() - Static method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

get an AnalysisFastQCBuilder

builder(HistoryDetails) - Static method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Constructs a new GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder.

builder(UUID) - Static method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Gets a AnalysisSubmission.Builder.

Builder() - Constructor for class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Builder(AnalysisSubmissionTemplate) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Create a new AnalysisSubmission.Builder from the given AnalysisSubmissionTemplate

Builder(UUID) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Creates a new AnalysisSubmission.Builder with a workflow id.

buildToolExecutionForOutputFile(String, String) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisProvenanceServiceGalaxy

Build up a provenance report for a specific file that's attached to the outputs of an analysis submission.

BuiltInAnalysisTypes - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis.type

Stores a number of constants for individual AnalysisTypes.

BuiltInAnalysisTypes() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

BYTES_PER_GB - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

BYTES_PER_KB - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

BYTES_PER_MB - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

C

ca.corefacility.bioinformatics.irida - package ca.corefacility.bioinformatics.irida

ca.corefacility.bioinformatics.irida.config.analysis - package ca.corefacility.bioinformatics.irida.config.analysis

ca.corefacility.bioinformatics.irida.config.data - package ca.corefacility.bioinformatics.irida.config.data

ca.corefacility.bioinformatics.irida.config.environment - package ca.corefacility.bioinformatics.irida.config.environment

ca.corefacility.bioinformatics.irida.config.repository - package ca.corefacility.bioinformatics.irida.config.repository

ca.corefacility.bioinformatics.irida.config.security - package ca.corefacility.bioinformatics.irida.config.security

ca.corefacility.bioinformatics.irida.config.services - package ca.corefacility.bioinformatics.irida.config.services

ca.corefacility.bioinformatics.irida.config.services.scheduled - package ca.corefacility.bioinformatics.irida.config.services.scheduled

ca.corefacility.bioinformatics.irida.config.web - package ca.corefacility.bioinformatics.irida.config.web

ca.corefacility.bioinformatics.irida.config.workflow - package ca.corefacility.bioinformatics.irida.config.workflow

ca.corefacility.bioinformatics.irida.constraints - package ca.corefacility.bioinformatics.irida.constraints

ca.corefacility.bioinformatics.irida.constraints.impl - package ca.corefacility.bioinformatics.irida.constraints.impl

ca.corefacility.bioinformatics.irida.database.changesets - package ca.corefacility.bioinformatics.irida.database.changesets

ca.corefacility.bioinformatics.irida.events - package ca.corefacility.bioinformatics.irida.events

ca.corefacility.bioinformatics.irida.events.annotations - package ca.corefacility.bioinformatics.irida.events.annotations

ca.corefacility.bioinformatics.irida.exceptions - package ca.corefacility.bioinformatics.irida.exceptions

ca.corefacility.bioinformatics.irida.exceptions.galaxy - package ca.corefacility.bioinformatics.irida.exceptions.galaxy

ca.corefacility.bioinformatics.irida.exceptions.pipelines - package ca.corefacility.bioinformatics.irida.exceptions.pipelines

ca.corefacility.bioinformatics.irida.jackson2.mixin - package ca.corefacility.bioinformatics.irida.jackson2.mixin

ca.corefacility.bioinformatics.irida.model - package ca.corefacility.bioinformatics.irida.model

ca.corefacility.bioinformatics.irida.model.announcements - package ca.corefacility.bioinformatics.irida.model.announcements

ca.corefacility.bioinformatics.irida.model.assembly - package ca.corefacility.bioinformatics.irida.model.assembly

ca.corefacility.bioinformatics.irida.model.enums - package ca.corefacility.bioinformatics.irida.model.enums

ca.corefacility.bioinformatics.irida.model.event - package ca.corefacility.bioinformatics.irida.model.event

ca.corefacility.bioinformatics.irida.model.export - package ca.corefacility.bioinformatics.irida.model.export

ca.corefacility.bioinformatics.irida.model.irida - package ca.corefacility.bioinformatics.irida.model.irida

ca.corefacility.bioinformatics.irida.model.joins - package ca.corefacility.bioinformatics.irida.model.joins

ca.corefacility.bioinformatics.irida.model.joins.impl - package ca.corefacility.bioinformatics.irida.model.joins.impl

ca.corefacility.bioinformatics.irida.model.project - package ca.corefacility.bioinformatics.irida.model.project

ca.corefacility.bioinformatics.irida.model.remote - package ca.corefacility.bioinformatics.irida.model.remote

ca.corefacility.bioinformatics.irida.model.remote.resource - package ca.corefacility.bioinformatics.irida.model.remote.resource

ca.corefacility.bioinformatics.irida.model.run - package ca.corefacility.bioinformatics.irida.model.run

ca.corefacility.bioinformatics.irida.model.sample - package ca.corefacility.bioinformatics.irida.model.sample

ca.corefacility.bioinformatics.irida.model.sample.metadata - package ca.corefacility.bioinformatics.irida.model.sample.metadata

ca.corefacility.bioinformatics.irida.model.sequenceFile - package ca.corefacility.bioinformatics.irida.model.sequenceFile

ca.corefacility.bioinformatics.irida.model.subscription - package ca.corefacility.bioinformatics.irida.model.subscription

ca.corefacility.bioinformatics.irida.model.upload - package ca.corefacility.bioinformatics.irida.model.upload

ca.corefacility.bioinformatics.irida.model.upload.galaxy - package ca.corefacility.bioinformatics.irida.model.upload.galaxy

ca.corefacility.bioinformatics.irida.model.user - package ca.corefacility.bioinformatics.irida.model.user

ca.corefacility.bioinformatics.irida.model.user.group - package ca.corefacility.bioinformatics.irida.model.user.group

ca.corefacility.bioinformatics.irida.model.workflow - package ca.corefacility.bioinformatics.irida.model.workflow

ca.corefacility.bioinformatics.irida.model.workflow.analysis - package ca.corefacility.bioinformatics.irida.model.workflow.analysis

ca.corefacility.bioinformatics.irida.model.workflow.analysis.type - package ca.corefacility.bioinformatics.irida.model.workflow.analysis.type

ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config - package ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config

ca.corefacility.bioinformatics.irida.model.workflow.config - package ca.corefacility.bioinformatics.irida.model.workflow.config

ca.corefacility.bioinformatics.irida.model.workflow.description - package ca.corefacility.bioinformatics.irida.model.workflow.description

ca.corefacility.bioinformatics.irida.model.workflow.execution - package ca.corefacility.bioinformatics.irida.model.workflow.execution

ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy - package ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

ca.corefacility.bioinformatics.irida.model.workflow.manager - package ca.corefacility.bioinformatics.irida.model.workflow.manager

ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy - package ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy

ca.corefacility.bioinformatics.irida.model.workflow.structure - package ca.corefacility.bioinformatics.irida.model.workflow.structure

ca.corefacility.bioinformatics.irida.model.workflow.submission - package ca.corefacility.bioinformatics.irida.model.workflow.submission

ca.corefacility.bioinformatics.irida.oauth2 - package ca.corefacility.bioinformatics.irida.oauth2

ca.corefacility.bioinformatics.irida.pipeline.results - package ca.corefacility.bioinformatics.irida.pipeline.results

ca.corefacility.bioinformatics.irida.pipeline.results.impl - package ca.corefacility.bioinformatics.irida.pipeline.results.impl

ca.corefacility.bioinformatics.irida.pipeline.results.updater - package ca.corefacility.bioinformatics.irida.pipeline.results.updater

ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl - package ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl

ca.corefacility.bioinformatics.irida.pipeline.upload - package ca.corefacility.bioinformatics.irida.pipeline.upload

ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy - package ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

ca.corefacility.bioinformatics.irida.plugins - package ca.corefacility.bioinformatics.irida.plugins

ca.corefacility.bioinformatics.irida.processing - package ca.corefacility.bioinformatics.irida.processing

ca.corefacility.bioinformatics.irida.processing.concatenate - package ca.corefacility.bioinformatics.irida.processing.concatenate

ca.corefacility.bioinformatics.irida.processing.concatenate.impl - package ca.corefacility.bioinformatics.irida.processing.concatenate.impl

ca.corefacility.bioinformatics.irida.processing.impl - package ca.corefacility.bioinformatics.irida.processing.impl

ca.corefacility.bioinformatics.irida.repositories - package ca.corefacility.bioinformatics.irida.repositories

ca.corefacility.bioinformatics.irida.repositories.analysis - package ca.corefacility.bioinformatics.irida.repositories.analysis

ca.corefacility.bioinformatics.irida.repositories.analysis.submission - package ca.corefacility.bioinformatics.irida.repositories.analysis.submission

ca.corefacility.bioinformatics.irida.repositories.assembly - package ca.corefacility.bioinformatics.irida.repositories.assembly

ca.corefacility.bioinformatics.irida.repositories.filesystem - package ca.corefacility.bioinformatics.irida.repositories.filesystem

ca.corefacility.bioinformatics.irida.repositories.joins.announcement - package ca.corefacility.bioinformatics.irida.repositories.joins.announcement

ca.corefacility.bioinformatics.irida.repositories.joins.project - package ca.corefacility.bioinformatics.irida.repositories.joins.project

ca.corefacility.bioinformatics.irida.repositories.joins.sample - package ca.corefacility.bioinformatics.irida.repositories.joins.sample

ca.corefacility.bioinformatics.irida.repositories.referencefile - package ca.corefacility.bioinformatics.irida.repositories.referencefile

ca.corefacility.bioinformatics.irida.repositories.relational.auditing - package ca.corefacility.bioinformatics.irida.repositories.relational.auditing

ca.corefacility.bioinformatics.irida.repositories.remote - package ca.corefacility.bioinformatics.irida.repositories.remote

ca.corefacility.bioinformatics.irida.repositories.remote.impl - package ca.corefacility.bioinformatics.irida.repositories.remote.impl

ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate - package ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate

ca.corefacility.bioinformatics.irida.repositories.sample - package ca.corefacility.bioinformatics.irida.repositories.sample

ca.corefacility.bioinformatics.irida.repositories.sequencefile - package ca.corefacility.bioinformatics.irida.repositories.sequencefile

ca.corefacility.bioinformatics.irida.repositories.specification - package ca.corefacility.bioinformatics.irida.repositories.specification

ca.corefacility.bioinformatics.irida.repositories.user - package ca.corefacility.bioinformatics.irida.repositories.user

ca.corefacility.bioinformatics.irida.ria.config - package ca.corefacility.bioinformatics.irida.ria.config

ca.corefacility.bioinformatics.irida.ria.config.filters - package ca.corefacility.bioinformatics.irida.ria.config.filters

ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker - package ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker

ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor - package ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor

ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util - package ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

ca.corefacility.bioinformatics.irida.ria.security - package ca.corefacility.bioinformatics.irida.ria.security

ca.corefacility.bioinformatics.irida.ria.utilities - package ca.corefacility.bioinformatics.irida.ria.utilities

ca.corefacility.bioinformatics.irida.ria.utilities.components - package ca.corefacility.bioinformatics.irida.ria.utilities.components

ca.corefacility.bioinformatics.irida.ria.utilities.converters - package ca.corefacility.bioinformatics.irida.ria.utilities.converters

ca.corefacility.bioinformatics.irida.ria.web - package ca.corefacility.bioinformatics.irida.ria.web

ca.corefacility.bioinformatics.irida.ria.web.activities - package ca.corefacility.bioinformatics.irida.ria.web.activities

ca.corefacility.bioinformatics.irida.ria.web.activities.dto - package ca.corefacility.bioinformatics.irida.ria.web.activities.dto

ca.corefacility.bioinformatics.irida.ria.web.admin - package ca.corefacility.bioinformatics.irida.ria.web.admin

ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics - package ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics

ca.corefacility.bioinformatics.irida.ria.web.ajax - package ca.corefacility.bioinformatics.irida.ria.web.ajax

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui - package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui

ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata - package ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata

ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto - package ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto

ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies - package ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies

ca.corefacility.bioinformatics.irida.ria.web.ajax.projects - package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects

ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto - package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto

ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings - package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings

ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto - package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto

ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions - package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions

ca.corefacility.bioinformatics.irida.ria.web.ajax.users - package ca.corefacility.bioinformatics.irida.ria.web.ajax.users

ca.corefacility.bioinformatics.irida.ria.web.analyses - package ca.corefacility.bioinformatics.irida.ria.web.analyses

ca.corefacility.bioinformatics.irida.ria.web.analysis - package ca.corefacility.bioinformatics.irida.ria.web.analysis

ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing - package ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing

ca.corefacility.bioinformatics.irida.ria.web.analysis.dto - package ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

ca.corefacility.bioinformatics.irida.ria.web.announcements - package ca.corefacility.bioinformatics.irida.ria.web.announcements

ca.corefacility.bioinformatics.irida.ria.web.announcements.dto - package ca.corefacility.bioinformatics.irida.ria.web.announcements.dto

ca.corefacility.bioinformatics.irida.ria.web.cart - package ca.corefacility.bioinformatics.irida.ria.web.cart

ca.corefacility.bioinformatics.irida.ria.web.cart.dto - package ca.corefacility.bioinformatics.irida.ria.web.cart.dto

ca.corefacility.bioinformatics.irida.ria.web.components - package ca.corefacility.bioinformatics.irida.ria.web.components

ca.corefacility.bioinformatics.irida.ria.web.components.agGrid - package ca.corefacility.bioinformatics.irida.ria.web.components.agGrid

ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification - package ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

ca.corefacility.bioinformatics.irida.ria.web.components.ant.table - package ca.corefacility.bioinformatics.irida.ria.web.components.ant.table

ca.corefacility.bioinformatics.irida.ria.web.components.datatables - package ca.corefacility.bioinformatics.irida.ria.web.components.datatables

ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config - package ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config

ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export - package ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export

ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models - package ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models

ca.corefacility.bioinformatics.irida.ria.web.dto - package ca.corefacility.bioinformatics.irida.ria.web.dto

ca.corefacility.bioinformatics.irida.ria.web.dto.list - package ca.corefacility.bioinformatics.irida.ria.web.dto.list

ca.corefacility.bioinformatics.irida.ria.web.errors - package ca.corefacility.bioinformatics.irida.ria.web.errors

ca.corefacility.bioinformatics.irida.ria.web.exceptions - package ca.corefacility.bioinformatics.irida.ria.web.exceptions

ca.corefacility.bioinformatics.irida.ria.web.files - package ca.corefacility.bioinformatics.irida.ria.web.files

ca.corefacility.bioinformatics.irida.ria.web.files.dto - package ca.corefacility.bioinformatics.irida.ria.web.files.dto

ca.corefacility.bioinformatics.irida.ria.web.launchPipeline - package ca.corefacility.bioinformatics.irida.ria.web.launchPipeline

ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos - package ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos

ca.corefacility.bioinformatics.irida.ria.web.linelist - package ca.corefacility.bioinformatics.irida.ria.web.linelist

ca.corefacility.bioinformatics.irida.ria.web.linelist.dto - package ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

ca.corefacility.bioinformatics.irida.ria.web.login - package ca.corefacility.bioinformatics.irida.ria.web.login

ca.corefacility.bioinformatics.irida.ria.web.models - package ca.corefacility.bioinformatics.irida.ria.web.models

ca.corefacility.bioinformatics.irida.ria.web.models.datatables - package ca.corefacility.bioinformatics.irida.ria.web.models.datatables

ca.corefacility.bioinformatics.irida.ria.web.models.export - package ca.corefacility.bioinformatics.irida.ria.web.models.export

ca.corefacility.bioinformatics.irida.ria.web.models.project - package ca.corefacility.bioinformatics.irida.ria.web.models.project

ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile - package ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile

ca.corefacility.bioinformatics.irida.ria.web.models.tables - package ca.corefacility.bioinformatics.irida.ria.web.models.tables

ca.corefacility.bioinformatics.irida.ria.web.models.user - package ca.corefacility.bioinformatics.irida.ria.web.models.user

ca.corefacility.bioinformatics.irida.ria.web.oauth - package ca.corefacility.bioinformatics.irida.ria.web.oauth

ca.corefacility.bioinformatics.irida.ria.web.pipelines - package ca.corefacility.bioinformatics.irida.ria.web.pipelines

ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto - package ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto

ca.corefacility.bioinformatics.irida.ria.web.projects - package ca.corefacility.bioinformatics.irida.ria.web.projects

ca.corefacility.bioinformatics.irida.ria.web.projects.dto - package ca.corefacility.bioinformatics.irida.ria.web.projects.dto

ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples - package ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

ca.corefacility.bioinformatics.irida.ria.web.projects.error - package ca.corefacility.bioinformatics.irida.ria.web.projects.error

ca.corefacility.bioinformatics.irida.ria.web.projects.metadata - package ca.corefacility.bioinformatics.irida.ria.web.projects.metadata

ca.corefacility.bioinformatics.irida.ria.web.projects.settings - package ca.corefacility.bioinformatics.irida.ria.web.projects.settings

ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto - package ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto

ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto - package ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto

ca.corefacility.bioinformatics.irida.ria.web.samples - package ca.corefacility.bioinformatics.irida.ria.web.samples

ca.corefacility.bioinformatics.irida.ria.web.samples.dto - package ca.corefacility.bioinformatics.irida.ria.web.samples.dto

ca.corefacility.bioinformatics.irida.ria.web.search - package ca.corefacility.bioinformatics.irida.ria.web.search

ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns - package ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns

ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto - package ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto

ca.corefacility.bioinformatics.irida.ria.web.services - package ca.corefacility.bioinformatics.irida.ria.web.services

ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs - package ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs

ca.corefacility.bioinformatics.irida.ria.web.settings - package ca.corefacility.bioinformatics.irida.ria.web.settings

ca.corefacility.bioinformatics.irida.ria.web.settings.dto - package ca.corefacility.bioinformatics.irida.ria.web.settings.dto

ca.corefacility.bioinformatics.irida.ria.web.users - package ca.corefacility.bioinformatics.irida.ria.web.users

ca.corefacility.bioinformatics.irida.ria.web.users.dto - package ca.corefacility.bioinformatics.irida.ria.web.users.dto

ca.corefacility.bioinformatics.irida.ria.web.utilities - package ca.corefacility.bioinformatics.irida.ria.web.utilities

ca.corefacility.bioinformatics.irida.security - package ca.corefacility.bioinformatics.irida.security

ca.corefacility.bioinformatics.irida.security.permissions - package ca.corefacility.bioinformatics.irida.security.permissions

ca.corefacility.bioinformatics.irida.security.permissions.analysis - package ca.corefacility.bioinformatics.irida.security.permissions.analysis

ca.corefacility.bioinformatics.irida.security.permissions.files - package ca.corefacility.bioinformatics.irida.security.permissions.files

ca.corefacility.bioinformatics.irida.security.permissions.metadata - package ca.corefacility.bioinformatics.irida.security.permissions.metadata

ca.corefacility.bioinformatics.irida.security.permissions.project - package ca.corefacility.bioinformatics.irida.security.permissions.project

ca.corefacility.bioinformatics.irida.security.permissions.sample - package ca.corefacility.bioinformatics.irida.security.permissions.sample

ca.corefacility.bioinformatics.irida.security.permissions.user - package ca.corefacility.bioinformatics.irida.security.permissions.user

ca.corefacility.bioinformatics.irida.service - package ca.corefacility.bioinformatics.irida.service

ca.corefacility.bioinformatics.irida.service.analysis.annotations - package ca.corefacility.bioinformatics.irida.service.analysis.annotations

ca.corefacility.bioinformatics.irida.service.analysis.execution - package ca.corefacility.bioinformatics.irida.service.analysis.execution

ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy - package ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy

ca.corefacility.bioinformatics.irida.service.analysis.workspace - package ca.corefacility.bioinformatics.irida.service.analysis.workspace

ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy - package ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

ca.corefacility.bioinformatics.irida.service.export - package ca.corefacility.bioinformatics.irida.service.export

ca.corefacility.bioinformatics.irida.service.impl - package ca.corefacility.bioinformatics.irida.service.impl

ca.corefacility.bioinformatics.irida.service.impl.analysis.submission - package ca.corefacility.bioinformatics.irida.service.impl.analysis.submission

ca.corefacility.bioinformatics.irida.service.impl.export - package ca.corefacility.bioinformatics.irida.service.impl.export

ca.corefacility.bioinformatics.irida.service.impl.processor - package ca.corefacility.bioinformatics.irida.service.impl.processor

ca.corefacility.bioinformatics.irida.service.impl.sample - package ca.corefacility.bioinformatics.irida.service.impl.sample

ca.corefacility.bioinformatics.irida.service.impl.user - package ca.corefacility.bioinformatics.irida.service.impl.user

ca.corefacility.bioinformatics.irida.service.impl.workflow - package ca.corefacility.bioinformatics.irida.service.impl.workflow

ca.corefacility.bioinformatics.irida.service.remote - package ca.corefacility.bioinformatics.irida.service.remote

ca.corefacility.bioinformatics.irida.service.remote.impl - package ca.corefacility.bioinformatics.irida.service.remote.impl

ca.corefacility.bioinformatics.irida.service.sample - package ca.corefacility.bioinformatics.irida.service.sample

ca.corefacility.bioinformatics.irida.service.user - package ca.corefacility.bioinformatics.irida.service.user

ca.corefacility.bioinformatics.irida.service.util - package ca.corefacility.bioinformatics.irida.service.util

ca.corefacility.bioinformatics.irida.service.util.impl - package ca.corefacility.bioinformatics.irida.service.util.impl

ca.corefacility.bioinformatics.irida.service.workflow - package ca.corefacility.bioinformatics.irida.service.workflow

ca.corefacility.bioinformatics.irida.util - package ca.corefacility.bioinformatics.irida.util

ca.corefacility.bioinformatics.irida.validators - package ca.corefacility.bioinformatics.irida.validators

ca.corefacility.bioinformatics.irida.validators.annotations - package ca.corefacility.bioinformatics.irida.validators.annotations

ca.corefacility.bioinformatics.irida.validators.annotations.validators - package ca.corefacility.bioinformatics.irida.validators.annotations.validators

ca.corefacility.bioinformatics.irida.validators.groups - package ca.corefacility.bioinformatics.irida.validators.groups

ca.corefacility.bioinformatics.irida.web.assembler.resource - package ca.corefacility.bioinformatics.irida.web.assembler.resource

ca.corefacility.bioinformatics.irida.web.assembler.resource.sample - package ca.corefacility.bioinformatics.irida.web.assembler.resource.sample

ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile - package ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile

ca.corefacility.bioinformatics.irida.web.controller.api - package ca.corefacility.bioinformatics.irida.web.controller.api

ca.corefacility.bioinformatics.irida.web.controller.api.exception - package ca.corefacility.bioinformatics.irida.web.controller.api.exception

ca.corefacility.bioinformatics.irida.web.controller.api.json - package ca.corefacility.bioinformatics.irida.web.controller.api.json

ca.corefacility.bioinformatics.irida.web.controller.api.projects - package ca.corefacility.bioinformatics.irida.web.controller.api.projects

ca.corefacility.bioinformatics.irida.web.controller.api.samples - package ca.corefacility.bioinformatics.irida.web.controller.api.samples

ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun - package ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun

ca.corefacility.bioinformatics.irida.web.filter - package ca.corefacility.bioinformatics.irida.web.filter

ca.corefacility.bioinformatics.irida.web.spring.view - package ca.corefacility.bioinformatics.irida.web.spring.view

CAGE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

calculateCoverageForSamplesInProject(Project, List<Long>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Calculate the coverage for a list of Samples within a Project.

canRead(Class<?>, MediaType) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

canUpdateRemoteObject(Object, Authentication) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission

Check if the given object is a remote object, and if so if the authentication is a ProjectSynchronizationAuthenticationToken object

canWrite(Class<?>, MediaType) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

CAPILLARY - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

cart() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

Cart - Class in ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs

Session object to hold samples that are currently in the cart.

Cart() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

CartAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.cart

AJAX controller for cart functionality

CartAjaxController(UICartService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

CartController - Class in ca.corefacility.bioinformatics.irida.ria.web.cart

Controller managing interactions with the selected sequences

CartController(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.CartController

CartGalaxyController - Class in ca.corefacility.bioinformatics.irida.ria.web.cart

Controller to handle all ajax requests made to the cart that have to do with Galaxy.

CartGalaxyController(UICartService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.CartGalaxyController

CartProjectModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart

Model for UI to represent a project and its sample within the cart.

CartProjectModel(Long, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel

CartProjectSample - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

Data transfer object for getting the samples that are in the cart and their relevant project identifier

CartProjectSample(Sample, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample

CartSampleModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used to represent a Sample on the UI Cart Page.

CartSampleModel(Sample, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CartSampleModel

CartSampleRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

Object to handle samples that have been sent to the server to be added to the cart.

CartSampleRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

CartSampleRequest(Long, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

CartSamplesByUserPermissions - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

Data transfer object for getting the samples that are in the cart.

CartSamplesByUserPermissions(List<CartProjectSample>, List<CartProjectSample>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSamplesByUserPermissions

CartUpdateResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

Return value for adding samples to the samples cart.

CartUpdateResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse

CDNA - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

CFH - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

CFM - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

CFS - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

CFT - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

changePassword(Long, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Change the password on the User account.

changePassword(Long, String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Change the password on the User account.

changeUserGroupRole(User, UserGroup, UserGroupJoin.UserGroupRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Change the role for the User in the UserGroup.

changeUserGroupRole(User, UserGroup, UserGroupJoin.UserGroupRole) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Change the role for the User in the UserGroup.

changeUserPassword(Long, String, String, Principal, HttpServletRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Change the password of a user

changeUserPassword(Long, String, String, Principal, HttpServletRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Change the password for a user

check(UserDetails) - Method in class ca.corefacility.bioinformatics.irida.security.IridaPostAuthenicationChecker

check(UserDetails) - Method in class ca.corefacility.bioinformatics.irida.security.PasswordExpiryChecker

Checks if the given UserDetails password has expired.

checkAPIStatus(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Check the status of a RemoteAPI

checkAPIStatus(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Check the currently logged in user's OAuth2 connection status to a given API

checkNullDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.AbstractExportModel

Check if a date is null.

checkNullId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.AbstractExportModel

Check if the ID of the object is null.

checkNullStrings(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.AbstractExportModel

Check if a string is null or empty.

ChecksumFileProcessor - Class in ca.corefacility.bioinformatics.irida.processing.impl

FileProcessor used to calculate a checksum using sha256 for uploaded SequenceFiles

ChecksumFileProcessor(SequenceFileRepository) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.ChecksumFileProcessor

CHIP - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

CHIPSEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

classLoaderTemplateResolver() - Method in class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig

Configure the template resolver

CLEANED - ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

Set when an analysis is finished being cleaned.

CLEANING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

Indicates this analysis is in the process of being cleaned.

CLEANING_ERROR - ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

Indicates that there was an error while cleaning a submission.

cleanupAnalysisSubmissionCondition() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Builds a condition object defining the conditions under which an analysis submission should be cleaned up.

CleanupAnalysisSubmissionCondition - Interface in ca.corefacility.bioinformatics.irida.service

Defines an interface for a condition on whether or not to clean up an AnalysisSubmission.

CleanupAnalysisSubmissionConditionAge - Class in ca.corefacility.bioinformatics.irida.service.impl.analysis.submission

A condition used to cleanup an AnalysisSubmission if it is too old.

CleanupAnalysisSubmissionConditionAge(Duration) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.CleanupAnalysisSubmissionConditionAge

Constructs a new CleanupAnalysisSubmissionConditionAge with the given time before cleanup.

cleanupAnalysisSubmissions() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any completed or error submissions and clean up results from the execution manager.

cleanupAnalysisSubmissions() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through any completed or errored AnalysisSubmissions and delete intermediate files in the execution manager.

cleanupAnalysisSubmissions() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through any completed or errored AnalysisSubmissions and delete intermediate files in the execution manager.

cleanupSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Cleans up any intermediate files in the execution manager for this submission.

cleanupSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Cleans up any intermediate files in the execution manager for this submission.

cleanupSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyCleanupAsync

Cleans up any intermediate files from this AnalysisSubmission in the execution manager.

clearProjectSampleMetadata(HttpSession, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

Clear any uploaded sample metadata stored into the session.

clearProjectSampleMetadata(HttpSession, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

Clear any uploaded sample metadata stored into the session.

CLIENT_ID_CONSTRAINT_NAME - Static variable in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

CLIENTS_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

ClientsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax

Controller to handle ajax request for IRIDA Clients.

ClientsAjaxController(UIClientService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

ClientTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients

Used to represent an IridaClientDetails in an ant.design table on the Clients page.

ClientTableModel(IridaClientDetails, int) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableModel

ClientTableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients

UI request for client details for the clients table.

ClientTableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableRequest

CLONE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

CLONEEND - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

code - Variable in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

compareTo(Announcement) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

compareTo(AnnouncementUserJoin) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

compareTo(Project) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

compareTo(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

compareTo(SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

compareTo(Sample) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

compareTo(OverrepresentedSequence) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

compareTo(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

compareTo(PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

compareTo(User) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

compareTo(JobError) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

compareTo(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

compareTo(AnalysisSubmissionTemplate) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

compareTo(AnnouncementUserReadDetails) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

compareTo(SequenceFileDetails) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

COMPLETE - ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

COMPLETED - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that has completed and been loaded into IRIDA.

completedSuccessfully() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Whether or not this workflow has completed successfully.

COMPLETING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that is complete but data needs to be transferred back into IRIDA.

ConcatenateException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when there's an issue with a SequencingObjectConcatenator

ConcatenateException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException

ConcatenateException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException

concatenateFiles(List<? extends SequencingObject>, String) - Method in class ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SequenceFilePairConcatenator

Concatenate a set of SequencingObjects of a given type

concatenateFiles(List<? extends SequencingObject>, String) - Method in class ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SingleEndSequenceFileConcatenator

Concatenate a set of SequencingObjects of a given type

concatenateFiles(List<? extends SequencingObject>, String) - Method in class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenator

Concatenate a set of SequencingObjects of a given type

concatenateSequenceFiles(Long, Set<Long>, String, boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Concatenate a collection of SequencingObjects

concatenateSequenceFiles(Long, Set<Long>, String, boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Concatenate a collection of SequencingObjects

concatenateSequences(List<SequencingObject>, String, Sample, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Concatenate a collection of SequencingObjects and save back to a Sample

concatenateSequences(List<SequencingObject>, String, Sample, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Concatenate a collection of SequencingObjects and save back to a Sample

ConfigurableJavaMailSenderImpl() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSenderImpl

configure(SpringApplicationBuilder) - Method in class ca.corefacility.bioinformatics.irida.ServletInitializer

configure(AuthenticationManagerBuilder) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

configureContentNegotiation(ContentNegotiationConfigurer) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

configureTasks(ScheduledTaskRegistrar) - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.IridaScheduledTasksConfig

connectToAPI(Long, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

Initiate a token request on a remote api if one does not yet exist.

consent(Principal, Map<String, Object>, String, String, String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTOAuthAuthorizationConsentController

Basic authorization consent controller for OAuth2

constructCollection(CollectionDescription, History) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Builds a new Dataset Collection given the description of this collection.

constructCollectionResourceLinks(ResourceCollection<SequencingRun>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Get custom links to the ResourceCollection being called by RESTGenericController.listAllResources().

constructCollectionResourceLinks(ResourceCollection<AnalysisSubmission>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get custom links to the ResourceCollection being called by RESTGenericController.listAllResources().

constructCollectionResourceLinks(ResourceCollection<Type>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Get custom links to the ResourceCollection being called by RESTGenericController.listAllResources().

constructCustomResourceLinks(Project) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

The RESTProjectsController should tell the client how to find the users for a specific Project.

constructCustomResourceLinks(User) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

A collection of custom links for a specific User.

constructCustomResourceLinks(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Construct a collection of Links for a specific resource.

constructCustomResourceLinks(Type) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Construct a collection of Links for a specific resource.

CONTENT_DISPOSITION - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

CONTENT_TYPE_APPLICATION_ZIP - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

CONTENT_TYPE_TEXT - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

ControllerExceptionHandler - Class in ca.corefacility.bioinformatics.irida.web.controller.api.exception

Globally handles exceptions thrown by controllers.

ControllerExceptionHandler() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

convert(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

Converts a file length property (bytes) to kilobytes.

convert(HttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationConverter

convertMetadataStringsToSet(Map<String, MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get the appropriate MetadataTemplateFields and MetadataEntrys for a given map of Strings

convertMetadataStringsToSet(Map<String, MetadataEntry>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get the appropriate MetadataTemplateFields and MetadataEntrys for a given map of Strings

convertToDatabaseColumn(Path) - Method in class ca.corefacility.bioinformatics.irida.model.PathConverter

convertToEntityAttribute(String) - Method in class ca.corefacility.bioinformatics.irida.model.PathConverter

copySampleToProject(Long, List<Long>, boolean, HttpServletResponse, Locale) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Copy an existing sample to a project.

count() - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

How many entities of Type exist in the database?

count() - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

How many entities of Type exist in the database?

count() - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

How many entities of Type exist in the database?

count() - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

How many entities of Type exist in the database?

count() - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

How many entities of Type exist in the database?

countActiveTokensForClient(IridaClientDetails) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Get the number of all tokens defined for a given IridaClientDetails that are valid and not expired.

countActiveTokensForClient(IridaClientDetails) - Method in interface ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService

Get the number of all tokens defined for a given IridaClientDetails that are valid and not expired.

countAnalysesRanByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the count of AnalysisSubmissions ran by user

countAnalysesRanGrouped(Date, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get a list of GenericStatModels for analyses ran in past n time period grouped by format provided.

countAnalysesRanInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the count of AnalysisSubmissions run in time period

countByAnalysisState(Collection<AnalysisState>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the analysis submissions that are currently in the given list of states

countProjectsCreatedGrouped(Date, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Get a list of GenericStatModels for projects created in the past n time period and grouped by the format provided.

countProjectsCreatedInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Get a count of all Projects created within time period

countReadsForAllAnnouncements() - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a map where the keys are Announcements and the values are Integers representing the number of Users who have read that announcement.

countReadsForAllAnnouncements() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a map where the keys are Announcements and the values are Integers representing the number of Users who have read that announcement.

countReadsForOneAnnouncement(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a count of the number of Users who have read Announcement

countReadsForOneAnnouncement(Announcement) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a count of the number of Users who have read Announcement

countSamplesCreatedGrouped(Date, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get a list of GenericStatModels for samples created in the past n time period and grouped by the format provided.

countSamplesCreatedInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get a count of all Samples created within time period

countSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Count the number of Samples in a given Project.

countSequenceFileLengthInBases(Path) - Method in class ca.corefacility.bioinformatics.irida.service.util.impl.BioJavaSequenceFileUtilitiesImpl

Calculate the length of a sequence file in bases

countSequenceFileLengthInBases(Path) - Method in interface ca.corefacility.bioinformatics.irida.service.util.SequenceFileUtilities

Calculate the length of a sequence file in bases

countTokensForClient(IridaClientDetails) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Get the number of tokens issued for a given IridaClientDetails

countTokensForClient(IridaClientDetails) - Method in interface ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService

Get the number of tokens issued for a given IridaClientDetails

countUsersCreatedGrouped(Date, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepository

Get a list of GenericStatModels for users created in the n time period grouped by the format provided.

countUsersCreatedInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepository

Get a count of all Users created within time period

countUsersForAnnouncement(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Count how many Users have read a specific Announcement

countUsersForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get the number of Users in a given Project

countUsersForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Count the number of Users in a given Project

countUsersForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Count the number of Users in a given Project

countUsersLoggedInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepository

Get a count of all Users logged in within time period

Coverage - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto

UI Model for the minimum and maximum coverage and genome size for a project

Coverage() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

Coverage(int, int, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

COVERAGE - ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryType

CoverageFileProcessor - Class in ca.corefacility.bioinformatics.irida.processing.impl

FileProcessor used to calculate coverage of a SequencingObject for a Projects

CoverageFileProcessor(QCEntryRepository, AnalysisRepository) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.CoverageFileProcessor

CoverageQCEntry - Class in ca.corefacility.bioinformatics.irida.model.sample

a QCEntry relating to the coverage of a sequence

CoverageQCEntry() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

CoverageQCEntry(SequencingObject, long) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

create(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Create a new object in the persistence store.

create(PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

create(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Create a new object in the persistence store.

create(Announcement) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Create a new object in the persistence store.

create(IridaClientDetails) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Create a new object in the persistence store.

create(NcbiExportSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Create a new object in the persistence store.

create(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Create a new object in the persistence store.

create(Project, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Create a new instance of Type in the database, then respond to the client with the location of the resource.

create(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl

Create a new object in the persistence store.

create(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

Create a new object in the persistence store.

create(RemoteAPIToken) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Add a token to the store for a given service

create(RemoteAPIToken) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService

Add a token to the store for a given service

create(SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

create(SequencingRun, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Create a new instance of Type in the database, then respond to the client with the location of the resource.

create(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Create a new object in the persistence store.

create(UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Create a new object in the persistence store.

create(User, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Create a new instance of Type in the database, then respond to the client with the location of the resource.

create(Analysis) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisServiceImpl

Create a new object in the persistence store.

create(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Create a new object in the persistence store.

create(AnalysisSubmission, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Create a new instance of Type in the database, then respond to the client with the location of the resource.

create(IridaWorkflowNamedParameters) - Method in class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

Create a new object in the persistence store.

create(Type) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Create a new object in the persistence store.

create(Type, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Create a new instance of Type in the database, then respond to the client with the location of the resource.

create(ValueType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Create a new object in the persistence store.

createAnalysisOutputFileZippedResponse(HttpServletResponse, String, Set<AnalysisOutputFile>) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Utility method for download a zip file containing all output files from an analysis.

createAndSendNewPasswordResetEmail(String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetAjaxController

Create a password reset for the given email address or username

createAndSendNewPasswordResetEmail(String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPasswordResetService

Create a password reset for the given email address or username

createAssemblyInSample(Sample, GenomeAssembly) - Method in interface ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService

Create a new GenomeAssembly in the given Sample

createAssemblyInSample(Sample, GenomeAssembly) - Method in class ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

Create a new GenomeAssembly in the given Sample

createAuthentication(HttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.web.filter.UnauthenticatedAnonymousAuthenticationFilter

Create the anonymous auth token with Authenticated set to false

createBatchAnalysisOutputFileZippedResponse(HttpServletResponse, String, Map<ProjectSampleAnalysisOutputInfo, AnalysisOutputFile>) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Utility method for download a zip file containing all output files from an analysis.

createClient(CreateUpdateClientDetails, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Create a new client.

CREATED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submission created and being populated

CREATED_DATE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

CREATED_DATE_SORT_PROPERTY - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

createdDate - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

createExpressionHandler() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

CreateLibraryException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

When there is an issue building a new data library.

CreateLibraryException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.CreateLibraryException

Constructs a new CreateLibraryException with no information.

CreateLibraryException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.CreateLibraryException

Constructs a new CreateLibraryException with the given message.

CreateLibraryException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.CreateLibraryException

Constructs a new CreateLibraryException with the given message and cause.

CreateLibraryException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.CreateLibraryException

Constructs a new CreateLibraryException with the given cause.

createMetadataTemplate(MetadataTemplate, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Create a new MetadataTemplate within a Project

createMetadataTemplateInProject(MetadataTemplate, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Create a new MetadataTemplate for a Project

createMetadataTemplateInProject(MetadataTemplate, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Create a new MetadataTemplate for a Project

createMultipleSampleSubmission(IridaWorkflow, Long, List<SingleEndSequenceFile>, List<SequenceFilePair>, Map<String, String>, IridaWorkflowNamedParameters, String, String, List<Project>, boolean, boolean, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Submit AnalysisSubmission for workflows allowing multiple one SequenceFile or SequenceFilePair

createMultipleSampleSubmission(IridaWorkflow, Long, List<SingleEndSequenceFile>, List<SequenceFilePair>, Map<String, String>, IridaWorkflowNamedParameters, String, String, List<Project>, boolean, boolean, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Submit AnalysisSubmission for workflows allowing multiple one SequenceFile or SequenceFilePair

CreateNamedParameterSetAjaxResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline

Response for creating a new set of named parameters on the pipeline launch page.

CreateNamedParameterSetAjaxResponse(SavedPipelineParameters) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.CreateNamedParameterSetAjaxResponse

createNewAnnouncement(AnnouncementRequest, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handles request to create a new announcement

createNewAnnouncement(AnnouncementRequest, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Creates a new announcement

createNewJobErrors(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyJobErrorsService

Get any JobError associated with an AnalysisSubmission

createNewMetadataTemplate(MetadataTemplate, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Create a new metadata template within a project

createNewProject(CreateProjectRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController

Create a new project.

createNewUserGroup(UserGroup, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Create a new UserGroup

createNewUserGroup(UserGroup, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Crate a new UserGroup

createOrUpdateClient(CreateUpdateClientDetails, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Create a new client

createProject(CreateProjectRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Create a new project based on a request sent by the UI.

CreateProjectRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Data transfer object for creating a new project.

CreateProjectRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

createProjectSampleMetadata(HttpSession, Long, MultipartFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

Upload CSV or Excel file containing sample metadata and extract the headers.

createProjectSampleMetadata(HttpSession, Long, MultipartFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

Upload CSV or Excel file containing sample metadata and extract the headers.

createProjectWithSamples(Project, List<Long>, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Create a Project with the given Samples contained

createProjectWithSamples(Project, List<Long>, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Create a Project with the given Samples contained

CreateRemoteProjectRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

Used to capture details about creating a new remote project through the UI

CreateRemoteProjectRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

CreateRemoteProjectRequest(String, ProjectSyncFrequency) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

createRequest(URI, HttpMethod) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.OAuthTokenRestTemplate

Add an OAuth token from the tokenRepository to the request

createResourceOpener() - Method in class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase

createSample(CreateSampleRequest, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService

Create a new sample in a project

createSampleInProject(CreateSampleRequest, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Create a new sample within a project

CreateSampleRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

UI Request to create a new sample

CreateSampleRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

CreateSampleRequest(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

CreateSampleRequest(String, String, String, List<FieldUpdate>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

createSequencingObjectInSample(SequencingObject, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Create a new SequencingObject associated with a Sample

createSequencingObjectInSample(SequencingObject, Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Create a new SequencingObject associated with a Sample

createSequencingRun(String, SequencingRun, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Create a Sequencing run

createSingleFileResponse(HttpServletResponse, AnalysisOutputFile) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Utility method for download single file from an analysis.

createSingleFileResponse(HttpServletResponse, AnalysisOutputFile, String) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Utility method for download single file from an analysis.

createSingleSampleSubmission(IridaWorkflow, Long, List<SingleEndSequenceFile>, List<SequenceFilePair>, Map<String, String>, IridaWorkflowNamedParameters, String, String, List<Project>, boolean, boolean, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Submit AnalysisSubmission for workflows requiring only one SequenceFile or SequenceFilePair

createSingleSampleSubmission(IridaWorkflow, Long, List<SingleEndSequenceFile>, List<SequenceFilePair>, Map<String, String>, IridaWorkflowNamedParameters, String, String, List<Project>, boolean, boolean, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Submit AnalysisSubmission for workflows requiring only one SequenceFile or SequenceFilePair

createSingleSampleSubmissionTemplate(IridaWorkflow, Long, Map<String, String>, IridaWorkflowNamedParameters, String, String, String, Project, boolean, boolean, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Create a new AnalysisSubmissionTemplate for a project with the given settings

createSingleSampleSubmissionTemplate(IridaWorkflow, Long, Map<String, String>, IridaWorkflowNamedParameters, String, String, String, Project, boolean, boolean, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Create a new AnalysisSubmissionTemplate for a project with the given settings

createSynchronizedProject(CreateRemoteProjectRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Create a new synchronized remote project

createSynchronizedProject(CreateRemoteProjectRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Add a new Synchronized Remote Project

createTokenFromAuthCode(String, RemoteAPI, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Get a new token from the given auth code

createTokenFromAuthCode(String, RemoteAPI, String) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService

Create a new RemoteAPIToken from a given auth code

CreateUpdateClientDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients

Used by the UI to send details for a new client.

CreateUpdateClientDetails() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

createUser(UserCreateRequest, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Submit a new user

createUser(UserCreateRequest, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Create a new user

createXml(NcbiExportSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Create the XML for an NcbiExportSubmission

crudService - Variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

service used for working with classes in the database.

CRUDService<IdentifierType extends java.io.Serializable,Type extends Timestamped<IdentifierType>> - Interface in ca.corefacility.bioinformatics.irida.service

All Service interfaces should extend this interface to inherit common methods relating to creating, reading, updating and deleting objects from persistence.

CRUDServiceImpl<KeyType extends java.io.Serializable,ValueType extends Timestamped<KeyType>> - Class in ca.corefacility.bioinformatics.irida.service.impl

A universal CRUD service for all types.

CRUDServiceImpl(IridaJpaRepository<ValueType, KeyType>, Validator, Class<ValueType>) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

CSS - ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

csv - ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportTypes

CSVView - Class in ca.corefacility.bioinformatics.irida.web.spring.view

Write out CSV files to the client.

CSVView() - Constructor for class ca.corefacility.bioinformatics.irida.web.spring.view.CSVView

Default constructor

CTS - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

CURRENT_USER_DETAILS - Static variable in class ca.corefacility.bioinformatics.irida.ria.config.UserSecurityInterceptor

CurrentUser - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Details about the currently logged in user for use by the UI.

CurrentUser(User) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

CurrentUserAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax

UI Controller to get information about the current user

CurrentUserAjaxController(UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.CurrentUserAjaxController

customPermissionAllowed(Authentication, NcbiExportSubmission) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadExportSubmissionPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Project) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ModifyProjectPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Project) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Project) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingRunPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateSequencingRunPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, MetadataEntry) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission

customPermissionAllowed(Authentication, MetadataTemplate) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, MetadataTemplate) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Sample) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Sample) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, UserGroup) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserGroupPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, User) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, Analysis) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisSubmissionPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

customPermissionAllowed(Authentication, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateSamplesFromAnalysisSubmissionPermission

customPermissionAllowed(Authentication, DomainObjectType) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.RepositoryBackedPermission

This method is called by RepositoryBackedPermission to evaluate the custom permissions provided by implementing classes.

D

DAILY - ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

DAILY - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

DashboardController - Class in ca.corefacility.bioinformatics.irida.ria.web

User Login Page Controller

DashboardController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.DashboardController

DataAddedToSampleProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event shown when SequenceFile data is added to a Sample for a Project

DataAddedToSampleProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent

DataAddedToSampleProjectEvent(Project, Sample) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent

DatasetCollectionType - Enum in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

The different types for a dataset collection.

DataStorage - Enum in ca.corefacility.bioinformatics.irida.pipeline.upload

Defines the location of data to upload on a filesystem.

DataTable - Class in ca.corefacility.bioinformatics.irida.ria.utilities.components

Static string used in the ResponseBody for DataTables calls.

DataTable() - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

DataTablesColumnDefinitions - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

Responsible for extracting and representing DataTables Columns

DataTablesExportable - Interface in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

This interface is responsible for enforcing that classes implementing DataTablesResponseModel and need to be exportable will be able to explicitly state which attributes and in which order they need to be exported.

DataTablesExportToFile - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

Used to export datatables to either excel or csv formatted files.

DataTablesExportToFile() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportToFile

DataTablesExportTypes - Enum in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

This class represents the types of files that can be exported from a datatable.

DataTablesParams - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

Represents all parameters within a DataTables request.

DataTablesParams() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

DataTablesParams(Integer, Integer, Integer, String, Sort, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

DataTablesRequest - Annotation Type in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config

Annotation for DataTablesParams This is used to handle an ajax request from a client for a DataTables response.

DataTablesRequestResolver - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config

Request resolver for DataTablesParams

DataTablesRequestResolver() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config.DataTablesRequestResolver

DataTablesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables

This is returned to client in an HttpServletResponse in the format the can be consumed by jQuery DataTables.

DataTablesResponse(DataTablesParams, long, List<DataTablesResponseModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

DataTablesResponse(DataTablesParams, Page<?>, List<? extends DataTablesResponseModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

DataTablesResponseModel - Interface in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models

Responsible for adding a DataTables rowId property to the response.

DATE - Static variable in interface ca.corefacility.bioinformatics.irida.ria.utilities.Formats

Default format for Date in DataTables

DateDeserializer() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateDeserializer

DateJson - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Class containing custom JSON serializers/deserializers for Dates.

DateJson() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson

DateJson.DateDeserializer - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Custom JSON deserializer date from format yyyy-MM-DD.

DateJson.DateSerializer - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Custom JSON serializer to format date as yyyy-MM-DD.

DateSerializer() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateSerializer

DateUtilities - Class in ca.corefacility.bioinformatics.irida.ria.web.utilities

Utilities class to help with date conversions.

