All Classes

Class	Description
AbsoluteToRelativePaths	Custom SQL change converting absolute paths to relative in the database
AbstractAnalysisSubmission	Abstract superclass for analysis submissions.
AbstractExportModel	Parent class of all export model to hold utility functions.
ActivitiesAjaxController	AJAX controller to handle actitivies
Activity	Model for an Activity (Event).
ActivityItem	Used to create either the subject or the predicate of an activity.
ActivityType	Define specific type activities.
AddSampleMetadataRequest	Used to handle requests from the UI to add a sample metadata.
AddSampleMetadataResponse	Used to handle responses to the UI to add a piece of sample metadata.
AddToCartRequest	Request sent from the UI to add Samples from a Project to the cart.
AdminBaseController	Admin Panel Page Controller
AdminStatisticsAjaxController	Controller to handle ajax requests for the Admin Panel statistics page.
AdminUsersTableRequest	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.
AgGridColumn	AgGrid column is used to represent a generic AgGrid Column
AjaxCreateItemSuccessResponse	UI Response for successfully creating an item.
AjaxErrorResponse	Response returned if there is an error creating a new item in IRIDA.
AjaxFormErrorResponse	AJAX response to return form errors to the client
AjaxItemNotFoundException	Error thrown if an item is not found on an Ajax Request
AjaxResponse	Generic parent response type for AJAX requests.
AjaxSuccessResponse	Response returned if an upload of an item is successful.
AjaxUpdateItemSuccessResponse	UI Response for successfully updating an item.
AnalysesFilters	Represents the filters on the Analyses Table.
AnalysesListRequest	Used to handle a UI Request for the Analyses Page.
AnalysesOutputsAjaxController	Controller for handling all ajax requests for Single Sample Analyses Outputs.
AnalysesTableAjaxController	Controller to handle ajax requests for the Analyses table
Analysis	An analysis object for storing results of an analysis execution.
AnalysisAjaxController	Controller for individual Analysis ajax requests (details page, analysis outputs, project analysis outputs)
AnalysisAlreadySetException	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.
AnalysisAudit	This class component is used for auditing AnalysisSubmission.
AnalysisCleanedState	Defines the state for cleaning up intermediate files of an analysis.
AnalysisCollectionServiceGalaxy	A service for constructing dataset collections of input files for workflows in galaxy.
AnalysisController	Controller for Analysis.
AnalysisDetails	Used as a response for encapsulating analysis details
AnalysisEmailPipelineResult	Used as a request to update if a user should receive email an email upon completion or error..
AnalysisExecutionScheduledTask	A service for executing AnalysisSubmission tasks.
AnalysisExecutionScheduledTaskImpl	Implementation of analysis execution tasks.
AnalysisExecutionService	Service for submission of AnalysisSubmissions to an execution manager.
AnalysisExecutionServiceAspect	Switches an AnalysisSubmission to an error state on an exception when being submitted for analysis.
AnalysisExecutionServiceConfig	Configuration for an AnalysisExecutionService class.
AnalysisExecutionServiceGalaxy	Service for performing analyses within a Galaxy execution manager.
AnalysisExecutionServiceGalaxyAsync	Service for executing AnalysisSubmission stages within a Galaxy execution manager asynchronously.
AnalysisExecutionServiceGalaxyCleanupAsync	Service for cleaning up an AnalysisSubmission within a Galaxy execution manager asynchronously.
AnalysisFastQC	Specific implementation of Analysis for storing properties created by FastQC.
AnalysisFastQC.AnalysisFastQCBuilder	Builder for creating instances of AnalysisFastQC.
AnalysisInfo	Used by UI to encapsulate analysis information
AnalysisInputFiles	Used as a response for encapsulating analysis input files data which includes the samples, reads, and reference file if it was required by workflow
AnalysisJobError	Used as a response for encapsulating galaxy job errors, the url of the galaxy instance, and the galaxy history id.
AnalysisModel	Used to represent an AnalysisSubmission for consumption by the user interface.
AnalysisOutputFile	Store file references to files produced by a workflow execution that we otherwise don't want to parse metadata from.
AnalysisOutputFileDownloadManager	This Spring Bean stores a temporary selection of ProjectSampleAnalysisOutputInfo and AnalysisOutputFile for batch download of the selected files.
AnalysisOutputFileInfo	DTO for AnalysisOutputFile text contents
AnalysisOutputFileRepository	A custom repository for managing AnalysisOutputFile objects.
AnalysisOutputFileRepositoryImpl	Custom implementation of FilesystemSupplementedRepositoryImpl for AnalysisOutputFile.
AnalysisParameterService<WorkflowInputsType extends WorkflowInputsGeneric>	A service for setting up parameters for an analysis.
AnalysisParameterServiceGalaxy	A Galaxy implementation for preparing parameters for an analysis.
AnalysisProjectShare	Represents the update for sharing an analysis with a project.
AnalysisProvenanceResponse	Used as a response for encapsulating the file provenance
AnalysisProvenanceServiceGalaxy	A class used to collect provenance data from Galaxy that corresponds to a specific output file generated by an analysis submission.
AnalysisRepository	A custom repository for managing Analysis objects.
AnalysisSampleProject	Used to return a sample linked to a project to the UI.
AnalysisSamples	Used as a response for encapsulating analysis paired end sample data
AnalysisSampleUpdater	A service for updating samples with results from a particular Analysis type.
AnalysisScheduledTaskConfig	Scheduled task configuration for running analysis pipelines
AnalysisService	Service for managing objects of type Analysis.
AnalysisServiceImpl	Implementation of AnalysisService.