DateUtilities() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities

DEFAULT - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

DEFAULT_CONTENT_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.web.spring.view.CSVView

DEFAULT_CONTENT_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.web.spring.view.FastaView

DEFAULT_CONTENT_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.web.spring.view.FastqView

DEFAULT_CONTENT_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.web.spring.view.GenbankView

DEFAULT_CONTENT_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.web.spring.view.NewickFileView

DEFAULT_DOWNLOAD_MEDIA_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.Fast5ObjectRemoteRepositoryImpl

DEFAULT_DOWNLOAD_MEDIA_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.GenomeAssemblyRemoteRepositoryImpl

DEFAULT_DOWNLOAD_MEDIA_TYPE - Static variable in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFileRemoteRepositoryImpl

DEFAULT_REFRESH_TOKEN_VALIDITY - Static variable in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

DEFAULT_TOKEN_VALIDITY - Static variable in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

DefaultFileProcessingChain - Class in ca.corefacility.bioinformatics.irida.processing.impl

Default implementation of FileProcessingChain.

DefaultFileProcessingChain(SequencingObjectRepository, QCEntryRepository, FileProcessor...) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

DefaultFileProcessingChain(SequencingObjectRepository, QCEntryRepository, List<FileProcessor>) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

defaultIridaWorkflows() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

A set of workflow ids to use as defaults.

delegate(MethodEvent) - Method in class ca.corefacility.bioinformatics.irida.events.ProjectEventHandler

Handle translation of a MethodEvent into the correct ProjectEvent subclass

delete(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Delete a token for the logged in user and a given RemoteAPI

delete(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService

Delete a token for the logged in user and a given RemoteAPI

delete(IdentifierType) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Delete the object with the specified identifier from the database.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Delete the instance of the resource identified by a specific identifier.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Delete the instance of the resource identified by a specific identifier.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Delete the instance of the resource identified by a specific identifier.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Delete the instance of the resource identified by a specific identifier.

delete(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Delete the instance of the resource identified by a specific identifier.

delete(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

delete(KeyType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Delete the object with the specified identifier from the database.

deleteAjaxAnalysisSubmission(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Delete an AnalysisSubmission by id.

deleteAnalysisSubmissions(List<Long>, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Delete a specific AnalysisSubmission

deleteAnalysisSubmissionTemplateForProject(Long, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Delete an AnalysisSubmissionTemplate from the given Project

deleteAnalysisSubmissionTemplateForProject(Long, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Delete an AnalysisSubmissionTemplate from the given Project

deleteAnnouncement(AnnouncementRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handles request to delete an existing announcement.

deleteAnnouncement(AnnouncementRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Delete an existing announcement.

deleteClient(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Delete a client

deleteClient(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Delete a client

deleteClientTokens(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Revoke all tokens for a client given its identifier

deleteClientTokens(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Revoke all tokens for a specific client

DELETED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submission deleted

deleteFilesFromSample(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Remove a sequencing object or genome assembly linked to a Sample

DeleteGalaxyObjectFailedException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

Exception when there is a failure to delete a Galaxy object.

DeleteGalaxyObjectFailedException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.DeleteGalaxyObjectFailedException

Constructs a new CreateLibraryException with the given message.

DeleteGalaxyObjectFailedException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.DeleteGalaxyObjectFailedException

Constructs a new DeleteGalaxyObjectFailedException with the given message and cause.

DeleteGalaxyObjectFailedException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.DeleteGalaxyObjectFailedException

Constructs a new DeleteGalaxyObjectFailedException with the given cause.

deleteGenomeAssemblyFromSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Remove a genome assembly linked to a Sample

deleteHistory(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Deletes a history from Galaxy with the given id.

deleteLibrary(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

Deletes the Galaxy library with the given id.

deleteMetadataTemplate(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Delete a MetadataTemplate within a Project

deleteMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Delete a metadata template from the project

deleteMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Ajax request handler for deleting a specific MetadataTemplate

deleteMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Remove a MetadataTemplate from a Project

deleteMetadataTemplateFromProject(Project, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Deleta a MetadataTemplate from a Project

deleteMetadataTemplateFromProject(Project, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Deleta a MetadataTemplate from a Project

deleteMultiple(Collection<Long>) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Delete multiple AnalysisSubmissions

deleteMultiple(Collection<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Delete multiple AnalysisSubmissions

deleteProject(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Delete a project

deleteProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Delete a project

deleteReferenceFile(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController

Delete a reference file.

deleteReferenceFile(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService

Delete a reference file.

deleteRemoteAPI(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Delete a Remote API Connection

deleteRemoteAPI(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Delete a specific RemoteAPI

deleteSequencingObjectFromSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Remove a sequencing object linked to a Sample

deleteSequencingRun(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

Delete a sequencing run.

deleteSequencingRun(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

Delete a sequencing run.

deleteUserGroup(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Delete a specific user group

deleteUserGroup(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Delete a specific user group

deleteWorkflow(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Deletes a workflow with the given id.

description(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the description

deserialize(JsonParser, DeserializationContext) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifestDeserializer

deserialize(JsonParser, DeserializationContext) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntryDeserializer

deserialize(JsonParser, DeserializationContext) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateDeserializer

destroy() - Method in class ca.corefacility.bioinformatics.irida.web.filter.HttpHeadFilter

destroy() - Method in class ca.corefacility.bioinformatics.irida.web.filter.SlashFilter

disabledAnalysisTypes() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Builds a AnalysisTypeSet of AnalysisTypes which are to be disabled from the UI.

DISCARDED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

DNASE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

DNASE_HYPERSENSITIVITY - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

DNBSEQ_G_400 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

DNBSEQ_G_50 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

DNBSEQ_T_7 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class ca.corefacility.bioinformatics.irida.ria.config.filters.SessionFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class ca.corefacility.bioinformatics.irida.web.filter.HttpHeadFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class ca.corefacility.bioinformatics.irida.web.filter.SlashFilter

doProcess(ITemplateContext, IProcessableElementTag, AttributeName, String, IElementTagStructureHandler) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerScriptAttributeTagProcessor

doProcess(ITemplateContext, IProcessableElementTag, IElementTagStructureHandler) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerCSSElementTagProcessor

doProcess(ITemplateContext, IProcessableElementTag, IElementTagStructureHandler) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerJavascriptElementTagProcessor

downloadAnalysis(Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Download the output files of an AnalysisSubmission

downloadAnalysisOutputsSelection(String, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Download the selected AnalysisOutputFile.

downloadAssembly(Long, Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Download a GenomeAssembly file

downloadAssembly(Long, Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Download a GenomeAssembly file

downloadDatasetTo(String, String, Path) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Given a particular dataset id within a Galaxy history download this dataset to the local filesystem.

downloadIndividualAnalysisOutputFile(Long, Long, String, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Download analysis output file

downloadIndividualFile(Long, Long, String, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Download single output files from an AnalysisSubmission

DOWNLOADING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Deprecated.

This is no longer a valid state. This must still exist in IRIDA in cases where this state has been recored in the audit tables.

downloadReferenceFile(Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController

Download a reference file based on the id passed.

downloadReferenceFile(Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService

Download a reference file based on the id passed.

downloadRemoteAssembly(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.GenomeAssemblyRemoteRepository

Download a GenomeAssembly fom the given RemoteAPI with a default MediaType

downloadRemoteAssembly(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.GenomeAssemblyRemoteRepositoryImpl

Download a GenomeAssembly fom the given RemoteAPI with a default MediaType

downloadRemoteAssembly(String, RemoteAPI, MediaType...) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.GenomeAssemblyRemoteRepository

Download a GenomeAssembly fom the given RemoteAPI

downloadRemoteAssembly(String, RemoteAPI, MediaType...) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.GenomeAssemblyRemoteRepositoryImpl

Download a GenomeAssembly fom the given RemoteAPI

downloadRemoteSequenceFile(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFileRemoteRepositoryImpl

Get a local copy of a SequenceFile with a default MediaType of application/fastq

downloadRemoteSequenceFile(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFileRemoteRepository

Get a local copy of a SequenceFile with a default MediaType of application/fastq

downloadRemoteSequenceFile(String, RemoteAPI, MediaType...) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFileRemoteRepositoryImpl

Get a local copy of a SequenceFile

downloadRemoteSequenceFile(String, RemoteAPI, MediaType...) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.SequenceFileRemoteRepository

Get a local copy of a SequenceFile

DownloadRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Request information to download samples from the project samples table

DownloadRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.DownloadRequest

downloadSamples(long, DownloadRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Download a zipped file containing sequencing reads for a list of samples.

downloadSamples(Long, List<Long>, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get the sequence files for a list of samples

downloadSamplesSpreadsheet(long, String, ProjectSamplesTableRequest, HttpServletResponse, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Export the current state of the Project Samples table as either a CSV or Excel file.

downloadSamplesSpreadsheet(Long, String, ProjectSamplesTableRequest, HttpServletResponse, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Download the currently filtered project samples table as either an xlsx or csv file.

downloadSelection(String, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Download the selected AnalysisOutputFile.

downloadSequenceFile(Long, Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.SequenceFileAjaxController

Download the sequence file

downloadSequenceFile(Long, Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

Download the sequence file

downloadTemplate(Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Download a MetadataTemplate as an Excel file.

DTProject - Class in ca.corefacility.bioinformatics.irida.ria.web.models.datatables

User interface model for DataTables for Project

DTProject(Project, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

DTProjectSamples - Class in ca.corefacility.bioinformatics.irida.ria.web.models.datatables

DataTables response object for ProjectSampleJoin

DTProjectSamples(ProjectSampleJoin, List<String>, Double) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

DuplicateSampleException - Exception in ca.corefacility.bioinformatics.irida.exceptions

If there is more than one SequenceFile from a Sample for a IridaWorkflow.

DuplicateSampleException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.DuplicateSampleException

duplicationLevelChart(AnalysisOutputFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the duplicationLevelChart

DYNAMIC_FIELD_PREFIX - Static variable in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

E

EmailController - Interface in ca.corefacility.bioinformatics.irida.service

Interface describing methods for emailing information to the user

EmailControllerImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

This class is responsible for all email sent to the server that are templated with Thymeleaf.

EmailControllerImpl(WebEmailConfig.ConfigurableJavaMailSender, TemplateEngine, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

emailPipelineResultCompleted - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

emailPipelineResultCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets if user should be emailed on pipeline completion

emailPipelineResultError - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

emailPipelineResultError(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets if user should be emailed on pipeline error

emailProjectEvents() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.EmailScheduledTaskConfig

Check for any new events for users who are subscribed to projects and email them

EmailScheduledTaskConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Scheduled taks configuration for sending digest emails

EmailScheduledTaskConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.EmailScheduledTaskConfig

emailTemplateEngine() - Method in class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig

emailUserTasks() - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventEmailScheduledTaskImpl

Task that checks for new events to mail to users then fires an email.

emailUserTasks() - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectEventEmailScheduledTask

Task that checks for new events to mail to users then fires an email.

empty() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Empty the cart and remove all sample names

EMPTY - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

emptyCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Completely empty the cart

emptyCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Remove all samples from the cart

emptyValuePlaceholder() - Static method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisProvenanceServiceGalaxy

Get an empty value placeholder

encoding(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the encoding

enhanceQcEntries(SequencingObject, Project) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Adds the Project to any QCEntry within a SequencingObject.

EntityExistsException - Exception in ca.corefacility.bioinformatics.irida.exceptions

When an entity to be created in the database shares an identifier with an existing entity.

EntityExistsException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException

Construct a new EntityExistsException with the specified message.

EntityExistsException(String, String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException

Construct a new EntityExistsException with the specified message.

EntityExistsException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException

Construct a new EntityExistsException with the specified message and cause.

EntityNotFoundException - Exception in ca.corefacility.bioinformatics.irida.exceptions

When an entity cannot be found in the database.

EntityNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException

Construct a new EntityNotFoundException with the specified message.

EntityNotFoundException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException

Construct a new EntityNotFoundException with the specified message and cause.

entries - Variable in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifest

EntriesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

Response for linelist to include total count

EntriesResponse(long, List<UISampleMetadata>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.EntriesResponse

ENTRY_ATTR - Static variable in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.WebpackerDialect

EQUAL - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

Equals method using remoteAPI and tokenString

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

equals(Object) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

ERROR - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that was not successfully able to run.

ERROR - ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

ERROR - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

An error occurred while synchronizing.

ERROR - ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

ERROR - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

ERROR - ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

ErrorNotification - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Consumed by the UI to display an error notification.

ErrorNotification(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.ErrorNotification

ErrorNotification(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.ErrorNotification

errorOccurred() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Whether or not this workflow is in an error state.

ErrorResponse - Class in ca.corefacility.bioinformatics.irida.web.controller.api.exception

Error message response class to be serialzed to Json and returned from the ControllerExceptionHandler

ErrorResponse() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

ErrorResponse(String) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

ErrorResponse(String, Map<String, Object>) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

errorViewResolver() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

EST - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

estimateCoverageForSample(Sample, long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Given the length of a reference file, estimate the total coverage for this sample.

estimateCoverageForSample(Sample, long) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Given the length of a reference file, estimate the total coverage for this sample.

estimateCoverageForSample(Sample, ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Given a ReferenceFile, estimate the total coverage for this sample.

estimateCoverageForSample(Sample, ReferenceFile) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Given a ReferenceFile, estimate the total coverage for this sample.

excel - ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportTypes

ExcelCol - Class in ca.corefacility.bioinformatics.irida.ria.web.dto

Used as a response for encapsulating excel column data

ExcelCol(int, Double) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

ExcelCol(int, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

ExcelData - Class in ca.corefacility.bioinformatics.irida.ria.web.dto

Used as a response for encapsulating parsed excel file data

ExcelData(List<ExcelHeader>, List<ExcelRow>, List<String>, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

ExcelHeader - Class in ca.corefacility.bioinformatics.irida.ria.web.dto

Used as a response for encapsulating excel header column data

ExcelHeader(String, int, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

ExcelRow - Class in ca.corefacility.bioinformatics.irida.ria.web.dto

Used as a response for encapsulating excel parsed row data

ExcelRow(List<ExcelCol>, int, int) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

ExceptionPropertyAndMessage - Class in ca.corefacility.bioinformatics.irida.ria.utilities

Class storing a property name and a message name to display if the property is in error.

ExceptionPropertyAndMessage(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.ExceptionPropertyAndMessage

Create an ExceptionPropertyAndMessage storing the affected property name and the message name to display if that property is in error.

ExceptionUtilities - Class in ca.corefacility.bioinformatics.irida.ria.web.utilities

Utilities class for Exception handling.

ExceptionUtilities() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.utilities.ExceptionUtilities

EXCLUDE_PROJECT - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

executableAnalysisTypes() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Gets all executable AnalysisTypes.

executableAnalysisTypes() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Gets all executable AnalysisTypes.

executeAnalyses() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any outstanding submissions and execute them.

executeAnalyses() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through any outstanding AnalysisSubmissions and execute them.

executeAnalyses() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through any outstanding AnalysisSubmissions and execute them.

executeAnalysis(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Executes the passed prepared AnalysisSubmission in an execution manager.

executeAnalysis(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Executes the passed prepared AnalysisSubmission in an execution manager.

executeAnalysis(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

Executes the passed prepared AnalysisSubmission in an execution manager.

executionManager() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

Builds a new ExecutionManagerGalaxy from the given properties.

ExecutionManager - Interface in ca.corefacility.bioinformatics.irida.model.workflow.manager

Defines an ExecutionManager for executing a workflow.

executionManagerAnalysisId(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the executionManagerAnalysisId

ExecutionManagerConfig - Class in ca.corefacility.bioinformatics.irida.config.analysis

Configuration for connections to an ExecutionManager in IRIDA.

ExecutionManagerConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

ExecutionManagerConfigurationException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception that gets thrown for an invalid configuration option for an execution manager.

ExecutionManagerConfigurationException(String, String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerConfigurationException

Constructs a new ExecutionManagerConfigurationException with the given property name.

ExecutionManagerConfigurationException(String, String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerConfigurationException

Constructs a new ExecutionManagerConfigurationException with the given message and cause.

ExecutionManagerDownloadException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when there is an issue downloading data from an execution manager.

ExecutionManagerDownloadException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerDownloadException

Constructs a new ExecutionManagerDownloadException with no information.

ExecutionManagerDownloadException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerDownloadException

Constructs a new ExecutionManagerDownloadException with the given message.

ExecutionManagerDownloadException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerDownloadException

Constructs a new ExecutionManagerDownloadException with the given message and cause.

ExecutionManagerDownloadException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerDownloadException

Constructs a new ExecutionManagerDownloadException with the given cause.

ExecutionManagerException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when dealing with data or workflows from an external execution manager (e.g.

ExecutionManagerException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException

Constructs a new ExecutionManagerException with no information.

ExecutionManagerException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException

Constructs a new ExecutionManagerException with the given message.

ExecutionManagerException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException

Constructs a new ExecutionManagerException with the given message and cause.

ExecutionManagerException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException

Constructs a new ExecutionManagerException with the given cause.

ExecutionManagerGalaxy - Class in ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy

Defines an ExecutionManager Galaxy implementation for interacting with Galaxy.

ExecutionManagerGalaxy(URL, String, GalaxyAccountEmail, DataStorage) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy

Builds a new ExecutionManagerGalaxy with the given information.

ExecutionManagerObjectNotFoundException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown if an object is not found by the execution manager

ExecutionManagerObjectNotFoundException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerObjectNotFoundException

Constructs a new ExecutionManagerObjectNotFoundException with no information.

ExecutionManagerObjectNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerObjectNotFoundException

Constructs a new ExecutionManagerObjectNotFoundException with the given message.

ExecutionManagerObjectNotFoundException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerObjectNotFoundException

Constructs a new ExecutionManagerObjectNotFoundException with the given message and cause.

ExecutionManagerObjectNotFoundException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerObjectNotFoundException

Constructs a new ExecutionManagerObjectNotFoundException with the given cause.

ExecutorConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Configuration for a task executor for running scheduled tasks.

ExecutorConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.ExecutorConfig

ExistingSampleNameException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when trying to add a Sample to a Project with a duplicate sample name

ExistingSampleNameException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExistingSampleNameException

ExistingSampleNameException(String, Sample) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExistingSampleNameException

ExistingSampleNameException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ExistingSampleNameException

exists(IdentifierType) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Check to see if an identifier for Type exists in the database.

exists(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Check to see if an identifier for Type exists in the database.

exists(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Check to see if an identifier for Type exists in the database.

exists(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Check to see if an identifier for Type exists in the database.

exists(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Check to see if an identifier for Type exists in the database.

exists(KeyType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Check to see if an identifier for Type exists in the database.

ExportFormatException - Exception in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export

Exception thrown when attempting to export a table with an unknown format.

ExportFormatException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.components.datatables.export.ExportFormatException

exportProjectsToFile(String, Boolean, HttpServletResponse, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Export Projects table as either an excel file or CSV

ExportToFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Used the get the form details submitted via a post to export samples to a CSV.

ExportToFileModel() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

ExportToFileModel(List<String>, List<Long>, String, Date, Date, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

ExportUploadService - Class in ca.corefacility.bioinformatics.irida.service.export

Class which handles uploading a NcbiExportSubmission to NCBI

ExportUploadService(NcbiExportSubmissionService, SampleService, MetadataTemplateService, TemplateEngine, EmailController) - Constructor for class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

ExportUploadState - Enum in ca.corefacility.bioinformatics.irida.model.enums

Status of an NcbiExportSubmission.

exportUploadTemplateEngine() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

EXTENSION_HTML_ZIP - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

EXTENSION_ZIP - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

F

FAILED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Failed immediately after submission

FAILED_METADATA - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

Fast5Object - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

SequencingObject implementation for storing .fast5 files.

Fast5Object() - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

Fast5Object(SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

Fast5Object.Fast5Type - Enum in ca.corefacility.bioinformatics.irida.model.sequenceFile

Type of file stored buy this fast5 object

Fast5ObjectRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

Repository for synchronizing Fast5Object from a RemoteAPI

Fast5ObjectRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

A repository implementaion for reading Fast5Object from remote locations using a OAuthTokenRestTemplate

Fast5ObjectRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.Fast5ObjectRemoteRepositoryImpl

Fast5ObjectRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

A service for reading Fast5Objects from a remote location

Fast5ObjectRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

An implementation of Fast5ObjectRemoteService using a Fast5ObjectRemoteRepository to read remote Fast5Object

Fast5ObjectRemoteServiceImpl(Fast5ObjectRemoteRepository, SequenceFileRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.Fast5ObjectRemoteServiceImpl

FASTA - ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

A FASTA formatted file.

FastaView - Class in ca.corefacility.bioinformatics.irida.web.spring.view

Write out FASTA formatted sequence files to the client.

FastaView() - Constructor for class ca.corefacility.bioinformatics.irida.web.spring.view.FastaView

Default constructor

FASTQ_SANGER - ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

The fastqsanger file type (quality scores are Phred+33).

FASTQ_SANGER_GZ - ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

The fastqsanger.gz (gzipped) file type (quality scores are Phred+33).

FASTQC - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

FastQCDetailsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.files.dto

Used by UI to encapsulate fastqc details.

FastQCDetailsResponse(SequencingObject, SequenceFile, AnalysisFastQC) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

FastqcFileProcessor - Class in ca.corefacility.bioinformatics.irida.processing.impl

Executes FastQC on a SequenceFile and stores the report in the database.

FastqcFileProcessor(MessageSource, SequenceFileRepository, AnalysisOutputFileRepository) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.FastqcFileProcessor

Create a new FastqcFileProcessor

FastQCImagesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.files.dto

Used by UI to encapsulate fastqc images data.

FastQCImagesResponse(byte[], byte[], byte[], String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

FastqcToFilesystem - Class in ca.corefacility.bioinformatics.irida.database.changesets

Liquibase update class for moving the fastqc analysis results off the AnalysisFastQC class (and out of the database).

FastqcToFilesystem() - Constructor for class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

fastqcVersion(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the fastqc version used in the analysis

FastqView - Class in ca.corefacility.bioinformatics.irida.web.spring.view

Write out FASTQ formatted sequence files to the client.

FastqView() - Constructor for class ca.corefacility.bioinformatics.irida.web.spring.view.FastqView

Default constructor

fetchAnalysesQueueCounts() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Fetch the current status of the analysis server.

FieldUpdate - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used by UI when any field needs to have its value updated.

FieldUpdate() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

FieldUpdate(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

FILE_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

FILE_SAMPLE_REL - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

FileProcessingChain - Interface in ca.corefacility.bioinformatics.irida.processing

A collection of FileProcessor that are executed, in order, on a specific SequencingObject.

fileProcessingChainExecutor() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

FileProcessingScheduledTaskConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Scheduled task configuration for running file processors

FileProcessingScheduledTaskConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.FileProcessingScheduledTaskConfig

FileProcessor - Interface in ca.corefacility.bioinformatics.irida.processing

Responsible for processing a SequenceFile after the file has been uploaded to the server.

fileProcessorChain(SequencingObjectRepository, QCEntryRepository, GzipFileProcessor, FastqcFileProcessor, ChecksumFileProcessor, CoverageFileProcessor, AutomatedAnalysisFileProcessor) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

FileProcessorErrorQCEntry - Class in ca.corefacility.bioinformatics.irida.model.sample

QCEntry for a failed FileProcessor

FileProcessorErrorQCEntry() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

FileProcessorErrorQCEntry(SequencingObject) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

FileProcessorException - Exception in ca.corefacility.bioinformatics.irida.processing

Exception thrown when a FileProcessor fails to complete execution.

FileProcessorException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.processing.FileProcessorException

FileProcessorException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.processing.FileProcessorException

FileProcessorTimeoutException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when the FileProcessingChain waits longer than a specified timeout for the SequencingObjectService to finish executing its transaction.

FileProcessorTimeoutException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.FileProcessorTimeoutException

files(Set<SingleEndSequenceFile>) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

set the single end files

FileSizeConverter - Class in ca.corefacility.bioinformatics.irida.ria.utilities.converters

Converts a files size (originally in bytes) to Kilobytes

FileSizeConverter() - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

filesToLibraryToHistory(Set<Path>, History, Library, DataStorage) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Uploads a set of files to a given history through the given library.

filesToLibraryWait(Set<Path>, Library, DataStorage) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

Uploads a set of files to a given library, waiting until all uploads are complete.

FilesystemSupplementedRepository<Type extends VersionedFileFields<java.lang.Long> & IridaThing> - Interface in ca.corefacility.bioinformatics.irida.repositories.filesystem

Custom implementation interface for writing the Path part of a SequenceFile to disk.

FilesystemSupplementedRepositoryImpl<Type extends VersionedFileFields<java.lang.Long> & IridaThing> - Class in ca.corefacility.bioinformatics.irida.repositories.filesystem

Custom implementation of a repository that writes the Path part of an entity to disk.

FilesystemSupplementedRepositoryImpl(EntityManager, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl

FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener - Class in ca.corefacility.bioinformatics.irida.repositories.filesystem

A JPA event listener to translate the relative paths stored in the database to absolute paths so that everyone after the repository knows where the file is actually stored.

fileToHistory(Path, InputFileType, History) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Uploads a file to a given history.

fileToLibrary(Path, InputFileType, Library, DataStorage) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

Uploads the given file to a library with the given information.

fileType(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the filetype

FileUtilities - Class in ca.corefacility.bioinformatics.irida.ria.utilities

Download a zip archive of all output files within an AnalysisSubmission

FileUtilities() - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

FileUtils - Class in ca.corefacility.bioinformatics.irida.util

A class containing a number of utilities for dealing with files.

FileUtils() - Constructor for class ca.corefacility.bioinformatics.irida.util.FileUtils

filterAnalyses(String, String, Set<AnalysisState>, User, Set<UUID>, Project, Boolean) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.AnalysisSubmissionSpecification

Search for analyses with a given name, AnalysisState, or Workflow UUID

filterChain(HttpSecurity) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig

filteredSequences(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the filteredSequences

filterUsersByUsername(String, UserGroup, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Filter the list of users in the UserGroup by username.

filterUsersByUsername(String, UserGroup, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Filter the list of users in the UserGroup by username.

findAccessTokensByRegisteredClientId(String) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

findAll() - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

List all objects of Type in the database.

findAll() - Method in class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

List all objects of Type in the database.

findAll(Specification<ProjectSampleJoin>, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

findAllByAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository

Find all JobError objects for a given AnalysisSubmission

findAllByAnalysisSubmission_WorkflowId(UUID) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository

Find all JobError objects for an IridaWorkflow

findAllMetadataFieldsByLabelQuery(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository

Get a List of MetadataTemplateField with a label that partially matches the query

findAllProjects(String, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Find a paged list of all projects (for admin) using the specified search criteria.

findAllProjects(String, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Find a paged list of all projects (for admin) using the specified search criteria.

findAllProjectsByNameExcludingProject(String, Project, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Load up a page of Projects, excluding the specified Project.

findAllProjectSubscriptionsByUser(User, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository

Find all the ProjectSubscription for the given user.

findAnalysesByState(Collection<AnalysisState>) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get a list of all AnalysisSubmissions with a given AnalysisState

findAnalysesByState(Collection<AnalysisState>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get a list of all AnalysisSubmissions with a given AnalysisState

findAnalysisSubmissionsForSequencingObject(SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the Set of AnalysisSubmissions which use a given SequencingObject

findAnalysisSubmissionsForSequencingObjectBySubmitter(SequencingObject, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the Set of AnalysisSubmissions which use a given SequencingObject for a given User

findByAnalysis(Analysis) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Finds the AnalysisSubmission that caused the passed Analysis to be created.

findByAnalysisState(AnalysisState) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Loads up a list of AnalysisSubmissions with the given state.

findByAnalysisState(AnalysisState, AnalysisCleanedState) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Loads up a list of AnalysisSubmissions with the given states.

findByAnalysisState(Collection<AnalysisState>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Loads up a list of AnalysisSubmissions with the given state.

findByClientId(String) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaRegisteredClientsRepository

findById(String) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

findById(String) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaRegisteredClientsRepository

findById(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Finds the history by it's ID.

findByProjectAndUser(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find the joins for a user and project.

findByProjectAndUserGroup(Project, UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find the join for a user group and project.

findByReferenceFile(ReferenceFile) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get the Set of AnalysisSubmissions making use of the given ReferenceFile.

findBySample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository

Gets a collection of SampleGenomeAssemblyJoin by the sample.

findBySampleAndAssemblyId(Long, Long) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository

Gets a GenomeAssembly from a Sample with the given id.

findBySubmitter(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Loads up all AnalysisSubmissions by the submitted User.

findByToken(String, OAuth2TokenType) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

findByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.PasswordResetRepository

Find any existing PasswordResets for the specified user.

findByWorkflowId(UUID) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.WorkflowNamedParametersRepository

Find all saved, named parameters for the specified workflow.

findByWorkflowIds(Collection<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Finds all AnalysisSubmissions corresponding to the given workflow ids.

findFastqcAnalysisForSequenceFile(SequenceFile) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository

Get the fastqc analysis for a specific file.

findFilesToProcess() - Method in class ca.corefacility.bioinformatics.irida.service.SequencingObjectProcessingService

Find new SequencingObjects to process and mark that this process is going to handle them

findFirstByAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.JobErrorRepository

Find first JobError for a given AnalysisSubmission

findGroupsByProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find all groups with access to the project.

findGroupsByProjectAndProjectRole(Project, ProjectRole) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find all groups with access to the project with a specific role.

findGroupsForProjectAndUser(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Get the UserGroupProjectJoin (potentially more than 1) between a given User and Project

findManageableProjectsByName(String, Project, User, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Load a page of Projects for a specific User, excluding a Project.

findMarkedProjectsToSync() - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Find projects which should be synchronized and launch a synchornization task.

findMetadataFieldByLabel(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository

Get a MetadataTemplateField based on its String label.

findMetadataFieldByStaticId(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository

Read a StaticMetadataTemplateField by its staticId

findNamedParametersForWorkflow(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

Get the named parameters saved for the specified workflow.

findNamedParametersForWorkflow(UUID) - Method in interface ca.corefacility.bioinformatics.irida.service.workflow.WorkflowNamedParametersService

Get the named parameters saved for the specified workflow.

findProjectsByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find the projects where the specified user is in a group on the project.

findProjectsByUserGroup(UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository

Find all projects linked to the group.

findProjectsForReferenceFile(ReferenceFile) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository

Get the collection of ReferenceFile for the specified Project.

findProjectsForUser(String, Integer, Integer, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Find a list of projects (for a user or admin) using the specified search criteria

findProjectsForUser(String, Integer, Integer, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Find a list of projects (for a user or admin) using the specified search criteria

findProjectsToMark() - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Method checking for remote projects that have passed their frequency time.

findProjectSubscriptionByUserAndProject(User, Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository

Find the ProjectSubscription for the given user and project.

findReferenceFilesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository

Get the collection of ReferenceFile for the specified Project.

findRevisions(IdentifierType) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Find all of the revisions for the specified identifier.

findRevisions(IdentifierType, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Returns a Page of revisions for the entity with the given id.

findRevisions(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Find all of the revisions for the specified identifier.

findRevisions(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Find all of the revisions for the specified identifier.

findRevisions(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Find all of the revisions for the specified identifier.

findRevisions(Long, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Returns a Page of revisions for the entity with the given id.

findRevisions(Long, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Returns a Page of revisions for the entity with the given id.

findRevisions(Long, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Returns a Page of revisions for the entity with the given id.

findRevisions(KeyType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Find all of the revisions for the specified identifier.

findRevisions(KeyType, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Returns a Page of revisions for the entity with the given id.

findSampleByNameInProject(Project, List<String>, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get a Page of Samples based on a list of Sample names

findSamplesForAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get the Samples associated with a given AnalysisSubmission

findSequencingObjectsForAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository

Get the SequencingObjects associated with a given AnalysisSubmission

findSequencingObjectsForSequencingRun(SequencingRun) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository

Get the SequencingObjects for a given SequencingRun

findStaticMetadataFields() - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository

Get a list of all StaticMetadataTemplateFields

findUserGroupsNotOnProject(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserGroupRepository

Find a collection of UserGroup not already attached to the Project.

findUsersInGroup(UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserGroupJoinRepository

Get a collection of users in a group.

findUsersNotInGroup(UserGroup, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserGroupJoinRepository

Get a collection of users not in a group.

FINISHED - ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

FINISHED_DOWNLOADING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Deprecated.

This is no longer a valid state. This must still exist in IRIDA in cases where this state has been recored in the audit tables.

FINISHED_RUNNING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that has finished running in the execution manager.

FINISHING - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

FIVE_METHYL - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

FL_CDNA - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

forbidJpqlUpdateDeletePostProcessor() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

ForbidJpqlUpdateDeletePostProcessor - Class in ca.corefacility.bioinformatics.irida.config.repository

A BeanPostProcessor that inspects the Query methods on a repository bean and dies when a query is written in JPQL that tries to modify the database with an update or delete.

ForbidJpqlUpdateDeletePostProcessor() - Constructor for class ca.corefacility.bioinformatics.irida.config.repository.ForbidJpqlUpdateDeletePostProcessor

FORCE - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Marked to have a full resync of all elements regardless of project hash

Formats - Interface in ca.corefacility.bioinformatics.irida.ria.utilities

This class is responsible for holding the formats of different Strings (e.g.

forwardMatches - Static variable in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

FRAGMENT_NAMES - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Given a string defining a state, converts this to a AnalysisState.

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Get an ExportUploadState from its string representation

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

Get a role from the given string code

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

Get a role from the given string code

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

Get a status from the given string

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole

Get a role from the given string

fromString(String) - Static method in enum ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

Get a operation from the given string operation

fromString(String) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Gets a AnalysisType from the given string.

fromString(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Gets a AnalysisType from the given string.

G

GALAXY_CALLBACK_URL - Static variable in class ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor

GALAXY_CLIENT_ID - Static variable in class ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor

GalaxyAccountEmail - Class in ca.corefacility.bioinformatics.irida.model.upload.galaxy

A GalaxyAccount object for storing credentials for an account in Galaxy.

GalaxyAccountEmail(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail

Builds a new GalaxyAccountEmail with the passed email address.

GalaxyDatasetException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

This exception is thrown when there is an error obtaining a Galaxy dataset.

GalaxyDatasetException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException

Constructs a new GalaxyDatasetException with no information.

GalaxyDatasetException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException

Constructs a new GalaxyDatasetException with the given message.

GalaxyDatasetException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException

Constructs a new GalaxyDatasetException with the given message and cause.

GalaxyDatasetException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException

Constructs a new GalaxyDatasetException with the given cause.

GalaxyDatasetNotFoundException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

Exception thrown if a given dataset is not found in galaxy

GalaxyDatasetNotFoundException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException

Constructs a new GalaxyDatasetNotFoundException with no information.

GalaxyDatasetNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException

Constructs a new GalaxyDatasetNotFoundException with the given message.

GalaxyDatasetNotFoundException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException

Constructs a new GalaxyDatasetNotFoundException with the given message and cause.

GalaxyDatasetNotFoundException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException

Constructs a new GalaxyDatasetNotFoundException with the given cause.

GalaxyExportAuthentication - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

UI Model to hold whether the current galaxy client has a valid security token.

GalaxyExportAuthentication(boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportAuthentication

GalaxyExportSample - Class in ca.corefacility.bioinformatics.irida.ria.web.cart.dto

UI Model to return sample links in the format that galaxy expects:

GalaxyExportSample(Sample, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportSample

galaxyHistoriesService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

GalaxyHistoriesService - Class in ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

Class for working with Galaxy Histories.

GalaxyHistoriesService(HistoriesClient, ToolsClient, GalaxyLibrariesService) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Builds a new GalaxyHistory object for working with Galaxy Histories.

galaxyInstance() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

galaxyJobErrorsService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

GalaxyJobErrorsService - Class in ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

Class to create new JobError objects using a Galaxy HistoriesClient, ToolsClient and JobsClient if an error occurred during an Galaxy pipeline AnalysisSubmission.

GalaxyJobErrorsService(HistoriesClient, ToolsClient, JobsClient) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyJobErrorsService

galaxyLibrariesService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

GalaxyLibrariesService - Class in ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

A service class for dealing with Galaxy libraries.

GalaxyLibrariesService(LibrariesClient, int, int, int) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService

Builds a new GalaxyLibrariesService with the given LibrariesClient.

GalaxyOutputsForWorkflowException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

An exception in getting outputs from Galaxy for a workflow.

GalaxyOutputsForWorkflowException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyOutputsForWorkflowException

Constructs a new NoGalaxyOutputsForWorkflowException with no information.

GalaxyOutputsForWorkflowException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyOutputsForWorkflowException

Constructs a new NoGalaxyOutputsForWorkflowException with the given message.

GalaxyOutputsForWorkflowException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyOutputsForWorkflowException

Constructs a new NoGalaxyOutputsForWorkflowException with the given message and cause.

GalaxyOutputsForWorkflowException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyOutputsForWorkflowException

Constructs a new NoGalaxyOutputsForWorkflowException with the given cause.

GalaxyProjectName - Class in ca.corefacility.bioinformatics.irida.model.upload.galaxy

A name for a Galaxy project (Library) used for checking the validity of the name.

GalaxyProjectName(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName

Builds a new GalaxyObjectName with the given name.

GalaxyRedirectionEndpointController - Class in ca.corefacility.bioinformatics.irida.ria.web.oauth

Controller for handling OAuth2 authorization codes for the Galaxy exporter

GalaxyRedirectionEndpointController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.oauth.GalaxyRedirectionEndpointController

galaxySessionInterceptor() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

GalaxySessionInterceptor - Class in ca.corefacility.bioinformatics.irida.ria.config

Interceptor to determine if the HttpServletRequest is from a Galaxy Instance.

GalaxySessionInterceptor() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor

galaxyToolDataService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

GalaxyToolDataService - Class in ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

A service class for dealing with Galaxy Tool Data Tables.

GalaxyToolDataService(ToolDataClient) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyToolDataService

Builds a new GalaxyToolDataService with the given ToolDataClient.

GalaxyToolDataTableException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

An exception that gets thrown when there a problem accessing a Galaxy Tool Data Table.

GalaxyToolDataTableException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyToolDataTableException

Constructs a new GalaxyToolDataTableException with no information.

GalaxyToolDataTableException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyToolDataTableException

Constructs a new GalaxyToolDataTableException with the given message.

GalaxyToolDataTableException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyToolDataTableException

Constructs a new GalaxyToolDataTableException with the given message and cause.

GalaxyToolDataTableException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyToolDataTableException

Constructs a new GalaxyToolDataTableException with the given cause.

galaxyWorkflowService() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

GalaxyWorkflowService - Class in ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

Handles operating with workflows in Galaxy.

GalaxyWorkflowService(WorkflowsClient, Charset) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Constructs a new GalaxyWorkflowSubmitter with the given information.

GalaxyWorkflowState - Enum in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

Defines the state of a workflow.

GalaxyWorkflowStatus - Class in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

Defines the status of a workflow.

GalaxyWorkflowStatus(GalaxyWorkflowState, Map<GalaxyWorkflowState, Set<String>>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Constructs a new GalaxyWorkflowStatus with the given information.

GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder - Class in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

Used to build a GalaxyWorkflowStatus from the underlying Galaxy objects.

GalaxyWorkflowStatusBuilder(HistoryDetails) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder

Constructs a new GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder.

gcContent(Short) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the gcContent

GenbankView - Class in ca.corefacility.bioinformatics.irida.web.spring.view

Write out GenBank formatted sequence files to the client.

GenbankView() - Constructor for class ca.corefacility.bioinformatics.irida.web.spring.view.GenbankView

Default constructor

generateLinkerCommand(NGSLinkerCmdRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.NGSLinkerService

Generate the full ngs-linker command.

generateStatements(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

generateStatements(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

generateStatements(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

generateStatements(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

GenericsException - Exception in ca.corefacility.bioinformatics.irida.web.controller.api.exception

An exception that can be used when the RESTGenericController fails to construct a resource.

GenericsException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.web.controller.api.exception.GenericsException

GenericsException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.web.controller.api.exception.GenericsException

Construct a GenericsException with a given message and cause

GenericStatModel - Class in ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics

Used to represent the time period and counts for statistics.

GenericStatModel(String, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel

GenomeAssembly - Class in ca.corefacility.bioinformatics.irida.model.assembly

Defines a genome assembly which can be associated with a sample.

GenomeAssembly() - Constructor for class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

GenomeAssembly(Date) - Constructor for class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

GenomeAssemblyFromAnalysis - Class in ca.corefacility.bioinformatics.irida.model.assembly

Defines a genome assembly from an IRIDA-based analysis.

GenomeAssemblyFromAnalysis(AnalysisSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

GenomeAssemblyRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

Repository for synchronizing GenomeAssembly from a RemoteAPI

GenomeAssemblyRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

A repository implementaion for reading GenomeAssembly from remote locations using a OAuthTokenRestTemplate

GenomeAssemblyRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.GenomeAssemblyRemoteRepositoryImpl

GenomeAssemblyRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

A service for reading UploadedAssemblys from a remote location

GenomeAssemblyRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

An implementation of GenomeAssemblyRemoteService using a GenomeAssemblyRemoteRepository to read remote GenomeAssembly

GenomeAssemblyRemoteServiceImpl(GenomeAssemblyRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

Create a new remote service that interacts with the given repository

GenomeAssemblyRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.assembly

A repository for storing and retrieving GenomeAssembly entities

GenomeAssemblyRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.assembly

A FilesystemSupplementedRepositoryImpl implementation for GenomeAssembly

GenomeAssemblyRepositoryImpl(EntityManager, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepositoryImpl

GenomeAssemblyService - Interface in ca.corefacility.bioinformatics.irida.service

A service for storing and retrieving GenomeAssembly entities.

GenomeAssemblyServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service implementation for storing and retrieving GenomeAssembly

GenomeAssemblyServiceImpl(GenomeAssemblyRepository, SampleGenomeAssemblyJoinRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

GENOMIC - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

GET_EVENTS_FOR_USER - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Query to get events for the specified user

getAccession() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getAccession() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getAccessTokenValiditySeconds() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getAccountEmail() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy

getActivate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getActivitiesForProject(Long, int, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIActivitiesService

Get a page of activities for a project

getAdditionalProperties() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getAdditionalProperties() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

Get the added properties

getAdminAnalysesStatistics(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

Get updated usage statistics for analyses for the provided time period

getAdminAnalysesStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns a dto with a list of GenericStatModels which contains the analyses ran counts and labels

getAdminAnalysisList(Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

Get the admin all Analysis list page

getAdminDashboard() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminBaseController

Get the index page

getAdminProjectStatistics(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

Get updated usage statistics for projects for the provided time period

getAdminProjectStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns a dto with a list of GenericStatModels which contains the projects created counts and labels

getAdminSampleStatistics(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

Get updated usage statistics for samples for the provided time period

getAdminSampleStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns a dto with a list of GenericStatModels which contains the samples created counts and labels

getAdminStatistics(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

Get basic usage statistics for projects, samples, analyses, and users for the provided time period

getAdminStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns a dto with basic stats (counts) for analyses, projects, users, and samples.

getAdminUserLoggedInStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns the number of users logged in for the time period

getAdminUserStatistics(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.AdminStatisticsAjaxController

Get updated usage statistics for users for the provided time period

getAdminUserStatistics(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

Returns a dto with a list of GenericStatModels which contains the users created counts and labels

getAffectedClass() - Method in exception ca.corefacility.bioinformatics.irida.exceptions.InvalidPropertyException

getAjaxAPIList(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Get a list of the current page for the Remote API Table

getAjaxDownloadAnalysisSubmission(Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Download all output files from an AnalysisSubmission

getAllAnalysisOutputInfoSharedWithProject(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get all ProjectSampleAnalysisOutputInfo for a Project.

getAllAnalysisOutputInfoSharedWithProject(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get all ProjectSampleAnalysisOutputInfo for a Project.

getAllAnalysisOutputInfoSharedWithProject(Long, Set<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get all ProjectSampleAnalysisOutputInfo shared with a Project.

getAllAnalysisOutputInfoSharedWithProject(Long, Set<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryCustom

Get all ProjectSampleAnalysisOutputInfo shared with a Project.

getAllAnalysisOutputInfoSharedWithProject(Long, Set<UUID>) - Method in class ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryImpl

Get all ProjectSampleAnalysisOutputInfo shared with a Project.

getAllAnnouncements() - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of all of the Announcements that currently exist

getAllAnnouncements() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of all of the Announcements that currently exist

getAllAutomatedAnalysisOutputInfoForAProject(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

getAllAutomatedAnalysisOutputInfoForAProject(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

getAllAutomatedAnalysisOutputInfoForAProject(Long, Set<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

getAllAutomatedAnalysisOutputInfoForAProject(Long, Set<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryCustom

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

getAllAutomatedAnalysisOutputInfoForAProject(Long, Set<UUID>) - Method in class ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryImpl

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

getAllDefaultWorkflowsByType(Set<AnalysisType>) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets all of the default workflows for a given Set of AnalysisTypes.

getAllMetadataFieldsByQueryString(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get a list of all MetadataTemplateFields that contain the query

getAllMetadataFieldsByQueryString(String) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get a list of all MetadataTemplateFields that contain the query

getAllPipelines(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Get a list of all pipelines in the IRIDA instance

getAllProjectsEvents(Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Get the events for all projects

getAllProjectsEvents(Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl

Get a list of events for all projects

getAllProjectsEvents(Pageable) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectEventService

Get a list of events for all projects

getAllProjectsPage(Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the admin projects page.

getAllRecentActivities(int, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.ActivitiesAjaxController

Get a specific page of recent activities for all projects

getAllRecentActivities(int, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIActivitiesService

Get a specific page of recent activities for all projects for admin

getAllSamplesInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Get a list of all samples in the cart, these will be separated out into samples that the user can and cannot modify.

getAllUserAnalysisOutputInfo() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Get all the user single sample analysis outputs

getAllUserAnalysisOutputInfo(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get all User generated AnalysisOutputFile info

getAllUserAnalysisOutputInfo(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

getAllUserAnalysisOutputInfo(Long) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepository

Get all User generated analysis output information.

getAllUserAnalysisOutputInfo(Long) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryCustom

Get all User generated analysis output information.

getAllUserAnalysisOutputInfo(Long) - Method in class ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionRepositoryImpl

Get all User generated analysis output information.

getAllWorkflowsByType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets all the workflows for a given AnalysisType.

getAnalysesRanGrouped(Date, StatisticTimePeriod) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get list of GenericStatModel of analyses run in the past n time period grouped by the format provided.

getAnalysesRanGrouped(Date, StatisticTimePeriod) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get list of GenericStatModel of analyses run in the past n time period grouped by the format provided.

getAnalysesRanInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get count of analyses run in the time period

getAnalysesRanInTimePeriod(Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get count of analyses run in the time period

getAnalysesStats() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

getAnalysis() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

getAnalysis() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnalysisCleanedState() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

getAnalysisDescription() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Get the description of the analysis

getAnalysisDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getAnalysisFastQC() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

getAnalysisForSubmission(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get the Analysis for an AnalysisSubmission.

getAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getAnalysisInfo(Long, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the analysis details

getAnalysisInputFilePairs(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get the SequenceFilePairs used for the AnalysisSubmission

getAnalysisInputUnpairedFiles(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

get the SequenceFiles not in SequenceFilePairs used for the AnalysisSubmission

getAnalysisName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnalysisName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

getAnalysisOutputFile(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get an analysis output file for a given submission

getAnalysisOutputFile(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Get an output file with the given key

getAnalysisOutputFileContents(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get the actual file contents for an analysis output file.

getAnalysisOutputFileId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisOutputFileKey() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisOutputFileNames() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Return the names of available output files from this analysis

getAnalysisOutputFiles() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

Get all output files produced by this Analysis.

getAnalysisOutputFilesMap() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getAnalysisPriority() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getAnalysisResults(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService

Gets an Analysis object containing the results for this analysis.

getAnalysisResults(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy

Gets an Analysis object containing the results for this analysis.

getAnalysisRunningTime(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit

Gets the running time of an analysis

getAnalysisSampleProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnalysisServiceStatus() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get the status of the analysis service.

getAnalysisServiceStatus() - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get the status of the analysis service.

getAnalysisState() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Gets the state of this analysis.

getAnalysisState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

getAnalysisState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnalysisStateModel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

getAnalysisStates(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Get a internationalized list of all Analysis pipeline states.

getAnalysisSubmission() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

getAnalysisSubmission() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getAnalysisSubmissionId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisSubmissionId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

getAnalysisSubmissionId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getAnalysisSubmissionId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

getAnalysisSubmissionName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds(Collection<UUID>) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Gets all AnalysisSubmissionServices accessible by the current user matching one of the workflow ids.

getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds(Collection<UUID>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Gets all AnalysisSubmissionServices accessible by the current user matching one of the workflow ids.

getAnalysisSubmissionsForCurrentUser() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Gets a Set of AnalysisSubmissions for the current User.

getAnalysisSubmissionsForCurrentUser() - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Gets a Set of AnalysisSubmissions for the current User.

getAnalysisSubmissionsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Gets a Set of AnalysisSubmissions for a User.

getAnalysisSubmissionsForUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Gets a Set of AnalysisSubmissions for a User.

getAnalysisSubmissionsSharedToProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get a collection of all AnalysisSubmissions shared with a Project.

getAnalysisSubmissionsSharedToProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get a collection of all AnalysisSubmissions shared with a Project.

getAnalysisSubmissionTemplatesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionTemplateRepository

Get all the AnalysisSubmissionTemplates for a given Project

getAnalysisTemplatesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get all the AnalysisSubmissionTemplates for a given Project

getAnalysisTemplatesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get all the AnalysisSubmissionTemplates for a given Project

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getAnalysisType() - Method in interface ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater

Gets the AnalysisType this updater service handles.

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.AssemblySampleUpdater

Gets the AnalysisType this updater service handles.

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.BioHanselSampleUpdater

Gets the AnalysisType this updater service handles.

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.SISTRSampleUpdater

getAnalysisType() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Gets the particular AnalysisType of the workflow to load.

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnalysisType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

getAnalysisTypes() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.config.AnalysisTypeSet

getAnalysisViewer() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Get the name of the viewer to use for this pipeline

getAnalysisViewer() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getAnnouncement(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handles request for getting an announcement.

getAnnouncement(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Get an announcement.

getAnnouncementID() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

getAnnouncementsAdmin(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handle request for getting a paged list of announcements for an administrator.

getAnnouncementsAdmin(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Returns a paged list of announcements for an administrator.

getAnnouncementsByCreator(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.AnnouncementRepository

Get all announcements created by a specific User

getAnnouncementsCreatedByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of Announcements created by specific admin User

getAnnouncementsCreatedByUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of Announcements created by specific admin User

getAnnouncementsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Get a collection of the Announcements related to a User, meaning the collection of Announcements read and unread by the User

getAnnouncementsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of Announcements that have been read and unread by User

getAnnouncementsForUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of Announcements that have been read and unread by User

getAnnouncementsPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementsController

Request for the page to display a list of read and unread announcements for user.

getAnnouncementsReadByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Get a collection of the Announcements related to a User, meaning the collection of Announcements marked as read by the User

getAnnouncementsUnreadByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Gets a collection of Announcements that have not been marked as read by the User.

getAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handle request for getting a list of read and unread announcements for a user.

getAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Returns a list of read and unread announcements for a user.

getAnnouncementUserJoin(Announcement, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Get a specific AnnouncementUserJoin by Announcement and User

getApi() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getAPIKey() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy

getApplicationContext() - Method in class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase.ApplicationContextSpringResourceOpener

getArgs() - Method in class ca.corefacility.bioinformatics.irida.events.MethodEvent

Get the arguments from the method call

getAssemblies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles

getAssemblies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles

getAssembliesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService

Get all GenomeAssembly for the given Sample

getAssembliesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

Get all GenomeAssembly for the given Sample

getAssemblyOutput() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

Get genome assembly AnalysisOutputFile.

getAssociated() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getAssociated() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectSamplesFilter

getAssociatedProjectIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest

getAssociatedProjects(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController

Get a list of all projects associated with the current project.

getAssociatedProjects(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService

Get a list of all projects associated with the current project.

getAssociatedProjectsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController

Get a list of all projects associated with the current project.

getAssociatedProjectsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService

Get a list of all projects associated with the current project.

getAuthorities() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getAuthority() - Method in enum ca.corefacility.bioinformatics.irida.model.user.Role

getAuthorizedGrantTypes() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getAutomatedAssembly() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getAutomatedAssembly() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getAutomatedPipelines(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Get a list of available automated pipelines within the IRIDA instance

getAutomatedProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getAutomatedSingleSampleOutputs(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Get all the automated single sample analysis outputs for the project

getAutomatedSingleSampleOutputs(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Get all the automated single sample analysis outputs for the project

getAvailableMembersForProject(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Get a filtered list of available IRIDA instance users for this project

getAvailableUserGroupsForProject(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Get a list of user groups that are not on the current project

getAvailableUserGroupsForProject(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Get a list of UserGroups that are not on the current Project

getAvailableUsersForProject(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Get a filtered list of available IRIDA instance users for this project

getAvailableUsersForUserGroup(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Get a listing of available users for the user group filtered by a text query

getAvailableUsersForUserGroup(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Get a list of system users who are not on the project yet.

getBackgroundColor() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Gets an optional Color object used to modify the background color in the "Select a Pipeline" page.

getBioProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getBioProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getBioProjectId() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getBioProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel

getBioSample() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getBioSample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getBioSample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getBioSampleFiles() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getBioSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getBytesForFile() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

Read the bytes for an image output file

getCapacity() - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Get the AnalysisExecutionService capacity for running new jobs.

getCapacity() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Get the AnalysisExecutionService capacity for running new jobs.

getCartPage(Model, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartController

Get the dedicated page for the Cart

getCartSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Get the sample ids of samples that are in the cart

getCartSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get a list of sample ids in the cart

getCartSamplesForNewProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get a list of samples that are currently loaded into the cart that can be added to a new project This requires a special method because the user can only add samples to the new project that they already can modify.

getCartSamplesForProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Get the samples that are in the cart for a specific project

getCgmlstDistance() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getCgmlstFoundAlleles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getCgmlstGenomeMatch() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getCgmlstMatchingAlleles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getCgmlstST() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getCgmlstSubspecies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getChangeUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

getChildren() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.TaxonomyEntry

getChildren() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Get a list of all the children of this node

getChoices() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Get the list of choices for this parameter

getChunk() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getChunksForEntryType(ServletContext, String, WebpackerTagType) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerManifestParser

Get a list of webpack chunks for a specific file type given an entry.

getClientId() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getClientId() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

getClientId() - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

getClientId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableModel

getClientId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getClientId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getClientId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableAdminModel

getClientList(ClientTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Get a listing of clients based on the table request.

getClientSecret() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getClientSecret() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

getClientSecret() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getClientSecret() - Method in class ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableAdminModel

getClientsList(ClientTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Get a page in the clients listing table based on the table request.

getCollectedBy() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getCollectedBy() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getCollectedBy() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getCollectionDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getCollectionDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getColumnName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions

Column Name

getColumnType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

getCommandLine() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getCommandLine() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getConcatenator(Class<T>) - Static method in class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenatorFactory

Get a SequencingObjectConcatenator for the given class type

getConcatenator(Collection<? extends SequencingObject>) - Static method in class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenatorFactory

Get a SequencingObjectConcatenator for a given collection of SequencingObjects

getConfirmationMessage() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

getConfirmationMessage() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

getConfirmationMessage() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

getConfirmationMessage() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

getContent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.list.PagedListResponse

getContent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.EntriesResponse

getContent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse

getCount() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse

getCoverage() - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

Get the coverage number for this QCEntry

getCoverage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getCoverage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getCoverage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getCoverageForSamplesInProject(Project, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get Coverage for samples within a project.

getCoverageForSamplesInProject(Project, List<Long>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get Coverage for samples within a project.

getCreated() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getCreatedByTool() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getCreatedByTool() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceConcatenation

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

getCreatedDate() - Method in interface ca.corefacility.bioinformatics.irida.model.Timestamped

Get the created date of the object

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Get the created date of the object

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel

getCreatedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

getCss() - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

getCurrent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

getCurrent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntPagination

Return the page number to request

getCurrent() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

getCurrentId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getCurrentPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Get the currently viewed page in the DataTable.

getCurrentUser() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Get the user account that is currently logged in.

getCurrentUserDetails() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.CurrentUserAjaxController

Get information about the current user

getData() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions

Column Data

getData() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

The data to be displayed in the table.

getDataIndex() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

getDataIndex() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

getDatasetForFileInHistory(String, String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Gets a Dataset object for a file with the given name in the given history.

getDataSource() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse

getDataStorage() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy

getDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

getDateRead() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserTableModel

getDays() - Method in enum ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

getDefaultGenomeAssembly() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getDefaultMetadataTemplateId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getDefaultSequencingObject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getDefaultSequencingObject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

getDefaultTemplateForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get the default MetadataTemplate for the given Project (if one exists)

getDefaultTemplateForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get the default MetadataTemplate for the given Project (if one exists)

getDefaultValue() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Gets the default value for this parameter.

getDefaultWorkflowByType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets the default workflow for a given type of analysis.

getDefaultWorkflowUUID() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Gets the UUID of the default implementation of the workflow to use.

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Get a description of the remote api

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

getDescription() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ProjectUserGroupsTableModel

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getDescription() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getDetails() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableModel

getDetailsPage(Long, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

View details about an individual analysis submission

getDirectoryPath() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getDisplayableIridaWorkflow(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Returns a workflow with the given id that is displayable.

getDisplayableWorkflowTypes() - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets a Set of disabled AnalysisTypes.

getDisplayColumn() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

getDisplayFormat() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

getDraw() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Get the draw counter.

getDraw() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

Get the draw counter.

getDT_RowId() - Method in interface ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel

Get the datatables row prefixed id

getDuplicationlevelChart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

getDuplicationLevelChart() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

Line chartshowing duplication-level as a PNG-formatted image in a byte array.

getDuration() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

getDuration() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

getDuration() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getDuration() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getDuration() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

getDurationInMilliseconds(Date, Date) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities

Get the milliseconds between two Dates

getDynamicSource() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Gets the dynamic source for the parameter.

getDynamicSources() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getEmail() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getEmail() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getEmail() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getEmail() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getEmailConfigured() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISettingsService

Get if email is configured.

getEmailConfigured() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.IRIDASettingsAjaxController

Get if email is configured.

getEmailPipelineResultCompleted() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Whether or not to send an email upon pipeline completion.

getEmailPipelineResultCompleted() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

getEmailPipelineResultError() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Whether or not to send an email upon pipeline error.

getEmailPipelineResultError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

getEmbedded() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportSample

Get a Map of all the file links

getEnabled() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getEnabledAnalysisSubmissionTemplatesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.AnalysisSubmissionTemplateRepository

Get only the enabled AnalysisSubmissionTemplates for a given Project

getEncoding() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getEnd() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getEndDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

Get the end date of the filter

getEndDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifest

getEntry() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

getEntryId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getEntryId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

getEntryValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

Returns the associated value to which the given key is mapped

getError() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

getError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxErrorResponse

getError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getErrorHandler() - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.OAuthTokenRestTemplate

getErrorMessage() - Method in exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIConstraintViolationException

getErrors() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxFormErrorResponse

getErrors() - Method in exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIConstraintViolationException

getErrors() - Method in exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIUserFormException

getErrorsFromDataIntegrityViolationException(DataIntegrityViolationException, Map<String, ExceptionPropertyAndMessage>, MessageSource, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.BaseController

Converts a DataIntegrityViolationException to a usable map of strings for displaying in the UI.

getErrorsFromViolationException(ConstraintViolationException) - Method in class ca.corefacility.bioinformatics.irida.ria.web.BaseController

Changes a ConstraintViolationException to a usable map of strings for displaying in the UI.

getEventClass() - Method in class ca.corefacility.bioinformatics.irida.events.MethodEvent

Get the class of event to be created

getEventsForProject(Project, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Get the events for a given project

getEventsForProject(Project, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl

Get the events for a given project

getEventsForProject(Project, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectEventService

Get the events for a given project

getEventsForUser(User, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Get the events on all projects for a given user

getEventsForUser(User, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl

Get the events on all projects for a given user

getEventsForUser(User, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectEventService

Get the events on all projects for a given user

getEventsForUserAfterDate(User, Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Get all ProjectEvents for a given User that occurred after a given Date

getEventsForUserAfterDate(User, Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl

Get a list of events for a User which occurred after the given date.

getEventsForUserAfterDate(User, Date) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectEventService

Get a list of events for a User which occurred after the given date.

getExcelCols() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

getExcelHeaders() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

getExcelRows() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

getExcelSheetNames() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

getExcelSheetNames(Workbook) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Extract the sheet names from the excel workbook

getExecutionManagerAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getExecutionManagerFileId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getExecutionManagerIdentifier() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getExecutionParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

getExecutionTimeParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

Get the parameters for execution time of a pipeline

getExitCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getExpiryDate() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

Get the date that this token expires

getExportableTableHeaders(MessageSource, Locale) - Method in interface ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportable

Get an ordered list of internationalized table headers for the datatable.

getExportableTableHeaders(MessageSource, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

Get an ordered list of internationalized table headers for the datatable.

getExportableTableRow() - Method in interface ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportable

Convert the attribute of the class into a ordered list.

getExportableTableRow() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

Convert the attribute of the class into a ordered list.

getExportDetails(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService

Get the details for an NcbiExportSubmission for the UI

getExportDetails(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get the details of a specific NCBI SRA submission

getExportedSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel

getFast5() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles

getFast5() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles

getFast5FilesForExportSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of fast5 sequence files for a sample

getFast5FilesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.Fast5ObjectRemoteService

Get all the Fast5Objects associated with a Sample

getFast5FilesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.Fast5ObjectRemoteServiceImpl

Get all the Fast5Objects associated with a Sample

getFast5FilesForSample(Sample, Project, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of fast5 sequence files for a sample

getFast5Type() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

getFastQCAnalysis() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getFastQCAnalysisForSequenceFile(SequencingObject, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisService

Get the AnalysisFastQC object for a given SequencingObject and SequenceFile ID

getFastQCAnalysisForSequenceFile(SequencingObject, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisServiceImpl

Get the AnalysisFastQC object for a given SequencingObject and SequenceFile ID

getFastQCCharts(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.SequenceFileAjaxController

Gets the fastqc charts for the file.

getFastQCCharts(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

Gets the fastqc charts for the file.

getFastQCDetails(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.SequenceFileAjaxController

Gets the details for the file fastqc results.

getFastQCDetails(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

Gets the details for the sequence file

getFastqcVersion() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getFastQCVersion() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

getField() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

getField() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

getField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

getField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

getField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

getFieldId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getFieldId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

getFieldKey() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

Key for displaying the field in the UI

getFieldKey() - Method in class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

getFieldKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

getFieldName() - Method in exception ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException

Get the field name that caused the exception

getFields() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getFields() - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

Gets the assembly file.

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

Gets the assembly file.

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

getFile() - Method in interface ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile

Get the location on the file system where the sequence file is stored

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getFile() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getFile() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SingleEndSequenceFileModel

getFileExt() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getFileExt(Path) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Get file extension from filepath.

getFileExtension(List<? extends SequencingObject>) - Method in class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenator

Get the extension of the files to concatenate

getFileId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

getFileIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getFileInfo() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

getFileInfo() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getFileLength() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getFilename() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getFilename() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getFilename() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

getFileName() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

getFileName() - Method in interface ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile

The base name of the file

getFileName() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getFileName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

getFileName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

getFilePath() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getFilePointer() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getFileProcessor() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getFileProcessors() - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessingChain

Get the collection of FileProcessor that this FileProcessingChain manages.

getFileProcessors() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

Get the collection of FileProcessor that this FileProcessingChain manages.

getFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

getFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

getFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getFileRevisionNumber() - Method in interface ca.corefacility.bioinformatics.irida.model.VersionedFileFields

Get the version of the instance.

getFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

This intentionally always returns 0.

getFiles() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getFiles() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

Get the SequenceFiles associated with this SequencingObject

getFiles() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

getFiles() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

Get the SequenceFiles associated with this SequencingObject

getFiles() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

Get the SequenceFiles associated with this SequencingObject

getFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UploadReferenceFilesResponse

getFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

getFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.PairedEndSequenceFileModel

getFilesForSample(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Get sequencing files associated with a sample

getFilesForSamples(List<Long>, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Get the set of files for samples by the sample identifiers

getFilesForSamples(List<Long>, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get details about the files belonging to a list of samples

getFileSize() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

Get human-readable file size.

getFileSize() - Method in interface ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile

Get the size of the file.

getFileSize() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Get the size of the file.

getFileSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SequenceFileModel

getFileSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

getFileSizeBytes() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

Get the size of the genome assembly files

getFileSizeBytes() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getFileType() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getFileType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

getFileType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getFileWithId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

Get the SequenceFile with the given id in this object's files collection

getFilter() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getFilteredProjectSamples(List<Project>, ProjectSampleJoinSpecification, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

getFilteredProjectSamples(List<Project>, ProjectSampleJoinSpecification, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

getFilteredSamplesForProjects(List<Project>, List<String>, String, String, String, Date, Date, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

getFilteredSamplesForProjects(List<Project>, List<String>, String, String, String, Date, Date, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

getFilteredSequences() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getFilters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesListRequest

getFilters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSamplesTableRequest

getFirstFileSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

getFirstFileSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getFirstJobError(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get first JobError for a AnalysisSubmission id

getFirstJobError(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get first JobError for a AnalysisSubmission id

getFirstLine() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getFirstName() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getFirstName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

getFirstName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getFirstName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getFirstName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getForceSync() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

getForward() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

getForwardSequenceFile() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

Gets the forward SequenceFile from the pair.

getFoundRows() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

getFoundSampleId() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

getFrequency() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

getFullCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get the entire cart flushed out into Projects with their Samples

getGalaxyExportForm() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartGalaxyController

Get a list of links for all Sample to be exported to the Galaxy Client.

getGalaxyHistoryId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

getGalaxyJobErrors() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

getGalaxyRedirect(String) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.GalaxyRedirectionEndpointController

Get the URL for the galaxy redirection location.

getGalaxyUrl() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

getGcContent() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getGenomeAssembliesForExportSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get any genome assemblies that are available for a sample

getGenomeAssembliesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get any genome assemblies that are available for a sample

getGenomeAssembliesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.GenomeAssemblyRemoteService

List the GenomeAssembly for a given Sample

getGenomeAssembliesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

List the GenomeAssembly for a given Sample

getGenomeAssemblyForSample(Sample, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService

Gets the genome assembly for a sample.

getGenomeAssemblyForSample(Sample, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

Gets the genome assembly for a sample.

getGenomeSize() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getGenomeSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

getGeographicLocationName() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getGeographicLocationName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getGrantType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getGroupByFormat() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

getGroupDetailsPage(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.UserGroupsController

Get the default index page for listing groups.

getH1() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getH2() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getHeaderName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getHeaders() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

getHelp() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse

getHistoryId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getHref() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.ActivityItem

getHtml() - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

getHtmlOutputForSubmission(Long, String, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

Get the html page from the file name provided.

getId() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getId() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

getId() - Method in class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

getId() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getId() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getId() - Method in interface ca.corefacility.bioinformatics.irida.model.IridaThing

Get the numerical identifier for this object

getId() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getId() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getId() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getId() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getId() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Get the entity id

getId() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

getId() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceConcatenation

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getId() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getId() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

getId() - Method in interface ca.corefacility.bioinformatics.irida.model.Timestamped

Get the identifier for this object

getId() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Get the numerical identifier for this object

getId() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

getId() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

getId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxCreateItemSuccessResponse

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CartSampleModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserTableModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

getId() - Method in interface ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel

Get the id of the object being displayed

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.MinimalModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectObject

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

getId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

getIdentifier() - Method in interface ca.corefacility.bioinformatics.irida.model.IridaThing

Get the id parameter as a string.

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

getIdentifier() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource

We don't want to expose the id for the relationship, but rather the id for the object of the relationship.

getIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel

getIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.MergeRequest

getImageFile(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get an image file associated with a specific AnalysisSubmission by file name.

getIndex() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

getIndex() - Method in class ca.corefacility.bioinformatics.irida.ria.web.UserGroupsController

Get the default index page for listing groups.

getInputParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Gets the input parameters for this submission.

getInputParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

getInputs() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getInputsObject() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy

Gets the WorkflowInputs object.

getInstrumentModel() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getInstrumentModel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getInstrumentModel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getIridaWorkflow(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Returns a workflow with the given id.

getIridaWorkflowIds() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowIdSet

getIridaWorkflowOrUnknown(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Returns a workflow associated with the given AnalysisSubmission, attempting to fill in as many details as possible if the workflow can't be found.

getIridaWorkflowOrUnknown(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Returns a workflow associated with the given UUID, attempting to fill in as many details as possible if the workflow can't be found.

getIridaWorkflows() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowSet

getIsolate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getIsolate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getIsolationSource() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getIsolationSource() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getItems() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

getJavascript() - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

getJobErrors(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get the JobError objects for a AnalysisSubmission id

getJobErrors(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get the JobError objects for a AnalysisSubmission id

getJobId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getKey() - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.MinimalModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableItem

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

getKey() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

Get a human readable label for this object.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.enums.UserGroupRemovedProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserGroupRoleSetProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getLabel() - Method in interface ca.corefacility.bioinformatics.irida.model.IridaThing

Get a human readable label for this object.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getLabel() - Method in interface ca.corefacility.bioinformatics.irida.model.joins.Join

By default, we will return the label of the subject of the join.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

Get a human readable label for this object.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceConcatenation

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

Get a human readable label for this object.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Get a human readable label for this object.

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getLabel() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.ActivityItem

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CartSampleModel

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectModel

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.SelectOption

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupRole

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

getLabel() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.Role

getLabel() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource

getLanguage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

getLastLogin() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getLastLogin() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getLastName() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getLastName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

getLastName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getLastName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getLastName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getLastUpdate() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getLastUpdate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getLatitude() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getLatitude() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getLayoutType() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getLength() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Number of records that the table can display in the current draw.

getLevel() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

getLevel() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

getLevel() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

getLibraryConstructionProtocol() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getLibraryConstructionProtocol() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getLibraryConstructionProtocol() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getLibraryName() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getLibraryName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getLibraryName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getLibrarySelection() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getLibrarySelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getLibrarySelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getLibrarySource() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getLibrarySource() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getLibrarySource() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getLibraryStrategy() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getLibraryStrategy() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getLibraryStrategy() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getLimit() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getLineListPage(Long, Long, Model, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Get the page to display the project samples linelist.

getLinelistTemplatePage(Long, Model, Locale, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Get the page to create new linelist templates

getLineListTemplates(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

Get a List of all MetadataTemplate associated with the project.

getLines() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getLink(String) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Returns the link with the given rel.

getLinkerCommand(NGSLinkerCmdRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.NGSLinkerAjaxController

Get the command for the ngs-linker script with project and sample information.

getLinks() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Returns all Links contained in this resource.

getLinks() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportSample

Get the Map for this sample

getLinks(HttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

Creates a response with a set of links used to discover the rest of the system.

getListOfRemoteApis() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Get a list of all available remote API f

getListOfRemoteApis() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Get a list of all RemoteAPIs

getLocale() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getLocale() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getLocale() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getLocale() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getLocales() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig.IridaLocaleList

getLocales() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISettingsService

Get a list of all locales.

getLocales() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.IRIDASettingsAjaxController

Get a list of all locales.

getLocation() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.manager.galaxy.ExecutionManagerGalaxy

getLocked() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSamplesByUserPermissions

getLocked() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getLockedSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get a list of the Sample ids that are not owned by the given project

getLockedSamplesInProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a list of Sample ids that are locked in this project.

getLockedSamplesInProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a list of Sample ids that are locked in this project.

getLoggedInUserPage(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersController

Get the currently logged in user's page

getLoginSuccessHandler() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig

getLongitude() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getLongitude() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getMappingForParameterId(ParameterBuilderGalaxy.ParameterId) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy

Gets the mapped object for the id of the parameter.

getMarkSync() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

getMashDistance() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getMashGenome() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getMashSerovar() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getMashSubspecies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getMaximum() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

getMaximumCoverage() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getMaxLength() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getMaxRoleForProjectAndGroups(ProjectUserJoin, Collection<UserGroupProjectJoin>) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

Static method to compare a ProjectUserJoin and a collection of UserGroupProjectJoin and return the max ProjectMetadataRole from them

getMaxRoleForProjectsAndGroups(ProjectUserJoin, Collection<UserGroupProjectJoin>) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

Compares and returns the highest level ProjectRole from a ProjectUserJoin and a collection of UserGroupProjectJoins.

getMembers() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getMessage() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getMessage() - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

getMessage() - Method in class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

getMessage() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

Get the message for the qc entry

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxSuccessResponse

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification

getMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails

getMessage() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

Get the message for this response

getMessage(String, Object[], String, Locale) - Method in class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

getMessage(String, Object[], Locale) - Method in class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

getMessage(MessageSourceResolvable, Locale) - Method in class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

getMessageName() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.ExceptionPropertyAndMessage

getMetadaFieldsForTemplate(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Get the metadata fields for a specific template

getMetadata() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.ProjectMetadataResponse

getMetadata() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

getMetadata() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadata

getMetadata() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.sample.SampleMetadataResponse

getMetadataEntriesCountBySamplesAndField(MetadataTemplateField, List<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository

Get count of MetadataEntry related to the MetadataTemplateField in the list of Sample

getMetadataEntry() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

getMetadataEntry() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getMetadataEntry() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

getMetadataEntry() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getMetadataEntryById(Long) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository

Get the MetadataEntry by id

getMetadataEntryBySampleAndField(MetadataTemplateField, Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository

Get the MetadataEntry related to the MetadataTemplateField attached to the given Sample

getMetadataEntryId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getMetadataField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

getMetadataField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getMetadataFieldId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getMetadataFieldRestrictions(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Get the list of all metadata restrictions that belong to the current project.

getMetadataFieldsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryCustom

Get all MetadataTemplateField associated with a Project

getMetadataFieldsForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryImpl

Get all MetadataTemplateField associated with a Project

getMetadataFieldsForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get all the MetadataTemplateFields on a given Project

getMetadataFieldsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Deprecated.

getMetadataFieldsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Get all the metadata fields in a project

getMetadataFieldsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Get all MetadataTemplateFields belonging to a Project

getMetadataFieldsForProjects(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Get all the metadata fields for a list of projects

getMetadataFieldsForProjects(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Get all MetadataTemplateFields belonging to a list of Projects

getMetadataFieldsForTemplate(MetadataTemplate) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepository

Get all MetadataTemplateFields in a given MetadataTemplate

getMetadataForAnalysisSamples(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the metadata associated with a template for an analysis.

getMetadataForProjectSamples(Project, List<Long>, List<MetadataTemplateField>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryCustom

Get all the MetadataEntry for a set of samples in a given project.

getMetadataForProjectSamples(Project, List<Long>, List<MetadataTemplateField>) - Method in class ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryImpl

Get all the MetadataEntry for a set of samples in a given project.

getMetadataForProjectSamples(Project, List<Long>, List<MetadataTemplateField>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the metadata collections for a set of samples in a project.

getMetadataForProjectSamples(Project, List<Long>, List<MetadataTemplateField>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the metadata collections for a set of samples in a project.

getMetadataForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository

Get all the MetadataEntry attached to the given Sample

getMetadataForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the MetadataEntry set associated with the given Sample

getMetadataForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the MetadataEntry set associated with the given Sample

getMetadataForSampleAndField(Sample, Collection<MetadataTemplateField>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository

Get a set of MetadataEntry related to the MetadataTemplateField attached to the given Sample

getMetadataKeysForProject(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Search all Metadata keys available for adding to a template.

getMetadataRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

getMetadataRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getMetadataRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

getMetadataRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getMetadataRestrictionForFieldAndProject(Project, MetadataTemplateField) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

getMetadataRestrictionForFieldAndProject(Project, MetadataTemplateField) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get the MetadataRestriction for the given MetadataTemplateField and Project

getMetadataRestrictions() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getMetadataRestrictions(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Get the list of all metadata restrictions that belong to the current project.

getMetadataRestrictionsForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

getMetadataRestrictionsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

List all the MetadataRestriction for the given Project

getMetadataRole() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getMetadataRole() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getMetadataRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

getMetadataRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ProjectUserGroupsTableModel

getMetadataRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectMemberTableModel

getMetadataTemplateField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getMetadataTemplateField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

getMetadataTemplateFields(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Generates a list of metadata fields for a five template.

getMetadataTemplateListPage(Long, Model, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Get the page to create a new MetadataTemplate

getMetadataTemplatePage(Long, Long, Principal, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Get a the page for a specific MetadataTemplate

getMetadataTemplates(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Get a List of MetadataTemplates for a specific Project

getMetadataTemplatesForAnalysis(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get a list of all MetadataTemplates for the AnalysisSubmission

getMetadataTemplatesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataTemplateRepository

Get all the MetadataTemplates for a given Project

getMetadataTemplatesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get a list of MetadataTemplates for a given Project

getMetadataTemplatesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get a list of MetadataTemplates for a given Project

getMinimalSampleDetailsForFilteredProject(Long, ProjectSamplesTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Get a list of all samples in the current project and associated project that have been filtered, return a minimal representation of them.

getMinimalSampleDetailsForFilteredProject(Long, ProjectSamplesTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of all samples in the current project and associated project that have been filtered, return a minimal * representation of them.

getMinimum() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

getMinimumCoverage() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getMinLength() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getMiseqRunId() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource

getModel() - Method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

getModels() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableResponse

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getModifiedDate() - Method in interface ca.corefacility.bioinformatics.irida.model.MutableIridaThing

Get the date that this object was last modified

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Get the date that this object was last modified

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getModifiedDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getName() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getName() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

get the name of the remote API.

getName() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getName() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail

The name of this account as a string.

getName() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName

The name of the object to upload.

getName() - Method in interface ca.corefacility.bioinformatics.irida.model.upload.UploaderAccountName

The name of this account as a string.

getName() - Method in interface ca.corefacility.bioinformatics.irida.model.upload.UploadProjectName

The name of the object to upload.

getName() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

getName() - Method in enum ca.corefacility.bioinformatics.irida.model.user.Role

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Gets the name of this parameter.

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

Get parameter choice i18n key

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

getName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportSample

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.BaseModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.MinimalModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectObject

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

getName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

getNamedParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Get the named parameters object used to build this submission.

getNamespace() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getNCBIExportsForAdmin(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get a paged list of NCBI Export Submission based on the current page information

getNCBIExportsForAdmin(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService

Get a Page of NcbiExportSubmission

getNCBIExportsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get a List of all NCBI Export Submissions on a Project

getNCBIExportsForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService

Get a List of all NcbiExportSubmission that have occurred on a Project

getNcbiNamespace() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getNcbiNamespace() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getNcbiPlatforms() - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get all the available NCBI Sequencing platforms.

getNcbiSelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get a list of NCBI allowed Library selection techniques

getNcbiSources() - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get a list of NCBI Library Sources

getNcbiStrategies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Get a list of NCBI allowed Library strategies

getNewick() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

getNewickForAnalysis(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get a newick file associated with a specific AnalysisSubmission.

getNewickTree(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Construct the model parameters for results with a newick output Analysis

getNewName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.MergeRequest

getNotifications() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse

getNumberAnalysesByUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get count of AnalysisSubmission for the user grouped by the format provided.

getNumberAnalysesByUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get count of AnalysisSubmission for the user grouped by the format provided.

getNumberOfAnalyses() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserStatisticsResponse

getNumberOfProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserStatisticsResponse

getNumberOfSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserStatisticsResponse

getNumberOfSamplesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the number of Samples for a given Project.

getNumberOfSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the number of Samples for a given Project.

getNumberOfSamplesInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Get the number of samples from all projects that are currently in the cart

getNumberOfSamplesInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get the number of samples in the cart

getNumericValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

getOAntigen() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

getObject() - Method in interface ca.corefacility.bioinformatics.irida.model.joins.Join

Get the owned object in the relationship.

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getObject() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

getOldTokenId(RemoteAPIToken) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Remove any old token for this user from the database

getOperation() - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

getOperation() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSearch

getOptionalProperties() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

Get the Map of optional properties

getOptionalProperties() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Get the Map of optional properties

getOptionalProperties() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getOptionalProperty(String) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

Get an individual optional property

getOptionalProperty(String) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Get an individual optional property

getOptions() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.InputWithOptions

getOrder() - Method in class ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor

getOrder() - Method in class ca.corefacility.bioinformatics.irida.config.repository.ForbidJpqlUpdateDeletePostProcessor

getOrder() - Method in class ca.corefacility.bioinformatics.irida.events.ProjectEventAspect

This event **must** happen outside of a transaction so that multiple events happening at the same time do not result in a deadlock exception.

getOrder() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSort

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectModel

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getOrganism() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

getOrganization() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getOrganization() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getOrganization() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getOtherProperties() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

Get the other properties defined in the map

getOutputFile(Long, Long, Long, Long, Long, Long, Long, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Read some lines or text from an AnalysisOutputFile.

getOutputFilesInfo(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

For an AnalysisSubmission, get info about each AnalysisOutputFile

getOutputName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getOutputNames(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Get list of workflow output names.

getOutputs() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getOutputsMap() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Gets a Map representation of the outputs of a workflow, linking the output name to the IridaWorkflowOutput entry.

getOverrepresentedSequenceCount() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getOverrepresentedSequences() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getOwner() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

getOwner() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

getPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunController

Display the listing page

getPagedAnalyses(AnalysesListRequest, Boolean, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Returns a list of analyses based on paging, sorting and filter requirements sent in AnalysesListRequest

getPagedProjects(TableRequest, Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Get the table contents for the projects listing table based on the user and table request.

getPagedProjectSamples(Long, ProjectSamplesTableRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Returns a Page of samples for a project based on the information in the ProjectSamplesTableRequest

getPagedProjectSamples(Long, ProjectSamplesTableRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a page of samples based on the current state of the table options (filters, sort, and pagination)

getPagedProjectsForUser(TableRequest, Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController

Handle request for getting a filtered and sorted list of projects for a user or administrator

getPageNumber(int, int) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

Helper method to get the page number based on the pageSize of the list and the current start

getPageSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

getPageSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntPagination

getPageSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

getPageSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

getPaired() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles

getPairedEndSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

getPairedFiles(List<MultipartFile>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer

Get Paths to all paired sequence files

getPairedSequenceFilesForExportSample(Sample, Project) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of paired end sequence files for a sample

getPairedSequenceFilesForSample(Sample, Project, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of paired end sequence files for a sample

getPairs() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getPairs() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getPairs() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getPairs() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles

getParameterColumn() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

getParameterIds() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy

Gets a Set of the starting part of the names of any parameters.

getParameterName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

The name of the parameter to adjust.

getParameterName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

getParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

getParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

getParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getParameterValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

getParameterWithOptions() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getParent() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Get the parent node

getParentMessageSource() - Method in class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

getParse_results_error() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

getPassword() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getPassword() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getPerbaseChart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

getPerBaseQualityScoreChart() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

Box and whisker plot showing per-base quality scores as a PNG-formatted image in a byte array.

getPercentage() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getPercentCompleteForAnalysisSubmission(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Given the id of an AnalysisSubmission gets the percentage complete.

getPercentCompleteForAnalysisSubmission(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Given the id of an AnalysisSubmission gets the percentage complete.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisSubmissionPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateSamplesFromAnalysisSubmissionPermission

getPermissionProvided() - Method in interface ca.corefacility.bioinformatics.irida.security.permissions.BasePermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingRunPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateSequencingRunPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ManageLocalProjectSettingsPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadExportSubmissionPermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission

Get the implementation-specific permission provided.

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserGroupPermission

getPermissionProvided() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserPermission

getPermittedFieldsForCurrentUser(Project, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get all MetadataTemplateField that the currently logged in user is allowed to read

getPermittedFieldsForCurrentUser(Project, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get all MetadataTemplateField that the currently logged in user is allowed to read

getPermittedFieldsForTemplate(MetadataTemplate) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get all MetadataTemplateField the current user is allowed to read for a MetadataTemplate

getPermittedFieldsForTemplate(MetadataTemplate) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get all MetadataTemplateField the current user is allowed to read for a MetadataTemplate

getPersequenceChart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

getPerSequenceQualityScoreChart() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

Line chartshowing per-sequence quality scores as a PNG-formatted image in a byte array.

getPhoneNumber() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getPhoneNumber() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getPhoneNumber() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getPhoneNumber() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getPinned() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getPipelineDetails(UUID, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Get the launch page for a specific IRIDA Workflow Pipeline.

getPipelineDetails(UUID, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

Get the information about a specific workflow pipeline

getPipelineInfo(UUID) - Method in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.PipelineController

Get IridaWorkflowDescription for a workflow/pipeline UUID.

getPipelineLaunchPage(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchController

Mapping for the pipeline launch page.

getPipelineParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.CreateNamedParameterSetAjaxResponse

getPipelineSamples(boolean, boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Get a list of the samples that are in the cart and get their associated sequence files that can be used on the current pipeline

getPipelineSamples(boolean, boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineSampleService

Get a list of the samples that are in the cart and get their associated sequence files that can be used on the current pipeline

getPlatforms() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatformInstrumentModel

getPlugins() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig.IridaPluginList

getPossibleSource() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getPotentialProjectsToShareTo(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController

Get a list of projects that the user can share sample to.

getPotentialProjectsToShareTo(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Get a list of projects that the user can share sample to.

getPreviousExecutionTools() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

getPreviousState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

getPreviousState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

getPreviousStateBeforeError(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit

Gets the state of analysis prior to error

getPreviousSteps() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getPrimary() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.MergeRequest

getPriorDateFromCronString(String) - Static method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventEmailScheduledTaskImpl

Get the last time the job was run from the given cron string

getPriorities() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities

getPriorities() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getPriority() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getPriority() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

getPriority() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

getProcessingState() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getProcessingState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

getProcessors(String) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.WebpackerDialect

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.ProjectMetadataResponse

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

getProject() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

getProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

getProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiExportSubmissionAdminTableModel

getProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getProject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getProjectActivities(Long, int, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.ActivitiesAjaxController

Get a specific page of activities for a project

getProjectActivityPage(Long, Model, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Request for a specific project details page.

getProjectAnalyses(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectAnalysisController

Get the list of AnalysisSubmissions associated with this Project.

getProjectAnalysesByType(Long, String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectAnalysisController

Get the list of AnalysisSubmissions for this Project by type of analysis.

getProjectAnalysisList(Long, Principal, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the page for analyses shared with a given Project

getProjectAnalysisTemplates(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.ProjectSettingsAjaxController

Get all the automated workflow (analysis templates) for the current project

getProjectAnalysisTemplates(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

List of existing automated workflows on a project

getProjectDescription() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getProjectDetails(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Get general details about the project.

getProjectForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get a collection of the Projects related to a Sample

getProjectHash() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ProjectHashResource

getProjectHash(Project) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl

Read the full project hash for the given project

getProjectHash(Project) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectHashingService

Get a deep hashsum for the full project

getProjectHash(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.ProjectRemoteService

Read the full project hash for the given project

getProjectHash(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Get the deep project hash for the requested project

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

getProjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

getProjectIdsInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Get a list of project identifiers for projects that have samples in the cart.

getProjectIdsInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get a set of identifiers for Projects in the cart

getProjectInfo(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Get information about a project as well as permissions

getProjectJoinForUser(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get the join object between a given Project and User

getProjectMembers(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Get a paged listing of project members passed on parameters set in the table request.

getProjectMembers(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Get a paged listing of project members passed on parameters set in the table request.

getProjectMetadataRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Get a list of all metadata roles

getProjectMetadataRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Get a list of all metadata roles

getProjectMetadataTemplateFields(long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

Get a list of all MetadataTemplateFields on a Project

getProjectMetadataTemplates(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Get a list of metadata templates for a specific project

getProjectMetadataTemplates(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Get a list of MetadataTemplate for a specific Project

getProjectName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getProjectName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getProjectName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getProjectName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

getProjectName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

getProjectReferenceFilesPage(Model, Principal, long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectReferenceFileController

Get the reference files page for a project

getProjectRemoteSettings(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectSettingsRemoteAjaxController

Gets the remote synchronization Project settings

getProjectRemoteSettings(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteProjectService

Gets the remote synchronization Project settings

getProjectResources() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseProjectResource

getProjectRole() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

Get the user's role on the project

getProjectRole() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getProjectRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

getProjectRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectMemberTableModel

getProjectRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController

Get a list of all roles available on a project

getProjectRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Get a list of all roles available on a project

getProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getProjectSample(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Get the representation of a specific sample that's associated with the project.

getProjectSampleBySequencerId(Long, String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Get samples by a given string name

getProjectSampleMetadata(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

Get all the sample metadata for a given Project

getProjectSampleMetadata(HttpSession, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

Get the currently stored metadata.

getProjectSampleMetadata(HttpSession, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

Get the currently stored metadata.

getProjectSamples(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Get the list of Sample associated with this Project.

getProjectSamplesMetadataEntries(long, int, int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

Get a List of Map containing information from MetadataEntry for a Page of Samples in a Project

getProjectSamplesMetadataUploadPage(Model, Long, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Handle the page request to upload Sample metadata

getProjectSamplesPage(Model, Principal, long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the samples for a given project

getProjectsCreated(Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get count of projects created in the time period

getProjectsCreated(Date) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get count of projects created in the time period

getProjectsCreatedGrouped(Date, StatisticTimePeriod) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get list of GenericStatModel of projects created in the past n time period and grouped by the format provided.

getProjectsCreatedGrouped(Date, StatisticTimePeriod) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get list of GenericStatModel of projects created in the past n time period and grouped by the format provided.

getProjectSettingsPage(Long, Principal, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the project settings page

getProjectsForAnalysisSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all Projects a given AnalysisSubmission is shared with

getProjectsForAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all Projects a given AnalysisSubmission is shared with

getProjectsForAPI(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Get a list of project available at a remote API

getProjectsForAPI(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Get a list of projects available on a remote API

getProjectsForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get the projects that a given sample is on

getProjectsForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get the projects that a given sample is on

getProjectsForSequencingObjects(Collection<? extends SequencingObject>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get a Set of all Projects referred to by a collection of SequencingObjects

getProjectsForSequencingObjects(Collection<? extends SequencingObject>) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get a Set of all Projects referred to by a collection of SequencingObjects

getProjectsForSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository

Get all Projects a given AnalysisSubmission is shared with

getProjectsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get all Projects associated with a particular User.

getProjectsForUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all Projects associated with a particular User.

getProjectsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all Projects associated with a particular User.

getProjectsForUserGroup(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Get a full listing of all projects that this user group is on

getProjectsForUserGroup(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Gets a list of projects that are on a user group

getProjectsForUserUnique(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all Projects associated with a particular User.

getProjectsForUserUnique(User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all Projects associated with a particular User.

getProjectsForUserWithEmailSubscriptions(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Get a List of all Projects that a given User is subscribed to.

getProjectsForUserWithEmailSubscriptions(User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService

Get a List of all Projects that a given User is subscribed to.

getProjectsForUserWithSubscriptions(User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository

Get a List of all Projects that a given User is subscribed to.

getProjectsIdsInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Get all the identifiers for projects that have samples in the cart.

getProjectSPA(Model, Principal, long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Default page handler for all UI routes loaded through the project SPA endpoint

getProjectsPage(Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Request for the page to display a list of all projects available to the currently logged in user.

getProjectsSharePage(Long, Model, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the page to share samples between projects

getProjectStats() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

getProjectSubmissionShare(AnalysisSubmission, Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository

Read a ProjectAnalysisSubmissionJoin object for a given AnalysisSubmission and Project

getProjectSubscriptionsForUser(User, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Get a page of project subscriptions associated with a user.

getProjectSubscriptionsForUser(User, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService

Get a page of project subscriptions associated with a user.

getProjectSubscriptionsForUser(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectSubscriptionsAjaxController

Get the projects associated with a user

getProjectSubscriptionsForUser(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSubscriptionService

Get all the project subscriptions associated with a user

getProjectsUsedInAnalysisSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all Projects that have data used within an AnalysisSubmission.

getProjectsUsedInAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all Projects that have data used within an AnalysisSubmission.

getProjectsWithRemoteSyncStatus(RemoteStatus.SyncStatus) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Get a list of Projects from remote sites that have a given RemoteStatus.SyncStatus

getProjectsWithRemoteSyncStatus(RemoteStatus.SyncStatus) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get a list of Projects from remote sites that have a given RemoteStatus.SyncStatus

getProjectsWithRemoteSyncStatus(RemoteStatus.SyncStatus) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get a list of Projects from remote sites that have a given RemoteStatus.SyncStatus

getProjectsWithUserGroup(UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Get all of the projects with group.

getProjectsWithUserGroup(UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Get all of the projects with group.

getProjectSyncFrequencies() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getProjectSyncFrequency() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getProjectSyncFrequency() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

getProjectTemplateDetails(Model, Principal, Project) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectControllerUtils

Adds to the current view model default template information: Sidebar Information If the current user is an admin

getProjectUserGroups(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Get a table page of ProjectUserGroupsTableModel

getProjectUserJoin(User, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get the ProjectRole of a User on a given Project

getProjectUserJoin(User, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get the ProjectRole of a User on a given Project

getProperties() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

getProperty() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSearch

getPropertyName() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.ExceptionPropertyAndMessage

getProportionComplete() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Gets the proportion of the workflow tasks complete.

getProvenanceByFile(Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the full analysis provenance

getProvenanceId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getProvenanceUUID() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.PairedEndSequenceFileModel

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SingleEndSequenceFileModel

getQcEntries() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getQCEntriesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository

find all the QCEntry associated with SequencingObjects in a given Sample

getQCEntriesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Find all the QCEntry associated with SequencingObjects in a given Sample

getQCEntriesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Find all the QCEntry associated with SequencingObjects in a given Sample

getQCEntriesForSamples(List<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository

find all the QCEntry associated with SequencingObjects in a given Sample for a list of Samples.

getQCEntriesForSamples(List<Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Find all the QCEntry associated with SequencingObjects in a given Sample for a list of Samples

getQCEntriesForSamples(List<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Find all the QCEntry associated with SequencingObjects in a given Sample for a list of Samples

getQcMessages() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getQcStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getQcStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getQuality() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getQueued() - Method in class ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService.AnalysisServiceStatus

getRead() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getReadAnnouncementsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of Announcements that have been read by User

getReadAnnouncementsForUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of Announcements that have been read by User

getReadAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handle request for getting a list of read announcements for a user.

getReadAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Returns a list of read announcements for a user.

getReadBy() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getReadDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

getReadUsersForAnnouncement(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get all of the Joins describing users that have comfirmed they've read a particular Announcement

getReadUsersForAnnouncement(Announcement) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get all of the Joins describing users that have comfirmed they've read a particular Announcement

getRecentActivities(int, Locale, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.ActivitiesAjaxController

Get a specific page of recent activities for a user

getRecentActivitiesForUser(int, Locale, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIActivitiesService

Get a page of recent activities for a user

getRecordsFiltered() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

Total records, after filtering (i.e.

getRecordsTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesResponse

Total records, before filtering (i.e.

getRedirectUri() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getRedirectURI() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getReference() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

Gets the reference label.

getReference() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getReferenceFile() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Gets the ReferenceFile.

getReferenceFile() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

getReferenceFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getReferenceFilesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl

Get the collection of ReferenceFile attached to the specified Project.

getReferenceFilesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ReferenceFileService

Get the collection of ReferenceFile attached to the specified Project.

getReferenceFilesForProject(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController

Get the reference files for a project

getReferenceFilesForProject(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService

Get the reference files for a project

getRefreshToken() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

getRefreshToken() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getRefreshTokenValiditySeconds() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getRegisteredRedirectUri() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getRegisteredWorkflows() - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets a Set of all installed workflows.

getRegisteredWorkflowTypes() - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Gets a Set of all registered AnalysisType for all workflows.

getRelatedProjectJoin(Project, Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository

Get the RelatedProjectJoin for a given project and related project

getRelatedProjects(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all RelatedProjectJoins for a given Project

getRelatedProjects(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all RelatedProjectJoins for a given Project

getRelatedProjectsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository

Get the List of Projects that are related to this project as a list of RelatedProjectJoins This method will return RelatedProjectJoins where the given project is the subject property.

getReleaseDate() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getReleaseDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getReleaseDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getRemoteAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy

Gets the analysis id this workflow.

getRemoteAnalysisId() - Method in interface ca.corefacility.bioinformatics.irida.model.workflow.execution.PreparedWorkflow

Gets the analysis id this workflow.

getRemoteAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Gets an analysis id for this workflow

getRemoteApi() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

getRemoteAPI() - Method in exception ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException

Get the service trying to be accessed when this exception was thrown

getRemoteAPI() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getRemoteApiDetails(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

Get details about a specific RemoteAPI

getRemoteApiForURI(String) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

Convenience method for getting the RemoteAPI for a given string URI

getRemoteAPIForUrl(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.RemoteAPIRepository

Find the RemoteAPI where the serviceURI is a substring of the given URL

getRemoteAPIForUrl(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

getRemoteAPIForUrl(String) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPIService

Find the RemoteAPI where the serviceURI is a substring of the given URL.

getRemoteDataId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy

Gets the id for a location used to store data for a workflow.

getRemoteDataId() - Method in interface ca.corefacility.bioinformatics.irida.model.workflow.execution.PreparedWorkflow

Gets the id for a location used to store data for a workflow.

getRemoteHashCode() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getRemoteInputDataId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Gets the id of a remote location to store input files.

getRemoteProjectHash() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getRemoteProjects() - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Get a list of all Projects from remote sites

getRemoteProjects() - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get a list of all Projects from remote sites

getRemoteProjects() - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get a list of all Projects from remote sites

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Get the RemoteStatus for this object if it was read from a remote source

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getRemoteStatus() - Method in interface ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable

Get the status of a remote object

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getRemoteStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getRemoteURL() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getRemoteURL() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getRemoteWorkflowId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Gets the remote workflow id.

getRemove() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getRequired() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.InputWithOptions

getResetPage(String, boolean, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetController

Get the password reset page

getResource() - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ListResourceWrapper

getResource() - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceWrapper

Get the resource

getResource() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource

getResource() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

Get the embedded resource

getResource() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseResource

getResource() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource

getResource(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Retrieve and serialize an individual instance of a resource by identifier.

getResource(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Retrieve and serialize an individual instance of a resource by identifier.

getResource(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Retrieve and serialize an individual instance of a resource by identifier.

getResource(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Retrieve and serialize an individual instance of a resource by identifier.

getResource(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Retrieve and serialize an individual instance of a resource by identifier.

getResources() - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList

Get the list of resources

getResources() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

The collection of ResourceCollection objects in this collection.

getResponseMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxUpdateItemSuccessResponse

getResponseMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

getRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

getRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

getRestriction() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

getRestrictionForFieldAndProject(Project, MetadataTemplateField) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository

Get the MetadataRestriction for a given Project and MetadataTemplateField.

getRestrictionForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository

List all MetadataRestriction for a given Project

getRestrictions() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getResult() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

getReturnValue() - Method in class ca.corefacility.bioinformatics.irida.events.MethodEvent

Get the return value for the method call

getReverse() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

getReverseRelatedProjects(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository

Get the list of Projects that this project is related to as a list of RelatedProjectJoins.

getReverseRelatedProjects(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get all RelatedProjectJoins where the given Project is the relatedProject property.

getReverseRelatedProjects(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get all RelatedProjectJoins where the given Project is the relatedProject property.

getReverseSequenceFile() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

Gets the reverse SequenceFile from the pair.

getRevision() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

getRole() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserGroupRoleSetProjectEvent

getRole() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

getRole() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ProjectUserGroupsTableModel

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupProjectTableModel

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getRole() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

getRoleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

getRow(String, String) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

Returns the row from storage given the sample name and column name

getRows() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

getRunning() - Method in class ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService.AnalysisServiceStatus

getRunningStates() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Get the AnalysisStates that denote an AnalysisSubmission that has been picked up and is currently being processed.

getSample() - Method in exception ca.corefacility.bioinformatics.irida.exceptions.ExistingSampleNameException

getSample() - Method in class ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent

getSample() - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent

getSample() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

getSample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample

getSample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

getSample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

getSample(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Read a Sample by its id

getSampleAnalyses(Long, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Get analyses for sample

getSampleAnalyses(Long, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesService

Get analyses for sample

getSampleBySampleName(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get a Sample with the given string sample name from a specific project.

getSampleBySampleName(Project, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the Sample with the given sample name

getSampleBySampleName(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the Sample with the given sample name

getSampleDetails(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Get Sample details for a specific sample.

getSampleDetails(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get full details for a Sample

getSampleExportFiles(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

getSampleFiles(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get the sequence files associated with a sample

getSampleForProject(Project, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a specific instance of a Sample that belongs to a Project.

getSampleForProject(Project, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a specific instance of a Sample that belongs to a Project.

getSampleForSequencingObject(SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository

Get the SampleSequencingObjectJoin for a given SequencingObject

getSampleForSequencingObject(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Find a Sample assocaited with a SequencingObject

getSampleForSequencingObject(SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Find a Sample assocaited with a SequencingObject

getSampleId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getSampleId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject

getSampleId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

getSampleId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

getSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

getSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.DownloadRequest

getSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest

getSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.RemoveSamplesRequest

getSampleIds() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getSampleIdsBySampleNameForProjects(List<Long>, List<String>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the Sample identifiers with the given list of sample names from a list of projects.

getSampleIdsBySampleNameForProjects(List<Long>, List<String>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the Sample identifiers with the given list of sample names from a list of projects.

getSampleIdsBySampleNameInProjects(List<Long>, List<String>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get the Sample identifiers with the given list of sample names from a list of projects.

getSampleMetadata(Sample) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SampleRemoteRepositoryImpl

Get the Sample metadata for a remote sample

getSampleMetadata(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.SampleRemoteRepository

Get the Sample metadata for a remote sample

getSampleMetadata(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

Get the Sample metadata for a remote sample

getSampleMetadata(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.SampleRemoteService

Get the Sample metadata for a remote sample

getSampleMetadata(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

Get the metadata for a given Sample

getSampleMetadata(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Get Sample metadata for a specific sample.

getSampleMetadata(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get all the metadata for a Sample

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

getSampleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

getSampleNameColumn() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

getSampleNames() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getSampleNamesInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Get the names of all the samples in the cart.

getSampleOrganismsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get a list of the organism fields stored for all Samples in a Project

getSampleOrganismsForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a list of the organism fields stored for all Samples in a Project

getSampleOrganismsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a list of the organism fields stored for all Samples in a Project

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesResponse

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

getSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectModel

getSamplesCreated(Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get count of samples created in the time period

getSamplesCreated(Date) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get count of samples created in the time period

getSamplesCreatedGrouped(Date, StatisticTimePeriod) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get list of GenericStatModel of samples created in the past n time period grouped by the format provided.

getSamplesCreatedGrouped(Date, StatisticTimePeriod) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get list of GenericStatModel of samples created in the past n time period grouped by the format provided.

getSampleSequenceFiles(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Get the SequenceFile entities associated with a specific Sample.

getSamplesForAnalysisSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a list of all Samples associated with a given AnalysisSubmission

getSamplesForAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a list of all Samples associated with a given AnalysisSubmission

getSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get the Samples associated with a Project

getSamplesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the list of Sample that belongs to a specific project.

getSamplesForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

Get the Samples that exist in a Project

getSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.SampleRemoteService

Get the Samples that exist in a Project

getSamplesForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the list of Sample that belongs to a specific project.

getSamplesForProjects() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Get a list of sample in the cart belonging to a list of projects

getSamplesForProjectShallow(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository

Get the Samples associated with a Project

getSamplesForProjectShallow(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

getSamplesForProjectShallow(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a shallow listing of the Samples in a Project.

getSamplesForProjectWithName(Project, String, int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get the Samples for a Project in page form

getSamplesForProjectWithName(Project, String, int, int, Sort.Direction, String...) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get the Samples for a Project in page form

getSamplesInProject(Project, List<Long>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get Sample in a Project given a list of Sample ids.

getSamplesInProject(Project, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Get a list of Sample in a Project given some Sample ids.

getSamplesInProject(Project, List<Long>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Get a list of Sample in a Project given some Sample ids.

getSampleStats() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

getSavedParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

getSavedPipelineParameters() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getScheduledCronString() - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventEmailScheduledTaskImpl

Ge the cron string for this scheduled task

getScope() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

getScopes() - Method in class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationToken

Returns the requested scope(s).

getSearch() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

getSearch() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

getSearch() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

getSearch() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getSearchMap() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Get all the searches on this columns in this table

getSearchValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions

Get the value searched for in this column

getSearchValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Get the value from the global search.

getSecondFileSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

getSelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager

Get the current selection of AnalysisOutputFile.

getSelfHref() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Convenience method for getting the self rel href for an object read from a remote site

getSequence() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

getSequenceFile() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

getSequenceFile() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

getSequenceFile() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

getSequenceFilePairId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

getSequenceFilePairsForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.SequenceFilePairRemoteServiceImpl

Get the SequenceFilePairs for a given remote Sample

getSequenceFilePairsForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.SequenceFilePairRemoteService

Get the SequenceFilePairs for a given remote Sample

getSequenceOfTypeForSample(Sample, Class<? extends SequencingObject>) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.SampleSequencingObjectSpecification

Get SampleSequencingObjectJoins that have a given Sample and whose SequencingObjects are of a given type

getSequenceReadsPaired() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

Gets the sequence reads paired label.

getSequenceReadsSingle() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

Gets the sequence reads single label.

getSequencerType() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

Get the sequencer type

getSequencerType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getSequencerType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel

getSequencesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository

Get the SequenceFiles associated with a sample

getSequencesForSampleOfType(Sample, Class<? extends SequencingObject>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type

getSequencesForSampleOfType(Sample, Class<? extends SequencingObject>) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type

getSequencingObject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

getSequencingObject() - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

getSequencingObjectId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

getSequencingObjectsForAnalysisSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Get the set of SequencingObjects associated with a given AnalysisSubmission

getSequencingObjectsForAnalysisSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Get the set of SequencingObjects associated with a given AnalysisSubmission

getSequencingObjectsForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Get all the SequencingObjects associate with a given Sample

getSequencingObjectsForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Get all the SequencingObjects associate with a given Sample

getSequencingObjectsForSequencingRun(SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Get all the SequencingObjects associated with a given SequencingRun

getSequencingObjectsForSequencingRun(SequencingRun) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Get all the SequencingObjects associated with a given SequencingRun

getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission, Class<Type>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Get all SequencingObjects of a given type associated with an AnalysisSubmission

getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission, Class<Type>) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Get all SequencingObjects of a given type associated with an AnalysisSubmission

getSequencingObjectsWithProcessingState(SequencingObject.ProcessingState) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository

Get all SequencingObjects with the given SequencingObject.ProcessingState

getSequencingObjectsWithProcessingStateAndProcessor(SequencingObject.ProcessingState, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository

Get SequencingObjects with a given processing state and the given processor string

getSequencingRun() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getSequencingRun(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

Get the details for a specific sequencing run.

getSequencingRun(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

Get the details for a specific sequencing run.

getSequencingRunDetails(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

Get the details for a specific sequencing run.

getSequencingRunDetails(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

Get the details for a specific sequencing run.

getSequencingRunFiles(long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

Get the files for a specific sequencing run.

getSequencingRunFiles(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

Get the files for a specific sequencing run.

getSerogroup() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getSerovar() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getSerovarAntigen() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getSerovarCgmlst() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

getServiceStatus(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

Get the status of the remote service

getServiceStatus(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.RemoteRepository

Get the status of the remote service

getServiceStatus(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

Get the status of the remote service

getServiceStatus(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.RemoteService

Get the status of the remote service

getServiceURI() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Get the base URI of this remote api

getServiceURI() - Method in class ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableAdminModel

getSessionModelFilter() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig

getSharedProjectsForAnalysis(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the status of projects that can be shared with the given analysis

getSharedSingleSampleOutputs(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Get all the shared single sample analysis outputs for the project

getSharedSingleSampleOutputs(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Get all the shared single sample analysis outputs for the project

getSingleEndSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

getSingleEndSequenceFilesForExportSample(Sample, Project) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of single end sequence files for a sample

getSingleEndSequenceFilesForSample(Sample, Project, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get a list of single end sequence files for a sample

getSingleFiles(List<MultipartFile>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer

Get Paths to all single sequence files

getSingles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getSingles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

getSingles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles

getSingles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles

getSingleSampleWorkflows() - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Get all registered single-sample workflow UUIDs for retrieving AnalysisOutputFile info with a 1-to-1 mapping to a Sample

getSistrAnalysis(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the sistr analysis information to display

getSistrTyping() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

getSize() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

getSort() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getSort() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

Since we he need an actual Sort object and cannot pass this from the client, we create one from the information fathered from the client Direction of sort Column (attribute) of sort

getSort() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Get the current table sort properties.

getSort() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

Build the Sort object to use in the page request.

getSort() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

Since we he need an actual Sort object and cannot pass this from the client, we create one from the information fathered from the client Direction of sort Column (attribute) of sort

getSortColumn() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

getSortDirection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

getSortDirection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

getSortDirection(String) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

Helper method to get the sort direction for the column.

getSortField() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

getStandardError() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getStandardOutput() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getStart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getStartDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

Get the start date of the filter

getStartDate() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getStartName() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

getStartSeek() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getState() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Gets the state of the workflow.

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getState() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

getStateForAnalysisSubmission(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Given an analysis submission id, gets the state of this analysis.

getStateForAnalysisSubmission(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Given an analysis submission id, gets the state of this analysis.

getStaticId() - Method in class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

getStaticMetadataFields() - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

getStaticMetadataFields() - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get a list of all StaticMetadataTemplateFields available

getStatistics() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.StatisticsResponse

getStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

Get the QCEntry status.

getStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

Get the QCEntry status.

getStatus() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

Get the QCEntry status.

getStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse

getStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

getStatusForHistory(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Given a history id returns the status for the given workflow.

getStatusMessage() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

getStatusMessage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

getStorage() - Method in exception ca.corefacility.bioinformatics.irida.ria.web.errors.SavedMetadataException

getStorage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.SavedMetadataErrorResponse

getStrain() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

getStyleName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

getSubject() - Method in interface ca.corefacility.bioinformatics.irida.model.joins.Join

Get the owning object in the relationship.

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getSubject() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

getSubmission() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

Get the AnalysisSubmission that created this metadata

getSubmissionsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.submission.ProjectAnalysisSubmissionJoinRepository

Gets all the ProjectAnalysisSubmissionJoins for a given Project.

getSubmissionsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.NcbiExportSubmissionRepository

Get a List of NcbiExportSubmission for the given Project

getSubmissionsForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.export.NcbiExportSubmissionService

Get a List of NcbiExportSubmission for the given Project

getSubmissionsForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Get a List of NcbiExportSubmission for the given Project

getSubmissionStatus() - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

getSubmissionsWithState(ExportUploadState) - Method in interface ca.corefacility.bioinformatics.irida.service.export.NcbiExportSubmissionService

Get a List of NcbiExportSubmission object with the given ExportUploadState

getSubmissionsWithState(ExportUploadState) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Get a List of NcbiExportSubmission object with the given ExportUploadState

getSubmissionsWithState(Set<ExportUploadState>) - Method in interface ca.corefacility.bioinformatics.irida.repositories.NcbiExportSubmissionRepository

Get a List of NcbiExportSubmission object with the given ExportUploadState

getSubmissionsWithState(Set<ExportUploadState>) - Method in interface ca.corefacility.bioinformatics.irida.service.export.NcbiExportSubmissionService

Get a List of NcbiExportSubmission objects which have one of the given ExportUploadStates

getSubmissionsWithState(Set<ExportUploadState>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Get a List of NcbiExportSubmission objects which have one of the given ExportUploadStates

getSubmittedProject() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

getSubmitter() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getSubmitter() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

getSubmitter() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel

getSubmitter() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

getSubmitter() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

getSupportedMediaTypes() - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

getSyncFrequency() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

getSynchronizeProjectPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Get the page to synchronize remote projects

getSyncStatus() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getSyncUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

getSystemRole() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getSystemRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISettingsService

Get a list of all system roles.

getSystemRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.IRIDASettingsAjaxController

Get a list of all system roles.

getTargetId() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

getTemplateNames(Locale, Project) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectControllerUtils

Get a List of MetadataTemplates available for the current Project

getText() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.TaxonomyEntry

getText() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getText() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisStateModel

getText() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTypeModel

getText() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter

getTextColor() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Gets an optional Color object used to modify the text color in the "Select a Pipeline" page.

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.AnnouncementUserJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

getTimestamp() - Method in interface ca.corefacility.bioinformatics.irida.model.joins.Join

Get the timestamp for this object

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

getTimestamp() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

getTitle() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getTitle() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

getTitle() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel

getTitle() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

getTitle() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

getToken(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Get a token for a given service

getToken(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService

Get a token for a given service

getTokenFromAuthCode(HttpServletRequest, HttpServletResponse, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

Receive the OAuth2 authorization code and request an OAuth2 token

getTokens() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableModel

getTokenString() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

getTokenValidity() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

getToolDataTable(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyToolDataService

Gets details about a given tool data table.

getToolDescription() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getToolId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getToolId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

The id of the tool to adjust.

getToolId() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

getToolName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getToolName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getToolName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getToolName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

getToolParameters() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Gets a list of tools whose values are affected by this parameter.

getToolRepositories() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getToolVersion() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getToolVersion() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

getToolVersion() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

getTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableResponse

getTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.list.PagedListResponse

getTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.EntriesResponse

getTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse

getTotal() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse

getTotalBases() - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

getTotalBases() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getTotalBasesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Given a sample gets the total number of bases in all sequence files in this sample.

getTotalBasesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Given a sample gets the total number of bases in all sequence files in this sample.

getTotalResources() - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList

Get the total number of resources in this list

getTotalSequences() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

getTreeDefault() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

getType() - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

getType() - Method in class ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry

getType() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

getType() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

getType() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

Return the type of qc entry.

getType() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

Gets the particular type of the analysis as a string.

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.activities.dto.Activity

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getType() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

getUnassociatedProjects(Project, String, Integer, Integer, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get a page of projects eligible to be marked as associated projects for the specified project.

getUnassociatedProjects(Project, String, Integer, Integer, Sort.Direction, String...) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get a page of projects eligible to be marked as associated projects for the specified project.

getUniqueFilename(Path, String, Long, Long) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Get a unique filename for a filePath from an analysis output file.

getUniqueSamplesForSequencingObjects(Set<T>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Gets a map of SequencingObjects and corresponding Sample s.

getUniqueSamplesForSequencingObjects(Set<T>) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Gets a map of SequencingObjects and corresponding Sample s.

getUnlocked() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSamplesByUserPermissions

getUnpairedFilesForSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.SingleEndSequenceFileRemoteServiceImpl

Get all the SingleEndSequenceFiles associated with a Sample

getUnpairedFilesForSample(Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.SingleEndSequenceFileRemoteService

Get all the SingleEndSequenceFiles associated with a Sample

getUnreadAnnouncementsForUser(User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of Announcements that have not been read by User

getUnreadAnnouncementsForUser(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of Announcements that have not been read by User

getUnreadAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handle request for getting a list of unread announcements for a user.

getUnreadAnnouncementsUser(Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Returns a list of unread announcements for a user.

getUnreadUsersForAnnouncement(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Get a list of all of the Users that have not confirmed they've read the Announcement

getUnreadUsersForAnnouncement(Announcement) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Get a list of all of the Users that have not confirmed they've read the Announcement

getUpdatedDate() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

getUpdatedProgress(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Get the updated state and duration of an analysis

getUpdatedProgress(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Get the updated state and duration of an analysis

getUpdatedSequencingObjects(Long, List<Long>, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Get updated sample sequencing objects for given sequencing object ids

getUpdatedSequencingObjects(Long, List<Long>, Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Get updated sample sequencing objects for given sequencing object ids

getUpdater(MetadataTemplateService, SampleService, IridaWorkflowsService) - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Get the AnalysisSampleUpdater if available for this analysis pipeline

getUpdateSamples() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Whether or not to update samples from results on completion.

getUpdateSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

getUploadSha256() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Get the sha256 checksum for a file when it was uploaded.

getUploadState() - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

getUploadStatus() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getUploadStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getUploadStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel

getUrl() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

getUrl() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

getUrl() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

getURL() - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

getUser() - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

getUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails

getUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementTableModel

getUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserTableModel

getUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel

getUser() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

getUser(Long, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Get the details for a specific user

getUserAnalysisList(Model, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

Get the user Analysis list page

getUserAnalysisOutputsPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

Get the user Analysis list page

getUserAnnouncementInfoTable(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handles request for getting user read status for current announcement

getUserAnnouncementInfoTable(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Get user read status for current announcement

getUserByUsername(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get a user from the database with the supplied username.

getUserByUsername(String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get a user from the database with the supplied username.

getUserDetails(Long, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Get the details for a specific user

getUserDetailsPage(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersController

Request for a specific user details page.

getUserFirstName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getUserGroup() - Method in class ca.corefacility.bioinformatics.irida.model.enums.UserGroupRemovedProjectEvent

getUserGroup() - Method in class ca.corefacility.bioinformatics.irida.model.event.UserGroupRoleSetProjectEvent

getUserGroupDetails(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Get the details about a user group

getUserGroupDetails(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Get details about a specific user group

getUserGroupProjectJoins(User, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Get a collection of UserGroupProjectJoins of a User on a given Project

getUserGroupProjectJoins(User, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Get a collection of UserGroupProjectJoins of a User on a given Project

getUserGroupRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Get a list of all user group roles

getUserGroupRoles(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Get a list of all user group roles with their translations

getUserGroups(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Gat a paged list of user groups

getUserGroups(TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Gat a paged list of user groups

getUserGroupsForProject(Long, TableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Get a table page of ProjectUserGroupsTableModel

getUserGroupsForProject(String, Project, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Get a page of UserGroupProjectJoin for a specific Project .

getUserGroupsForProject(String, Project, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Get a page of UserGroupProjectJoin for a specific Project .

getUserGroupsNotOnProject(Project, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Get a collection of UserGroup that aren't already on a Project.

getUserGroupsNotOnProject(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Get a collection of UserGroup that aren't already on a Project.

getUserId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getUserId() - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

getUserID() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getUserLastName() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getUsername() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

getUsername() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

getUsername() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

getUsername() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

getUserName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

getUserProjects(String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Get the collection of projects for a specific user.

getUsersAvailableForProject(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepository

Get the list of Users that are not associated with the current project.

getUsersAvailableForProject(Project, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get the list of Users that are not associated with the current project.

getUsersAvailableForProject(Project, String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get the list of Users that are not associated with the current project.

getUsersByAnnouncementRead(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Get a collection of the Users that have read an Announcement

getUsersByAnnouncementUnread(Announcement) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.announcement.AnnouncementUserJoinRepository

Get a collection of the Users that have not read an Announcement

getUsersCreatedGrouped(Date, StatisticTimePeriod) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get list of GenericStatModel of users created in the past n time period grouped by the format provided.

getUsersCreatedGrouped(Date, StatisticTimePeriod) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get list of GenericStatModel of users created in the past n time period grouped by the format provided.

getUsersCreatedInTimePeriod(Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get count of users created during the time period

getUsersCreatedInTimePeriod(Date) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get count of users created during the time period

getUsersForGroup(UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Get all of the users in the group.

getUsersForGroup(UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Get all of the users in the group.

getUsersForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get all Users associated with a project.

getUsersForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get all users associated with a particular project.

getUsersForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get all users associated with a particular project.

getUsersForProject(Project, String, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get a page of Users associated with a project.

getUsersForProject(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Get all users associated with a project.

getUsersForProjectByRole(Project, ProjectRole) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository

Get Users for a Project that have a particular role

getUsersForProjectByRole(Project, ProjectRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get Users for a Project that have a particular role

getUsersForProjectByRole(Project, ProjectRole) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get Users for a Project that have a particular role

getUserSingleSampleOutputs() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Get all the logged in user single sample analysis outputs

getUsersLoggedIn() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

getUsersLoggedIn(Date) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get count of users logged on during the time period

getUsersLoggedIn(Date) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get count of users logged on during the time period

getUsersNotInGroup(UserGroup, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Get the set of User that are not currently in the UserGroup.

getUsersNotInGroup(UserGroup, String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Get the set of User that are not currently in the UserGroup.

getUsersPage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersController

Request for the page to display a list of all projects available to the currently logged in user.

getUsersPagedList(AdminUsersTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Get a paged listing of users for the administration user.

getUsersPagedList(AdminUsersTableRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Get a paged listing of users for the administration user.

getUserStatistics(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserStatisticsService

Get basic user usage statistics for dashboard

getUserStatistics(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UserStatisticsAjaxController

Get basic user usage statistics for dashboard

getUserStats() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

getUsersWithEmailSubscriptions() - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Get a List of all Users that are subscribed to any Projects.

getUsersWithEmailSubscriptions() - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService

Get a List of all Users that are subscribed to any Projects.

getUsersWithSubscriptions() - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectSubscriptionRepository

Get a list of all Users who are subscribed to any Project.

getValue() - Method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

getValue() - Method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

getValue() - Method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

getValue() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

getValue() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

Get parameter choice acceptable Galaxy workflow value

getValue() - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectModel

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.TaxonomyEntry

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.InputWithOptions

Getter for the value, if there is no value, the value of the first option is returned.

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.SelectOption

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupRole

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisStateModel

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTypeModel

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSearch

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.Role

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

getValue() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

getValue() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Get the value stored by this node

getValues() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

getVersion() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

getVersion() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getVersion() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController.ResponseVersion

getViewerForAnalysisType(AnalysisType) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Get the viewer for a given AnalysisType

getViewerForAnalysisType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Get the viewer for a given AnalysisType

getWarnings() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseResource

getWorkbookHeaders(Row) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Extract the headers from an excel file.

getWorkflowDescription() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getWorkflowDescription() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

getWorkflowDetails(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Gets details about a given workflow.

getWorkflowFile() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure

getWorkflowId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

getWorkflowId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Gets the id of the implementing workflow for this analysis.

getWorkflowId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

getWorkflowIdentifier() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

Gets a unique identifier for this workflow.

getWorkflowInputId(WorkflowDetails, String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Given a WorkflowDetails an a workflowInputLabel find the corresponding id for this input.

getWorkflowInputs() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy

Gets the inputs to a workflow.

getWorkflowInputs() - Method in interface ca.corefacility.bioinformatics.irida.model.workflow.execution.PreparedWorkflow

Gets the inputs to a workflow.

getWorkflowName() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

getWorkflowsPath() - Method in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Gets a Path to a directory containing the workflows to load.

getWorkflowStatus(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Gets the status for the given submitted analysis.

getWorkflowStatus(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Gets the status for the given submitted analysis.

getWorkflowStructure() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

getWorkflowTypes(Boolean, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

Get a list of pipeline workflows, if the automated flag is set then only those pipelines that can be run automated will be returned

getWorkflowTypes(Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysesTableAjaxController

Returns a list of localized names for all available AnalysisTypes.

getWrite() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

GREATER_THAN - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

GREATER_THAN_EQUAL - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

GRID_ION - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

GROUP_MEMBER - ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole

GROUP_OWNER - ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole

groups() - Method in annotation type ca.corefacility.bioinformatics.irida.constraints.MetadataRoleValidate

groups() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Latitude

groups() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Longitude

groups() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName

groups() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName

GzipFileProcessor - Class in ca.corefacility.bioinformatics.irida.processing.impl

Handle gzip-ed files (if necessary).

GzipFileProcessor(SequenceFileRepository) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

GzipFileProcessor(SequenceFileRepository, Boolean) - Constructor for class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

H

handleAccessDeniedException(AccessDeniedException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle AccessDeniedException.

handleAccessDeniedException(AccessDeniedException, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Handle an AccessDeniedException

handleAllOtherExceptions(Exception) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle Exception.

handleArgumentException(IllegalArgumentException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle IllegalArgumentException .

handleConstraintViolations(ConstraintViolationException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle ConstraintViolationException.

handleError(ClientHttpResponse) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.IridaOAuthErrorHandler

Overriding this method to throw a IridaOAuthException in case of an HTTP UNAUTHORIZED response.

handleExistsException(EntityExistsException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle EntityExistsException .

handleInvalidJsonException(HttpMessageNotReadableException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle JsonParseException.

handleInvalidPropertyException(InvalidPropertyException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle InvalidPropertyException .

handleIOException(IOException, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Catch and handle IOExceptions.

handleMediaTypeNotSupportedException(HttpMediaTypeNotSupportedException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle a HttpMediaTypeNotSupportedException exception.

handleMethodNotSupportedException(HttpRequestMethodNotSupportedException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle HttpRequestMethodNotSupportedException.

handleNotFoundException(EntityNotFoundException) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ControllerExceptionHandler

Handle EntityNotFoundException .

handleOAuthException(HttpServletRequest, IridaOAuthException) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

Handle an IridaOAuthException by launching an authentication flow

handleOAuthProblemException(OAuthProblemException) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Catch an OAuthProblemException and return an http 500 error

handleOtherExceptions(Exception, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Catch and handle all other exception types and respond with 500 status code.

handleProjectEvent(JoinPoint, LaunchesProjectEvent, Object) - Method in class ca.corefacility.bioinformatics.irida.events.ProjectEventAspect

Get the return value of a method to send to the ProjectEventHandler

handleProjectEventWithoutReturn(JoinPoint, LaunchesProjectEvent) - Method in class ca.corefacility.bioinformatics.irida.events.ProjectEventAspect

Get the arguments of a method to send to the ProjectEventHandler

handleResourceNotFoundException(EntityNotFoundException, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Handle an EntityNotFoundException

handleStorageException(StorageException, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

Catch and handle all StorageExceptions.

hasChoices() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Does this parameter have a set of restricted choices?

hasDynamicSource() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Whether or not this parameter pulls its value from a Dynamic Source (eg.

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

Hashcode using remoteAPI and tokenString

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

hashCode() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

hashCode() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

hashCode() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

hashCode() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

hasLink(String) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Returns whether the resource contains a Link with the given rel.

hasLinks() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Returns whether the resource contains Links at all.

hasPermission(Authentication, Serializable, String, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator

hasPermission(Authentication, Object, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator

hasRegisteredAnalysisSampleUpdater(AnalysisType) - Method in interface ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor

Whether or not there exists a registered AnalysisSampleUpdater for the corresponding AnalysisType.

hasRegisteredAnalysisSampleUpdater(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl

Whether or not there exists a registered AnalysisSampleUpdater for the corresponding AnalysisType.

hasRemoteAnalysisId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Whether or not a remoteAnalysisId exists for this submission.

hasRemoteInputDataId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Whether or not a remoteInputDataId exists for this submission.

hasRemoteWorkflowId() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Whether or not a remoteWorkflowId exists for this submission.

HI_SEQ_LIQUIBASE_PRO_PACKAGED_X_TEN - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

HI_SEQ_X_FIVE - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

HIGH - ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority

historiesClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

HMPR - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

HOURLY - ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

HTML - ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

HttpHeadFilter - Class in ca.corefacility.bioinformatics.irida.web.filter

Servlet filter that presents a HEAD request as a GET.

HttpHeadFilter() - Constructor for class ca.corefacility.bioinformatics.irida.web.filter.HttpHeadFilter

humanReadableByteCount(long, boolean) - Static method in interface ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile

From (http://stackoverflow.com/questions/3758606/how-to-convert-byte-size- into-human-readable-format-in-java)

humanReadableByteCount(long, boolean) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

From (http://stackoverflow.com/questions/3758606/how-to-convert-byte-size- into-human-readable-format-in-java)

HYBRID - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

I

id - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

IGNORE_DEFAULT_VALUE - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Can be passed as the value of a parameter instructing IRIDA to ignore the default value.

ILLUMINA - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

ILLUMINA_GENOME_ANALYZER - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_GENOME_ANALYZER_II - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_GENOME_ANALYZER_IIX - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SCAN_SQ - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_1000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_1500 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_2000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_2500 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_3000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_4000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_HI_SEQ_X - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_I_SEQ_100 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_MI_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_MINI_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ILLUMINA_NOVA_SEQ_6000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

IMG_DUPLICATION_LEVEL - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

IMG_PERBASE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

IMG_PERSEQUENCE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

IN - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

incrementFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

incrementFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

incrementFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

incrementFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

incrementFileRevisionNumber() - Method in interface ca.corefacility.bioinformatics.irida.model.VersionedFileFields

Internally modify the file revision number to something new.

incrementFileRevisionNumber() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile

This intentionally does nothing.

INFO - ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

InfoNotification - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Consumed by the UI to display an information notification.

InfoNotification(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.InfoNotification

InfoNotification(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.InfoNotification

init() - Method in class ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator

Initialize the permission evaluator

init(FilterConfig) - Method in class ca.corefacility.bioinformatics.irida.web.filter.HttpHeadFilter

init(FilterConfig) - Method in class ca.corefacility.bioinformatics.irida.web.filter.SlashFilter

initialize() - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevListener

Initialize the listener by getting dependencies

initialize(Latitude) - Method in class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LatitudeValidator

initialize(Longitude) - Method in class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LongitudeValidator

initLinks() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

Initialize a collection of all controllers in the system.

InMemoryTaxonomyService - Class in ca.corefacility.bioinformatics.irida.service.impl

A TaxonomyService leveraging Apache Jena's in memory storage service and Apache Lucene's text searching abilities.

InMemoryTaxonomyService(Path) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.InMemoryTaxonomyService

Input - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui

Used in the UI to render a Irida Workflow Pipeline Parameter option

Input() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

Input(String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

INPUT_FILES_PAIRED_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

INPUT_FILES_UNPAIRED_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

inputFiles - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

inputFiles(Set<SequencingObject>) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets the inputFilesPaired for this submission.

InputFileType - Enum in ca.corefacility.bioinformatics.irida.model.workflow.execution

Defines acceptable file types for input to a workflow.

inputParameter(String, String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Adds an individual input parameter.

inputParameters - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

inputParameters(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets the input parameters for this submission.

InputWithOptions - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui

Represents a IRIDA Workflow Pipeline Parameter that has specific options to be rendered within the UI.

InputWithOptions(String, String, String, List<SelectOption>, Boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.InputWithOptions

installedLocales() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

instrumentModel(NcbiInstrumentModel) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Sequencer model that created these files

InvalidPropertyException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when a property cannot be set or retrieved by a service class.

InvalidPropertyException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.InvalidPropertyException

InvalidPropertyException(String, Class<? extends Object>) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.InvalidPropertyException

Create a new InvalidPropertyException with the given invalid class

InvalidPropertyException(String, Class<? extends Object>, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.InvalidPropertyException

ION_GENE_STUDIO_S_5 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_GENE_STUDIO_S_5_PLUS - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_GENE_STUDIO_S_5_PRIME - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_TORRENT - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

ION_TORRENT_PGM - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_TORRENT_PROTON - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_TORRENT_S_5 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_TORRENT_S_5_XL - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

ION_UNSPECIFIED - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

IridaAccountDisabledException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when a password reset is requested by a user whose account is disabled

IridaAccountDisabledException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaAccountDisabledException

IridaAnalysisTypesServiceConfig - Class in ca.corefacility.bioinformatics.irida.config.workflow

Class to load up AnalysisTypesService.

IridaAnalysisTypesServiceConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.workflow.IridaAnalysisTypesServiceConfig

IridaApiAspectsConfig - Class in ca.corefacility.bioinformatics.irida.config.services

Configures the aspects in IRIDA

IridaApiAspectsConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig

IridaApiFilesystemRepositoryConfig - Class in ca.corefacility.bioinformatics.irida.config.repository

Configuration for filesystem repositories in IRIDA

IridaApiFilesystemRepositoryConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

IridaApiJdbcDataSourceConfig - Class in ca.corefacility.bioinformatics.irida.config.data

Configuration for IRIDA's JDBC Datasource

IridaApiJdbcDataSourceConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig

IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase - Class in ca.corefacility.bioinformatics.irida.config.data

Custom implementation of the SpringLiquibase bean (for doing liquibase on spring startup) that exposes the application context so that we can have access to the application context in custom java changesets.

IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase.ApplicationContextSpringResourceOpener - Class in ca.corefacility.bioinformatics.irida.config.data

Custom SpringResourceOpener that gives access to the application context.

IridaApiPropertyPlaceholderConfig - Class in ca.corefacility.bioinformatics.irida.config.services

Configuration class for loading properties files.

IridaApiPropertyPlaceholderConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaApiPropertyPlaceholderConfig

IridaApiRepositoriesConfig - Class in ca.corefacility.bioinformatics.irida.config.repository

Configuration for repository/data storage classes.

IridaApiRepositoriesConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig

IridaApiSecurityConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Configuration for IRIDA's spring security modules

IridaApiSecurityConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

IridaApiServicesConfig - Class in ca.corefacility.bioinformatics.irida.config.services

Configuration for the IRIDA platform.

IridaApiServicesConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

IridaApiServicesConfig.IridaLocaleList - Class in ca.corefacility.bioinformatics.irida.config.services

Inner class storing the enabled locales for IRIDA

IridaApplication - Class in ca.corefacility.bioinformatics.irida

Entry point to Spring Boot application

IridaApplication() - Constructor for class ca.corefacility.bioinformatics.irida.IridaApplication

IridaClientDetails - Class in ca.corefacility.bioinformatics.irida.model

Object representing a client that has been registered to communicate with this API via OAuth2

IridaClientDetails() - Constructor for class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

Default constructor with empty scopes, grant types, and redirect uris

IridaClientDetails(String, String, Set<String>, Set<String>) - Constructor for class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

Construct new IridaClientDetails with the following params

IridaClientDetailsRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for storing and retriving IridaClientDetails.

IridaClientDetailsService - Interface in ca.corefacility.bioinformatics.irida.service

Service for storing and reading IridaClientDetails objects

IridaClientDetailsServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service for storing and retrieving IridaClientDetails object.

IridaClientDetailsServiceImpl(IridaClientDetailsRepository, OAuth2AuthorizationService, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

IridaClientDetailsSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification class for IridaClientDetails

IridaClientDetailsSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.IridaClientDetailsSpecification

IridaCustomExceptionHandler - Class in ca.corefacility.bioinformatics.irida.ria.web.errors

Exception Handler for when a user is navigating around in the web interface.

IridaCustomExceptionHandler() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.errors.IridaCustomExceptionHandler

IridaEnvironmentPostProcessor - Class in ca.corefacility.bioinformatics.irida.config.environment

EnvironmentPostProcessor to translate deprecated properties into valid properties.

IridaEnvironmentPostProcessor(Log) - Constructor for class ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor

IridaJpaRepository<Type,Identifier extends java.io.Serializable> - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository type that extends PagingAndSortingRepository, JpaSpecificationExecutor, and RevisionRepository.

IridaLocaleList(List<Locale>) - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig.IridaLocaleList

IridaOAuth2AuthorizationService - Class in ca.corefacility.bioinformatics.irida.oauth2

A customized version of JdbcOAuth2AuthorizationService that adds a method to find OAuth2Authorizations with OAuth2AccessTokens for a specific RegisteredClient.

IridaOAuth2AuthorizationService(JdbcOperations, RegisteredClientRepository) - Constructor for class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

IridaOAuthErrorHandler - Class in ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate

Error handler for use in OAuthTokenRestTemplate.

IridaOAuthErrorHandler() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.IridaOAuthErrorHandler

IridaOAuthException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when attempting to read from a remote API via OAuth2 fails.

IridaOAuthException(String, RemoteAPI) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException

Create a new IridaOAuthException with the given message and service

IridaOAuthException(String, RemoteAPI, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException

Create a new IridaOAuthException with the given message and service

IridaOauthSecurityConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Configuration for REST API security using OAuth2

IridaOauthSecurityConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig

IridaOauthSecurityConfig.AuthorizationServerConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Class for configuring the OAuth authorization server

IridaOauthSecurityConfig.JWKConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Class for configuring the JSON Web Key for JSON Web Tokens used in OAuth2

IridaOauthSecurityConfig.ResourceServerConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Class for configuring the OAuth resource server security

IridaPermissionEvaluator - Class in ca.corefacility.bioinformatics.irida.security.permissions

Custom permission evaluator to determine whether or not an authenticated user has authorization to view or modify a resource.

IridaPermissionEvaluator(RepositoryBackedPermission<?, ?>...) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator

IridaPermissionEvaluator(Collection<BasePermission<?>>) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.IridaPermissionEvaluator

iridaPipelinePlugins() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig

Get the list of IRIDA pipeline plugins

iridaPipelinePluginStyle() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Gets a String containing pipeline plugin styles (CSS).

IridaPlugin - Interface in ca.corefacility.bioinformatics.irida.plugins

Interface describing the methods which must be exposed by an IRIDA pipeline plugin

IridaPluginConfig - Class in ca.corefacility.bioinformatics.irida.config.services

Configuration file for loading IRIDA plugins

IridaPluginConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig

IridaPluginConfig.IridaPluginList - Class in ca.corefacility.bioinformatics.irida.config.services

Class containing the list of all loaded IridaPlugin

IridaPluginException - Exception in ca.corefacility.bioinformatics.irida.plugins

An exception thrown when initializing IRIDA pipelines

IridaPluginException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.plugins.IridaPluginException

IridaPluginException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.plugins.IridaPluginException

IridaPluginList(List<IridaPlugin>) - Constructor for class ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig.IridaPluginList

IridaPluginMessageSource - Class in ca.corefacility.bioinformatics.irida.util

A MessageSource used to store and search through MessageSources for IRIDA Plugins.

IridaPluginMessageSource(List<MessageSource>) - Constructor for class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

Builds a new IridaPluginMessageSource which makes use of the given sources.

IridaPostAuthenicationChecker - Class in ca.corefacility.bioinformatics.irida.security

Expired credentials should be ignored when a user is trying to change their password.

IridaPostAuthenicationChecker() - Constructor for class ca.corefacility.bioinformatics.irida.security.IridaPostAuthenicationChecker

IridaPostAuthenticationFailureHandler - Class in ca.corefacility.bioinformatics.irida.ria.security

AuthenticationFailureHandler used to handle specific AuthenticationException's.

IridaPostAuthenticationFailureHandler(PasswordResetService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.security.IridaPostAuthenticationFailureHandler

IridaRegisteredClientsRepository - Class in ca.corefacility.bioinformatics.irida.oauth2

A converter implementation of RegisteredClientRepository, that transforms IridaClientDetails to/from RegisteredClient.

IridaRegisteredClientsRepository(IridaClientDetailsRepository) - Constructor for class ca.corefacility.bioinformatics.irida.oauth2.IridaRegisteredClientsRepository

IridaRepresentationModel - Class in ca.corefacility.bioinformatics.irida.model

Adds a collection of Links to extending objects.

IridaRepresentationModel() - Constructor for class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

IridaRestApiWebConfig - Class in ca.corefacility.bioinformatics.irida.config.web

Configuration for IRIDA REST API.

IridaRestApiWebConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

IridaScheduledTasksConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Config for only activating scheduled tasks in certain profiles.

IridaScheduledTasksConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.IridaScheduledTasksConfig

IridaSequenceFile - Interface in ca.corefacility.bioinformatics.irida.model.irida

Describes fields that must be made available for a Sequence File in IRIDA

IRIDASettingsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.settings

Handles asynchronous requests for IRIDA settings.

IRIDASettingsAjaxController(UISettingsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.settings.IRIDASettingsAjaxController

IridaThing - Interface in ca.corefacility.bioinformatics.irida.model

An interface for all model classes in the IRIDA system.

IridaToolParameter - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

A parameter for a particular tool in a workflow.

IridaToolParameter() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

IridaToolParameter(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

Builds a new IridaToolParameter object with the given information.

IridaUIWebConfig - Class in ca.corefacility.bioinformatics.irida.config.web

IridaUIWebConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

IridaWebSecurityConfig - Class in ca.corefacility.bioinformatics.irida.config.security

Configuration for web security using OAuth2

IridaWebSecurityConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig

IridaWebSecurityConfig.UISecurityConfig - Class in ca.corefacility.bioinformatics.irida.config.security

UI security config for IRIDA

IridaWorkflow - Class in ca.corefacility.bioinformatics.irida.model.workflow

Describes a workflow for IRIDA.

IridaWorkflow(IridaWorkflowDescription, IridaWorkflowStructure) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

Defines a new IridaWorkflow with the given information.

IridaWorkflowAnalysisTypeException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception for when there is an issue building a particular Analysis type.

IridaWorkflowAnalysisTypeException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowAnalysisTypeException

Constructs a new IridaWorkflowAnalysisTypeException with the given message.

IridaWorkflowAnalysisTypeException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowAnalysisTypeException

Constructs a new IridaWorkflowAnalysisTypeException with the given message and cause.

IridaWorkflowDefaultException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when attempting to set a default workflow for an analysis type that already has a default workflow set.

IridaWorkflowDefaultException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowDefaultException

Constructs a new IridaWorkflowDefaultException with the given message.

IridaWorkflowDefaultException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowDefaultException

Constructs a new IridaWorkflowDefaultException with the given message and cause.

IridaWorkflowDescription - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Class providing access to generic information about a workflow.

IridaWorkflowDescription() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

IridaWorkflowDescription(UUID, String, String, AnalysisType, IridaWorkflowInput, List<IridaWorkflowOutput>, List<IridaWorkflowToolRepository>, List<IridaWorkflowParameter>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Generates a new IridaWorkflowDescription with the given information.

IridaWorkflowDynamicSourceGalaxy - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Class providing access to information about a Dynamic Parameter Source that is supplied by Galaxy.

IridaWorkflowDynamicSourceGalaxy() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

IridaWorkflowDynamicSourceGalaxy(String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

IridaWorkflowException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown for any Irida workflows.

IridaWorkflowException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowException

Constructs a new IridaWorkflowException with the given message.

IridaWorkflowException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowException

Constructs a new IridaWorkflowException with the given message and cause.

IridaWorkflowIdSet - Class in ca.corefacility.bioinformatics.irida.model.workflow.config

A class wrapping around a Set of UUIDs for IRIDA workflows.

IridaWorkflowIdSet(Set<UUID>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowIdSet

Builds a new IridaWorkflowIdSet of workflow ids.

IridaWorkflowInput - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Defines the input labels for a workflow.

IridaWorkflowInput() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

IridaWorkflowInput(String, String, String, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

Builds a new IridaWorkflowInput object with the given information.

iridaWorkflowLoaderService() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Constructs a service for loading up workflows for IRIDA.

IridaWorkflowLoaderService - Class in ca.corefacility.bioinformatics.irida.service.workflow

Used to load up IRIDA workflows.

IridaWorkflowLoaderService(Unmarshaller, AnalysisTypesService) - Constructor for class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Builds a new IridaWorkflowLoaderService with the given unmarshaller.

IridaWorkflowLoadException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception that gets thrown when attempting to load a workflow.

IridaWorkflowLoadException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowLoadException

Constructs a new IridaWorkflowLoadException with the given message.

IridaWorkflowLoadException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowLoadException

Constructs a new IridaWorkflowLoadException with the given message and cause.

IridaWorkflowNamedParameters - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Users can create, save, and re-use named parameters in their workflow submissions.

IridaWorkflowNamedParameters(String, UUID, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters

IridaWorkflowNoParameterException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Defines an exception in cases of no parameters within an IRIDA workflow.

IridaWorkflowNoParameterException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNoParameterException

Constructs a new IridaWorkflowNoParameterException with the given message.

IridaWorkflowNoParameterException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNoParameterException

Constructs a new IridaWorkflowNoParameterException with the given message and cause.

IridaWorkflowNotDisplayableException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown if a workflow is not displayable.

IridaWorkflowNotDisplayableException(AnalysisType) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotDisplayableException

Constructs a new IridaWorkflowNotDisplayableException with the given analysis type.

IridaWorkflowNotDisplayableException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotDisplayableException

Constructs a new IridaWorkflowNotDisplayableException with the given workflow name.

IridaWorkflowNotDisplayableException(UUID) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotDisplayableException

Constructs a new IridaWorkflowNotDisplayableException with the given workflow identifier.

IridaWorkflowNotFoundException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown if a workflow is not found.

IridaWorkflowNotFoundException(AnalysisType) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotFoundException

Constructs a new IridaWorkflowNotFoundException with the given analysis type.

IridaWorkflowNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotFoundException

Constructs a new IridaWorkflowNotFoundException with the given workflow name.

IridaWorkflowNotFoundException(UUID) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowNotFoundException

Constructs a new IridaWorkflowNotFoundException with the given workflow identifier.

IridaWorkflowOutput - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Defines the output files and file names for a workflow.

IridaWorkflowOutput() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

IridaWorkflowOutput(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowOutput

Defines a new IridaWorkflowOutput object for descripting the output files of a workflow.

IridaWorkflowParameter - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Defines input parameters for a workflow which can be adjusted.

IridaWorkflowParameter() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

IridaWorkflowParameter(String, boolean, IridaWorkflowDynamicSourceGalaxy, List<IridaToolParameter>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Creates a new IridaWorkflowParameter which maps to the given tool parameters.

IridaWorkflowParameter(String, boolean, List<IridaWorkflowParameterChoice>, List<IridaToolParameter>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Creates a new IridaWorkflowParameter which maps to the given tool parameters.

IridaWorkflowParameter(String, String, List<IridaToolParameter>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Creates a new IridaWorkflowParameter which maps to the given tool parameters.

IridaWorkflowParameterChoice - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Defines a valid choice for a parameter of a workflow.

IridaWorkflowParameterChoice() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

IridaWorkflowParameterChoice(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

Parameter choice with informative name and acceptable Galaxy workflow value for the parameter

IridaWorkflowParameterException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Defines an exception for parameters within an IRIDA workflow.

IridaWorkflowParameterException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException

Constructs a new IridaWorkflowParameterException with the given message.

IridaWorkflowParameterException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException

Constructs a new IridaWorkflowParameterException with the given message and cause.

iridaWorkflows(Path) - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Builds a set of workflows to load up into IRIDA.

IridaWorkflowsConfig - Class in ca.corefacility.bioinformatics.irida.config.workflow

Class used to load up test workflows.

IridaWorkflowsConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

IridaWorkflowSet - Class in ca.corefacility.bioinformatics.irida.model.workflow.config

Wraps around a Set of IridaWorkflows to allow it to be handled as a spring managed bean.

IridaWorkflowSet(Set<IridaWorkflow>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.config.IridaWorkflowSet

Builds a new IridaWorkflowSet of workflows.

iridaWorkflowsService(IridaWorkflowSet, IridaWorkflowIdSet, AnalysisTypeSet) - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Builds a new IridaWorkflowsService.

IridaWorkflowsService - Class in ca.corefacility.bioinformatics.irida.service.workflow

Class used to load up installed workflows in IRIDA.

IridaWorkflowsService(IridaWorkflowSet, IridaWorkflowIdSet) - Constructor for class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Builds a new IridaWorkflowsService for loading up installed workflows.

IridaWorkflowsService(IridaWorkflowSet, IridaWorkflowIdSet, AnalysisTypeSet) - Constructor for class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Builds a new IridaWorkflowsService for loading up installed workflows.

IridaWorkflowStructure - Class in ca.corefacility.bioinformatics.irida.model.workflow.structure

Defines the structure of a workflow for IRIDA.

IridaWorkflowStructure(Path) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure

Builds a new IridaWorkflowStructure with the given information.

IridaWorkflowToolRepository - Class in ca.corefacility.bioinformatics.irida.model.workflow.description

Defines a Galaxy ToolShed repository containing dependency tools for a workflow.

IridaWorkflowToolRepository() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

IridaWorkflowToolRepository(String, String, URL, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

Builds a new IridaWorkflowToolRepository with the given information.

iridaWorkflowTypesPath() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Gets the Path for all IRIDA workflow types.

isAcceptsPairedSequenceFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

isAcceptsSingleSequenceFiles() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

isAccountNonExpired() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

isAccountNonLocked() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

isAdmin() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CurrentUser

isAdmin() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

isAdmin() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

isAdmin(User) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.utilities.RoleUtilities

Check if the user is an Admin

isAllowed(Authentication, Object) - Method in interface ca.corefacility.bioinformatics.irida.security.permissions.BasePermission

Is the authenticated user allowed to perform some action on the target domain object?

isAllowed(Authentication, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission

isAllowed(Authentication, Object) - Method in class ca.corefacility.bioinformatics.irida.security.permissions.RepositoryBackedPermission

Is the authenticated user allowed to perform some action on the target domain object?

isAllowedToModifySample() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isAssociated() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.AssociatedProject

isAuthenticated() - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.GalaxyExportAuthentication

isAutomated() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Whether this pipeline was run as part of an automated process

isCanCreatePasswordReset() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

isCanEditUserInfo() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

isCanEditUserStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

isCanManage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

isCanManage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel

isCanManage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

isCanManage() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.ProjectCurrentUserModel

isCanManageRemote() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

isCanShareToSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isCartEmpty() - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Determine if the cart is empty

isCheckboxSelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isChoicesEmpty() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Is the list of choices empty?

isCompleted() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

isCompleted() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

isConfigured() - Method in interface ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSender

Check to see if the mail server has been configured correctly.

isConfigured() - Method in class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig.ConfigurableJavaMailSenderImpl

Check to see if the mail server has been configured correctly.

isCredentialsNonExpired() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

isEditable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isEmailPipelineResultCompleted() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isEmailPipelineResultError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isEmailSubscribed() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

isEmailSubscription() - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

isEnabled() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

isEnabled() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

isEnabled() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.AnalysisTemplate

isEnabled() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

isError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

isError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

isExpired() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

Test if this token has expired

isGzipped(Path) - Static method in class ca.corefacility.bioinformatics.irida.util.FileUtils

Determines if a file is compressed.

isHeaderCheckboxSelection() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isHide() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isInCart() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

isInputTool() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

Indicates whether or not this tool is an input tool or data source.

isLock() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

isLockPinned() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isLockPosition() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isMailConfigured() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

isMailConfigured() - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Is the mail server configured?

isMailConfigured() - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Is the mail server configured?

isMailConfigured() - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

isManager() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

isModifiable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisModel

isModifiable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

isOrderable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions

Column Orderable: end user's ability to order this column.

isOwnAccount() - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

isOwner() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

Whether the Project has modification rights to the Sample

isOwner() - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CartSampleModel

isOwner() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

isOwner() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProjectSamples

isOwner() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

isParseError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

isProjectDefault() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

isRead() - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementUserReadDetails

isRemote() - Method in interface ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable

Check if this entity was read from a remote api

isRemote() - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.datatables.DTProject

isRemote() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

isRemote() - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectModel

isRequired() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Whether or not this parameter is required to be set manually before launching a pipeline.

isRequiresReference() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

isResizable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

isRunning() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

Whether or not this workflow is still running.

isSampleInCart(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Determine if a sample is in the cart.

isSampleInCart(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Find if a sample is currently in the cart.

isSaved() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

isScoped() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

isSearchable() - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesColumnDefinitions

Column searchable Defined if DataTables should include this column in the filterable data in the table.

isSecretRequired() - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

isShareStatus() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

isTreeDefault() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

isUpdatePermission() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isUpdateSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

isUpdateSamples() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

isValid(AnalysisType) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Whether or not this analysis type is valid (has been registered).

isValid(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Whether or not this analysis type is valid (has been registered).

isValid(Object, ConstraintValidatorContext) - Method in class ca.corefacility.bioinformatics.irida.constraints.impl.ProjectMetadataRoleValidator

isValid(String, ConstraintValidatorContext) - Method in class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LatitudeValidator

isValid(String, ConstraintValidatorContext) - Method in class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LongitudeValidator

isZippedFile(Path) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Determine if a file is a zip file.

iterator() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

J

javaMailSender() - Method in class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig

JobError - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

Galaxy Job failure information when a tool in a IRIDA workflow produces an error state for an AnalysisSubmission

JobError() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

for hibernate

JobError(AnalysisSubmission, JobDetails, HistoryContentsProvenance, Tool) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

JobErrorRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

A repository for managing JobError objects

jobsClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

Join<SubjectType extends IridaThing,ObjectType extends IridaThing> - Interface in ca.corefacility.bioinformatics.irida.model.joins

Interface that the join classes should extend.

JS - ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

JWKConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.JWKConfig

jwkSource(String, String) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.JWKConfig

jwtAuthenticationConverter() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.ResourceServerConfig

jwtCustomizer() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

jwtDecoder(JWKSource<SecurityContext>) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.JWKConfig

jwtEncoder(JWKSource<SecurityContext>) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.JWKConfig

L

label - Variable in enum ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

label - Variable in enum ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

label - Variable in enum ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

LabelledRelationshipResource<Owner extends IridaThing,Child extends IridaThing> - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

An implementation of a resource that only has a label and an identifier.

LabelledRelationshipResource(String, Join<Owner, Child>) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource

Latitude - Annotation Type in ca.corefacility.bioinformatics.irida.validators.annotations

Validates geographic latitude coordinate values.

LatitudeValidator - Class in ca.corefacility.bioinformatics.irida.validators.annotations.validators

Validator for validating latitude portion of a geographic coordinate.

LatitudeValidator() - Constructor for class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LatitudeValidator

LaunchAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.launchPipeline

Controller to handle AJAX requests from the UI for Workflow Pipelines

LaunchAjaxController(UIPipelineService, UIPipelineStartService, UIPipelineSampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

launchChain(Long) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessingChain

Launch the chain of FileProcessor on the specific SequencingObject.

launchChain(Long) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

Launch the chain of FileProcessor on the specific SequencingObject.

LaunchController - Class in ca.corefacility.bioinformatics.irida.ria.web.launchPipeline

Controller for workflow launch pages.

LaunchController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchController

LaunchesProjectEvent - Annotation Type in ca.corefacility.bioinformatics.irida.events.annotations

Annotation to be put on methods which should create a ProjectEvent.

launchPipeline(UUID, LaunchRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Launch a new IRIDA Workflow Pipeline

LaunchRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos

Information required to launch a IRIDA Workflow Pipeline

LaunchRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

LaunchSample - Class in ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos

Represents a sample within the cart on the pipeline launch page.

LaunchSample(Sample, Project, SequencingObject) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

launchUpload() - Method in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Check for new NcbiExportSubmissions to be uploaded and begin their upload

LESS_THAN - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

LESS_THAN_EQUAL - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

LEVEL_1 - ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

LEVEL_2 - ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

LEVEL_3 - ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

LEVEL_4 - ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

librariesClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

libraryConstructionProtocol(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

String describing the library construction protocol

libraryDatasetToHistory(String, History) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Transfers a dataset from a Galaxy library into a history for a workflow.

libraryName(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Name of the library for these files

librarySelection(NcbiLibrarySelection) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Method used to select the library for these files

librarySource(NcbiLibrarySource) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Set the library source

libraryStrategy(NcbiLibraryStrategy) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Strategy used for generating this library

LineListController - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist

This controller is responsible for AJAX handling for the line list page, which displays sample metadata.

LineListController(ProjectService, SampleService, MetadataTemplateService, ProjectOwnerPermission, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

LinkNotFoundException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when there is no link for a given rel when reading from an API

LinkNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.LinkNotFoundException

list() - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

Get the remote apis listing page

list(int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

List objects of Type in the database, limited to some specific page

list(int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

List objects of Type in the database, limited to some specific page

list(int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

List objects of Type in the database, limited to some specific page

list(int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

List objects of Type in the database, limited to some specific page

list(int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

List objects of Type in the database, limited to some specific page

list(int, int, Sort.Direction) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.

list(int, int, Sort.Direction) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.

list(int, int, Sort.Direction) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.

list(int, int, Sort.Direction) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.

list(int, int, Sort.Direction, String...) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

List objects of Type in the database, limited to some specific page.

list(int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

List objects of Type in the database, limited to some specific page.

list(int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

List objects of Type in the database, limited to some specific page.

list(int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

List objects of Type in the database, limited to some specific page.

list(int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

List objects of Type in the database, limited to some specific page.

list(int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

List objects of Type in the database, limited to some specific page.

list(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

List the resources available from this service

list(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SampleRemoteRepositoryImpl

List the resources available from this service

list(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.RemoteRepository

List the resources available from this service

list(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

List the resources available from this service

list(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.RemoteService

List the resources available from this service

LIST - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

Describes a list of files within a collection.

LIST_PAIRED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

Describes a list of paired end files.

LIST_PROJECTS_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

listAllResources() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Get all resources in the application.

listAllResources() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get all resources in the application.

listAllResources() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Get all resources in the application.

listAllResources() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Get all resources in the application.

listAllResources() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Get all resources in the application.

listAllSubmissions(String, String, Set<AnalysisState>, Set<UUID>, PageRequest) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get a page of all AnalysisSubmissions in the system

listAllSubmissions(String, String, Set<AnalysisState>, Set<UUID>, PageRequest) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get a page of all AnalysisSubmissions in the system

listAssembliesForSample(Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

List all the GenomeAssemblys for a given Sample

ListItem - Class in ca.corefacility.bioinformatics.irida.ria.web.dto.list

Generic List item for UI responses.

ListItem() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.list.ListItem

listOfType(String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Get all analyses of a given type

listProjectsForAPI(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl

List all of the projects for a given RemoteAPI

listProjectsForAPI(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.ProjectRemoteService

List all of the projects for a given RemoteAPI

ListResourceWrapper<Type extends IridaRepresentationModel> - Class in ca.corefacility.bioinformatics.irida.model.remote.resource

Object wrapping a list of returned resources from a remote IRIDA API.

ListResourceWrapper() - Constructor for class ca.corefacility.bioinformatics.irida.model.remote.resource.ListResourceWrapper

listSequencingObjectsOfTypeForSample(Long, String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

List all SequencingObjects of a given type for a Sample

listSequencingRuns(SequencingRunsListRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

Get the current page contents for a table displaying sequencing runs.

listSequencingRuns(SequencingRunsListRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

Get the current page contents for a table displaying sequencing runs.

listSubmissionsForProject(String, String, Set<AnalysisState>, Set<UUID>, Project, PageRequest) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get a page of the AnalysisSubmissions shared with a project.

listSubmissionsForProject(String, String, Set<AnalysisState>, Set<UUID>, Project, PageRequest) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get a page of the AnalysisSubmissions shared with a project.

listSubmissionsForUser(String, String, Set<AnalysisState>, User, Set<UUID>, PageRequest) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get a page of AnalysisSubmissions the given user has submitted.

listSubmissionsForUser(String, String, Set<AnalysisState>, User, Set<UUID>, PageRequest) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get a page of AnalysisSubmissions the given user has submitted.

listTypeReference - Variable in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

loadAllWorkflowImplementations(Path) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Loads up a set of IridaWorkflows from the given directory.

loadClientByClientId(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Get the IridaClientDetails by clientDetails

loadClientByClientId(String) - Method in interface ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService

Get the IridaClientDetails by clientDetails

loadClientDetailsByClientId(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.IridaClientDetailsRepository

Get a client by the given id

loadIridaWorkflow(Path, Path) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Loads up an IridaWorkflow from the given information files.

loadIridaWorkflowFromDirectory(Path) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Loads up a workflow from the given directory.

loadUserByEmail(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom

Get a user from the database with the supplied email address

loadUserByEmail(String) - Method in class ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryImpl

Get a user from the database with the supplied email address

loadUserByEmail(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get a user from the database with the supplied email address

loadUserByEmail(String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get a user from the database with the supplied email address

loadUserByUsername(String) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepository

Get a user from the database with the supplied username.

loadUserByUsername(String) - Method in class ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryImpl

loadUserByUsername(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

loadUserByUsername(String) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

loadWorkflowDescription(Path) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Loads up the workflow description from the given file.

loadWorkflowStructure(Path) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

Loads up the structure of the workflow given the file.

LOCAL - ca.corefacility.bioinformatics.irida.pipeline.upload.DataStorage

LOCAL implies the data to upload is on the same filesystem as the remote site (e.g.

Locale - Class in ca.corefacility.bioinformatics.irida.ria.web.settings.dto

Stores locale info.

Locale(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

localeResolver() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

LoginController - Class in ca.corefacility.bioinformatics.irida.ria.web.login

LoginController(EmailController) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.login.LoginController

LoginSuccessHandler - Class in ca.corefacility.bioinformatics.irida.ria.security

Handles actions for when a user is successfully logged in.

LoginSuccessHandler(UserRepository, LocaleResolver) - Constructor for class ca.corefacility.bioinformatics.irida.ria.security.LoginSuccessHandler

Longitude - Annotation Type in ca.corefacility.bioinformatics.irida.validators.annotations

Validates geographic longitude coordinate values.

LongitudeValidator - Class in ca.corefacility.bioinformatics.irida.validators.annotations.validators

Validator for validating longitude portion of a geographic coordinate.

LongitudeValidator() - Constructor for class ca.corefacility.bioinformatics.irida.validators.annotations.validators.LongitudeValidator

LOW - ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority

LS_454_GS - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS_454_GS_20 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS_454_GS_FLX - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS_454_GS_FLX_PLUS - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS_454_GS_FLX_TITANIUM - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS_454_GS_JUNIOR - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

LS454 - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

M

main(String[]) - Static method in class ca.corefacility.bioinformatics.irida.IridaApplication

main(String[]) - Static method in class ca.corefacility.bioinformatics.irida.util.SchemaExporter

main(String[]) - Static method in class ca.corefacility.bioinformatics.irida.util.ToolsListExporter

ManageLocalProjectSettingsPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.project

Permission checking if a user can update local project settings

ManageLocalProjectSettingsPermission(ProjectRepository, UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.project.ManageLocalProjectSettingsPermission

Construct an instance of ManageLocalProjectSettingsPermission.

MANAGER_IN_GROUP - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

MANAGER_ON_PROJECT - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

markAnnouncementAsReadByUser(Announcement, User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Mark an Announcement object as read by a User

markAnnouncementAsReadByUser(Announcement, User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Mark an Announcement object as read by a User

markAnnouncementAsReadByUser(Long, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Marks an announcement as read.

markAnnouncementAsUnreadByUser(Announcement, User) - Method in interface ca.corefacility.bioinformatics.irida.service.AnnouncementService

Mark an Announcement as unread by a User

markAnnouncementAsUnreadByUser(Announcement, User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Mark an Announcement as unread by a User

markAnnouncementRead(Long, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Marks the announcement as read by the current user.

MARKED - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Marked to be synchronized

markFileProcessor(Long, String, SequencingObject.ProcessingState) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository

Update a sequencing object's file processing state with the given status

MATCH - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

MATCH_END - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

MATCH_IN - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

MATCH_START - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

MAX_IN_MEMORY_SIZE - Static variable in class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

maxLength(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the maxLength

MBD2 - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

MEDIP_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

MEDIUM - ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority

merge(MetadataEntry) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

Merges the passed metadata entry into this metadata entry.

merge(MetadataEntry) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

Merges the passed metadata entry into this metadata entry.

MergeRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

DTO to handle merging 2 samples

MergeRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.MergeRequest

mergeSampleMetadata(Sample, Set<MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Merge the given set of MetadataEntry into the given Sample.

mergeSampleMetadata(Sample, Set<MetadataEntry>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Merge the given set of MetadataEntry into the given Sample.

mergeSamples(Project, Sample, Collection<Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Merge multiple samples into one.

mergeSamples(Project, Sample, Collection<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Merge multiple samples into one.

mergeSamples(Long, MergeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Merge 1 or more samples into another sample.

mergeSamples(Long, MergeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Merge 1 or more samples into another sample

message() - Method in annotation type ca.corefacility.bioinformatics.irida.constraints.MetadataRoleValidate

message() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Latitude

message() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Longitude

message() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName

message() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName

messageSource() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

METADATA_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

METADATA_ROLE_KEY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

MetadataAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata

Ajax controller for project metadata templates.

MetadataAjaxController(UIMetadataService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

MetadataEntry - Class in ca.corefacility.bioinformatics.irida.model.sample.metadata

Class for storing generic metadata for a Sample

MetadataEntry() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

MetadataEntry(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

MetadataEntry(String, String, MetadataTemplateField) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

MetadataEntryRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Repository for saving and reading MetadataEntry

MetadataEntryRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Custom repository methods for retrieving MetadataEntrys

MetadataEntryRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.sample

Implementation of the custom methods for retrieving MetadataEntry

MetadataEntryRepositoryImpl(DataSource, EntityManager) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepositoryImpl

MetadataFieldRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

A repository for storing and reading MetadataTemplateFields

MetadataFieldRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Custom repository methods for getting MetadataTemplateFields

MetadataFieldRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.sample

Custom repository methods for getting MetadataTemplateFields

MetadataFieldRepositoryImpl(EntityManager, DataSource) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.sample.MetadataFieldRepositoryImpl

MetadataImportFileTypeNotSupportedError - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception to be thrown if the upload metadata file does not match any of the predetermined formats.

MetadataImportFileTypeNotSupportedError(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.MetadataImportFileTypeNotSupportedError

MetadataRestriction - Class in ca.corefacility.bioinformatics.irida.model.sample.metadata

A class to define restrictions on which metadata fields can be viewed by a ProjectRole on a Project

MetadataRestriction() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

MetadataRestriction(Project, MetadataTemplateField, ProjectMetadataRole) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

MetadataRestrictionRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Interface for storing and retrieving MetadataRestriction

MetadataRoleValidate - Annotation Type in ca.corefacility.bioinformatics.irida.constraints

Validation annotation to validate that if the projectRole is set to PROJECT_OWNER for a user/usergroup then the metadataRole must be set to the highest level An array of fields (projectRole, metadataRole) must be supplied

MetadataTemplate - Class in ca.corefacility.bioinformatics.irida.model.sample

Stores a collection of MetadataTemplateFields that will often used together

MetadataTemplate() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

MetadataTemplate(String, List<MetadataTemplateField>) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

MetadataTemplate(String, List<MetadataTemplateField>, Project) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

MetadataTemplateField - Class in ca.corefacility.bioinformatics.irida.model.sample

Describes an individual field in a MetadataTemplate.

MetadataTemplateField() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

MetadataTemplateField(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

MetadataTemplateRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

A repository for storing and reading MetadataTemplates

MetadataTemplateService - Interface in ca.corefacility.bioinformatics.irida.service.sample

Service for managing MetadataTemplates and related Projects

MetadataTemplateServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.sample

Service for storing and reading MetadataTemplates

MetadataTemplateServiceImpl(MetadataTemplateRepository, MetadataFieldRepository, Validator, MetadataRestrictionRepository, UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

METAGENOMIC - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

METATRANSCRIPTOMIC - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

METHOD_SECURITY_ORDER - Static variable in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

MethodEvent - Class in ca.corefacility.bioinformatics.irida.events

Captures the arguments and return value of a method call.

MethodEvent(Class<? extends ProjectEvent>, Object, Object[]) - Constructor for class ca.corefacility.bioinformatics.irida.events.MethodEvent

MF - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

MGISEQ_2000_RS - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

MIN_ION - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

MinimalModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models

Basic implementation for items that want to return a smaller model to the UI Usually should stay as just name and id.

MinimalModel(Long, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.MinimalModel

minLength(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the minLength

mirrorAssembly(UploadedAssembly) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.GenomeAssemblyRemoteService

Download the given UploadedAssembly to the local server

mirrorAssembly(UploadedAssembly) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

Download the given UploadedAssembly to the local server

mirrorSequencingObject(Type) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.SequencingObjectRemoteServiceImpl

mirrorSequencingObject(Type) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.SequencingObjectRemoteService

Mirror a remote SequencingObject to the local system

MISEQ_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

MissingRequiredParametersException - Exception in ca.corefacility.bioinformatics.irida.exceptions.pipelines

This exception is thrown if a pipeline is attempted to be launched that has required parameters that haven't been provided

MissingRequiredParametersException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.pipelines.MissingRequiredParametersException

MLST_MENTALIST - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

MNASE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

MNASE_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

MOD_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

MODEL_ERROR_ATTR - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.BaseController

ModelKeys - Enum in ca.corefacility.bioinformatics.irida.ria.web.models

Use as prefixes when generating UI model keys.

MODIFIED_DATE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

modifiedDate - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

modifiesFile() - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

modifiesFile() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.AutomatedAnalysisFileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

modifiesFile() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.ChecksumFileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

modifiesFile() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.CoverageFileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

modifiesFile() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.FastqcFileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

modifiesFile() - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.

ModifyProjectPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.project

Superclass permission whether a user can modify project settings.

ModifyProjectPermission(ProjectRepository, UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.project.ModifyProjectPermission

Construct an instance of ModifyProjectPermission.

monitorRunningAnalyses() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any submissions running in Galaxy and monitor the status.

monitorRunningAnalyses() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through any AnalysisSubmissions currently running and mark as complete any completed analyses.

monitorRunningAnalyses() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through any AnalysisSubmissions currently running and mark as complete any completed analyses.

MONTHLY - ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

MONTHLY - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

moveSampleBetweenProjects(Project, Project, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Move a Sample from one Project to another

moveSampleBetweenProjects(Project, Project, Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Move a Sample from one Project to another

moveSamples(Project, Project, Collection<Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Move a list of Samples between 2 Project

moveSamples(Project, Project, Collection<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Move a list of Samples between 2 Project

MRE_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

MSLL - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

multipartResolver() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

MutableIridaThing - Interface in ca.corefacility.bioinformatics.irida.model

An object that can be modified

N

name - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

name - Variable in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

name(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets a name for this submission.

namedParameters - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

namespace(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

Namespace for generating the submission identifier

NCBI_ACCESSION_METADATA_LABEL - Static variable in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

NCBIAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web

Spring Ajax Controller to handle NCBI requests.

NCBIAjaxController(UINcbiService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

NcbiBioSampleFiles - Class in ca.corefacility.bioinformatics.irida.model.export

SequenceFiles and SequenceFilePairs associated with a NcbiExportSubmission.

NcbiBioSampleFiles() - Constructor for class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

NcbiBioSampleFiles(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

NcbiBioSampleFiles(String, Set<SingleEndSequenceFile>, Set<SequenceFilePair>, NcbiInstrumentModel, String, NcbiLibrarySelection, NcbiLibrarySource, NcbiLibraryStrategy, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

NcbiBioSampleFiles.Builder - Class in ca.corefacility.bioinformatics.irida.model.export

Builder class for NcbiBioSampleFiles

NcbiBioSampleModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Describes an NCBI SRA Submission's BioSample's files for the UI.

NcbiBioSampleModel(NcbiBioSampleFiles) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel

NcbiExportSubmission - Class in ca.corefacility.bioinformatics.irida.model

Class storing a request to upload sequence data to NCBI.

NcbiExportSubmission() - Constructor for class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

NcbiExportSubmission(Project, User, String, String, String, Date, List<NcbiBioSampleFiles>) - Constructor for class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

NcbiExportSubmissionAdminTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Represents a NcbiExportSubmission for viewing by an Administrator.

NcbiExportSubmissionAdminTableModel(NcbiExportSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiExportSubmissionAdminTableModel

NcbiExportSubmissionRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for storing and reading NcbiExportSubmissions

NcbiExportSubmissionService - Interface in ca.corefacility.bioinformatics.irida.service.export

Service for exporting SequenceFile data to NCBI

NcbiExportSubmissionServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.export

Service impl for submitting data to NCBI

NcbiExportSubmissionServiceImpl(NcbiExportSubmissionRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

NcbiExportSubmissionTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Represents a NcbiExportSubmission for use within the UI.

NcbiExportSubmissionTableModel(NcbiExportSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel

NcbiInstrumentModel - Enum in ca.corefacility.bioinformatics.irida.model.export

 * Instrument model for NCBI Upload.

NcbiLibrarySelection - Enum in ca.corefacility.bioinformatics.irida.model.export

Library selection of an ncbi export

NcbiLibrarySource - Enum in ca.corefacility.bioinformatics.irida.model.export

Library source of an NCBI export

NcbiLibraryStrategy - Enum in ca.corefacility.bioinformatics.irida.model.export

Library strategy of an ncbi export

NcbiPlatform - Enum in ca.corefacility.bioinformatics.irida.ria.web.models.export

List of all available NCBI Platforms

NcbiPlatformInstrumentModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Represents the relationship between sequencing platforms and instruments allowed by NCBI

NcbiPlatformInstrumentModel() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatformInstrumentModel

NCBISubmission - Interface in ca.corefacility.bioinformatics.irida.validators.groups

A group definition for fields that are required when submitting to NCBI repositories.

NcbiSubmissionModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Describes an NCBI SRA Submission for the UI

NcbiSubmissionModel(NcbiExportSubmission, List<NcbiBioSampleModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel

NCBISubmissionOneOf - Interface in ca.corefacility.bioinformatics.irida.validators.groups

NCBI defines some attributes as a "one-of" must not be null.

NcbiSubmissionRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Request for submitting to the NCBI SRA

NcbiSubmissionRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

NcbiSubmissionSample - Class in ca.corefacility.bioinformatics.irida.ria.web.models.export

Represents a sample in a NcbiSubmissionRequest

NcbiSubmissionSample() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

ncbiUpload() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.NcbiUploadScheduledTaskConfig

Launch the NCBI uploader

NcbiUploadScheduledTaskConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Scheduled task configuration for uploading to NCBI

NcbiUploadScheduledTaskConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.NcbiUploadScheduledTaskConfig

ncbiUploadStatus() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.NcbiUploadScheduledTaskConfig

Launch the NCBI status checking

NcbiXmlParseException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when there's an error parsing NCBI responses

NcbiXmlParseException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException

Create NcbiXmlParseException with message

NcbiXmlParseException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException

Create NcbiXmlParseException with message and cause

NEGATIVE - ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

NEVER - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

NEVER_CLEANUP - Static variable in interface ca.corefacility.bioinformatics.irida.service.CleanupAnalysisSubmissionCondition

Condition which never cleans up analysis submissions.

NEW - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Occurs when an analysis is first entered for submission.

NEW - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Newly created submission

NEW - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

newHistoryForWorkflow() - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Creates a new History for running a workflow.

NewickFileView - Class in ca.corefacility.bioinformatics.irida.web.spring.view

Write out Newick formatted tree files to the client.

NewickFileView() - Constructor for class ca.corefacility.bioinformatics.irida.web.spring.view.NewickFileView

Default constructor

NewMemberRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used to send information to the server about a user to be added as a project member

NewMemberRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

NewMemberRequest(Long, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

NewProjectMetadataRestriction - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Helper class when creating a project with samples from the cart to indicate which restriction level the metadata attached should have.

NewProjectMetadataRestriction() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

NewProjectMetadataRestriction(Long, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

newRevision(Object) - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevListener

NEXT_SEQ_1000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

NEXT_SEQ_2000 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

NEXT_SEQ_500 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

NEXT_SEQ_550 - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

NGSLinkerAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects

Controller to handle asynchronous request for the ngs-linker

NGSLinkerAjaxController(NGSLinkerService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.NGSLinkerAjaxController

NGSLinkerCmdRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Data transfer object for creating a command for the ngs-linker.pl

NGSLinkerCmdRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest

NGSLinkerService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service for converting data for creating the ngs-linker command.

NGSLinkerService(ProjectService, SampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.NGSLinkerService

NoGalaxyHistoryException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

An exception that gets thrown when there is no history in Galaxy that can be found.

NoGalaxyHistoryException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.NoGalaxyHistoryException

Constructs a new NoGalaxyHistoryException with no information.

NoGalaxyHistoryException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.NoGalaxyHistoryException

Constructs a new NoGalaxyHistoryException with the given message.

NoGalaxyHistoryException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.NoGalaxyHistoryException

Constructs a new NoGalaxyHistoryException with the given message and cause.

NoGalaxyHistoryException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.NoGalaxyHistoryException

Constructs a new NoGalaxyHistoryException with the given cause.

NoPercentageCompleteException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception that gets thrown when no percentage complete exists for an AnalysisSubmission.

NoPercentageCompleteException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NoPercentageCompleteException

Constructs a new NoPercentageComplete with the given message.

NoSuchValueException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when attempting to access a value that does not currently exist.

NoSuchValueException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NoSuchValueException

Constructs a new NoSuchValueException with no information.

NoSuchValueException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NoSuchValueException

Constructs a new NoSuchValueException with the given message.

NoSuchValueException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NoSuchValueException

Constructs a new NoSuchValueException with the given message and cause.

NoSuchValueException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.NoSuchValueException

Constructs a new NoSuchValueException with the given cause.

NOT_CLEANED - ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

A state where intermediate files exists for this analysis.

NOT_EQUAL - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

NOT_IN - ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

Notification - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Abstract class to represent an Ant Design UI notification.

Notification(NotificationType, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification

Notification(NotificationType, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.Notification

NotificationType - Enum in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Different types of notification found in Ant Design

O

OAuth2ResourceOwnerPasswordAuthenticationConverter - Class in ca.corefacility.bioinformatics.irida.oauth2

Attempts to extract an Access Token Request from HttpServletRequest for the OAuth 2.0 Resource Owner Password Credentials Grant and then converts it to an OAuth2ResourceOwnerPasswordAuthenticationToken used for authenticating the authorization grant.

OAuth2ResourceOwnerPasswordAuthenticationConverter() - Constructor for class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationConverter

OAuth2ResourceOwnerPasswordAuthenticationProvider - Class in ca.corefacility.bioinformatics.irida.oauth2

An AuthenticationProvider impementation for the OAuth 2.0 Resource Owner Password Credentials Grant.

OAuth2ResourceOwnerPasswordAuthenticationProvider(AuthenticationManager, OAuth2AuthorizationService, OAuth2TokenGenerator<? extends OAuth2Token>) - Constructor for class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationProvider

Constructs an OAuth2ResourceOwnerPasswordAuthenticationProvider using the provided parameters.

OAuth2ResourceOwnerPasswordAuthenticationToken - Class in ca.corefacility.bioinformatics.irida.oauth2

An Authentication implementation used for the OAuth 2.0 Resource Owner Password Credentials Grant.

OAuth2ResourceOwnerPasswordAuthenticationToken(AuthorizationGrantType, Authentication, Set<String>, Map<String, Object>) - Constructor for class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationToken

Constructs an OAuth2ResourceOwnerPasswordAuthenticationToken using the provider parameters.

oAuth2TokenGenerator(JwtEncoder, OAuth2TokenCustomizer<JwtEncodingContext>) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

oAuthClient() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

oauthClientAuthProvider(RegisteredClientRepository, OAuth2AuthorizationService) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

OAuthTokenRestTemplate - Class in ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate

Rest Template used to communicate with OAuth2 enabled REST APIs.

OAuthTokenRestTemplate(RemoteAPITokenService, RemoteAPI) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.OAuthTokenRestTemplate

Create a new OAuthTokenRestTemplate with the given RemoteAPITokenService and connecting to the given RemoteAPI

objectLabels - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Filetype labels for different SequencingObject subclasses.

objectTypeReference - Variable in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

OK - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

The workflow will be in this state when everything is complete.

OltuAuthorizationController - Class in ca.corefacility.bioinformatics.irida.ria.web.oauth

Controller for handling OAuth2 authorizations

OltuAuthorizationController(RemoteAPITokenService, RemoteAPIService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

onAuthenticationFailure(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ca.corefacility.bioinformatics.irida.ria.security.IridaPostAuthenticationFailureHandler

Custom authentication failure handling for specific AuthenticationException's otherwise default to SimpleUrlAuthenticationFailureHandler behaviour.

onAuthenticationSuccess(HttpServletRequest, HttpServletResponse, Authentication) - Method in class ca.corefacility.bioinformatics.irida.ria.security.LoginSuccessHandler

OpenAPIConfig - Class in ca.corefacility.bioinformatics.irida.config.web

Configuration for IRIDA REST API documentation.

OpenAPIConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.web.OpenAPIConfig

ORDER - Static variable in class ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor

The default order for the processor.

OTHER - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

OTHER - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

OTHER - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

outputFileBaseDirectory() - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

outputFilesExist(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService

Checks if all output files from a given AnalysisSubmission are available on galaxy.

outputFilesExist(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy

Checks if all output files from a given AnalysisSubmission are available on galaxy.

OverrepresentedSequence - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

A SequenceFile may have 0 or more over-represented sequences.

OverrepresentedSequence(String, int, BigDecimal, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

overrepresentedSequences(Set<OverrepresentedSequence>) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the overrepresentedSequences

OWNER - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

OXFORD_NANOPORE - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

P

PAC_BIO_RS - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

PAC_BIO_RS_II - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

PACBIO_SMRT - ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

PAGE_ANALYSIS_LIST - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

PAGE_USER_ANALYSIS_OUPUTS - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

PagedListResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.dto.list

UI Response for returning a paged list to the UI.

PagedListResponse(long, List<ListItem>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.list.PagedListResponse

PAIRED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

Describes a set of paired files (sequence read paired-end files).

PAIRED_END - ca.corefacility.bioinformatics.irida.model.run.SequencingRun.LayoutType

PairedEndSequenceFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile

Describes a SequenceFilePair for the UI

PairedEndSequenceFileModel - ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

PairedEndSequenceFileModel(SequenceFilePair) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.PairedEndSequenceFileModel

pairs(Set<SequenceFilePair>) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles.Builder

set the file pairs

PARAMETER_NAME_SEPARATOR - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

A separator character for nested parameter names.

ParameterBuilderGalaxy - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

A class used to build up the parameter data structures used for Galaxy.

ParameterBuilderGalaxy() - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy

Builds a new ParameterBuilderGalaxy.

ParameterBuilderGalaxy.ParameterId - Class in ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy

An id for a particular parameter.

ParameterId(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

Builds a new parameter id with the given information.

PARENT_FRAME_RELOAD_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

parseCSV(Long, InputStream) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataFileImportService

Parse metadata from an csv file.

parseDataTablesParams(HttpServletRequest) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesParams

Static initializer to get the params for all DataTablesRequest

parseExcel(Long, InputStream, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataFileImportService

Parse metadata from an excel file.

parseExcelFile(AnalysisOutputFile, int) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Parse the data from an AnalysisOutputFile excel file.

parseExcelFile(Long, String, Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Parse excel file and return an ExcelData dto which contains the row data as well as the headers.

parseWebpackManifestFile(File) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerManifestParser

Parse the webpack manifest file

passAuthCode(Model, HttpServletRequest, HttpSession) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.GalaxyRedirectionEndpointController

Receive the OAuth2 authorization code from IRIDA and pass it on to the client-side code

PASSWORD_RESET_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetController

passwordEncoder() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

PasswordExpiryChecker - Class in ca.corefacility.bioinformatics.irida.security

Checks whether a user's password has changed within the configured expiry time.

PasswordExpiryChecker(UserRepository, int) - Constructor for class ca.corefacility.bioinformatics.irida.security.PasswordExpiryChecker

Build a PasswordExpiryChecker with a given UserRepository and configured password expiry date

PasswordReset - Class in ca.corefacility.bioinformatics.irida.model.user

A password reset object.

PasswordReset() - Constructor for class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

PasswordReset(User) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.PasswordReset

PasswordResetAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.login

Handles asynchronous requests for password resets.

PasswordResetAjaxController(UIPasswordResetService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetAjaxController

PasswordResetController - Class in ca.corefacility.bioinformatics.irida.ria.web.login

Controller for handling password reset flow

PasswordResetController(PasswordResetService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetController

PasswordResetRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.user

A repository to store password resets for a user.

PasswordResetService - Interface in ca.corefacility.bioinformatics.irida.service.user

Service for managing PasswordReset entities.

PasswordResetServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.user

Implementation for managing PasswordReset

PasswordResetServiceImpl(PasswordResetRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

PasswordReusedException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when a user attempts to update a password with one they've already used.

PasswordReusedException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.PasswordReusedException

Create a new PasswordReusedException with the given message

PathConverter - Class in ca.corefacility.bioinformatics.irida.model

Converts a Path to a String before persisting a value to a column in a database.

PathConverter() - Constructor for class ca.corefacility.bioinformatics.irida.model.PathConverter

PathJson - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Serialization class for java Path objects.

PathJson() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson

PathJson.PathSerializer - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Serializer for Java Path objects.

PathSerializer() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson.PathSerializer

PAUSED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

payload() - Method in annotation type ca.corefacility.bioinformatics.irida.constraints.MetadataRoleValidate

payload() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Latitude

payload() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.Longitude

payload() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName

payload() - Method in annotation type ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName

PCR - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

perBaseQualityScoreChart(AnalysisOutputFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

set the perBaseQualityScoreChart

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission

PERMISSION_PROVIDED - Static variable in class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission

perSequenceQualityScoreChart(AnalysisOutputFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the perSequenceQualityScoreChart

PHYLOGENOMICS - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

Pipeline - Class in ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto

Analysis Workflow pipeline for consumption by the UI.

Pipeline(String, String, UUID, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.pipelines.dto.Pipeline

PIPELINE_STATUS_TEMPLATE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

PipelineController - Class in ca.corefacility.bioinformatics.irida.ria.web.pipelines

Controller for pipeline related views

PipelineController(IridaWorkflowsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.pipelines.PipelineController

PipelineProvidedMetadataEntry - Class in ca.corefacility.bioinformatics.irida.model.sample.metadata

MetadataEntry that has been created by an analysis pipeline

PipelineProvidedMetadataEntry(String, String, MetadataTemplateField, AnalysisSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

PipelineProvidedMetadataEntry(String, String, AnalysisSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.PipelineProvidedMetadataEntry

Build a PipelineProvidedMetadataEntry with the given value, type and AnalysisSubmission

PLUGIN_API_VERSION - Static variable in interface ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Defines the particular IRIDA Plugin API version.

POOLCLONE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

POSITIVE - ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

POST_PROCESSING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis currently undergoing post processing

postCreateRemoteAPI(RemoteAPI, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

Create a new client

postHandle(HttpServletRequest, HttpServletResponse, Object, ModelAndView) - Method in class ca.corefacility.bioinformatics.irida.ria.config.AnalyticsHandlerInterceptor

postHandle(HttpServletRequest, HttpServletResponse, Object, ModelAndView) - Method in class ca.corefacility.bioinformatics.irida.ria.config.BreadCrumbInterceptor

postHandle(HttpServletRequest, HttpServletResponse, Object, ModelAndView) - Method in class ca.corefacility.bioinformatics.irida.ria.config.UserSecurityInterceptor

postProcessAfterInitialization(Object, String) - Method in class ca.corefacility.bioinformatics.irida.config.repository.ForbidJpqlUpdateDeletePostProcessor

postProcessBeforeInitialization(Object, String) - Method in class ca.corefacility.bioinformatics.irida.config.repository.ForbidJpqlUpdateDeletePostProcessor

postProcessEnvironment(ConfigurableEnvironment, SpringApplication) - Method in class ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor

PostProcessingException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when a AnalysisSampleUpdater fails during post processing

PostProcessingException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.PostProcessingException

PostProcessingException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.PostProcessingException

postProcessResults() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any transferred submissions and perform post-processing

postProcessResults() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through any transferred AnalysisSubmissions and perform post processing as necessary

postProcessResults() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through any transferred AnalysisSubmissions and perform post processing as necessary

postProcessResults(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Performs any post processing required for an AnalysisSubmission.

postProcessResults(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Performs any post processing required for an AnalysisSubmission.

postProcessResults(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

Calls the AnalysisSubmissionSampleProcessor to perform any post processing required on a given AnalysisSubmission

postVisitDirectory(Path, IOException) - Method in class ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor

PREFIX - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

preHandle(HttpServletRequest, HttpServletResponse, Object) - Method in class ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor

prepareAnalyses() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any submissions and prepare them for execution.

prepareAnalyses() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through new AnalysisSubmissions and prepare them for execution.

prepareAnalyses() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through new AnalysisSubmissions and prepare them for execution.

prepareAnalysisFiles(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService

Uploads and prepares the files and other necessary data structures of a workflow for an analysis given an analysis submission.

prepareAnalysisFiles(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy

Uploads and prepares the files and other necessary data structures of a workflow for an analysis given an analysis submission.

prepareAnalysisOutputsSelectionDownload(List<ProjectSampleAnalysisOutputInfo>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

Prepare the download of multiple AnalysisOutputFile by adding them to a selection.

prepareAnalysisParameters(Map<String, String>, IridaWorkflow) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisParameterService

Prepares any parameters for this IridaWorkflow.

prepareAnalysisParameters(Map<String, String>, IridaWorkflow) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisParameterServiceGalaxy

Prepares any parameters for this IridaWorkflow.

prepareAnalysisWorkspace(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.workspace.AnalysisWorkspaceService

Prepares the workspace for an analysis given an analysis submission.

prepareAnalysisWorkspace(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisWorkspaceServiceGalaxy

Prepares the workspace for an analysis given an analysis submission.

PREPARED - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Occurs when an analysis is finished preparing.

prepareDownload(List<ProjectSampleAnalysisOutputInfo>, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analyses.AnalysesOutputsAjaxController

Prepare the download of multiple AnalysisOutputFile by adding them to a selection.

PreparedWorkflow<WorkflowInputsType extends WorkflowInputsGeneric> - Interface in ca.corefacility.bioinformatics.irida.model.workflow.execution

A Workflow that has been prepared for execution.

PreparedWorkflowGalaxy - Class in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

A Galaxy workflow that has been prepared for execution.

PreparedWorkflowGalaxy(String, String, WorkflowInputsGalaxy) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy

Builds a new PreparedWorkflowGalaxy with the given parameters.

prepareSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Prepares the given AnalysisSubmission to be executed within an execution manager.

prepareSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Prepares the given AnalysisSubmission to be executed within an execution manager.

prepareSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

Prepares the given AnalysisSubmission to be executed within an execution manager.

PREPARING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Occurs when an analysis is starting to be submitted.

preVisitDirectory(Path, BasicFileAttributes) - Method in class ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor

Priorities - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto

UI model for the priority and available priorities for a projects automated pipelines

Priorities() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities

priority - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

priority(AnalysisSubmission.Priority) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets the AnalysisSubmission.Priority of the analysis run

process(SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessor

Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain.

process(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.AutomatedAnalysisFileProcessor

Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain.

process(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.ChecksumFileProcessor

Create an sha256sum for the files in a SequencingObject and save it with the file.

process(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.CoverageFileProcessor

process(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.FastqcFileProcessor

process(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain.

PROCESSED_ERROR - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Processing completed with error(s)

PROCESSED_OK - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Processing completed successfully

processFiles() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.FileProcessingScheduledTaskConfig

Check for newly uploaded files to process

processFiles() - Method in class ca.corefacility.bioinformatics.irida.service.SequencingObjectProcessingService

Process SequencingObjects that have been locked for processing

PROCESSING - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Processing started

PROCESSING - ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryType

PROCESSING - ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

processSingleFile(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

Process a single SequenceFile

productionExecutor() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.ExecutorConfig

Task executor for running in regular production or development modes

Project - Class in ca.corefacility.bioinformatics.irida.model.project

A project object.

Project - ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

Project() - Constructor for class ca.corefacility.bioinformatics.irida.model.project.Project

Project(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.project.Project

Create a new Project with the given name

PROJECT_HASH_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

rel used for the project status hash

PROJECT_ID - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

PROJECT_MANAGER_PERMISSION - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

PROJECT_NAME - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

PROJECT_NAME_LIKE - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Sub-expressions for filtering and paging projects on different property names.

PROJECT_OWNER - ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

PROJECT_PERMISSIONS - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

PROJECT_SAMPLE_ADDED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_SAMPLE_DATA_ADDED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_SAMPLE_REMOVED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_SAMPLES_REL - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

PROJECT_USER - ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

PROJECT_USER_GROUP_ADDED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_USER_GROUP_REMOVED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_USER_REMOVED - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

PROJECT_USER_ROLE - ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

ProjectAnalysisSubmissionJoin - Class in ca.corefacility.bioinformatics.irida.model.workflow.submission

Join connection between an AnalysisSubmission and Project

ProjectAnalysisSubmissionJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

ProjectAnalysisSubmissionJoin(Project, AnalysisSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin

ProjectAnalysisSubmissionJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

repository for storing and reading ProjectAnalysisSubmissionJoins

ProjectAssociatedProjectsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings

Ajax Controller for handling associated projects

ProjectAssociatedProjectsAjaxController(UIAssociatedProjectsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController

ProjectCartSample - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

This class is USED ONLY for when a user selects all sample to be added to the cart from the project samples page.

ProjectCartSample(ProjectSampleJoin) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectCartSample

ProjectControllerUtils - Class in ca.corefacility.bioinformatics.irida.ria.web.projects

Common functions for project related controllers

ProjectControllerUtils(UserService, MetadataTemplateService, ProjectOwnerPermission, ManageLocalProjectSettingsPermission) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectControllerUtils

ProjectCurrentUserModel - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Details about how the current user can interact with a specific project

ProjectCurrentUserModel() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.ProjectCurrentUserModel

ProjectDetailsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings

Handle asynchronous requests for the UI project details page.

ProjectDetailsAjaxController(ProjectService, UIProjectsService, UIMetadataService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

ProjectDetailsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Encapsulates information about the project as well as permissions.

ProjectDetailsResponse(Project, boolean, boolean, MetadataTemplate) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

ProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Class storing events that happen on a Project.

ProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

ProjectEvent(Project) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.ProjectEvent

projectEventAspect(ProjectEventRepository, ProjectSampleJoinRepository, ProjectRepository, SampleRepository) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig

ProjectEventAspect - Class in ca.corefacility.bioinformatics.irida.events

Aspect used to create project events for methods annotated with event annotations

ProjectEventAspect(ProjectEventHandler) - Constructor for class ca.corefacility.bioinformatics.irida.events.ProjectEventAspect

ProjectEventEmailScheduledTask - Interface in ca.corefacility.bioinformatics.irida.service

Scheduled task for emailing new ProjectEvents to Users

ProjectEventEmailScheduledTaskImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Implementation of ProjectEventEmailScheduledTask which sends emails to users when they have new events

ProjectEventEmailScheduledTaskImpl(ProjectEventService, ProjectService, EmailController, ProjectSubscriptionService) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventEmailScheduledTaskImpl

ProjectEventHandler - Class in ca.corefacility.bioinformatics.irida.events

Handles the creation of ProjectEvents from methods annotated with LaunchesProjectEvent

ProjectEventHandler(ProjectEventRepository, ProjectSampleJoinRepository, ProjectRepository, SampleRepository) - Constructor for class ca.corefacility.bioinformatics.irida.events.ProjectEventHandler

ProjectEventRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for storing events that occurred on a project

ProjectEventService - Interface in ca.corefacility.bioinformatics.irida.service

Service for reading and managing ProjectEvents

ProjectEventServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Implementation of ProjectEventService using a ProjectEventRepository

ProjectEventServiceImpl(ProjectEventRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.ProjectEventServiceImpl

ProjectHashingService - Class in ca.corefacility.bioinformatics.irida.service.remote

Component used to compute a deep hashcode of a full project.

ProjectHashingService(SampleService, SequencingObjectService, GenomeAssemblyService) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.ProjectHashingService

ProjectHashResource - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

Resource class for storing a full project hash for the REST API

ProjectHashResource() - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ProjectHashResource

ProjectHashResource(Integer) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ProjectHashResource

ProjectLineListController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.metadata

Handles requests for the metadata in a project

ProjectLineListController(ProjectService, SampleService, MetadataTemplateService, ProjectControllerUtils, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

ProjectMembersAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects

Controller for all asynchronous request from the UI for Project Members

ProjectMembersAjaxController(UIProjectMembersService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

ProjectMemberTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Represents a Project member in the UI.

ProjectMemberTableModel(User, String, String, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectMemberTableModel

ProjectMetadataField - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto

A representation of a MetadataTemplateField specifically for a project.

ProjectMetadataField(MetadataTemplateField, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

ProjectMetadataResponse - Class in ca.corefacility.bioinformatics.irida.model.sample.metadata

Object grouping a project and all the metadata for samples within that project.

ProjectMetadataResponse(Project, Map<Long, Set<MetadataEntry>>) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.metadata.ProjectMetadataResponse

ProjectMetadataRole - Enum in ca.corefacility.bioinformatics.irida.model.enums

Role for a user's level of metadata access for a project.

ProjectMetadataRoleValidator - Class in ca.corefacility.bioinformatics.irida.constraints.impl

Hibernate validator to validate if a user/usegroup is a manager on a project then their metadata role should be set to the highest level.

ProjectMetadataRoleValidator() - Constructor for class ca.corefacility.bioinformatics.irida.constraints.impl.ProjectMetadataRoleValidator

ProjectMetadataTemplate - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto

Used to represent a project metadata template in the UI.

ProjectMetadataTemplate(MetadataTemplate, List<ProjectMetadataField>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

ProjectMinimalModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.project

Minimal model for a Project in the UI

ProjectMinimalModel(Project) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.project.ProjectMinimalModel

ProjectModel - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Representation of a Project used in the UI Projects listing table.

ProjectModel(Project, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectModel

ProjectObject - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

Representation of a Project used in the Project Samples table.

ProjectObject(Project) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectObject

ProjectOwnerPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.project

Confirms that a given user is the owner of a project

ProjectOwnerPermission(ProjectRepository, UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.project.ProjectOwnerPermission

Construct an instance of ProjectOwnerPermission.

ProjectReferenceFileController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings

Controller for ajax request dealing with project reference files.

ProjectReferenceFileController(ProjectService, ProjectControllerUtils) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectReferenceFileController

ProjectReferenceFileJoin - Class in ca.corefacility.bioinformatics.irida.model.project

Join-type relating Project to ReferenceFile.

ProjectReferenceFileJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

ProjectReferenceFileJoin(Project, ReferenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.model.project.ProjectReferenceFileJoin

ProjectReferenceFileJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.project

Repository for interacting with ProjectReferenceFileJoin.

ProjectRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

Service for reading Project objects from a remote IRIDA API

ProjectRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

Remote repository for retrieving Projects from RemoteAPIs

ProjectRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.ProjectRemoteRepositoryImpl

Create a new ProjectRemoteRepositoryImpl with the given RemoteAPITokenService

ProjectRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

Service for reading Project objects from a remote IRIDA API

ProjectRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Remote service for retrieving Projects

ProjectRemoteServiceImpl(ProjectRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl

ProjectRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Specialized repository for Project.

ProjectRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories

Custom repository methods for Projects

ProjectRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories

Implementation of custom repository methods for Projects

ProjectRepositoryImpl(EntityManager) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryImpl

ProjectRole - Enum in ca.corefacility.bioinformatics.irida.model.enums

Roles for users accessing projects.

PROJECTS_BOOKMARK - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl

PROJECTS_DIR - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

ProjectsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects

Controller for handling all ajax requests for Projects.

ProjectsAjaxController(UIProjectsService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsAjaxController

ProjectSampleAnalysisOutputInfo - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

Class to store basic AnalysisOutputFile and associated Sample, Project and AnalysisSubmission information from a native SQL query.

ProjectSampleAnalysisOutputInfo() - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

ProjectSampleAnalysisOutputInfo(Long, String, Long, String, String, Long, AnalysisType, UUID, Date, String, Long, Long, String, String, Long) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

ProjectSampleJoin - Class in ca.corefacility.bioinformatics.irida.model.joins.impl

ProjectSampleJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

ProjectSampleJoin(Project, Sample, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

ProjectSampleJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.project

Repository for managing ProjectUserJoin.

ProjectSampleJoinSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification for searching ProjectSampleJoins

ProjectSampleJoinSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.ProjectSampleJoinSpecification

ProjectSampleMetadataAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.metadata

This class is designed to be used for bulk actions on MetadataEntry within a Project.

ProjectSampleMetadataAjaxController(UIMetadataImportService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

ProjectSampleModel - Class in ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models

Used for exporting the project samples table.

ProjectSampleModel(ProjectSampleJoin, List<QCEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.ProjectSampleModel

ProjectSamplesAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects

AJAX Controller for handling asynchronous requests for project samples.

ProjectSamplesAjaxController(UIProjectSampleService, UISampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

ProjectSamplesFilter - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

DTO to handle filtering samples in a project

ProjectSamplesFilter() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectSamplesFilter

ProjectSamplesMetadataTemplateController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.metadata

Handles requests for MetadataTemplates in a Project

ProjectSamplesMetadataTemplateController(ProjectService, ProjectControllerUtils, MetadataTemplateService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

ProjectSamplesTableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

DTO for representing a page request in the Project Samples table

ProjectSamplesTableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSamplesTableRequest

ProjectSampleTableItem - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Representation of a row used in the Project Samples table.

ProjectSampleTableItem(ProjectSampleJoin, List<String>, String, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSampleTableItem

ProjectsController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects

Controller for project related views

ProjectsController(ProjectService, SampleService, UserService, ProjectControllerUtils, TaxonomyService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

ProjectService - Interface in ca.corefacility.bioinformatics.irida.service

A specialized service layer for projects.

ProjectServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

A specialized service layer for projects.

ProjectServiceImpl(ProjectRepository, SampleRepository, UserRepository, ProjectUserJoinRepository, ProjectSampleJoinRepository, RelatedProjectRepository, ReferenceFileRepository, ProjectReferenceFileJoinRepository, UserGroupProjectJoinRepository, SampleSequencingObjectJoinRepository, ProjectAnalysisSubmissionJoinRepository, SequencingObjectRepository, ProjectSubscriptionService, UserGroupJoinRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

ProjectSettingsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings

Controller to handle all asynchronous call from the project settings UI.

ProjectSettingsAjaxController(UIPipelineService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.ProjectSettingsAjaxController

ProjectSettingsRemoteAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings

Controller for managing settings for a remotely sync'd project asynchronously

ProjectSettingsRemoteAjaxController(UIRemoteProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectSettingsRemoteAjaxController

ProjectSubscription - Class in ca.corefacility.bioinformatics.irida.model.subscription

Class for storing email subscriptions to Projects for Users .

ProjectSubscription() - Constructor for class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

Construct an instance of ProjectSubscription with no properties set.

ProjectSubscription(User, Project, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

Construct an instance of ProjectSubscription with all properties set.

ProjectSubscriptionRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for storing, removing, and retrieving ProjectSubscriptions

ProjectSubscriptionsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.projects

Controller for handling AJAX requests for ProjectSubscription

ProjectSubscriptionsAjaxController(UIProjectSubscriptionService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectSubscriptionsAjaxController

ProjectSubscriptionService - Interface in ca.corefacility.bioinformatics.irida.service

A specialized service layer for project subscriptions.

ProjectSubscriptionServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

A specialized service layer for project subscriptions.

ProjectSubscriptionServiceImpl(ProjectSubscriptionRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

ProjectSyncFrequency - Enum in ca.corefacility.bioinformatics.irida.model.project

Describes how often a project should be synchronized by a remote api

ProjectSynchronizationAuthenticationToken - Class in ca.corefacility.bioinformatics.irida.security

An authentication token used to identify when an action is being taken during project synchronization.

ProjectSynchronizationAuthenticationToken(User) - Constructor for class ca.corefacility.bioinformatics.irida.security.ProjectSynchronizationAuthenticationToken

Create a new ProjectSynchronizationAuthenticationToken for a given User.

ProjectSynchronizationException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception thrown when there is an error synchronizing a project.

ProjectSynchronizationException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ProjectSynchronizationException

ProjectSynchronizationService - Class in ca.corefacility.bioinformatics.irida.service.remote

Service class to run a project synchornization task.

ProjectSynchronizationService(ProjectService, SampleService, SequencingObjectService, MetadataTemplateService, GenomeAssemblyService, ProjectRemoteService, SampleRemoteService, SingleEndSequenceFileRemoteService, SequenceFilePairRemoteService, GenomeAssemblyRemoteService, Fast5ObjectRemoteService, RemoteAPITokenService, EmailController) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

ProjectSyncScheduledTaskConfig - Class in ca.corefacility.bioinformatics.irida.config.services.scheduled

Scheduled task configuration for synchronizing projects from other IRIDA installations

ProjectSyncScheduledTaskConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.scheduled.ProjectSyncScheduledTaskConfig

ProjectUserGroupsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects

UI Ajax Controller for handling project user groups

ProjectUserGroupsAjaxController(UIProjectUserGroupsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

ProjectUserGroupsTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

UI Model for user groups that are associated with a project

ProjectUserGroupsTableModel(UserGroup, String, String, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ProjectUserGroupsTableModel

ProjectUserJoin - Class in ca.corefacility.bioinformatics.irida.model.joins.impl

A join table and class for users and projects.

ProjectUserJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

ProjectUserJoin(Project, User, ProjectRole) - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

ProjectUserJoin(Project, User, ProjectRole, ProjectMetadataRole) - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

ProjectUserJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.project

A repository for ProjectUserJoin.

ProjectWithoutOwnerException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown if role change is not allowed

ProjectWithoutOwnerException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.ProjectWithoutOwnerException

PROMETH_ION - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

propertySourcesPlaceholderConfigurer() - Static method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiPropertyPlaceholderConfig

propertySourcesPlaceholderConfigurer() - Static method in class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig

propertySourcesPlaceholderConfigurer() - Static method in class ca.corefacility.bioinformatics.irida.ria.config.WebStylesConfig

providerSettings() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.AuthorizationServerConfig

PUBLIC_CONTROLLERS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

A collection of the controllers in our system accessible by all authenticated users.

Q

QCEntry - Class in ca.corefacility.bioinformatics.irida.model.sample

Abstract class describing quality control entries for a SequencingObject

QCEntry() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

QCEntry(SequencingObject) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.QCEntry

QCEntry.QCEntryStatus - Enum in ca.corefacility.bioinformatics.irida.model.sample

Status of a QCEntry, whether checks are positive, negative, or can't be calculated.

QCEntry.QCEntryType - Enum in ca.corefacility.bioinformatics.irida.model.sample

The type of QCEntry

QCEntryRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Repository for saving and retrieving QCEntry objects

qcFileTypes - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

QUARTERLY - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

QUEUED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Queued for processing

QUEUED - ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

QUEUED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

R

RACE - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

RANDOM - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

RANDOMPCR - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

read(IdentifierType) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Read the object type by unique identifier.

read(Class<? extends Path>, HttpInputMessage) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Read the object type by unique identifier.

read(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

Read the object type by unique identifier.

read(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

read(String) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

Read individual resource at the given URI.

read(String) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.RemoteService

Read individual resource at the given URI.

read(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

Read an individual resource

read(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.RemoteRepository

Read an individual resource

read(String, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

Read an individual resource

read(String, RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.remote.RemoteService

Read an individual resource

read(KeyType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Read the object type by unique identifier.

ReadAnalysisPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.analysis

Confirms if a User can read a Analysis.

ReadAnalysisPermission(AnalysisRepository, UserRepository, AnalysisSubmissionRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisPermission

Constructs a new ReadAnalysisPermission with the given information.

ReadAnalysisSubmissionPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.analysis

Confirms if a User can read a AnalysisSubmission.

ReadAnalysisSubmissionPermission(AnalysisSubmissionRepository, UserRepository, SequencingObjectRepository, ReadSequencingObjectPermission, ProjectAnalysisSubmissionJoinRepository, ReadProjectPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.analysis.ReadAnalysisSubmissionPermission

Constructs a new ReadAnalysisSubmissionPermission with the given information.

readAnalysisSubmissionTemplateForProject(Long, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Get an AnalysisSubmissionTemplate on the given Project

readAnalysisSubmissionTemplateForProject(Long, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Get an AnalysisSubmissionTemplate on the given Project

readAssemblyForSample(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

Read an individual GenomeAssembly for a given Sample

readChunk(RandomAccessFile, Long, Long) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Read bytes of length chunk of a file starting at byte seek.

ReadExportSubmissionPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.project

Whether or not a User can read a given NcbiExportSubmission

ReadExportSubmissionPermission(NcbiExportSubmissionRepository, ReadProjectPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadExportSubmissionPermission

Construct an instance of ReadExportSubmissionPermission.

readLinesFromFilePointer(RandomAccessFile, Long) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Read lines from file using a RandomAccessFile.

readLinesLimit(BufferedReader, Long, Long, Long) - Static method in class ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Read a specified number of lines from a file.

ReadMetadataEntryPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.metadata

Permission for reading individual MetadataEntry for a sample

ReadMetadataEntryPermission(MetadataEntryRepository, ProjectSampleJoinRepository, MetadataRestrictionRepository, ProjectUserJoinRepository, UserRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission

readMetadataField(Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

readMetadataField(Long) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get a MetadataTemplateField by its Long identifier

readMetadataFieldByKey(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

readMetadataFieldByKey(String) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Read a MetadataTemplateField by its key

readMetadataFieldByLabel(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Get a MetadataTemplateField by its String label

readMetadataFieldByLabel(String) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Get a MetadataTemplateField by its String label

ReadMetadataTemplatePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.metadata

Permission for reading MetadataTemplate

ReadMetadataTemplatePermission(MetadataTemplateRepository, ReadProjectPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission

readMultiple(Iterable<IdentifierType>) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<Long>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Read multiple objects by the given collection of identifiers

readMultiple(Iterable<KeyType>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Read multiple objects by the given collection of identifiers

readObjectForSample(Sample, Long) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository

Read a SampleSequencingObjectJoin with the given Sample and SequencingObject by id

readProjectHash(Project) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.ProjectRemoteRepositoryImpl

Read the full project hash for the given project

readProjectHash(Project) - Method in interface ca.corefacility.bioinformatics.irida.repositories.remote.ProjectRemoteRepository

Read the full project hash for the given project

ReadProjectMetadataResponsePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.metadata

Permission for checking that a user should have access to the given MetadataTemplateFields in a ProjectMetadataResponse.

ReadProjectMetadataResponsePermission(UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository, MetadataRestrictionRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission

ReadProjectPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.project

Confirms that the authenticated user is allowed to read a project.

ReadProjectPermission(ProjectRepository, UserRepository, ProjectUserJoinRepository, UserGroupProjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission

Construct an instance of ReadProjectPermission.

readQCForSequenceFile(Long, String, Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Get the fastqc metrics for a SequenceFile

ReadReferenceFilePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.files

Permission testing if a given user can read a given reference file.

ReadReferenceFilePermission(ReferenceFileRepository, ProjectReferenceFileJoinRepository, AnalysisSubmissionRepository, ReadProjectPermission, ReadAnalysisSubmissionPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission

readSampleForProject(Project, Sample) - Method in interface ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository

Get a specific ProjectSampleJoin for a Project and Sample

ReadSamplePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.sample

Confirms that the authenticated user is allowed to read a sample.

ReadSamplePermission(SampleRepository, ProjectSampleJoinRepository, ReadProjectPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission

Construct an instance of ReadSamplePermission

readSequenceFileForSequencingObject(Long, String, Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Read a single SequenceFile for a given Sample and SequencingObject

readSequencingObject(Long, String, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Read a single SequencingObject of the given type from a Sample

readSequencingObjectForSample(Sample, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Read a SequencingObject and verify that it belongs to a given Sample.

readSequencingObjectForSample(Sample, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Read a SequencingObject and verify that it belongs to a given Sample.

ReadSequencingObjectPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.files

Evaluate whether or not a user can read a SequencingObject

ReadSequencingObjectPermission(SequencingObjectRepository, ReadSamplePermission, SampleSequencingObjectJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission

Construct an instance of ReadSequencingObjectPermission.

ReadSequencingRunPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.files

Permission allowing a user to read a SequencingRun

ReadSequencingRunPermission(SequencingRunRepository, UserRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingRunPermission

readTokenForApiAndUser(RemoteAPI, User) - Method in interface ca.corefacility.bioinformatics.irida.repositories.RemoteApiTokenRepository

Get an API token from the repository for a given service and user

RecursiveDeleteVisitor - Class in ca.corefacility.bioinformatics.irida.util

Delete an entire directory structure recursively.

RecursiveDeleteVisitor() - Constructor for class ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor

REDUCED_REPRESENTATION - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

referenceFile - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

referenceFile(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Sets the referenceFile for this submission.

ReferenceFile - Class in ca.corefacility.bioinformatics.irida.model.project

A reference file to be associated with a Project.

ReferenceFile() - Constructor for class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

ReferenceFile(Path) - Constructor for class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

ReferenceFileAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax

Controller for ajax actions for reference files

ReferenceFileAjaxController(UIProjectReferenceFileService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.ReferenceFileAjaxController

referenceFileBaseDirectory() - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

ReferenceFileRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.referencefile

Repository for interacting with ReferenceFile.

ReferenceFileRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.referencefile

Custom implementation of FilesystemSupplementedRepositoryImpl for ReferenceFile.

ReferenceFileRepositoryImpl(EntityManager, SequenceFileUtilities, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepositoryImpl

ReferenceFileRequiredException - Exception in ca.corefacility.bioinformatics.irida.exceptions.pipelines

This exception is thrown if a pipeline is attempted to be launched that requires a reference file, but does not have one.

ReferenceFileRequiredException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.pipelines.ReferenceFileRequiredException

ReferenceFileService - Interface in ca.corefacility.bioinformatics.irida.service

Interface for interactions with ReferenceFile.

ReferenceFileServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service for storing and reading ReferenceFile objects

ReferenceFileServiceImpl(ReferenceFileRepository, ProjectReferenceFileJoinRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.ReferenceFileServiceImpl

REFSEQ_MASHER - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

regenerateClientSecret(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Create a secret for a client

regenerateClientSecret(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Generate a new client secret

registerDefaultTypes() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Register some default AnalysisTypes from the BuiltInAnalysisTypes list

registerDefaultTypes() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Register some default AnalysisTypes from the BuiltInAnalysisTypes list

registerRunnableType(AnalysisType) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Register a new AnalysisType that can be run as a pipeline

registerRunnableType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Register a new AnalysisType that can be run as a pipeline

registerRunnableType(AnalysisType, String) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Register a new AnalysisType thatcna be run as a pipeline.

registerRunnableType(AnalysisType, String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Register a new AnalysisType thatcna be run as a pipeline.

registerUnrunnableType(AnalysisType) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Register an AnalysisType that cannot be run as a pipeline

registerUnrunnableType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Register an AnalysisType that cannot be run as a pipeline

registerWorkflow(IridaWorkflow) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Registers the given workflow with this service.

registerWorkflows(Set<IridaWorkflow>) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Registers the set of workflows with IRIDA.

REL_ASSEMBLY_ANALYSIS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

REL_AUTOMATED_ASSEMBLY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

rel for automated analyses associated with sequencing object

REL_COLLECTION - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Link back to the collection after deletion of a resource.

REL_PAIR - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel to the SequenceFile pair

REL_PAIR_FORWARD - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

rel for forward and reverse files

REL_PAIR_REVERSE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_PAIR_SAMPLE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_PROJECT - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Rel to get to the project that this sample belongs to.

REL_PROJECT - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

rel used for accessing an individual project.

REL_PROJECT_SAMPLE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

REL_PROJECT_SAMPLES - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

rel used for accessing the list of samples associated with a project.

REL_PROJECT_USERS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Rel to get to the list of users associated with a project.

REL_QC_SEQFILE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_RELATIONSHIP - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Rel used for terminating a relationship between resources.

REL_SAMPLE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

REL_SAMPLE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel to get back to the Sample.

REL_SAMPLE_ASSEMBLIES - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

REL_SAMPLE_SEQUENCE_FILE_FAST5 - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.Fast5ObjectRemoteServiceImpl

REL_SAMPLE_SEQUENCE_FILE_FAST5 - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_SAMPLE_SEQUENCE_FILE_PAIRS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel for paired sequence files for a given sample

REL_SAMPLE_SEQUENCE_FILE_UNPAIRED - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

rel for the unpaired sequence files for a given sample

REL_SAMPLE_SEQUENCE_FILES - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel to get to the new location of the SequenceFile.

REL_SEQ_OBJECT - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel to a sequencefile's sequencing object

REL_SEQ_QC - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Rel for a sequencefile's fastqc info

REL_SEQUENCEFILE_SAMPLE - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_SISTR_TYPING - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

REL_USER_PROJECTS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

a rel for getting a handle on the projects that a user belongs to.

RELATED_RESOURCES_NAME - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

name of related resources sent back to the client.

RelatedProjectJoin - Class in ca.corefacility.bioinformatics.irida.model.joins.impl

Relationship between two Projects.

RelatedProjectJoin() - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

RelatedProjectJoin(Project, Project) - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.RelatedProjectJoin

RelatedProjectRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.project

Repository for managing RelatedProjectJoins

relativePath(VersionedFileFields<Long>) - Method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener

Before persisting a VersionedFileFields to the database, we need to translate it to a relative path by stripping the storage directory for the type.

relativePathTranslatorListener(Path, Path, Path, Path) - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

RelativePathTranslatorListener() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener

REMOTE - ca.corefacility.bioinformatics.irida.pipeline.upload.DataStorage

REMOTE implies the data to upload is on a separate filesystem as the remote site (e.g.

RemoteAPI - Class in ca.corefacility.bioinformatics.irida.model

Description of a remote Irida API that this API can communicate with via OAuth2

RemoteAPI() - Constructor for class ca.corefacility.bioinformatics.irida.model.RemoteAPI

RemoteAPI(String, String, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.RemoteAPI

RemoteAPIAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax

Controller for asynchronous requests for remote api functionality.

RemoteAPIAjaxController(RemoteAPIService, UIRemoteAPIService, MessageSource, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.RemoteAPIAjaxController

RemoteAPIController - Class in ca.corefacility.bioinformatics.irida.ria.web.oauth

Controller handling basic operations for listing, viewing, adding, and removing RemoteAPIs

RemoteAPIController(RemoteAPIService, ProjectRemoteService, OltuAuthorizationController) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

RemoteAPIModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

UI Model to represent the details of a RemoteAPI

RemoteAPIModel(RemoteAPI) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteAPIModel

RemoteAPIRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

A repository to store RemoteAPI instances that this IRIDA instance can connect to

RemoteAPIService - Interface in ca.corefacility.bioinformatics.irida.service

Service for storing and retrieving RemoteAPIs that this API can connect to

RemoteAPIServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service implementation for storing and retrieving RemoteAPI objects from a RemoteAPIRepository

RemoteAPIServiceImpl(RemoteAPIRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

RemoteAPISpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification class for RemoteAPI

RemoteAPISpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.RemoteAPISpecification

RemoteAPITableAdminModel - Class in ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto

Represents a RemoteAPI in the Remote API table.

RemoteAPITableAdminModel(RemoteAPI) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableAdminModel

RemoteAPITableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto

Represents a RemoteAPI in the Remote API table.

RemoteAPITableModel(RemoteAPI) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.rempoteapi.dto.RemoteAPITableModel

RemoteAPIToken - Class in ca.corefacility.bioinformatics.irida.model

OAuth2 token for communicating with a RemoteAPI for a given User

RemoteAPIToken() - Constructor for class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

RemoteAPIToken(String, RemoteAPI, Date) - Constructor for class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

RemoteAPIToken(String, String, RemoteAPI, Date) - Constructor for class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

RemoteApiTokenRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

Repository for storing an reading RemoteAPITokens

RemoteAPITokenService - Interface in ca.corefacility.bioinformatics.irida.service

Service for saving and reading tokens for Remote APIs

RemoteAPITokenServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Service implementation for storing and reading remote api tokens

RemoteAPITokenServiceImpl(RemoteApiTokenRepository, UserRepository, OAuthClient) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

RemoteFileNotCachedException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when a remote file is attempted to be used before it has been cached locally.

RemoteFileNotCachedException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.RemoteFileNotCachedException

RemoteFileNotCachedException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.RemoteFileNotCachedException

RemoteProjectModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

Used to represent a remote project for selecting from available remote projects in the create remote synchronized project form

RemoteProjectModel(Project) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectModel

RemoteProjectSettings - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

Used as a response for encapsulating a remote synchronized project settings

RemoteProjectSettings(RemoteStatus, Date, RemoteAPI, ProjectSyncFrequency[], ProjectSyncFrequency, User) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

RemoteProjectSettingsUpdateRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote

Used to handle requests from the UI to update settings for a remote sync'd project.

RemoteProjectSettingsUpdateRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

RemoteProjectSettingsUpdateRequest(boolean, boolean, boolean, ProjectSyncFrequency) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

RemoteRepository<Type extends IridaRepresentationModel> - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

A repository for storing and retrieving objects from a remote api

RemoteRepositoryImpl<Type extends IridaRepresentationModel> - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

Remote repository to request from remote IRIDA instances using OAuthTokenRestTemplates

RemoteRepositoryImpl(RemoteAPITokenService, UserService, ParameterizedTypeReference<ListResourceWrapper<Type>>, ParameterizedTypeReference<ResourceWrapper<Type>>) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

Create a new repository with the given rest template and object params

RemoteService<Type extends IridaRepresentationModel & IridaThing> - Interface in ca.corefacility.bioinformatics.irida.service.remote

Service for communicating with a remote IRIDA instance

RemoteServiceImpl<Type extends IridaRepresentationModel & IridaThing> - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Remote service to request from remote IRIDA instances using OAuth2

RemoteServiceImpl(RemoteRepository<Type>, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

Create a new remote service that interacts with the given repository

RemoteStatus - Class in ca.corefacility.bioinformatics.irida.model.remote

Information about an entity that was copied from a remote api.

RemoteStatus() - Constructor for class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

RemoteStatus(String, RemoteAPI) - Constructor for class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

RemoteStatus.SyncStatus - Enum in ca.corefacility.bioinformatics.irida.model.remote

The status of the synchronized object

RemoteSynchronizable - Interface in ca.corefacility.bioinformatics.irida.model.remote

Marks an object which can be synchronized from a RemoteAPI

remove(OAuth2Authorization) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

removeAnalysisProjectShare(AnalysisSubmission, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Cancel the share of an AnalysisSubmission with a given Project

removeAnalysisProjectShare(AnalysisSubmission, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Cancel the share of an AnalysisSubmission with a given Project

removeAssociatedProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectAssociatedProjectsAjaxController

Remove an associated project linkage

removeAssociatedProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService

Remove an associated project linkage

removeDefaultMetadataTemplateForProject(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Remove the default MetadataTemplate from the project.

removeDefaultMetadataTemplateForProject(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Remove the default MetadataTemplate from the project.

removeGalaxySession(HttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartGalaxyController

Remove the Galaxy attributes from the session.

removeGenomeAssemblyFromSample(Sample, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService

Deletes the given genome assembly from the given sample.

removeGenomeAssemblyFromSample(Sample, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

Deletes the given genome assembly from the given sample.

removeLinks() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Removes all Links added to the resource so far.

removeMemberFromUserGroup(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Remove a member from the user group

removeMemberFromUserGroup(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Remove a user from an user group

removeProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Remove an entire project from the cart

removeProject(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Remove all samples from a specific project from the cart

removeProject(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Remove all samples from a specific project from the cart.

removeProjectAnalysisTemplates(long, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.ProjectSettingsAjaxController

Remove an automated workflow (analysis templates) for the current project

removeProjectAutomatedPipeline(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

Remove an automated workflow from a project

removeProjectSubscriptionForProjectAndUser(Project, User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Remove the project subscription associated with a Project and User.

removeProjectSubscriptionForProjectAndUser(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectSubscriptionService

Remove the project subscription associated with a Project and User.

removeReferenceFileFromProject(Project, ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove a ReferenceFile from a Project

removeReferenceFileFromProject(Project, ReferenceFile) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove a ReferenceFile from a Project

removeRelatedProject(RelatedProjectJoin) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove a RelatedProjectJoin

removeRelatedProject(RelatedProjectJoin) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove a RelatedProjectJoin

removeRelatedProject(Project, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove a RelatedProjectJoin for the given project and related project

removeRelatedProject(Project, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove a RelatedProjectJoin for the given project and related project

removeRows() - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

remove all rows

removeSample(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.sessionAttrs.Cart

Remove a sample from the cart.

removeSample(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.CartAjaxController

Remove a sample from the cart

removeSample(Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

Remove a specific sample from the cart.

removeSampleFromProject(Project, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove the specified Sample from the Project.

removeSampleFromProject(Project, Sample) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove the specified Sample from the Project.

removeSampleFromProject(Long, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Remove a specific Sample from the collection of Samples associated with a Project.

removeSampleMetadata(Long, Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Remove metadata field and entry from Sample

removeSampleMetadata(Long, Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Remove metadata from the sample

removeSamplesFromProject(long, RemoveSamplesRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Remove 1 or more samples from a project.

removeSamplesFromProject(Project, Iterable<Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove a collection of Samples from a Project

removeSamplesFromProject(Project, Iterable<Sample>) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove a collection of Samples from a Project

removeSamplesFromProject(Long, List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Remove 1 or more samples from a project.

RemoveSamplesRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

DTO for removing samples from a project

RemoveSamplesRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.RemoveSamplesRequest

removeSequenceFileFromSample(Long, String, Long) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Remove a SequencingObject from a Sample.

removeSequencingObjectFromSample(Sample, SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Remove a SequencingObject from a given Sample.

removeSequencingObjectFromSample(Sample, SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Remove a SequencingObject from a given Sample.

removeUserFromGroup(User, UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Remove the User from the UserGroup.

removeUserFromGroup(User, UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserGroupService

Remove the User from the UserGroup.

removeUserFromProject(Project, User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove the specified User from the Project.

removeUserFromProject(Project, User) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove the specified User from the Project.

removeUserFromProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Remove a user from the project

removeUserFromProject(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Remove a user from the project

removeUserFromProject(Long, String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Remove the relationship between a Project and a User.

removeUserGroupFromProject(long, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Remove a user group from a project

removeUserGroupFromProject(long, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Remove a UserGroup from a Project

removeUserGroupFromProject(Project, UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Remove the specified UserGroup from the Project.

removeUserGroupFromProject(Project, UserGroup) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Remove the specified UserGroup from the Project.

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.spring.view.CSVView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.spring.view.FastaView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.spring.view.FastqView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.spring.view.GenbankView

renderMergedOutputModel(Map<String, Object>, HttpServletRequest, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.web.spring.view.NewickFileView

repository - Variable in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

RepositoryBackedPermission<DomainObjectType,IdentifierType extends java.io.Serializable> - Class in ca.corefacility.bioinformatics.irida.security.permissions

Superclass for permissions on objects which can be read from a CrudRepository.

RepositoryBackedPermission(Class<DomainObjectType>, Class<IdentifierType>, CrudRepository<DomainObjectType, IdentifierType>) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.RepositoryBackedPermission

Constructor with handles on the type of repository and type of domain object.

REQUEST_PARAM_DRAW - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

REQUEST_PARAM_LENGTH - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

REQUEST_PARAM_SEARCH_VALUE - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

REQUEST_PARAM_SORT_COLUMN - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

REQUEST_PARAM_SORT_DIRECTION - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

REQUEST_PARAM_START - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

Request Parameters

requiresDynamicSource() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Whether or not this workflow requires a data from a dynamic source such as a Galaxy Tool Data Table.

requiresReference() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

Whether or not this workflow requires a reference file.

requiresSingleSample() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowInput

Whether or not this workflow requires a single sample.

RESET_TEMPLATE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

resolveArgument(MethodParameter, ModelAndViewContainer, NativeWebRequest, WebDataBinderFactory) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config.DataTablesRequestResolver

RESOURCE_NAME - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

name of the objects used to render the view classes.

ResourceAdditionalProperties<Type extends IridaRepresentationModel> - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

Class to be used when returning additional properties about a model object via the REST API.

ResourceAdditionalProperties(Type) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

ResourceCollection<Type> - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

Wraps a collection of ResourceCollection objects to be sent to the client.

ResourceCollection() - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

Default constructor, empty set of resources.

ResourceCollection(long) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

Constructor with a pre-defined size for the set of resources.

ResourceList<Type extends IridaRepresentationModel> - Class in ca.corefacility.bioinformatics.irida.model.remote.resource

Class to hold a list of resources when being read from a remote Irida API

ResourceList() - Constructor for class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList

ResourceServerConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.ResourceServerConfig

resourceServerSecurityFilterChain(HttpSecurity) - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaOauthSecurityConfig.ResourceServerConfig

ResourceWrapper<Type extends IridaRepresentationModel> - Class in ca.corefacility.bioinformatics.irida.model.remote.resource

Object wrapping a resource read from an Irida API

ResourceWrapper() - Constructor for class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceWrapper

RESPONSE_PARAM_DATA - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

RESPONSE_PARAM_DRAW - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

Response Parameters

RESPONSE_PARAM_RECORDS_FILTERED - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

RESPONSE_PARAM_RECORDS_TOTAL - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

RESPONSE_PARAM_SORT_COLUMN - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

RESPONSE_PARAM_SORT_DIRECTION - Static variable in class ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

ResponseDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.dto

Used as a response for ajax result

ResponseDetails() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails

ResponseDetails(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails

responseMessage - Variable in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxUpdateItemSuccessResponse

ResponseProjectResource<Type> - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

The resource for displaying the API project response.

ResponseProjectResource(Type) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseProjectResource

ResponseResource<Type> - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

The resource for displaying the API responses.

ResponseResource(Type) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseResource

ResponseVersion(String) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController.ResponseVersion

RESTAnalysisSubmissionController - Class in ca.corefacility.bioinformatics.irida.web.controller.api

REST controller to manage sharing of AnalysisSubmission, Analysis, and AnalysisOutputFile classes.

RESTAnalysisSubmissionController(AnalysisSubmissionService, SampleService, SequencingObjectService, IridaWorkflowsService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

RESTGenericController<Type extends IridaRepresentationModel & IridaThing & java.lang.Comparable<Type>> - Class in ca.corefacility.bioinformatics.irida.web.controller.api

A controller that can serve any model from the database.

RESTGenericController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

The type used to serialize/de-serialize the Type to the client.

RESTGenericController(CRUDService<Long, Type>, Class<Type>) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Construct an instance of RESTGenericController.

RESTOAuthAuthorizationConsentController - Class in ca.corefacility.bioinformatics.irida.web.controller.api

Controller class for serving custom OAuth2 authorization consent pages

RESTOAuthAuthorizationConsentController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTOAuthAuthorizationConsentController

RESTProjectAnalysisController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.projects

Controller for managing relationships between Project and AnalysisSubmission.

RESTProjectAnalysisController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectAnalysisController

RESTProjectAnalysisController(ProjectService, AnalysisSubmissionService, IridaWorkflowsService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectAnalysisController

RESTProjectSamplesController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.projects

Controller for managing relationships between Project and Sample.

RESTProjectSamplesController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

RESTProjectSamplesController(ProjectService, SampleService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

RESTProjectsController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.projects

Controller for managing Projects in the database.

RESTProjectsController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Default constructor.

RESTProjectsController(ProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Constructor for RESTProjectsController, requires a reference to a ProjectService.

RESTProjectUsersController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.projects

Controller for managing relationships between Project and User.

RESTProjectUsersController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

RESTProjectUsersController(UserService, ProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

RESTRICTED_CONTROLLERS - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

A collection of the controllers in our system accessible by users with `ROLE_ADMIN` or `ROLE_SEQUENCER` authorization.

RESTRICTION_DIGEST - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

RESTRootController - Class in ca.corefacility.bioinformatics.irida.web.controller.api

A basis for clients to begin discovering other URLs in our API.

RESTRootController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

RESTRootController.ResponseVersion - Class in ca.corefacility.bioinformatics.irida.web.controller.api

A convenient class for returning the api version.

RESTSampleAssemblyController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.samples

Controller for viewing and downloading assemblies for samples

RESTSampleAssemblyController(SampleService, GenomeAssemblyService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

RESTSampleMetadataController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.samples

REST controller to handle storing and retrieving metadata from a Sample

RESTSampleMetadataController(SampleService, MetadataTemplateService, ProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

RESTSampleSequenceFilesController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.samples

Controller for managing relationships between Sample and SequenceFile.

RESTSampleSequenceFilesController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

RESTSampleSequenceFilesController(SampleService, SequencingRunService, SequencingObjectService, AnalysisService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

RESTSequencingRunController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun

RESTSequencingRunController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Default constructor.

RESTSequencingRunController(SequencingRunService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Constructor for RESTProjectsController, requires a reference to a ProjectService.

RESTSequencingRunSequenceFilesController - Class in ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun

RESTSequencingRunSequenceFilesController(SequencingRunService, SequencingObjectService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunSequenceFilesController

RESTUsersController - Class in ca.corefacility.bioinformatics.irida.web.controller.api

Controller for managing users.

RESTUsersController() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

RESTUsersController(UserService, ProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Constructor, requires a reference to a UserService and a ProjectService.

RESUBMITTED - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

RETRIED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Retried processing of failed action(s

reverseMatches - Static variable in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

revisionListener() - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig

revokeTokensForClient(IridaClientDetails) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Revoke all OAuth2 tokens for a given IridaClientDetails

revokeTokensForClient(IridaClientDetails) - Method in interface ca.corefacility.bioinformatics.irida.service.IridaClientDetailsService

Revoke all OAuth2 tokens for a given IridaClientDetails

RNA_SEQ - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

Role - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto

Represents a ProjectRole in the interface, including it's translation.

Role - Class in ca.corefacility.bioinformatics.irida.ria.web.settings.dto

Stores role info.

Role - Enum in ca.corefacility.bioinformatics.irida.model.user

Roles for authorization in the application.

Role(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.Role

Role(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

ROLE_ADMIN - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for administrative role.

ROLE_ANONYMOUS - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for anonymous role.

ROLE_MANAGER - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for the manager role

ROLE_SEQUENCER - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for the sequencer role.

ROLE_TECHNICIAN - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for technician role.

ROLE_USER - ca.corefacility.bioinformatics.irida.model.user.Role

Constant reference for user role.

roleChangeErrorHandler(Exception) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Handle a ProjectWithoutOwnerException error.

RoleMixin - Class in ca.corefacility.bioinformatics.irida.jackson2.mixin

This mixin class is used to serialize/deserialize Role.

RoleMixin(String) - Constructor for class ca.corefacility.bioinformatics.irida.jackson2.mixin.RoleMixin

rolesClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

RoleUtilities - Class in ca.corefacility.bioinformatics.irida.ria.web.utilities

Utilities class to help with role access.

RoleUtilities() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.utilities.RoleUtilities

RootResource - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource

Resource for sending links back when a client requests the root resource.

RootResource() - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.RootResource

ROW_ID_PREFIX - Static variable in interface ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel

RTPCR - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

run() - Method in class ca.corefacility.bioinformatics.irida.service.impl.processor.SequenceFileProcessorLauncher

RUN_AS_USER_ORDER - Static variable in class ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect

runAsSubmissionUserAspect() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig

Aspect for setting the user in the security context to be the user in the AnalysisSubmission

RunAsUser - Annotation Type in ca.corefacility.bioinformatics.irida.service.analysis.annotations

Annotation saying the function should be run as the User identified in the RunAsUser.value().

RunAsUserAspect - Class in ca.corefacility.bioinformatics.irida.service.analysis.annotations

Aspect to update the Authentication object in the SecurityContext to be the user specified in the annotation using SpEL.

RunAsUserAspect() - Constructor for class ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect

RUNNING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that is running in the execution manager.

RUNNING - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

runProcessingJob() - Method in class ca.corefacility.bioinformatics.irida.service.SequencingObjectProcessingService

Process new SequencingObjects uploaded and find new sequences to process next time around

runWorkflow(WorkflowInputsGalaxy) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Attempts to run the workflow definined by the given WorkflowInputs object.

S

Sample - Class in ca.corefacility.bioinformatics.irida.model.sample

A biological sample.

Sample() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.Sample

Sample(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.Sample

Create a new Sample with the given name

SAMPLE_ASSEMBLY_REL - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

SAMPLE_ID - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

SAMPLE_NAME - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

SAMPLE_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

SAMPLE_SEQENCE_FILE_PAIRS_REL - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SequenceFilePairRemoteServiceImpl

SAMPLE_SEQENCE_FILE_UNPAIRED_REL - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SingleEndSequenceFileRemoteServiceImpl

SampleAddedProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event created when a Sample is added to a Project

SampleAddedProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent

SampleAddedProjectEvent(ProjectSampleJoin) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent

SampleAnalyses - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to return analyses ran with Sample sequencing objects back to the user interface.

SampleAnalyses(AnalysisSubmission, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleAnalyses

SampleAnalysisDuplicateException - Exception in ca.corefacility.bioinformatics.irida.exceptions

If there is a duplicate Sample which is being sent for analysis.

SampleAnalysisDuplicateException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.SampleAnalysisDuplicateException

Construct a new SampleAnalysisDuplicateException with the specified message.

SampleAnalysisDuplicateException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.SampleAnalysisDuplicateException

Construct a new SampleAnalysisDuplicateException with the specified message and original cause.

SampleDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to return details of a Sample back to the user interface.

SampleDetails(Sample, boolean, Project, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails

SampleExportFiles - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

SampleExportFiles(List<SingleEndSequenceFileModel>, List<PairedEndSequenceFileModel>, List<SequencingObject>, List<GenomeAssembly>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleExportFiles

SampleFiles - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Collection of different files that can be on a sample

SampleFiles(List<SampleSequencingObjectFileModel>, List<SampleSequencingObjectFileModel>, List<SampleSequencingObjectFileModel>, List<SampleGenomeAssemblyFileModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles

SampleFilesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Response for getting details about the files belonging to multiple samples

SampleFilesResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleFilesResponse

SampleGenomeAssemblyFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to send genome assembly object information with file size to the UI

SampleGenomeAssemblyFileModel(GenomeAssembly, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

SampleGenomeAssemblyJoin - Class in ca.corefacility.bioinformatics.irida.model.joins.impl

Relationship between a Sample and a GenomeAssembly.

SampleGenomeAssemblyJoin(Sample, GenomeAssembly) - Constructor for class ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin

SampleGenomeAssemblyJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.sample

Repository for storing and retrieving SampleGenomeAssemblyJoins.

SampleMergeException - Exception in ca.corefacility.bioinformatics.irida.ria.web.projects.error

Error thrown during the samples merge process

SampleMergeException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.projects.error.SampleMergeException

SampleMetadata - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to return Sample metadata back to the user interface.

SampleMetadata(List<SampleMetadataFieldEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadata

SampleMetadataFieldEntry - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to return metadata field and entry back to the user interface.

SampleMetadataFieldEntry(Long, String, String, Long, ProjectMetadataRole) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

SampleMetadataResponse - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource.sample

Response class for grouping MetadataEntrys for response in the REST API

SampleMetadataResponse(Set<MetadataEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.sample.SampleMetadataResponse

SampleMetadataStorage - Class in ca.corefacility.bioinformatics.irida.ria.utilities

Used to store information relating to sample metadata during upload.

SampleMetadataStorage() - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

SampleMetadataStorageRow - Class in ca.corefacility.bioinformatics.irida.ria.utilities

Used to store information relating to sample metadata rows during upload.

SampleMetadataStorageRow(Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

SampleNameValidationResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

UI Response to indicate the value of validating a proposed sample name.

SampleNameValidationResponse(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse

SampleObject - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples

Representation of a Sample used in the Project Samples table.

SampleObject(Sample) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject

SamplePairer - Class in ca.corefacility.bioinformatics.irida.ria.web.samples

Utility class for pairing up sequence files with common prefixes and expected characters for forward and reverse sequence files.

SamplePairer(List<MultipartFile>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer

SampleRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

Repository to read Samples from a RemoteAPI

SampleRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

An implementation of SampleRemoteRepository

SampleRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SampleRemoteRepositoryImpl

SampleRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

Service for reading Samples

SampleRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Implementation of SampleRemoteService using SampleRemoteRepository

SampleRemoteServiceImpl(SampleRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

SampleRemovedProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event for when a sample is removed from a project.

SampleRemovedProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent

SampleRemovedProjectEvent(Project, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.SampleRemovedProjectEvent

SampleRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

A repository for storing Sample objects

SampleRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories.sample

Custom repository methods for Samples

SampleRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.sample

Implementation of custom repository methods for Samples

SampleRepositoryImpl(EntityManager) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryImpl

SAMPLES_CACHE_NAME - Static variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

SamplesAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.samples

Controller for asynchronous requests for a Sample

SamplesAjaxController(UISampleService, UIAnalysesService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

SampleSequencingObjectFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to send sequencing object information with file sizes to the UI

SampleSequencingObjectFileModel(SequencingObject, String, String, Set<QCEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

SampleSequencingObjectFileModel(SequencingObject, String, String, Set<QCEntry>, AnalysisSubmission) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

SampleSequencingObjectJoin - Class in ca.corefacility.bioinformatics.irida.model.sample

Relationship between a Sample and a SequencingObject

SampleSequencingObjectJoin(Sample, SequencingObject) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin

SampleSequencingObjectJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.sample

Repository for storing and retrieving SampleSequencingObjectJoins

SampleSequencingObjectSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification for searching through SampleSequencingObjectJoins

SampleSequencingObjectSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.SampleSequencingObjectSpecification

SampleService - Interface in ca.corefacility.bioinformatics.irida.service.sample

A service class for working with samples.

SampleServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.sample

Service class for managing Sample.

SampleServiceImpl(SampleRepository, ProjectSampleJoinRepository, AnalysisRepository, SampleSequencingObjectJoinRepository, QCEntryRepository, SequencingObjectRepository, SampleGenomeAssemblyJoinRepository, UserRepository, MetadataEntryRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Constructor.

save(GenomeAssembly) - Method in class ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepositoryImpl

save(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepositoryImpl

Persist an entity to disk and database.

save(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepositoryImpl

Persist an entity to disk and database.

save(AnalysisOutputFile) - Method in class ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepositoryImpl

Persist an entity to disk and database.

save(RegisteredClient) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaRegisteredClientsRepository

save(OAuth2Authorization) - Method in class ca.corefacility.bioinformatics.irida.oauth2.IridaOAuth2AuthorizationService

save(S) - Method in interface ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisOutputFileRepository

Save is overridden here instead of in FilesystemSupplementedRepository as it would throw a compilation error

save(S) - Method in interface ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository

save(S) - Method in interface ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository

Save is overridden here instead of in FilesystemSupplementedRepository as it would throw a compilation error

save(S) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository

Save is overridden here instead of in FilesystemSupplementedRepository as it would throw a compilation error

save(Type) - Method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl

Persist an entity to disk and database.

SavedMetadataErrorResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.dto

Returns the SampleMetadataStorage on error.

SavedMetadataErrorResponse(SampleMetadataStorage) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.SavedMetadataErrorResponse

SavedMetadataException - Exception in ca.corefacility.bioinformatics.irida.ria.web.errors

Returns the SampleMetadataStorage on error.

SavedMetadataException(SampleMetadataStorage) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.errors.SavedMetadataException

SavedPipelineParameters - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline

Used by the UI for displaying a named pipeline parameter set.

SavedPipelineParameters() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

SavedPipelineParameters(Long, String, List<Input>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

saveInternal(Type) - Method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl

Actually persist the entity to disk and to the database.

saveLinelistTemplate(Long, String, List<Map<String, String>>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Save a new line list template.

saveLineListTemplate(UIMetadataTemplate, Long, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

Save or update a MetadataTemplate

saveMetadata(Type) - Method in interface ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepository

Save an entity without updating any of the Path entries within the file.

saveMetadata(Type) - Method in class ca.corefacility.bioinformatics.irida.repositories.filesystem.FilesystemSupplementedRepositoryImpl

Save an entity without updating any of the Path entries within the file.

saveMetadataEntry(long, String, String, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.linelist.LineListController

Save an updated sample metadata entry

saveMetadataField(MetadataTemplateField) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

saveMetadataField(MetadataTemplateField) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Save a new metadata fields

saveMetadataTemplate(long, String, List<String>, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectLineListController

Save a list a MetadataTemplateField as a MetadataTemplate

saveMetadataTemplate(Long, Long, String, List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSamplesMetadataTemplateController

Save or update a MetadataTemplate within a Project

saveNewPipelineParameters(UUID, SavePipelineParametersRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchAjaxController

Save a new set of named pipeline parameters

saveNewPipelineParameters(UUID, SavePipelineParametersRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

Save a new set of IridaWorkflowNamedParameters

SavePipelineParametersRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline

Used to save new values for Saved Pipeline Parameters on the Pipeline Launch Page

SavePipelineParametersRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

SavePipelineParametersRequest(String, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

saveProjectSampleMetadata(Locale, HttpSession, Long, List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

Save uploaded metadata from the session into IRIDA.

saveProjectSampleMetadata(Locale, HttpSession, Long, List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

Save uploaded metadata

saveResultsToSamples(Long, Locale, HttpServletResponse) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Save the results of an analysis back to the samples

saveSampleMetadata(Long, Map<String, MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

Save new metadata for a Sample.

SchemaExporter - Class in ca.corefacility.bioinformatics.irida.util

Export the current hibernate-generated schema (with auditing tables).

SchemaExporter() - Constructor for class ca.corefacility.bioinformatics.irida.util.SchemaExporter

search(String) - Method in class ca.corefacility.bioinformatics.irida.service.impl.InMemoryTaxonomyService

Search for a tree of taxonomy terms with a given search term

search(String) - Method in interface ca.corefacility.bioinformatics.irida.service.TaxonomyService

Search for a tree of taxonomy terms with a given search term

search(String, boolean, Model) - Method in class ca.corefacility.bioinformatics.irida.ria.web.search.SearchController

Get the search view with a given query

search(Specification<Announcement>, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Search for an entity of Type and PageRequest

search(Specification<IridaClientDetails>, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

Search for an entity of Type and PageRequest

search(Specification<RemoteAPI>, int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPIServiceImpl

Search for an entity of Type with a given specification

search(Specification<UserGroup>, int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Search for an entity of Type with a given specification

search(Specification<UserGroup>, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Search for an entity of Type and PageRequest

search(Specification<User>, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Search for an entity of Type and PageRequest

search(Specification<Type>, int, int, Sort.Direction, String...) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Search for an entity of Type with a given specification

search(Specification<Type>, Pageable) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Search for an entity of Type and PageRequest

search(Specification<ValueType>, int, int, Sort.Direction, String...) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Deprecated.

search(Specification<ValueType>, Pageable) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Search for an entity of Type and PageRequest

searchAllSamples(String, Integer, Integer, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Search all Samples in the database on the given query

searchAllSamples(String, Integer, Integer, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Search all Samples in the database on the given query

searchAnnouncement(String) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.AnnouncementSpecification

Search for Announcement by name.

searchClient(String) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.IridaClientDetailsSpecification

Search for a IridaClientDetails object with a given search term

SearchController - Class in ca.corefacility.bioinformatics.irida.ria.web.search

Controller to manage global searching

SearchController(ProjectService, SampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.search.SearchController

SearchCriteria - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Define a search criteria for a given key and value.

SearchCriteria() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

SearchCriteria(String, Object, SearchOperation) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

SearchOperation - Enum in ca.corefacility.bioinformatics.irida.repositories.specification

Search operations available to use in SearchCriteria's

searchProjects(String, boolean, DataTablesParams) - Method in class ca.corefacility.bioinformatics.irida.ria.web.search.SearchController

Search all projects a user is a member of based on a query string

searchRemoteAPI(String) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.RemoteAPISpecification

Search for a RemoteAPI object with a given search term

searchSamples(String, boolean, DataTablesParams) - Method in class ca.corefacility.bioinformatics.irida.ria.web.search.SearchController

Search all Samples in projects for a user based on a query string

searchSamplesForUser(String, Integer, Integer, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Search all Samples in projects the current logged in user has access to

searchSamplesForUser(String, Integer, Integer, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Search all Samples in projects the current logged in user has access to

searchTaxonomy(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies.TaxonomyAjaxController

Query the taxonomy ontology and return a list of taxonomy with their children

searchTaxonomy(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Search for taxonomy terms.

searchUser(String) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.UserSpecification

Search for a User by firstname, lastname, email, and username

searchUserGroup(String) - Static method in class ca.corefacility.bioinformatics.irida.repositories.specification.UserGroupSpecification

Search for UserGroup by name.

searchUsersForProject(Project, String, int, int, Sort) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Get a page of user accounts on a project filtered by username.

searchUsersForProject(Project, String, int, int, Sort) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Get a page of user accounts on a project filtered by username.

SelectOption - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui

Generically represents a UI Select Option

SelectOption(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.SelectOption

SEMIMONTHLY - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

sendEmailOnCompletion() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

Check to see if an email should be sent on pipeline completion

sendEmailOnError() - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

Check to see if an email should be sent on pipeline errors.

sendFilesystemExceptionEmail(String, Exception) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send an e-mail to the administrative user with an exception when there's a serious storage related exception.

sendFilesystemExceptionEmail(String, Exception) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send an e-mail to the administrative user with an exception when there's a serious storage related exception.

sendFilesystemExceptionEmail(String, Exception) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendNCBIUploadExceptionEmail(String, Exception, Long) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send an email to the administrators with an exception when there's an error uploading data or getting upload status from NCBI's SRA.

sendNCBIUploadExceptionEmail(String, Exception, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send an email to the administrators with an exception when there's an error uploading data or getting upload status from NCBI's SRA.

sendNCBIUploadExceptionEmail(String, Exception, Long) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendPasswordResetLinkEmail(User, PasswordReset) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send a PasswordReset link to a User

sendPasswordResetLinkEmail(User, PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send a PasswordReset link to a User

sendPasswordResetLinkEmail(User, PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendPipelineStatusEmail(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send pipeline status email to a user when a pipeline that they have launched is completed or has an error

sendPipelineStatusEmail(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send pipeline status email to a user when a pipeline that they have launched is completed or has an error

sendPipelineStatusEmail(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendProjectSyncUnauthorizedEmail(Project) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Email user responsible for a synchronized project when the sync job's credentials expire

sendProjectSyncUnauthorizedEmail(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Email user responsible for a synchronized project when the sync job's credentials expire

sendProjectSyncUnauthorizedEmail(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendSubscriptionUpdateEmail(User, List<ProjectEvent>) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send a subscription email to the given User containing the given ProjectEvents

sendSubscriptionUpdateEmail(User, List<ProjectEvent>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send a subscription email to the given User containing the given ProjectEvents

sendSubscriptionUpdateEmail(User, List<ProjectEvent>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

sendWelcomeEmail(User, User, PasswordReset) - Method in interface ca.corefacility.bioinformatics.irida.service.EmailController

Send welcome email to a user who joined the platform

sendWelcomeEmail(User, User, PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Send welcome email to a user who joined the platform

sendWelcomeEmail(User, User, PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

SEQUEL - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

SEQUEL_II - ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

SEQUENCE_FILE_ID_KEY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

The key used in the request to add an existing SequenceFile to a Sample.

SequenceConcatenation - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

Class storing when 2 SequencingObjects are concatenated into a new SequencingObject

SequenceConcatenation(SequencingObject, List<SequencingObject>) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceConcatenation

SequenceConcatenationRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sequencefile

Repository for SequenceConcatenations

SequenceFile - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

A file that may be stored somewhere on the file system and belongs to a particular Sample.

SequenceFile() - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

SequenceFile(Path) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Create a new SequenceFile with the given file Path

SEQUENCEFILE_ID_KEY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunSequenceFilesController

key used in map when adding sequencefile to miseqrun.

SequenceFileAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.files

Ajax controller to get data for the fastqc page.

SequenceFileAjaxController(UISequenceFileService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.files.SequenceFileAjaxController

SequenceFileAnalysisException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when there is an issue with a SequenceFile analysis.

SequenceFileAnalysisException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.SequenceFileAnalysisException

Construct a new SequenceFileAnalysisException with the specified message.

SequenceFileAnalysisException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.SequenceFileAnalysisException

Construct a new SequenceFileAnalysisException with the specified message and original cause.

sequenceFileBaseDirectory() - Method in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiFilesystemRepositoryConfig

SequenceFileDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto

Data transfer object for retrieving SequenceFile details from a SequencingRun.

SequenceFileDetails(SequenceFile, Long, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails

SequenceFileMessageConverter - Class in ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate

Message markdownConverter for converting application/fastq HTTP responses to a Java Path temporary file

SequenceFileMessageConverter(String) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

SequenceFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile

UI Model for a SequenceFile

SequenceFileModel - ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

SequenceFileModel(SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SequenceFileModel

SequenceFilePair - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

A pair of sequence files in forward/reverse orientation.

SequenceFilePair() - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

SequenceFilePair(SequenceFile, SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

SequenceFilePairConcatenator - Class in ca.corefacility.bioinformatics.irida.processing.concatenate.impl

SequencingObjectConcatenator for SequenceFilePairs

SequenceFilePairConcatenator() - Constructor for class ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SequenceFilePairConcatenator

SequenceFilePairRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

RemoteRepository for reading SequenceFilePair objects

SequenceFilePairRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

RemoteRepositoryImpl for reading and listing SequenceFilePair objects.

SequenceFilePairRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFilePairRemoteRepositoryImpl

SequenceFilePairRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

Remote service for reading sequence file pairs from a remote api

SequenceFilePairRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Remote service implementation for reading sequence file pairs from a remote api

SequenceFilePairRemoteServiceImpl(SequenceFilePairRemoteRepository, SequenceFileRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.SequenceFilePairRemoteServiceImpl

SequenceFileProcessorLauncher - Class in ca.corefacility.bioinformatics.irida.service.impl.processor

SequenceFile processor which launches a FileProcessingChain on a collection of SequenceFile ids

SequenceFileProcessorLauncher(FileProcessingChain, Long, SecurityContext) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.processor.SequenceFileProcessorLauncher

sequenceFileRemoteRepository - Variable in class ca.corefacility.bioinformatics.irida.service.remote.impl.SequencingObjectRemoteServiceImpl

SequenceFileRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

Repository for reading SequenceFiles from a Remote IRIDA installation

SequenceFileRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

Implementation of SequenceFileRemoteRepository using OAuthTokenRestTemplate for making requests

SequenceFileRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFileRemoteRepositoryImpl

Create a new SequenceFileRemoteRepositoryImpl

SequenceFileRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sequencefile

A repository to store information about sequence files.

SequenceFileRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.sequencefile

Custom implementation of FilesystemSupplementedRepositoryImpl for SequenceFile.

SequenceFileRepositoryImpl(EntityManager, Path) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepositoryImpl

SequenceFileResource - Class in ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile

Resource wrapper for SequenceFile.

SequenceFileResource() - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource

SequenceFileResource(SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource

SequenceFileUtilities - Interface in ca.corefacility.bioinformatics.irida.service.util

Utility class for executing common functions on sequence files

SequencerUILoginException - Exception in ca.corefacility.bioinformatics.irida.security

Thrown if an authentication request is rejected because the account's role is ROLE_SEQUENCER.

SequencerUILoginException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.security.SequencerUILoginException

Constructs a SequencerUILoginException with the specified message.

SequencerUILoginException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.security.SequencerUILoginException

Constructs a SequencerUILoginException with the specified message and root cause.

SequencingObject - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

Objects that were obtained from some sequencing platform.

SequencingObject() - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

SequencingObject.ProcessingState - Enum in ca.corefacility.bioinformatics.irida.model.sequenceFile

The status of the file processing upon upload

SequencingObjectConcatenator<Type extends SequencingObject> - Class in ca.corefacility.bioinformatics.irida.processing.concatenate

Class to concatenate multiple SequencingObjects and return a single new SequencingObject.

SequencingObjectConcatenator() - Constructor for class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenator

SequencingObjectConcatenatorFactory - Class in ca.corefacility.bioinformatics.irida.processing.concatenate

Factory class for returning an instance of SequencingObjectConcatenator for a given filetype

SequencingObjectConcatenatorFactory() - Constructor for class ca.corefacility.bioinformatics.irida.processing.concatenate.SequencingObjectConcatenatorFactory

SequencingObjectProcessingService - Class in ca.corefacility.bioinformatics.irida.service

Service used to run a FileProcessingChain on incoming SequencingObjects.

SequencingObjectProcessingService(SequencingObjectRepository, ThreadPoolTaskExecutor, FileProcessingChain) - Constructor for class ca.corefacility.bioinformatics.irida.service.SequencingObjectProcessingService

SequencingObjectRemoteService<Type extends SequencingObject> - Interface in ca.corefacility.bioinformatics.irida.service.remote

Service for reading SequencingObjects from remote sources

SequencingObjectRemoteServiceImpl<Type extends SequencingObject> - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Service to read SequencingObjects from a remote api.

SequencingObjectRemoteServiceImpl(RemoteRepository<Type>, SequenceFileRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.SequencingObjectRemoteServiceImpl

SequencingObjectRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.sequencefile

Repository for storing and retrieving SequencingObjects

SequencingObjectService - Interface in ca.corefacility.bioinformatics.irida.service

Service for managing SequencingObjects and relationships with related objects

SequencingObjectServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

Implementation of SequencingObjectService using a SequencingObjectRepository and SampleSequencingObjectJoinRepository to persist and load objects.

SequencingObjectServiceImpl(SequencingObjectRepository, SequenceFileRepository, SampleSequencingObjectJoinRepository, SequenceConcatenationRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

SequencingRun - Class in ca.corefacility.bioinformatics.irida.model.run

This class represents a collection of sequence files that have come off one run of a sequencer.

SequencingRun() - Constructor for class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

SequencingRun(SequencingRun.LayoutType, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

SequencingRun.LayoutType - Enum in ca.corefacility.bioinformatics.irida.model.run

The type of layout for the run.

SequencingRunAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns

Controller to handle AJAX requests for sequencing run data

SequencingRunAjaxController(UISequencingRunService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunAjaxController

SequencingRunController - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns

Controller for displaying and interacting with SequencingRun objects

SequencingRunController() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.SequencingRunController

SequencingRunDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto

Data transfer object for retrieving sequencing run details from a sql query.

SequencingRunDetails(SequencingRun) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails

SequencingRunModel - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto

Model to format a SequencingRun into a format that can be used in the UI Table.

SequencingRunModel(SequencingRun, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel

SequencingRunRepository - Interface in ca.corefacility.bioinformatics.irida.repositories

SequencingRunService - Interface in ca.corefacility.bioinformatics.irida.service

Service layer for SequencingRun objects

SequencingRunServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl

SequencingRunServiceImpl(SequencingRunRepository, SequenceFileRepository, SequencingObjectRepository, SampleSequencingObjectJoinRepository, SampleRepository, AnalysisSubmissionRepository, UserRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

SequencingRunsListRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto

Request for data for the sequencing run listing page.

SequencingRunsListRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunsListRequest

SequencingRunUploadStatus - Enum in ca.corefacility.bioinformatics.irida.model.enums

Encodes the status of an uploaded SequencingRun.

serialize(Path, JsonGenerator, SerializerProvider) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson.PathSerializer

serialize(Date, JsonGenerator, SerializerProvider) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.json.DateJson.DateSerializer

serialize(Date, JsonGenerator, SerializerProvider) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson.TimestampSerializer

SERVICE_URI_CONSTRAINT_NAME - Static variable in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

ServletInitializer - Class in ca.corefacility.bioinformatics.irida

Servlet Initializer for Spring Boot application

ServletInitializer() - Constructor for class ca.corefacility.bioinformatics.irida.ServletInitializer

SessionFilter - Class in ca.corefacility.bioinformatics.irida.ria.config.filters

Filter to be used to add constants to the session for templating

SessionFilter() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.filters.SessionFilter

setAcceptsPairedSequenceFiles(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setAcceptsSingleSequenceFiles(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setAccession(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

setAccessTokenValiditySeconds(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setAdditionalProperties(Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

Set the map of additional properties

setAdmin(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAdmin(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setAllowedToModifySample(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setAnalysesStats(List<GenericStatModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

setAnalysis(Analysis) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Set the Analysis generated as a result of this submission.

setAnalysis(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAnalysisCleanedState(AnalysisCleanedState) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Sets the AnalysisCleanedState.

setAnalysisDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Set the description of the analysis for this submission

setAnalysisDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setAnalysisExecutionService(AnalysisExecutionServiceGalaxyCleanupAsync) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

setAnalysisFastQC(AnalysisFastQC) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

setAnalysisId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setAnalysisName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAnalysisName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

setAnalysisOutputFileId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisOutputFileKey(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisPriority(AnalysisSubmission.Priority) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setAnalysisSampleProjects(List<AnalysisSampleProject>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAnalysisState(AnalysisState) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Sets the state of this analysis.

setAnalysisState(AnalysisState) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

setAnalysisState(AnalysisState) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAnalysisStateModel(AnalysisStateModel) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

setAnalysisSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssemblyFromAnalysis

setAnalysisSubmissionId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisSubmissionId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

setAnalysisSubmissionId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setAnalysisSubmissionId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

setAnalysisSubmissionName(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

setAnalysisType(AnalysisType) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setAnalysisType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setAnalysisViewer(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setApplicationContext(ApplicationContext) - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

setApplicationContext(ApplicationContext) - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevListener

setAssociated(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setAssociated(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectSamplesFilter

setAssociatedProjectIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest

setAuthorizedGrantTypes(Set<String>) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setAutomatedAssembly(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setAutomatedProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setBioProject(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setBioProjectId(String) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setBioSample(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setBioSampleFiles(List<NcbiBioSampleFiles>) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setCanCreatePasswordReset(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setCanEditUserInfo(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setCanEditUserStatus(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setCanManage(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel

setCanManage(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setCanManage(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.ProjectCurrentUserModel

setCanManageRemote(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setCanShareToSamples(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setCartService(UICartService) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.LaunchController

setCgmlstDistance(Float) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setCgmlstFoundAlleles(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setCgmlstGenomeMatch(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setCgmlstMatchingAlleles(Integer) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setCgmlstST(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setCgmlstSubspecies(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setChangeUser(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

setCheckboxSelection(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setChunk(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setClientId(Long) - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

setClientId(String) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setClientId(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

setClientId(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setClientSecret(String) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setClientSecret(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

setCollectedBy(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setCollectionDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setColumnType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

setCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

setCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setConnectionDetails(String, int, String, String, String) - Method in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Manually configure connection details for this service

setContent(List<T>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse

setCount(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartUpdateResponse

setCoverage(Coverage) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setCreatedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setCredentialsNonExpired(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setCss(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

setCurrent(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

setCurrent(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

setCurrentId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setDataIndex(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

setDataIndex(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

setDefaultGenomeAssembly(GenomeAssembly) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setDefaultMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Set a default metadata template for a project

setDefaultMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Set a default metadata template for a project

setDefaultMetadataTemplate(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Set the default MetadataTemplate for a Project

setDefaultMetadataTemplateId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setDefaultSequencingObject(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setDefaultWorkflow(UUID) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Sets the given workflow as a default workflow for it's analysis type.

setDefaultWorkflows(Set<UUID>) - Method in class ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

Sets the given set of workflow ids as default workflows.

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Set the description for the remote api

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setDescription(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setDirection(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSort

setDirectoryPath(String) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setDisableFileProcessor(boolean) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

Disables this file processor from processing files.

setDuplicationlevelChart(byte[]) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

setDuration(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

setDuration(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

setDuration(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setDuration(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setDynamicSources(List<InputWithOptions>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setEmail(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setEmailPipelineResult(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setEmailPipelineResultCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets flag to indicate whether or not user should be emailed upon pipeline completion.

setEmailPipelineResultCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setEmailPipelineResultCompleted(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

setEmailPipelineResultError(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets flag to indicate whether or not user should be emailed upon pipeline error.

setEmailPipelineResultError(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setEmailPipelineResultError(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisEmailPipelineResult

setEmailSubscription(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

setEnabled(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setEnabled(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

setEnd(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setEndDate(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

setEndDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setEntry(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

setEntryId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setEntryId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

setError(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

setError(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setError(String) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

setError(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setExcelCols(List<ExcelCol>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

setExcelHeaders(List<ExcelHeader>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

setExcelRows(List<ExcelRow>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

setExcelSheetNames(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

setExecutionParameters(ArrayList<AnalysisToolExecutionParameters>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

setExpiryDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

Set the date that this token expires

setFast5Type(Fast5Object.Fast5Type) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

setFastFail(Boolean) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessingChain

Set whether or not the FileProcessingChain should fail on *all* exceptions.

setFastFail(Boolean) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

setFastQCAnalysis(AnalysisFastQC) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Set the AnalysisFastQC for this SequenceFile.

setFastQCVersion(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

setField(MetadataTemplateField) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

setField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

setField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

setField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

setFieldId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setFieldId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

setFieldKey(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

setFieldName(String) - Method in exception ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException

Set the field name that was in duplicate and caused the exception

setFields(List<MetadataTemplateField>) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setFields(List<ProjectMetadataField>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setFile(Path) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

setFile(Path) - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

setFile(Path) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

setFileExt(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setFileId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

setFileIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setFileInfo(GenomeAssembly) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

setFileInfo(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

setFileLength(Long) - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

setFilename(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setFilename(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setFilename(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

setFileOpener(ResourceAccessor) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

setFileOpener(ResourceAccessor) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

setFileOpener(ResourceAccessor) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

setFileOpener(ResourceAccessor) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

setFilePath(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setFilePointer(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setFileProcessor(String) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setFiles(List<SampleSequencingObjectFileModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchSample

setFiles(Set<SequenceFile>) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

Set the SequenceFiles in this pair.

setFiles(Set<SingleEndSequenceFile>) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

setFileSizeBytes(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setFilter(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setFilters(AnalysesFilters) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesListRequest

setFilters(ProjectSamplesFilter) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectSamplesTableRequest

setFirstFileSize(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel

setFirstFileSize(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

setFirstLine(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setFirstName(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setForceSync(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

setForward(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

setFoundSampleId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

setFrequency(ProjectSyncFrequency) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

setGalaxyHistoryId(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

setGalaxyJobErrors(List<JobError>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

setGalaxyUrl(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisJobError

setGenomeSize(Long) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setGenomeSize(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

setGeographicLocationName(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setGrantType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setH1(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setH2(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setHeaderCheckboxSelection(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setHeaders(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

setHide(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setHtml(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setId(Long) - Method in interface ca.corefacility.bioinformatics.irida.model.MutableIridaThing

Set the numerical identifier for this object

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Set the entity id

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Set the numerical identifier for this object

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

setId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setId(String) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

setIdentifier(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setIdentifier(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

setIdentifier(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

setIdentifier(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails

setIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel

setIndex(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

setInstrumentModel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setIsolate(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setIsolationSource(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setJavascript(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

setKey(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelRow

setKey(String) - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

setKey(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel

setKey(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

setLabel(String) - Method in interface ca.corefacility.bioinformatics.irida.model.IridaThing

Method supporting JSON deserialzation.

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartSampleRequest

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setLabel(String) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.LabelledRelationshipResource

setLanguage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

setLastName(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setLastUpdate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setLastUpdate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setLatitude(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setLevel(ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction

setLibraryConstructionProtocol(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setLibraryName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setLibrarySelection(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setLibrarySource(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setLibraryStrategy(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setLimit(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setLines(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setLocale(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setLock(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setLocked(Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setLockPinned(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setLockPosition(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setLongitude(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setMailConfigured(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setMarkSync(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

setMashDistance(Float) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setMashGenome(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setMashSerovar(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setMashSubspecies(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setMaximum(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

setMaximumCoverage(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setMessage(String) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

setMessage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

setMessage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

setMessage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails

setMessage(String) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

Set the message for this response

setMetadata(List<FieldUpdate>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

setMetadata(Map<MetadataTemplateField, MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.sample.SampleMetadataResponse

setMetadataEntry(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

setMetadataEntry(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setMetadataEntry(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

setMetadataEntry(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setMetadataEntryId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setMetadataField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

setMetadataField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setMetadataFieldId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setMetadataRestriction(ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

setMetadataRestriction(Project, MetadataTemplateField, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

setMetadataRestriction(Project, MetadataTemplateField, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Adds or updates the MetadataRestriction for a project and field

setMetadataRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

setMetadataRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setMetadataRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setMetadataRestrictions(List<NewProjectMetadataRestriction>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setMetadataRole(ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

setMetadataRole(ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

setMetadataRole(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

setMetadataTemplateField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setMetadataTemplateField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleMetadataFieldEntry

setMinimum(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Coverage

setMinimumCoverage(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setMiseqRunId(Long) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.sequencefile.SequenceFileResource

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setModifiedDate(Date) - Method in interface ca.corefacility.bioinformatics.irida.model.MutableIridaThing

Set the modification time of this object

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.project.ReferenceFile

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object

Throws UnsupportedOperationException because you should not be able to update a file.

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

Throws UnsupportedOperationException because you should not be able to update a file.

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

Set the modification time of this object

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setModifiedDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setName(String) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setName(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Set the name of the remote API.

setName(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setName(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

setName(String) - Method in enum ca.corefacility.bioinformatics.irida.model.user.Role

setName(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataTemplate

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Locale

setName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

setName(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

setNamespace(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setNcbiNamespace(String) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setNewick(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisTreeResponse

setNewPassword(String, String, Model, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPasswordResetService

Set the password for the User

setNumericValue(Double) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

setOAntigen(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setOperation(SearchOperation) - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

setOptionalProperties(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

Set the Map of optional properties

setOrder(List<AntSort>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setOrganism(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setOrganization(String) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setOrganization(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setOtherProperties(Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.exception.ErrorResponse

Set the additional properties to display for this response

setOutputName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setOwnAccount(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setOwner(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

setPageSize(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

setPageSize(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

setPagination(AntPagination) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

setPairedEndSamples(List<AnalysisSamples>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

setPairs(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setPairs(Set<SequenceFilePair>) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

setParameterName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

setParameters(List<Input>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavedPipelineParameters

setParameters(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.pipeline.SavePipelineParametersRequest

setParameters(Map<String, String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setParameterValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecutionParameters

setParameterWithOptions(List<InputWithOptions>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setParent(TreeNode<ValueType>) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Set the parent node

setParentMessageSource(MessageSource) - Method in class ca.corefacility.bioinformatics.irida.util.IridaPluginMessageSource

setParse_results_error(Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

setParseError(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData

setPassword(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setPerbaseChart(byte[]) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

setPersequenceChart(byte[]) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCImagesResponse

setPhoneNumber(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setPinned(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setPreviousExecutionTools(ArrayList<AnalysisToolExecution>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

setPreviousState(AnalysisState) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

setPreviousState(AnalysisState) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setPriorities(AnalysisSubmission.Priority[]) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setPriorities(List<SelectOption>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities

setPriority(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

setPriority(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

setPriority(AnalysisSubmission.Priority) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

setPriority(AnalysisSubmission.Priority) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSubmissionInfo

setPriority(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.dto.Priorities

setPriority(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setPriority(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ProjectDetailsResponse

setProcessingState(SequencingObject.ProcessingState) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setProject(Project) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setProject(Project) - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

setProject(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample

setProjectDefault(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate

setProjectDescription(String) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataRequest

setProjectId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

setProjectRole(ProjectRole) - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectUserJoin

Set the user's role on the project

setProjectRole(ProjectRole) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

setProjectRole(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NewMemberRequest

setProjects(List<SelectOption>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setProjects(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setProjectSampleMetadataSampleId(HttpSession, Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.metadata.ProjectSampleMetadataAjaxController

Add the metadata to specific Sample based on the selected column to correspond to the Sample id.

setProjectSampleMetadataSampleId(HttpSession, Long, String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

Add the metadata to specific Sample based on the selected column to correspond to the Sample id.

setProjectStats(List<GenericStatModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

setProjectSyncFrequencies(ProjectSyncFrequency[]) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setProjectSyncFrequency(ProjectSyncFrequency) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setProjectSyncFrequency(ProjectSyncFrequency) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettingsUpdateRequest

setProperties(Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

setProperty(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntSort

setQcEntries(Set<QCEntry>) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setQcEntries(Set<QCEntry>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

setQcMessages(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setQcStatus(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setRead(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setReadBy(User) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setRedirectURI(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setReference(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setReferenceFile(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets the reference file.

setReferenceFile(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

Sets the reference file.

setReferenceFile(ReferenceFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

setReferenceFiles(List<UIReferenceFile>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setRefreshToken(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setRefreshToken(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

setRefreshTokenValiditySeconds(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setRegisteredRedirectUri(String) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setReleaseDate(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setRemoteAnalysisId(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Sets the remote analysis id.

setRemoteApi(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

setRemoteAPI(RemoteAPI) - Method in exception ca.corefacility.bioinformatics.irida.exceptions.IridaOAuthException

Set the service for this exception

setRemoteAPI(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.IridaOAuthErrorHandler

Set the RemoteAPI to return to the caller if an error occurs

setRemoteAPI(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.OAuthTokenRestTemplate

Set the API this rest template will communicate with

setRemoteAPI(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setRemoteHashCode(int) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setRemoteInputDataId(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Sets the id of a remote location to store input files.

setRemoteProjectHash(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

Set the RemoteStatus for this object if it was read from a remote source

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setRemoteStatus(RemoteStatus) - Method in interface ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable

Set the RemoteStatus of a remote object

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setRemoteStatus(RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setRemoteStatus(T, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.Fast5ObjectRemoteRepositoryImpl

setRemoteStatus(T, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.RemoteRepositoryImpl

Set the RemoteStatus of a read remote entity

setRemoteStatus(T, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SequenceFilePairRemoteRepositoryImpl

Set the RemoteStatus of a read remote entity

setRemoteStatus(T, RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SingleEndSequenceFileRemoteRepositoryImpl

setRemoteURL(String) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setRemoteURL(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setRemoteWorkflowId(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

Sets the remote workflow id.

setRemove(Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setRemoveCompressedFiles(boolean) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

Decide whether or not to delete the original compressed files that are uploaded once they're unzipped.

setRequiresReference(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setResizable(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setResource(ResourceList<Type>) - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ListResourceWrapper

setResource(Type) - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceWrapper

Set the resource

setResource(Type) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceAdditionalProperties

Set the resource of this object

setResources(List<Type>) - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList

Set the list of resources

setResponseMessage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxUpdateItemSuccessResponse

setResponseMessage(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.AddSampleMetadataResponse

setRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

setRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.NewProjectMetadataRestriction

setRestriction(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

setRestrictions(List<ShareMetadataRestriction>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setResult(SistrResult) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

setReverse(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

setRole(UserGroupJoin.UserGroupRole) - Method in class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

setRole(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.settings.dto.Role

setRows(List<SampleMetadataStorageRow>) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

setSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

setSample(Sample) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.CartProjectSample

setSampleId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setSampleId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSampleProject

setSampleId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

setSampleId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

setSampleIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.cart.dto.AddToCartRequest

setSampleIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.NGSLinkerCmdRequest

setSampleIds(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setSampleName(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setSampleName(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setSampleName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

setSampleName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

setSampleName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSistrResults

setSampleNameColumn(String) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorage

setSampleNames(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setSamples(List<CartSampleModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.cart.CartProjectModel

setSamples(List<ValidateSampleNameModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest

setSamples(List<NcbiSubmissionSample>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest

setSamples(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.CreateProjectRequest

setSampleStats(List<GenericStatModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

setSaved(Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.utilities.SampleMetadataStorageRow

setSavedParameters(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setSavedPipelineParameters(List<SavedPipelineParameters>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setScope(Set<String>) - Method in class ca.corefacility.bioinformatics.irida.model.IridaClientDetails

setSearch(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

setSearch(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

Set the search term for the TableRequest.

setSearch(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setSearch(List<AntSearch>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableRequest

setSecondFileSize(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

setSecurityContextFromAnalysisSubmission(ProceedingJoinPoint, RunAsUser) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect

Advice around a method annotated with RunAsUser.

setSelection(List<ProjectSampleAnalysisOutputInfo>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager

Set the selected AnalysisOutputFile

setSequenceFile(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

setSequenceFile(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSingleEndSamples

setSequenceFile(SequenceFile) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

setSequenceFilePairId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisSamples

setSequencerType(String) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

setSequencingObject(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.ria.web.files.dto.FastQCDetailsResponse

setSequencingRun(SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setSerogroup(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setSerovar(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setSerovarAntigen(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setSerovarCgmlst(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

setServerBase(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

Set the base URL of this server

setServiceURI(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

Set the base URI of this remote service

setShareStatus(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProjectShare

setSingleEndSamples(List<AnalysisSingleEndSamples>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInputFiles

setSingles(List<Long>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionSample

setSistrTyping(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject

setSleepDuration(Integer) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessingChain

Set the amount of time (in seconds) that the processor chain should sleep each time it sleeps.

setSleepDuration(Integer) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

Set the amount of time (in seconds) that the processor chain should sleep each time it sleeps.

setSort(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.agGrid.AgGridColumn

setSortColumn(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.ClientTableRequest

setSortColumn(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

setSortColumn(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.AdminUsersTableRequest

setSortDirection(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

setSortDirection(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

setSortField(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

setStart(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setStartDate(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

setStartDate(Date) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setStartSeek(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setState(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

setStatistics(List<GenericStatModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.StatisticsResponse

setStatusMessage(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmissionTemplate

setStrain(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

setSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel

setSubmissionStatus(ExportUploadState) - Method in class ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles

setSubmitter(User) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets the User who is submitting this analysis.

setSyncFrequency(ProjectSyncFrequency) - Method in class ca.corefacility.bioinformatics.irida.model.project.Project

setSyncStatus(RemoteStatus.SyncStatus) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setSyncUser(User) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.RemoteProjectSettings

setSystemRole(Role) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setTargetId(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

setText(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setText(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter

setTimeout(Integer) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessingChain

Set the total amount of time (in seconds) that the processor chain should wait for the SequencingObject to appear before failing.

setTimeout(Integer) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

Set the total amount of time (in seconds) that the processor chain should wait for the SequencingObject to appear before failing.

SETTING_METADATA - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

setTitle(String) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

setTitle(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.dto.AnnouncementRequest

setTitle(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelHeader

setTokenString(String) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

setTokenValidity(int) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

setToolName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setToolName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisToolExecution

setTools(AnalysisToolExecution) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisProvenanceResponse

setToolVersion(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

setTotal(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse

setTotalBases(long) - Method in class ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry

setTotalResources(Long) - Method in class ca.corefacility.bioinformatics.irida.model.remote.resource.ResourceList

Set the total number of resources

setTreeDefault(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisInfo

setTreeDefault(Boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

setType(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

setType(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

setType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.dto.ProjectMetadataField

setType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setType(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.dto.ExportToFileModel

setType(List<String>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysesFilters

setUp() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

setUp() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

setUp() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

setUp() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

setUpdatePermission(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setUpdateSamples(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets flag to indicate whether or not samples in the submission should be updated with analysis results following completion.

setUpdateSamples(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setUpdateSamples(boolean) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.LaunchRequest

setUpdateSamples(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

setUploadSha256(String) - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile

setUploadState(ExportUploadState) - Method in class ca.corefacility.bioinformatics.irida.model.NcbiExportSubmission

setUrl(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.remote.CreateRemoteProjectRequest

setURL(String) - Method in class ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus

setUser(User) - Method in class ca.corefacility.bioinformatics.irida.model.announcements.Announcement

setUser(User) - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

setUser(User) - Method in class ca.corefacility.bioinformatics.irida.model.run.SequencingRun

setUser(User) - Method in class ca.corefacility.bioinformatics.irida.model.subscription.ProjectSubscription

setUser(User) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails

setUser(UserDetailsModel) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

setUserFirstName(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setUserId(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setUserId(Long) - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

setUserLastName(String) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setUsername(String) - Method in class ca.corefacility.bioinformatics.irida.model.user.User

setUsersLoggedIn(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

setUserStats(List<GenericStatModel>) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.BasicStatsResponse

setValue(Long) - Method in class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel

setValue(Object) - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.FieldUpdate

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ui.Input

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelCol

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

setValue(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

setValue(ValueType) - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

Set the value for this node

setVersion(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setWarnings(List<String>) - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResponseResource

setWorkflowDescription(IridaWorkflowDescription) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setWorkflowId(UUID) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

setWorkflowId(UUID) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Sets the id of the workflow for this analysis.

setWorkflowName(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisDetails

setWrite(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.clients.CreateUpdateClientDetails

shareAnalysisSubmissionWithProject(AnalysisSubmission, Project) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Share an AnalysisSubmission with a given Project

shareAnalysisSubmissionWithProject(AnalysisSubmission, Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Share an AnalysisSubmission with a given Project

ShareMetadataRestriction - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Helper class used when sharing / moving samples to indicate, which restriction level the metadata attached should have.

ShareMetadataRestriction() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

ShareMetadataRestriction(Long, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction

shareSamples(Project, Project, Collection<Sample>, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Share a list of Samples between two Projects.

shareSamples(Project, Project, Collection<Sample>, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Share a list of Samples between two Projects.

ShareSamplesRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Handles data transfer for sharing samples between projects

ShareSamplesRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest

shareSamplesWithProject(ShareSamplesRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Share / Move samples between projects

shareSamplesWithProject(ShareSamplesRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

shouldCleanupSubmission(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.CleanupAnalysisSubmissionCondition

Whether or not the passed AnalysisSubmission should be cleaned up.

shouldCleanupSubmission(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.CleanupAnalysisSubmissionConditionAge

Whether or not the passed AnalysisSubmission should be cleaned up.

shouldProcessFile(SequencingObject) - Method in interface ca.corefacility.bioinformatics.irida.processing.FileProcessor

This method asks the file processor whether it should act on this file.

shouldProcessFile(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.AutomatedAnalysisFileProcessor

shouldProcessFile(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.FastqcFileProcessor

shouldProcessFile(SequencingObject) - Method in class ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

showHistoryContents(String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Show the history contents for the specified history identifier

showIndex() - Method in class ca.corefacility.bioinformatics.irida.ria.web.DashboardController

Get the index page

showLogin(Model, Boolean, Principal) - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.LoginController

Get the login page

showProvenance(String, String) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService

Show the history provenance contents for the specified history identifiers.

showSplash() - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.LoginController

Get the index page

SINGLE - ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type

SINGLE_END - ca.corefacility.bioinformatics.irida.model.run.SequencingRun.LayoutType

SingleEndSequenceFile - Class in ca.corefacility.bioinformatics.irida.model.sequenceFile

SequencingObject from a single ended sequence run.

SingleEndSequenceFile(SequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile

SingleEndSequenceFileConcatenator - Class in ca.corefacility.bioinformatics.irida.processing.concatenate.impl

SequenceFilePairConcatenator for SingleEndSequenceFiles

SingleEndSequenceFileConcatenator() - Constructor for class ca.corefacility.bioinformatics.irida.processing.concatenate.impl.SingleEndSequenceFileConcatenator

SingleEndSequenceFileModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile

IRIDA UI model to represent SingleEndSequenceFile

SingleEndSequenceFileModel - ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

SingleEndSequenceFileModel(SingleEndSequenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.sequenceFile.SingleEndSequenceFileModel

SingleEndSequenceFileRemoteRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.remote

RemoteRepository for storing and reading SingleEndSequenceFiles

SingleEndSequenceFileRemoteRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.remote.impl

Implementation of a SingleEndSequenceFileRemoteRepository extending RemoteRepositoryImpl

SingleEndSequenceFileRemoteRepositoryImpl(RemoteAPITokenService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.remote.impl.SingleEndSequenceFileRemoteRepositoryImpl

SingleEndSequenceFileRemoteService - Interface in ca.corefacility.bioinformatics.irida.service.remote

Service for storing and retrieving SingleEndSequenceFiles from a RemoteAPI

SingleEndSequenceFileRemoteServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.remote.impl

Implementation of SingleEndSequenceFileRemoteService using a SingleEndSequenceFileRemoteRepository

SingleEndSequenceFileRemoteServiceImpl(SingleEndSequenceFileRemoteRepository, SequenceFileRemoteRepository, RemoteAPIRepository) - Constructor for class ca.corefacility.bioinformatics.irida.service.remote.impl.SingleEndSequenceFileRemoteServiceImpl

SISTR_TYPING - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

SistrResult - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis.dto

Used as a response for encapsulating a SISTR result object

SistrResult() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

SistrResult(String, String, String, String, String, String, String, String, String, Long, String, String, Float, Integer, Integer, String, String, String, Float) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.SistrResult

SISTRSampleUpdater - Class in ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl

AnalysisSampleUpdater that adds a number of results from a SISTR run to the metadata of a Sample

SISTRSampleUpdater(MetadataTemplateService, SampleService, IridaWorkflowsService) - Constructor for class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.SISTRSampleUpdater

size() - Method in class ca.corefacility.bioinformatics.irida.web.assembler.resource.ResourceCollection

Get the number of elements in the collection.

SIZE_FRACTIONATION - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

SlashFilter - Class in ca.corefacility.bioinformatics.irida.web.filter

A simple filter that wraps HttpServletRequest to replace any incoming requests with two or more slashes with a single slash.

SlashFilter() - Constructor for class ca.corefacility.bioinformatics.irida.web.filter.SlashFilter

springLiquibase(DataSource, ApplicationContext) - Method in class ca.corefacility.bioinformatics.irida.config.data.IridaApiJdbcDataSourceConfig

Create an instance of SpringLiquibase to update the database schema with liquibase change sets.

start(UUID, LaunchRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineStartService

Start a new pipeline

STATE_PERCENTAGE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

A Map defining the progress transitions points for each state in an AnalysisSubmission.

StateFilter - Class in ca.corefacility.bioinformatics.irida.ria.web.analysis

Class for conversion from JSON.

StateFilter() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.analysis.StateFilter

STATIC_FIELD_PREFIX - Static variable in class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

StaticMetadataTemplateField - Class in ca.corefacility.bioinformatics.irida.model.sample

A MetadataTemplateField with a special key "irida-static-*" to specify that it is statically added to a Sample and not part of the sample metadata.

StaticMetadataTemplateField() - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

StaticMetadataTemplateField(String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.sample.StaticMetadataTemplateField

StatisticsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics

UI Response to to encapsulate statistics.

StatisticsResponse(List<GenericStatModel>, StatisticTimePeriod) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.StatisticsResponse

StatisticTimePeriod - Enum in ca.corefacility.bioinformatics.irida.model.enums

Defines a arrays of time periods and group by formats used for getting statistics for the Admin Panel.

StorageException - Exception in ca.corefacility.bioinformatics.irida.exceptions

When a database error occurs

StorageException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.StorageException

Construct a new StorageException with the specified message.

StorageException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.StorageException

Construct a new StorageException with the specified message and original cause.

stringToState(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

Given a string defining a state, converts this to a GalaxyWorkflowState.

SubmissionIds - Class in ca.corefacility.bioinformatics.irida.ria.web.components

This class is used to store workflow submission ids in the session.

SubmissionIds() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.SubmissionIds

SUBMISSIONS_REL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

submitNcbiExport(NcbiSubmissionRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.NCBIAjaxController

Submit a NCBI SRA Submission

submitNcbiExport(NcbiSubmissionRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService

Create a new submission to the NCBI SRA.

SUBMITTED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submitted to NCBI

submitter - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

submitter(User) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Set the user who submitted the pipeline

SUBMITTING - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Occurs when an analysis is first submitting.

SUBSCRIPTION_TEMPLATE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

SUCCESS - ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

SuccessNotification - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Consumed by the UI to display a success notification.

SuccessNotification(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.SuccessNotification

SuccessNotification(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.SuccessNotification

SUPPORTED_TYPES - Static variable in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

supports(Class<?>) - Method in class ca.corefacility.bioinformatics.irida.oauth2.OAuth2ResourceOwnerPasswordAuthenticationProvider

supportsParameter(MethodParameter) - Method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.config.DataTablesRequestResolver

switchInconsistentSubmissionsToError() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionCleanupService

This examines all possible analysis submissions and moves any submissions not in a valid state to AnalysisState.ERROR.

switchInconsistentSubmissionsToError() - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionCleanupServiceImpl

This examines all possible analysis submissions and moves any submissions not in a valid state to AnalysisState.ERROR.

SYNC_EXPIRED_TEMPLATE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

SYNC_NEW_PROJECT_PAGE - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

syncAssembly(UploadedAssembly, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize a given UploadedAssembly to the local installation

syncFast5File(Fast5Object, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize a given Fast5Object to the local installation

SYNCHRONIZED - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Up to date

syncProject() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.ProjectSyncScheduledTaskConfig

Find projects which must be synchronized from remote sites

syncSample(Sample, Project, Map<String, Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize a given Sample to the local installation.

syncSampleMetadata(Sample, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize the given sample's metadata

syncSequenceFilePair(SequenceFilePair, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize a given SequenceFilePair to the local installation.

syncSingleEndSequenceFile(SingleEndSequenceFile, Sample) - Method in class ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

Synchronize a given SingleEndSequenceFile to the local installation

SYNTHETIC - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

T

TableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.table

Used as the base class of any item to be represented in an ant.design Table.

TableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Used as the base class of any item to be represented in an ant.design Table.

TableModel(Long, String, Date, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableModel

TableModel(Long, String, Date, Date) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableModel

TableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.table

Handles the conversion of the HttpRequestBody into an object.

TableRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Default for request for table contents.

TableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableRequest

TableRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

TableRequest(int, int, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest

TableResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.table

Contains information needed for listing of items in an ag-grid table

TableResponse<T extends TableModel> - Class in ca.corefacility.bioinformatics.irida.ria.web.models.tables

Response sent when items are requested for a table.

TableResponse(List<? extends TableModel>, long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.table.TableResponse

TableResponse(List<T>, Long) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse

TaxonomyAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies

Handle asynchronous request related to the taxonomy ontology.

TaxonomyAjaxController(TaxonomyService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.ontologies.TaxonomyAjaxController

TaxonomyEntry - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used by the UI to generate a select input based on a search within the taxonomy.

TaxonomyEntry(TreeNode<String>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.TaxonomyEntry

taxonomyService() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

TaxonomyService - Interface in ca.corefacility.bioinformatics.irida.service

Service for reading taxonomy information

templateEngine() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

TestEmailController - Class in ca.corefacility.bioinformatics.irida.service.impl

Email controller used for testing.

TestEmailController() - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

TestEmailController(WebEmailConfig.ConfigurableJavaMailSender, TemplateEngine, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.TestEmailController

testExecutor() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.ExecutorConfig

Task executor for running in test modes.

testRelativePaths() - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

Check that files exist in expected locations

throwConstraintViolationException(TransactionSystemException, Locale, MessageSource) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.utilities.ExceptionUtilities

Method to unwrap a TransactionSystemException to create the error message from the root ConstraintViolationException cause and throw a UIConstraintViolationException.

Timestamped<Identifier> - Interface in ca.corefacility.bioinformatics.irida.model

An object with a timestamp and ID

TimestampJson - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Serialization class for java Date objects.

TimestampJson() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson

TimestampJson.TimestampSerializer - Class in ca.corefacility.bioinformatics.irida.web.controller.api.json

Default serializer for Date objects.

TimestampMixin - Class in ca.corefacility.bioinformatics.irida.jackson2.mixin

This mixin class is used to serialize/deserialize Timestamp.

TimestampMixin() - Constructor for class ca.corefacility.bioinformatics.irida.jackson2.mixin.TimestampMixin

TimestampSerializer() - Constructor for class ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson.TimestampSerializer

toErrorStateOnCleaningException(AnalysisSubmission, Exception) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect

Aspect that matches any asynchronous calls for cleaning analysis submissions and switches to a cleaned error state.

toErrorStateOnException(AnalysisSubmission, Exception) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect

Aspect that matches any asynchronous calls for performing analysis submissions and switches the submission to an error state on an exception.

TOKEN_ENDPOINT - Static variable in class ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

toolDataClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

ToolExecution - Class in ca.corefacility.bioinformatics.irida.model.workflow.analysis

A historical record of how a tool was executed by a workflow execution manager to produce some set of outputs.

ToolExecution(Long, Set<ToolExecution>, String, String, String, Map<String, String>) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

Construct a new instance of ToolExecution.

ToolExecution(Set<ToolExecution>, String, String, String, Map<String, String>, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

Construct a new instance of ToolExecution.

toolsClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

ToolsListExporter - Class in ca.corefacility.bioinformatics.irida.util

Exports a YAML configuration file containing the list of all tools necessary in Galaxy to run this IRIDA instance.

ToolsListExporter() - Constructor for class ca.corefacility.bioinformatics.irida.util.ToolsListExporter

toPredicate(Root<ProjectSampleJoin>, CriteriaQuery<?>, CriteriaBuilder) - Method in class ca.corefacility.bioinformatics.irida.repositories.specification.ProjectSampleJoinSpecification

toString() - Method in class ca.corefacility.bioinformatics.irida.events.MethodEvent

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Return the String representation of the ExportUploadState

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

toString() - Method in class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

toString() - Method in class ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin

toString() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPI

toString() - Method in class ca.corefacility.bioinformatics.irida.model.RemoteAPIToken

toString() - Method in class ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

toString() - Method in class ca.corefacility.bioinformatics.irida.model.sample.Sample

toString() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.OverrepresentedSequence

toString() - Method in class ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair

toString() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyAccountEmail

toString() - Method in class ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.user.Role

toString() - Method in class ca.corefacility.bioinformatics.irida.model.user.User

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ProjectSampleAnalysisOutputInfo

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDescription

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowDynamicSourceGalaxy

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameterChoice

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus

toString() - Method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.structure.IridaWorkflowStructure

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

toString() - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission

toString() - Method in class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

toString() - Method in enum ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

toString() - Method in enum ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

toString() - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.AnalysisOutputFileInfo

toString() - Method in enum ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

toString() - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.ParameterBuilderGalaxy.ParameterId

toString() - Method in class ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService.AnalysisServiceStatus

toString() - Method in class ca.corefacility.bioinformatics.irida.util.TreeNode

totalBases(Long) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the totalBases

totalSequences(Integer) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC.AnalysisFastQCBuilder

Set the total sequences

TRANSACTION_MANAGEMENT_ORDER - Static variable in class ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig

The order for transaction management.

TRANSCRIPTOMIC - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

transferAnalysesResults() - Method in class ca.corefacility.bioinformatics.irida.config.services.scheduled.AnalysisScheduledTaskConfig

Cycle through any completed submissions and transfer the results.

transferAnalysesResults() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisExecutionScheduledTask

Cycle through any completed AnalysisSubmissions and transfer the results to IRIDA.

transferAnalysesResults() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

Cycle through any completed AnalysisSubmissions and transfer the results to IRIDA.

transferAnalysisResults(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService

Downloads and saves the results of an AnalysisSubmission that was previously submitted from an execution manager.

transferAnalysisResults(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxy

Downloads and saves the results of an AnalysisSubmission that was previously submitted from an execution manager.

transferAnalysisResults(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

Downloads and saves the results of an AnalysisSubmission that was previously submitted from an execution manager.

TRANSFERRED - ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

An analysis that has been transferred to IRIDA, but has not had post processing performed.

TreeNode<ValueType> - Class in ca.corefacility.bioinformatics.irida.util

Simple generic tree node with links to parent and a list of children

TreeNode(ValueType) - Constructor for class ca.corefacility.bioinformatics.irida.util.TreeNode

Create a new TreeNode with a given value

U

UIActivitiesService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI service for converting events into UI activities.

UIActivitiesService(ProjectService, ProjectEventService, MessageSource, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIActivitiesService

UIAddAssociatedProjectException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Error to throw if there is an error adding an associated project to a project

UIAddAssociatedProjectException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIAddAssociatedProjectException

UIAdminStatisticsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for formatting responses for the admin statistics page UI.

UIAdminStatisticsService(ProjectService, UserService, SampleService, AnalysisSubmissionService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIAdminStatisticsService

UIAnalysesOutputsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for all things related to project single sample analysis outputs.

UIAnalysesOutputsService(AnalysisSubmissionService, IridaWorkflowsService, UserService, AnalysisOutputFileDownloadManager) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesOutputsService

UIAnalysesService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for analyses

UIAnalysesService(SampleService, SequencingObjectService, UserService, AnalysisSubmissionRepository, IridaWorkflowsService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesService

UIAnnouncementsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for formatting responses for the announcements page UI.

UIAnnouncementsService(AnnouncementService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

UIAssociatedProjectsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service for handling associated projects

UIAssociatedProjectsService(ProjectService, ProjectOwnerPermission, MessageSource, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIAssociatedProjectsService

UICartService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service for handling all aspects of interaction with the Cart.

UICartService(Cart, ProjectService, SampleService, UpdateSamplePermission, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UICartService

UIClientService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service to handle IRIDA Clients

UIClientService(IridaClientDetailsService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

UIConstraintViolationException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Used by UI to contain internationalized constraint violations.

UIConstraintViolationException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIConstraintViolationException

UIConstraintViolationException(Map<String, String>) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIConstraintViolationException

UIEmailSendException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to be thrown by the UI when an email failed to send.

UIEmailSendException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIEmailSendException

UIEntityNotFoundException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to be thrown by the UI when the entity does not exist.

UIEntityNotFoundException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIEntityNotFoundException

UIMetadataField - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

This is a generic class to represent all possible headers (MetadataFields) in a line list.

UIMetadataField(MetadataTemplateField, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataField

UIMetadataFieldDefault - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

Represents metadata fields that are not part of the sample metadata, but are included on the line list page.

UIMetadataFieldDefault(String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataFieldDefault

UIMetadataFileImportService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI service to handle parsing metadata files so they can be saved to the session.

UIMetadataFileImportService(ProjectService, SampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataFileImportService

UIMetadataImportService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI service to handle importing metadata files, so they can be saved to the session.

UIMetadataImportService(MessageSource, ProjectService, SampleService, MetadataTemplateService, UIMetadataFileImportService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataImportService

UIMetadataService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service for Metadata Templates in the user interface

UIMetadataService(ProjectService, MetadataTemplateService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

UIMetadataTemplate - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

User interface model for a MetadataTemplate This is required for creating a new MetadataTemplate since the UI create new MetadataTemplateField only lists String representations of them.

UIMetadataTemplate() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate

UIMetadataTemplate(Long, String, List<AgGridColumn>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UIMetadataTemplate

UINcbiService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Utility class for formatting responses for NCBI Export Listing page UI.

UINcbiService(ProjectService, NcbiExportSubmissionService, SequencingObjectService, UserService, UISampleService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UINcbiService

UIPasswordResetService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Handles service calls for password resets.

UIPasswordResetService(UserService, PasswordResetService, EmailController, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIPasswordResetService

UIPipelineDetailsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos

Model class to send details about a workflow pipeline to the UI Used on the launch pipeline page.

UIPipelineDetailsResponse() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.launchPipeline.dtos.UIPipelineDetailsResponse

UIPipelineSampleService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for all things related to samples within the pipeline

UIPipelineSampleService(UISampleService, UICartService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineSampleService

UIPipelineService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for all things related to workflow pipelines.

UIPipelineService(UICartService, IridaWorkflowsService, WorkflowNamedParametersService, ProjectService, ReferenceFileService, AnalysisSubmissionSampleProcessor, UpdateSamplePermission, GalaxyToolDataService, AnalysisSubmissionService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineService

UIPipelineStartService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service to handle starting of IridaWorkflows through the UI.

UIPipelineStartService(IridaWorkflowsService, SequencingObjectService, AnalysisSubmissionService, ProjectService, WorkflowNamedParametersService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIPipelineStartService

UIProjectMembersService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service class for the UI for handling project members actions.

UIProjectMembersService(ProjectService, UserService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

UIProjectReferenceFileService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for formatting responses for the project reference files page UI.

UIProjectReferenceFileService(ProjectService, ReferenceFileService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectReferenceFileService

UIProjectSampleService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service to handle samples within a project.

UIProjectSampleService(ProjectService, SampleService, MetadataTemplateService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService

UIProjectsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for formatting responses for the project members page UI.

UIProjectsService(ProjectService, SampleService, MessageSource, ProjectOwnerPermission, ManageLocalProjectSettingsPermission, MetadataTemplateService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

UIProjectSubscriptionService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for formatting responses for the project subscriptions page UI.

UIProjectSubscriptionService(ProjectSubscriptionService, UserService, ProjectService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSubscriptionService

UIProjectUserGroupsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service to handle requests for project user groups.

UIProjectUserGroupsService(ProjectService, UserGroupService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

UIProjectWithoutOwnerException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to be thrown by the UI when the member being removed from the project, would leave the project without a manager.

UIProjectWithoutOwnerException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIProjectWithoutOwnerException

UIReferenceFile - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references

Represents a reference file in the UI.

UIReferenceFile(Join<Project, ReferenceFile>, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

UIReferenceFile(ReferenceFile) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UIReferenceFile

UIRemoteAPIService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service to handle request for Remote APIs

UIRemoteAPIService(RemoteAPIService, RemoteAPITokenService, ProjectRemoteService, ProjectService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteAPIService

UIRemoteProjectService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

A utility class for doing operations on remote project sync settings.

UIRemoteProjectService(MessageSource, ProjectService, ProjectRemoteService, UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteProjectService

UIRemoveAssociatedProjectException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to through if there is an error removing an associated project from a project

UIRemoveAssociatedProjectException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIRemoveAssociatedProjectException

UISampleFilter - Class in ca.corefacility.bioinformatics.irida.ria.web.models

User Interface model for available field to filter the Project Samples by.

UISampleFilter() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.UISampleFilter

UISampleMetadata - Class in ca.corefacility.bioinformatics.irida.ria.web.linelist.dto

Represents Sample metadata in the linelist table.

UISampleMetadata(Project, Sample, boolean, Set<MetadataEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

UISampleService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for samples

UISampleService(SampleService, ProjectService, UpdateSamplePermission, SequencingObjectService, GenomeAssemblyService, MessageSource, UICartService, MetadataTemplateService, MetadataEntryRepository, MetadataRestrictionRepository) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

UISecurityConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig

UISequenceFileService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for handling requests related to SequenceFiles

UISequenceFileService(AnalysisService, SequencingObjectService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

UISequencingRunService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for handling requests related to SequencingRuns

UISequencingRunService(SequencingRunService, SequencingObjectService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService

UISettingsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Handles service calls for settings in IRIDA.

UISettingsService(IridaApiServicesConfig.IridaLocaleList, EmailController, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UISettingsService

UIShareSamplesException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to through if there is an error sharing samples between projects

UIShareSamplesException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIShareSamplesException

UIUserFormException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to be thrown by the UI when a user cannot be created or updated.

UIUserFormException(Map<String, String>) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIUserFormException

UIUserGroupsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Service class for the UI for handling UserGroups

UIUserGroupsService(UserGroupService, UserService, MessageSource) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

UIUsersService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

Handles service call for the administration of the IRIDA users.

UIUsersService(UserService, EmailController, MessageSource, PasswordEncoder, PasswordResetService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

UIUserStatisticsService - Class in ca.corefacility.bioinformatics.irida.ria.web.services

UI Service for handling requests related to user statistics

UIUserStatisticsService(UserService, ProjectService, SampleService, AnalysisSubmissionService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserStatisticsService

UIUserStatusException - Exception in ca.corefacility.bioinformatics.irida.ria.web.exceptions

Exception to throw if there is an error updating the user status

UIUserStatusException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIUserStatusException

UnauthenticatedAnonymousAuthenticationFilter - Class in ca.corefacility.bioinformatics.irida.web.filter

Anonymous authentication filter that sets anonymous tokens as being unauthenticated

UnauthenticatedAnonymousAuthenticationFilter(String) - Constructor for class ca.corefacility.bioinformatics.irida.web.filter.UnauthenticatedAnonymousAuthenticationFilter

Creates a filter with a principal named "anonymousUser" and the single authority "ROLE_ANONYMOUS".

UnauthenticatedAnonymousAuthenticationFilter(String, Object, List<GrantedAuthority>) - Constructor for class ca.corefacility.bioinformatics.irida.web.filter.UnauthenticatedAnonymousAuthenticationFilter

Create a new UnauthenticatedAnonymousAuthenticationFilter with the given key, principal, and authorities.

UNAUTHORIZED - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

No active OAuth2 token to synchronize this project

UNAVAILABLE - ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

UndefinedPermissionException - Exception in ca.corefacility.bioinformatics.irida.security.permissions

Thrown when the IridaPermissionEvaluator is asked to test a permission that it doesn't know about.

UndefinedPermissionException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.security.permissions.UndefinedPermissionException

UNKNOWN - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

used for undefined states

UNKNOWN - ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type

UNKNOWN - Static variable in class ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes

UNLIMITED_UPLOAD_SIZE - Static variable in class ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

named constant for allowing unlimited upload sizes.

UNPROCESSED - ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

UNSPECIFIED - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

UnsupportedReferenceFileContentError - Error in ca.corefacility.bioinformatics.irida.exceptions

Error that's thrown when BioJava can't parse an uploaded reference file.

UnsupportedReferenceFileContentError(String, Error) - Constructor for error ca.corefacility.bioinformatics.irida.exceptions.UnsupportedReferenceFileContentError

UNSYNCHRONIZED - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Entity should not be synchronized

update(Announcement) - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnnouncementServiceImpl

Update an object

update(IridaClientDetails) - Method in class ca.corefacility.bioinformatics.irida.service.impl.IridaClientDetailsServiceImpl

update(NcbiExportSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.export.NcbiExportSubmissionServiceImpl

Update an object

update(Project) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Update an object

update(SequencingRun) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

Update an object

update(Sample) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Update an object

update(ProjectSubscription) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectSubscriptionServiceImpl

Update an object

update(UserGroup) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Update an object

update(PasswordReset) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

update(User) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Throws an UnsupportedOperationException telling user to use UserServiceImpl.updateFields(Long, Map) instead.

update(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Update an object

update(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Update some of the fields of an individual resource in the database.

update(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Update some of the fields of an individual resource in the database.

update(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController

Update some of the fields of an individual resource in the database.

update(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Update some of the fields of an individual resource in the database.

update(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Update some of the fields of an individual resource in the database.

update(Collection<Sample>, AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.pipeline.results.updater.AnalysisSampleUpdater

Updates a collection of samples with a particular analysis result.

update(Collection<Sample>, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.AssemblySampleUpdater

Updates a collection of samples with a particular analysis result.

update(Collection<Sample>, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.BioHanselSampleUpdater

Add bio_hansel results to the metadata of the given Sample.

update(Collection<Sample>, AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.SISTRSampleUpdater

Add SISTR results to the metadata of the given Samples

update(Type) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Update an object

update(ValueType) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Update an object

UpdateAnalysisSubmissionPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.analysis

Confirms if a User can update a AnalysisSubmission.

UpdateAnalysisSubmissionPermission(AnalysisSubmissionRepository, UserRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission

Constructs a new UpdateAnalysisSubmissionPermission with the given information.

updateAnnouncement(AnnouncementRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.announcements.AnnouncementAjaxController

Handles request to update an existing announcement

updateAnnouncement(AnnouncementRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIAnnouncementsService

Update an existing announcement

updateClient(CreateUpdateClientDetails, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Update the details of a client

UpdatedAnalysisProgress - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used by the UI to to update the state and duration of an analysis.

UpdatedAnalysisProgress(AnalysisState, AnalysisState, Long, Boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress

UpdatedAnalysisTableProgress - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used by the UI to to update the state and duration of an analysis.

UpdatedAnalysisTableProgress(AnalysisStateModel, Long, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisTableProgress

updateDefaultGenomeAssemblyForSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Update the default genome assembly for the sample

updateDefaultGenomeAssemblyForSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Update the default genome assembly for the sample

updateDefaultMetadataTemplateForProject(Project, MetadataTemplate) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Update which MetadataTemplate is the default for the given Project

updateDefaultMetadataTemplateForProject(Project, MetadataTemplate) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Update which MetadataTemplate is the default for the given Project

updateDefaultSequencingObjectForSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Update the default sequencing object for the sample

updateDefaultSequencingObjectForSample(Long, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Update the default sequencing object for the sample

updateEmailSubscription(User, Project, boolean) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Update a ProjectUserJoin to subscribe or unsubscribe a User to a given Project

updateEmailSubscription(User, Project, boolean) - Method in interface ca.corefacility.bioinformatics.irida.service.user.UserService

Update a ProjectUserJoin to subscribe or unsubscribe a User to a given Project

UpdateException - Exception in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions

Thrown if there was an error during the update.

UpdateException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.settings.exceptions.UpdateException

updateFields(IdentifierType, Map<String, Object>) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Update properties of the given object by given fields.

updateFields(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Update properties of the given object by given fields.

updateFields(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Update properties of the given object by given fields.

updateFields(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

Update properties of the given object by given fields.

updateFields(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Update properties of the given object by given fields.

updateFields(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

Update properties of the given object by given fields.

updateFields(String, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.user.PasswordResetServiceImpl

updateFields(KeyType, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Update properties of the given object by given fields.

updateGroupDetails(Long, FieldUpdate) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Update the details within a user group

updateLogin(User, Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryCustom

Update the last login date for the given User

updateLogin(User, Date) - Method in class ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryImpl

Update the last login date for the given User

updateMetadataProjectField(Long, Long, ProjectMetadataRole, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Update a restriction level on a metadata field for a project

updateMetadataTemplate(MetadataTemplate, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Updated the fields in a MetadataTemplate

updateMetadataTemplate(MetadataTemplate, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIMetadataService

Update details within a MetadataTemplate

updateMetadataTemplateInProject(MetadataTemplate) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

Update a MetadataTemplate within a Project

updateMetadataTemplateInProject(MetadataTemplate) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService

Update a MetadataTemplate within a Project

UpdateMetadataTemplatePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.metadata

Permission for updating a MetadataTemplate

UpdateMetadataTemplatePermission(MetadataTemplateRepository, ManageLocalProjectSettingsPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission

updateMultiple(Collection<Sample>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Update multiple objects at once

updateMultiple(Collection<Type>) - Method in interface ca.corefacility.bioinformatics.irida.service.CRUDService

Update multiple objects at once

updateMultiple(Collection<ValueType>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

Update multiple objects at once

updatePassword(String, String, Model, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetAjaxController

Update the password for the User

updatePriority(AnalysisSubmission, AnalysisSubmission.Priority) - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

Update the priority of an AnalysisSubmission

updatePriority(AnalysisSubmission, AnalysisSubmission.Priority) - Method in class ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

Update the priority of an AnalysisSubmission

updateProcessingCoverage(long, Coverage, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Update the minimum/maximum coverage or genome size for the project

updateProcessingCoverage(Coverage, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Update the minimum, maximum coverage or genome size for a project.

updateProcessingPriority(long, AnalysisSubmission.Priority, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Update the priority for analyses for a project.

updateProcessingPriority(Long, AnalysisSubmission.Priority, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Update the priority for a projects automated pipelines.

UpdateProjectAttributeRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto

Used to handle requests from the UI to update a specific attribute on a project.

UpdateProjectAttributeRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

UpdateProjectAttributeRequest(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.dto.UpdateProjectAttributeRequest

updateProjectDetails(Long, UpdateProjectAttributeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectDetailsAjaxController

Update a field within the project details.

updateProjectDetails(Long, UpdateProjectAttributeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectsService

Update a field within the project details.

updateProjectMetadataFieldRestriction(Long, Long, ProjectMetadataRole, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.metadata.MetadataAjaxController

Update a restriction level on a metadata field for a project

updateProjectModifiedDate(Project, Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryCustom

Update the modifiedDate in a Project to the specified date.

updateProjectModifiedDate(Project, Date) - Method in class ca.corefacility.bioinformatics.irida.repositories.ProjectRepositoryImpl

Update the modifiedDate in a Project to the specified date.

updateProjectSettings(Project, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Update select Project settings

updateProjectSettings(Project, Map<String, Object>) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Update select Project settings

updateProjectShare(Long, AnalysisProjectShare, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisAjaxController

Update the share status of a given AnalysisSubmission for a given Project

updateProjectSubscription(Long, boolean, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectSubscriptionsAjaxController

Update a ProjectSubscription

updateProjectSubscription(Long, boolean, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSubscriptionService

Update an existing project subscription

updateProjectSyncSettings(Long, RemoteProjectSettingsUpdateRequest, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.projects.settings.ProjectSettingsRemoteAjaxController

Update the remote project sync settings

updateProjectSyncSettings(Long, RemoteProjectSettingsUpdateRequest, Principal, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIRemoteProjectService

Update the project sync settings

UpdateReferenceFilePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.files

Confirms that the authenticated user is allowed to modify a reference file.

UpdateReferenceFilePermission(ReferenceFileRepository, ProjectReferenceFileJoinRepository, ProjectOwnerPermission) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission

updateRemoteStatus(Long, RemoteStatus) - Method in class ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

Update the RemoteStatus for a SequencingObject

updateRemoteStatus(Long, RemoteStatus) - Method in interface ca.corefacility.bioinformatics.irida.service.SequencingObjectService

Update the RemoteStatus for a SequencingObject

updateRunningUploads() - Method in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Check local database for submissions which may have updates on the NCBI server and update them as necessary.

updateSample(UpdateSampleRequest, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService

Update a sample in a project

updateSample(Long, Map<String, Object>) - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Update a Sample details.

UpdateSampleAttributeRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to handle requests from the UI to update a specific attribute on a sample.

UpdateSampleAttributeRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

UpdateSampleAttributeRequest(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleAttributeRequest

updateSampleDetails(Long, UpdateSampleAttributeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Update a field within the sample details.

updateSampleDetails(Long, UpdateSampleAttributeRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Update a field within the sample details.

updateSampleInProject(UpdateSampleRequest, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Update a sample within a project

updateSampleMetadata(Sample, Set<MetadataEntry>) - Method in class ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl

Set the given set of MetadataEntry on the given Sample and save it to the database

updateSampleMetadata(Sample, Set<MetadataEntry>) - Method in interface ca.corefacility.bioinformatics.irida.service.sample.SampleService

Set the given set of MetadataEntry on the given Sample and save it to the database

updateSampleMetadata(Long, UpdateSampleMetadataRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Update a metadata field entry for Sample

updateSampleMetadata(Long, UpdateSampleMetadataRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Update metadata for the sample

UpdateSampleMetadataRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.samples.dto

Used to handle requests from the UI to update a sample metadata field/entry/restriction.

UpdateSampleMetadataRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

UpdateSampleMetadataRequest(Long, Long, String, Long, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.samples.dto.UpdateSampleMetadataRequest

updateSampleModifiedDate(Sample, Date) - Method in interface ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryCustom

Update the modifiedDate in a Sample to the specified value.

updateSampleModifiedDate(Sample, Date) - Method in class ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepositoryImpl

Update the modifiedDate in a Sample to the specified value.

UpdateSamplePermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.sample

Custom permission implementation for updating Sample.

UpdateSamplePermission(SampleRepository, ProjectOwnerPermission, ProjectSampleJoinRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission

Constructs a new instance of UpdateSamplePermission.

UpdateSampleRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

UI Request to update an existing sample

UpdateSampleRequest(String, String, String, List<FieldUpdate>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdateSampleRequest

updateSamples - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

updateSamples(boolean) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Turns on/off updating of samples from results for this analysis submission.

updateSamples(AnalysisSubmission) - Method in interface ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor

Updates the samples associated with an AnalysisSubmission to contain information from the Analysis.

updateSamples(AnalysisSubmission) - Method in class ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl

Updates the samples associated with an AnalysisSubmission to contain information from the Analysis.

UpdateSamplesFromAnalysisSubmissionPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.analysis

Permission for whether a user can update samples in a given analysis submission.

UpdateSamplesFromAnalysisSubmissionPermission(AnalysisSubmissionRepository, UpdateSamplePermission, ReadAnalysisSubmissionPermission, SampleRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateSamplesFromAnalysisSubmissionPermission

Constructs a new UpdateSamplesFromAnalysisSubmissionPermission.

UpdateSequencingRunPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.files

Permission checking if a user is the owner of a SequencingRun or if they are ROLE_SEQUENCER

UpdateSequencingRunPermission(SequencingRunRepository, UserRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateSequencingRunPermission

Construct an instance of UpdateSequencingRunPermission.

updateTokenFromRefreshToken(RemoteAPI) - Method in class ca.corefacility.bioinformatics.irida.service.impl.RemoteAPITokenServiceImpl

Update a given RemoteAPI's OAuth token by refresh token if available

updateTokenFromRefreshToken(RemoteAPI) - Method in interface ca.corefacility.bioinformatics.irida.service.RemoteAPITokenService

Update a given RemoteAPI's OAuth token by refresh token if available

updateUser(Long, UserEditRequest, Principal, HttpServletRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Submit a user edit

updateUser(Long, UserEditRequest, Principal, HttpServletRequest, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Submit a user edit

updateUserGroupDetails(Long, FieldUpdate) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Update user group details

updateUserGroupMetadataRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Update the project metadata role of a user group on the current project

updateUserGroupMetadataRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Update the ProjectMetadataRole of a UserGroup on the current Project

UpdateUserGroupPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.user

Confirms that the authenticated user is allowed to modify a user group.

UpdateUserGroupPermission(UserGroupRepository, UserGroupJoinRepository, UserRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserGroupPermission

Construct an instance of UpdateUserGroupPermission.

updateUserGroupProjectMetadataRole(Project, UserGroup, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

updateUserGroupProjectMetadataRole(Project, UserGroup, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Update a UserGroup's ProjectMetadataRole on a Project

updateUserGroupProjectRole(Project, UserGroup, ProjectRole, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Update a UserGroup's ProjectRole on a Project

updateUserGroupProjectRole(Project, UserGroup, ProjectRole, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Update a UserGroup's ProjectRole on a Project

updateUserGroupRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectUserGroupsAjaxController

Update the project role of a user group on the current project

updateUserGroupRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectUserGroupsService

Update the ProjectRole of a UserGroup on the current Project

updateUserMetadataRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Update a users metadata role on a project

updateUserMetadataRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Update a users metadata role on a project

UpdateUserPermission - Class in ca.corefacility.bioinformatics.irida.security.permissions.user

Confirms that the authenticated user is allowed to modify another (or their own) user account.

UpdateUserPermission(UserRepository) - Constructor for class ca.corefacility.bioinformatics.irida.security.permissions.user.UpdateUserPermission

Construct an instance of UpdateUserPermission.

updateUserProjectMetadataRole(Project, User, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

updateUserProjectMetadataRole(Project, User, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Update a User's ProjectMetadataRole on a Project

updateUserProjectRole(Project, User, ProjectRole, ProjectMetadataRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Update a User's ProjectRole on a Project

updateUserProjectRole(Project, User, ProjectRole, ProjectMetadataRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Update a User's ProjectRole on a Project

updateUserRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectMembersAjaxController

Update a users role on a project

updateUserRoleOnProject(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectMembersService

Update a users role on a project

updateUserRoleOnUserGroup(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

Update a group members role on the user groups

updateUserRoleOnUserGroup(Long, Long, String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUserGroupsService

Update a users role on a project

updateUserStatus(Long, boolean, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIUsersService

Update a user status (if the user is enabled within IRIDA).

updateUserStatus(Long, boolean, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

Update a user status (if the user is enabled within IRIDA).

UPDATING - ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Currently being copied

UPLOAD - ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

UPLOAD_ERROR - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submission where an error occurred while uploading

uploadAssemblies(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Upload assemblies to the given sample

uploadAssemblies(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Upload GenomeAssembly's to a sample

UploadConnectionException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown when a connection to a remote site for uploading data fails.

UploadConnectionException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadConnectionException

Constructs a new UploadConnectionException with no information.

UploadConnectionException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadConnectionException

Constructs a new UploadConnectionException with the given message.

UploadConnectionException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadConnectionException

Constructs a new UploadConnectionException with the given message and cause.

UploadConnectionException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadConnectionException

Constructs a new UploadConnectionException with the given cause.

UPLOADED - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submission which has been successfully uploaded

UploadedAssembly - Class in ca.corefacility.bioinformatics.irida.model.assembly

A GenomeAssembly implementation that was uploaded by a user or service

UploadedAssembly() - Constructor for class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

UploadedAssembly(Path) - Constructor for class ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly

UploaderAccountName - Interface in ca.corefacility.bioinformatics.irida.model.upload

An account name for setting up permissions of uploaded files to a remote endpoint.

UploadErrorException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when there is an error while uploading data to a separate data management system (e.g.

UploadErrorException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadErrorException

Constructs a new UploadErrorException with no information.

UploadErrorException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadErrorException

Constructs a new UploadErrorException with the given message.

UploadErrorException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadErrorException

Constructs a new UploadErrorException with the given message and cause.

UploadErrorException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadErrorException

Constructs a new UploadErrorException with the given cause.

UploadException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when uploading data to a separate data management system (e.g.

UploadException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadException

Constructs a new UploadException with no information.

UploadException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadException

Constructs a new UploadException with the given message.

UploadException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadException

Constructs a new UploadException with the given message and cause.

UploadException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadException

Constructs a new UploadException with the given cause.

uploadExecutor() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

uploadFast5Files(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Upload fast5 files to the given sample

uploadFast5Files(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Upload Fast5Object's to a sample

uploadGalaxyWorkflow(Path) - Method in class ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService

Uploads a workflow definined in the given file to Galaxy.

UPLOADING - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Submission currently being uploaded

UPLOADING - ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

UploadProjectName - Interface in ca.corefacility.bioinformatics.irida.model.upload

Defines the name of a project to be uploaded to a remote site.

UploadReferenceFilesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references

Used by UI to handle the return of a successful upload on one or more reference files.

UploadReferenceFilesResponse(List<UIReferenceFile>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.references.UploadReferenceFilesResponse

uploadSequenceFiles(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.samples.SamplesAjaxController

Upload SequenceFile's to a sample

uploadSequenceFiles(Long, MultipartHttpServletRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService

Upload SequenceFile's to a sample

uploadSequenceFilesPaired(Map<Sample, SequenceFilePair>, History, Library) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisCollectionServiceGalaxy

Uploads a list of paired sequence files belonging to the given samples to Galaxy.

uploadSequenceFilesSingleEnd(Map<Sample, SingleEndSequenceFile>, History, Library) - Method in class ca.corefacility.bioinformatics.irida.service.analysis.workspace.galaxy.AnalysisCollectionServiceGalaxy

Uploads a list of single sequence files belonging to the given samples to Galaxy.

uploadSubmission(NcbiExportSubmission, String) - Method in class ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Upload an NcbiExportSubmission's files and submission xml to the configured ftp site

UploadTimeoutException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when there is a timeout while uploading data to a separate data management system (e.g.

UploadTimeoutException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadTimeoutException

Constructs a new UploadTimeoutException with no information.

UploadTimeoutException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadTimeoutException

Constructs a new UploadTimeoutException with the given message.

UploadTimeoutException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadTimeoutException

Constructs a new UploadTimeoutException with the given message and cause.

UploadTimeoutException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UploadTimeoutException

Constructs a new UploadTimeoutException with the given cause.

User - Class in ca.corefacility.bioinformatics.irida.model.user

A user object.

User - ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

User() - Constructor for class ca.corefacility.bioinformatics.irida.model.user.User

Construct an instance of User with no properties set.

User(Long, String, String, String, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.User

Construct an instance of User with all properties set.

User(String, String, String, String, String, String) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.User

Construct an instance of User with all properties (except identifier) set.

USER_EMAIL_CONSTRAINT_NAME - Static variable in class ca.corefacility.bioinformatics.irida.model.user.User

USER_ID_KEY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

key used in map when adding user to project.

USER_IN_GROUP - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

USER_ON_PROJECT - Static variable in interface ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Sub-expressions for filtering and paging projects on permissions (via user groups and project membership).

USER_PROJECTS_MAP_LABEL - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

a map label for the projects associated with a user.

USER_ROLE_KEY - Static variable in class ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Key used in map for role when adding user to project

USER_USERNAME_CONSTRAINT_NAME - Static variable in class ca.corefacility.bioinformatics.irida.model.user.User

UserCreateRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Data transfer object for creating a new user account.

UserCreateRequest(String, String, String, String, String, String, String, boolean, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserCreateRequest

UserDetailsModel - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Describes a User in a ant.design table.

UserDetailsModel(User) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsModel

UserDetailsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Returns an AjaxResponse with user details.

UserDetailsResponse(UserDetailsModel, boolean, boolean, boolean, boolean, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserDetailsResponse

UserEditRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Data transfer object for editing user details.

UserEditRequest(String, String, String, String, String, String, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserEditRequest

UserGroup - Class in ca.corefacility.bioinformatics.irida.model.user.group

A collection of User accounts is a UserGroup.

UserGroup(String) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.group.UserGroup

UserGroupDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used to return details about a user group to the UI.

UserGroupDetails(UserGroup, List<UserGroupMember>, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupDetails

UserGroupJoin - Class in ca.corefacility.bioinformatics.irida.model.user.group

A relationship between an individual User account and a UserGroup.

UserGroupJoin(User, UserGroup, UserGroupJoin.UserGroupRole) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin

Create a new UserGroupJoin.

UserGroupJoin.UserGroupRole - Enum in ca.corefacility.bioinformatics.irida.model.user.group

The role of a user in the group

UserGroupJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.user

Repository for working with UserGroupJoin.

UserGroupMember - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used to send information about a user group member to the UI.

UserGroupMember(UserGroupJoin) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupMember

UserGroupProjectJoin - Class in ca.corefacility.bioinformatics.irida.model.user.group

A relationship between a UserGroup and Project.

UserGroupProjectJoin(Project, UserGroup, ProjectRole, ProjectMetadataRole) - Constructor for class ca.corefacility.bioinformatics.irida.model.user.group.UserGroupProjectJoin

Create a new UserGroupProjectJoin.

UserGroupProjectJoinRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.joins.project

Repository for UserGroupProjectJoin.

UserGroupProjectTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Used to send information about a project in a user group to the UI.

UserGroupProjectTableModel(UserGroupProjectJoin, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupProjectTableModel

UserGroupRemovedProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.enums

Event created when a UserGroup is removed from a Project.

UserGroupRemovedProjectEvent(Project, UserGroup) - Constructor for class ca.corefacility.bioinformatics.irida.model.enums.UserGroupRemovedProjectEvent

UserGroupRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.user

A repository for UserGroup.

UserGroupRole - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Represents a user group role in the UI.

UserGroupRole(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupRole

UserGroupRoleSetProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event created when a UserGroup is added or has role changed on a Project.

UserGroupRoleSetProjectEvent(UserGroupProjectJoin) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.UserGroupRoleSetProjectEvent

UserGroupsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.users

Controller for asynchronous request for User Groups

UserGroupsAjaxController(UIUserGroupsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.users.UserGroupsAjaxController

UserGroupsController - Class in ca.corefacility.bioinformatics.irida.ria.web

Controller for interacting with UserGroup.

UserGroupsController(UserGroupService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.UserGroupsController

Create a new groups controller.

UserGroupService - Interface in ca.corefacility.bioinformatics.irida.service.user

Service for working with UserGroups.

UserGroupServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.user

Implementation of UserGroupService.

UserGroupServiceImpl(UserGroupRepository, UserGroupJoinRepository, UserRepository, UserGroupProjectJoinRepository, ProjectSubscriptionService, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.user.UserGroupServiceImpl

Create a new UserGroupServiceImpl.

UserGroupSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Search specification for UserGroup.

UserGroupSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.UserGroupSpecification

UserGroupTableModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Represent a UserGroup in the UI

UserGroupTableModel(UserGroup, boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserGroupTableModel

UserGroupWithoutOwnerException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception thrown when a change to membership of a UserGroup causes that group to have no owner.

UserGroupWithoutOwnerException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.UserGroupWithoutOwnerException

userHasProjectRole(User, Project, ProjectRole) - Method in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

Check if a User has a given ProjectRole on a Project

userHasProjectRole(User, Project, ProjectRole) - Method in interface ca.corefacility.bioinformatics.irida.service.ProjectService

Check if a User has a given ProjectRole on a Project

UserMinimalModel - Class in ca.corefacility.bioinformatics.irida.ria.web.models.user

Minimal model for a User in the UI.

UserMinimalModel(User) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.models.user.UserMinimalModel

UserMixin - Class in ca.corefacility.bioinformatics.irida.jackson2.mixin

This mixin class is used to serialize/deserialize User.

UserMixin() - Constructor for class ca.corefacility.bioinformatics.irida.jackson2.mixin.UserMixin

UserPasswordResetDetails - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.dto

Data transfer object for user's password reset details

UserPasswordResetDetails(String, User) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UserPasswordResetDetails

UserProjectDetailsModel - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

Used to represent user Projects on the UI user account projects page.

UserProjectDetailsModel(ProjectSubscription, ProjectRole) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserProjectDetailsModel

UserRemovedProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event for when a User is removed from a Project

UserRemovedProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent

UserRemovedProjectEvent(Project, User) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent

UserRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.user

Specialized repository for User.

UserRepositoryCustom - Interface in ca.corefacility.bioinformatics.irida.repositories.user

Custom repository methods for UserRepository

UserRepositoryImpl - Class in ca.corefacility.bioinformatics.irida.repositories.user

Custom implementation of UserRepository that throws UsernameNotFoundException.

UserRepositoryImpl(EntityManager) - Constructor for class ca.corefacility.bioinformatics.irida.repositories.user.UserRepositoryImpl

UserRevEntity - Class in ca.corefacility.bioinformatics.irida.repositories.relational.auditing

Envers Revision class storing the timestamp, user, and oauth client used to make a change.

UserRevEntity() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevEntity

UserRevListener - Class in ca.corefacility.bioinformatics.irida.repositories.relational.auditing

UserRevListener() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.relational.auditing.UserRevListener

UserRoleSetProjectEvent - Class in ca.corefacility.bioinformatics.irida.model.event

Event created when a User is added to or has a role changed on a Project.

UserRoleSetProjectEvent() - Constructor for class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

UserRoleSetProjectEvent(ProjectUserJoin) - Constructor for class ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent

UsersAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.users

Handles asynchronous requests for the administration users table.

UsersAjaxController(UIUsersService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.UsersAjaxController

UsersController - Class in ca.corefacility.bioinformatics.irida.ria.web.users

Controller for all User related views

UsersController(UserService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.UsersController

userSecurityInterceptor() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

UserSecurityInterceptor - Class in ca.corefacility.bioinformatics.irida.ria.config

Interceptor Adaptor to add the user to the Model each server call.

UserSecurityInterceptor() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.UserSecurityInterceptor

UserService - Interface in ca.corefacility.bioinformatics.irida.service.user

Customized service for accessing user objects.

UserServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.user

Implementation of the UserService.

UserServiceImpl(UserRepository, AnnouncementUserJoinRepository, ProjectUserJoinRepository, PasswordEncoder, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.user.UserServiceImpl

Constructor, requires a handle on a validator and a repository.

UserSpecification - Class in ca.corefacility.bioinformatics.irida.repositories.specification

Specification for searching a User

UserSpecification() - Constructor for class ca.corefacility.bioinformatics.irida.repositories.specification.UserSpecification

UserStatisticsAjaxController - Class in ca.corefacility.bioinformatics.irida.ria.web.users

Controller for user statistics

UserStatisticsAjaxController(UIUserStatisticsService) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.UserStatisticsAjaxController

UserStatisticsResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.users.dto

UI Response to to encapsulate user statistics.

UserStatisticsResponse(int, int, int) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.users.dto.UserStatisticsResponse

V

VALID_LOCAL_SETTINGS - Variable in class ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl

validate(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AbsoluteToRelativePaths

validate(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedAnalysisToTemplate

validate(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate

validate(Database) - Method in class ca.corefacility.bioinformatics.irida.database.changesets.FastqcToFilesystem

validateClientId(String) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIClientService

Validate a client identifier for a new client

validateClientName(String, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.ClientsAjaxController

Check to see if the client identifier that a user wants to use for a new client is not already used

validateNewSampleName(String, long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Ensure a potential sample name meets criteria

validateNewSampleName(String, Long, Locale) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService

Validate a sample name to ensure can be stored correctly.

validateParameters(JoinPoint) - Method in class ca.corefacility.bioinformatics.irida.validators.ValidMethodParametersAspect

Aspect that matches any method execution in our package with one or more parameters that have the Valid annotation.

ValidateSampleNameModel - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto

Model for UI to represent a sample.

ValidateSampleNameModel(List<Long>, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel

validateSampleNames(Long, ValidateSampleNamesRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.ProjectSamplesAjaxController

Validate a list of samples names

validateSampleNames(Long, ValidateSampleNamesRequest) - Method in class ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService

Validate a list of sample names

ValidateSampleNamesRequest - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto

UI request to validate sample names.

ValidateSampleNamesRequest() - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest

ValidateSampleNamesResponse - Class in ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto

Return a list of sample names.

ValidateSampleNamesResponse(List<ValidateSampleNameModel>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesResponse

validator - Variable in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

validator() - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiServicesConfig

ValidMethodParametersAspect - Class in ca.corefacility.bioinformatics.irida.validators

This aspect automatically invokes a Validator for method parameters annotated with the Valid annotation.

ValidMethodParametersAspect(Validator) - Constructor for class ca.corefacility.bioinformatics.irida.validators.ValidMethodParametersAspect

validMethodsParametersAspect(Validator) - Method in class ca.corefacility.bioinformatics.irida.config.services.IridaApiAspectsConfig

ValidProjectName - Annotation Type in ca.corefacility.bioinformatics.irida.validators.annotations

Custom validation annotation that implements a block-list of unacceptable characters in resources that can be named.

ValidProjectName.ValidProjectNameBlocklist - Class in ca.corefacility.bioinformatics.irida.validators.annotations

Invalid characters in a project name

ValidProjectNameBlocklist() - Constructor for class ca.corefacility.bioinformatics.irida.validators.annotations.ValidProjectName.ValidProjectNameBlocklist

ValidSampleName - Annotation Type in ca.corefacility.bioinformatics.irida.validators.annotations

A collection of patterns that validate the name of a sample.

ValidSampleName.ValidSampleNameBlocklist - Class in ca.corefacility.bioinformatics.irida.validators.annotations

Characters not allowed in a sample name

ValidSampleNameBlocklist() - Constructor for class ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName.ValidSampleNameBlocklist

value - Variable in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

value() - Method in annotation type ca.corefacility.bioinformatics.irida.events.annotations.LaunchesProjectEvent

The type of ProjectEvent that should be created on this annotated method

value() - Method in annotation type ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUser

SpEL expression denoting the user to add to the security context prior to running the annotated method

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.run.SequencingRun.LayoutType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.user.Role

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.pipeline.upload.DataStorage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportTypes

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

Returns the enum constant of this type with the specified name.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisCleanedState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.AnalysisState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.ProjectRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiInstrumentModel

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySelection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus.SyncStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.run.SequencingRun.LayoutType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.sample.QCEntry.QCEntryType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject.ProcessingState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.user.group.UserGroupJoin.UserGroupRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.user.Role

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.DatasetCollectionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.execution.InputFileType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Priority

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.pipeline.upload.DataStorage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerTagType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.activities.ActivityType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportTypes

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiPlatform

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ca.corefacility.bioinformatics.irida.ria.web.models.ModelKeys

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in interface ca.corefacility.bioinformatics.irida.service.AnalysisTypesService

Gets all AnalysisTypes as a Collection.

values() - Method in class ca.corefacility.bioinformatics.irida.service.impl.AnalysisTypesServiceImpl

Gets all AnalysisTypes as a Collection.

valueType - Variable in class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

version() - Method in class ca.corefacility.bioinformatics.irida.web.controller.api.RESTRootController

Creates a response with the current build version.

VersionedFileFields<VersionType extends java.io.Serializable> - Interface in ca.corefacility.bioinformatics.irida.model

An instance of a class may have a property with Version or may have an internally managed version representation.

viewResolver() - Method in class ca.corefacility.bioinformatics.irida.config.web.IridaUIWebConfig

VIRALRNA - ca.corefacility.bioinformatics.irida.model.export.NcbiLibrarySource

visitFile(Path, BasicFileAttributes) - Method in class ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor

visitFileFailed(Path, IOException) - Method in class ca.corefacility.bioinformatics.irida.util.RecursiveDeleteVisitor

W

WAITING - ca.corefacility.bioinformatics.irida.model.enums.ExportUploadState

Waiting for other files to continue processing

WARN - ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.NotificationType

WarnNotification - Class in ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification

Consumed by the UI to display a warning notification.

WarnNotification(String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.WarnNotification

WarnNotification(String, String) - Constructor for class ca.corefacility.bioinformatics.irida.ria.web.components.ant.notification.WarnNotification

WCS - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

WebEmailConfig - Class in ca.corefacility.bioinformatics.irida.config.services

Configuration class for loading properties files.

WebEmailConfig() - Constructor for class ca.corefacility.bioinformatics.irida.config.services.WebEmailConfig

WebEmailConfig.ConfigurableJavaMailSender - Interface in ca.corefacility.bioinformatics.irida.config.services

An extension of JavaMailSender that allows checking to see if it's configured.

WebEmailConfig.ConfigurableJavaMailSenderImpl - Class in ca.corefacility.bioinformatics.irida.config.services

Implementation of WebEmailConfig.ConfigurableJavaMailSender.

WebpackAssetsManifest - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Container for the assets manifest file deserialization

WebpackAssetsManifest(Map<String, WebpackEntry>) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifest

WebpackAssetsManifestDeserializer - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Deserializer for the webpack assets-manifest file

WebpackAssetsManifestDeserializer() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackAssetsManifestDeserializer

WebpackEntry - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Each webpack entry with have at least one JavaScript file, and possibly css files and html (translatons)

WebpackEntry() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntry

WebpackEntryDeserializer - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Deserializer for the webpack manifest file entry.

WebpackEntryDeserializer() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackEntryDeserializer

WebpackerCSSElementTagProcessor - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor

Thymeleaf Tag Processor for elements with the tag `webpack:css` This processor will: - determine which css files need to be loaded from the webpack manifest file.

WebpackerCSSElementTagProcessor(String, WebpackerManifestParser) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerCSSElementTagProcessor

WebpackerDialect - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker

Webpacker Dialect.

WebpackerDialect(boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.WebpackerDialect

WebpackerJavascriptElementTagProcessor - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor

Thymeleaf Tag Processor for webpacker elements.

WebpackerJavascriptElementTagProcessor(String, WebpackerManifestParser) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerJavascriptElementTagProcessor

WebpackerManifestParser - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Responsible for parsing the webpack manifest file and passing along the chunks for js, css, and html resources.

WebpackerManifestParser(boolean) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util.WebpackerManifestParser

WebpackerScriptAttributeTagProcessor - Class in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor

Thymeleaf Tag Processor for elements with the attr `webpack:script="entry_name"` This is a special case handler for when the link to an entry is within an attribute on an element.

WebpackerScriptAttributeTagProcessor(String, WebpackerManifestParser) - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.processor.WebpackerScriptAttributeTagProcessor

WebpackerTagType - Enum in ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.util

Enum for available webpacker tag types

WebpackParserException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Thrown web there is an error parsing the webpack assets-manifest file.

WebpackParserException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WebpackParserException

webSecurityCustomizer() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaWebSecurityConfig.UISecurityConfig

webSecurityExpressionHandler() - Method in class ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

Default DefaultWebSecurityExpressionHandler.

WebStylesConfig - Class in ca.corefacility.bioinformatics.irida.ria.config

Configuration for Ant Design theme styles from properties file.

WebStylesConfig() - Constructor for class ca.corefacility.bioinformatics.irida.ria.config.WebStylesConfig

WEEKLY - ca.corefacility.bioinformatics.irida.model.project.ProjectSyncFrequency

WELCOME_TEMPLATE - Static variable in class ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

WGS - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

withNamedParameters(IridaWorkflowNamedParameters) - Method in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Use the specified set of named parameters to run this workflow.

workflowDescriptionUnmarshaller() - Method in class ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

Sets up an Unmarshaller for workflow objects.

WorkflowException - Exception in ca.corefacility.bioinformatics.irida.exceptions

Exception that gets thrown when there is an issue running a workflow.

WorkflowException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowException

Constructs a new WorkflowException with no information.

WorkflowException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowException

Constructs a new WorkflowException with the given message.

WorkflowException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowException

Constructs a new WorkflowException with the given message and cause.

WorkflowException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowException

Constructs a new WorkflowException with the given cause.

workflowId - Variable in class ca.corefacility.bioinformatics.irida.model.workflow.submission.AbstractAnalysisSubmission

Defines the id of an installed workflow in IRIDA for performing this analysis.

WorkflowInputsGalaxy - Class in ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy

Describes a set of workflow inputs for a Galaxy workflow.

WorkflowInputsGalaxy(WorkflowInvocationInputs) - Constructor for class ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy

Builds a new WorkflowInputsGalaxy to wrap around a WorkflowInputs.

WorkflowInputsGeneric - Interface in ca.corefacility.bioinformatics.irida.model.workflow.execution

Describes a generic set of inputs to a workflow.

WorkflowInvalidException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception thrown if a workflow is invalid.

WorkflowInvalidException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowInvalidException

Constructs a new WorkflowInvalidException with no information.

WorkflowInvalidException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowInvalidException

Constructs a new WorkflowInvalidException with the given message.

WorkflowInvalidException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowInvalidException

Constructs a new WorkflowInvalidException with the given message and cause.

WorkflowInvalidException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowInvalidException

Constructs a new WorkflowInvalidException with the given cause.

WorkflowNamedParametersRepository - Interface in ca.corefacility.bioinformatics.irida.repositories.analysis.submission

Repository for working with named parameter sets.

WorkflowNamedParametersService - Interface in ca.corefacility.bioinformatics.irida.service.workflow

Service for interacting with named parameter sets.

WorkflowNamedParametersServiceImpl - Class in ca.corefacility.bioinformatics.irida.service.impl.workflow

Service for interacting with named parameter sets.

WorkflowNamedParametersServiceImpl(WorkflowNamedParametersRepository, Validator) - Constructor for class ca.corefacility.bioinformatics.irida.service.impl.workflow.WorkflowNamedParametersServiceImpl

WorkflowPreprationException - Exception in ca.corefacility.bioinformatics.irida.exceptions

An exception that gets thrown during the preparation of a workflow.

WorkflowPreprationException() - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowPreprationException

Constructs a new WorkflowPreprationException with no information.

WorkflowPreprationException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowPreprationException

Constructs a new WorkflowPreprationException with the given message.

WorkflowPreprationException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowPreprationException

Constructs a new WorkflowPreprationException with the given message and cause.

WorkflowPreprationException(Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.WorkflowPreprationException

Constructs a new WorkflowPreprationException with the given cause.

workflowsClient() - Method in class ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig

WorkflowUploadException - Exception in ca.corefacility.bioinformatics.irida.exceptions.galaxy

Exception that gets thrown when there is an error uploading a workflow to Galaxy.

WorkflowUploadException(String) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.WorkflowUploadException

Construct a new WorkflowUploadException with the specified message.

WorkflowUploadException(String, Throwable) - Constructor for exception ca.corefacility.bioinformatics.irida.exceptions.galaxy.WorkflowUploadException

Constructs a new WorkflowUploadException with the given message and cause.

write(Path, MediaType, HttpOutputMessage) - Method in class ca.corefacility.bioinformatics.irida.repositories.remote.resttemplate.SequenceFileMessageConverter

writeFile(DataTablesExportTypes, HttpServletResponse, String, List<? extends DataTablesExportable>, List<String>) - Static method in class ca.corefacility.bioinformatics.irida.ria.web.components.datatables.DataTablesExportToFile

Write data within datatable to an excel formatted file.

WXS - ca.corefacility.bioinformatics.irida.model.export.NcbiLibraryStrategy

Y

YEARLY - ca.corefacility.bioinformatics.irida.model.enums.StatisticTimePeriod

Z

ZIPPED - ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object.Fast5Type

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