AnalysisSingleEndSamples	Used as a response for encapsulating analysis single end sample data
AnalysisSistrResults	Used as a response for encapsulating a SISTR result object as well as the sample name and if there was a parsing error
AnalysisState	Defines a set of states for an AnalysisSubmission.
AnalysisStateModel	UI Representation of an Analysis Submission state.
AnalysisSubmission	Defines a submission to an AnalysisService for executing a remote workflow.
AnalysisSubmission.Builder	Used to build up an AnalysisSubmission.
AnalysisSubmission.Priority	Enum encoding the priority of analysis submissions
AnalysisSubmissionCleanupService	A service for cleaning up certain aspects of AnalysisSubmissions.
AnalysisSubmissionCleanupServiceImpl	Implementation for a service to cleanup inconsistencies with AnalysisSubmissions.
AnalysisSubmissionInfo	Used as a request to update the analysis name and/or priority.
AnalysisSubmissionRepository	A repository for managing AnalysisSubmission objects.
AnalysisSubmissionRepositoryCustom	Interface for methods using native SQL queries to get AnalysisOutputFile info for Project and User
AnalysisSubmissionRepositoryImpl	Implementation of AnalysisSubmissionRepositoryCustom with methods using native SQL queries to get AnalysisOutputFile info for Project and User
AnalysisSubmissionSampleProcessor	Updates samples from an AnalysisSubmission with results from the analysis.
AnalysisSubmissionSampleProcessorImpl	Updates samples from an AnalysisSubmission with results from the analysis.
AnalysisSubmissionService	A service for AnalysisSubmissions.
AnalysisSubmissionService.AnalysisServiceStatus	Class to store the number of running and queued analyses
AnalysisSubmissionServiceImpl	Implementation of an AnalysisSubmissionService.
AnalysisSubmissionSpecification	Specification for searching AnalysisSubmission properties
AnalysisSubmissionTemplate	Shell for an analysis template to be submitted automatically when data is uploaded to a project.
AnalysisSubmissionTemplateRepository	Repository for storing and retrieving AnalysisSubmissionTemplates
AnalysisTemplate	Response class for easily formatting analysis templates for the project settings page
AnalysisToolExecution	Used as a response for encapsulating the tools used in the provenance as well as the execution parameters for these tools
AnalysisToolExecutionParameters	Used as a response for encapsulating tool execution parameters
AnalysisTreeResponse	Used as a response for encapsulating a newick string and an optional server message.
AnalysisType	Defines a particular type of Analysis available in IRIDA.
AnalysisTypeModel	UI Representation of an Analysis Type
AnalysisTypeSet	A class wrapping around AnalysisType to contain them in a set for Spring configuration.
AnalysisTypesService	A service for managing registered AnalysisTypes.
AnalysisTypesServiceImpl	A service for managing registered AnalysisTypes.
AnalysisWorkspaceService	Defines a service used to perform the tasks for execution of a workflow.
AnalysisWorkspaceServiceGalaxy	A service for performing tasks for analysis in Galaxy.
AnalyticsHandlerInterceptor	Interceptor to add analytics to every page.
Announcement	An announcement object.
AnnouncementAjaxController	Controller for all ajax requests from the UI for announcements.
AnnouncementRepository	Repository for managing Announcements
AnnouncementRequest	Data transfer object for requesting information about an announcement.
AnnouncementsController	Controller for handling Announcement views
AnnouncementService
AnnouncementServiceImpl	Service for managing @{link Announcements}
AnnouncementSpecification	A specification for searching for Announcements
AnnouncementTableModel	User interface model for administration of Announcement
AnnouncementUserJoin	AnnouncementUserJoin object This is created whenever a User has confirmed that they have read an Announcement
AnnouncementUserJoinRepository	Repository for managing AnnouncementUserJoins
AnnouncementUserReadDetails	Data transfer object for retrieving announcement details from a sql query.
AnnouncementUserTableModel	User interface model for viewing Announcement
AntPagination	Class to represent a page request in a AntD Table Request.
AntSearch	Class to represent a single column search in a AntD Table Request.
AntSort	Class to represent a single column sort in a AntD Table Request.
AntTableItem	Base class to be used to represent a row in a AntD table.
AntTableRequest	Table request for an Ant Design UI Table
AntTableResponse<T extends AntTableItem>	Base class to be used to represent a single page in a AntD table.
AssemblySampleUpdater	Updates a sample with the results from a genome assembly.
AssociatedProject	Representation of an Associated Project for the project associated projects page.
AutomatedAnalysisFileProcessor	File processor used to launch an automated analysis for uploaded data.
AutomatedAnalysisToTemplate	Liquibase update to convert the project settings for automated Assembly and SISTR checkboxes to analysis templates.
AutomatedSISTRUpdate	Class to translate automated SISTR analyses into metadata entries for associated samples.
BaseController	Base class for controllers so that they all can have access to common functionality.
BaseModel	Base for UI models
BasePermission<DomainObjectType>	Root interface for any permissions being built within IRIDA.
BasicStatsResponse	UI Response to to encapsulate basic usage statistics.
BioHanselSampleUpdater	AnalysisSampleUpdater for bio_hansel results to be written to metadata of Samples.
BioJavaSequenceFileUtilitiesImpl	Sequence file utilities class using BioJava for calculation
BreadCrumbInterceptor	Interceptor for handling UI BreadCrumbs
BuiltInAnalysisTypes	Stores a number of constants for individual AnalysisTypes.
Cart	Session object to hold samples that are currently in the cart.
CartAjaxController	AJAX controller for cart functionality
CartController	Controller managing interactions with the selected sequences
CartGalaxyController	Controller to handle all ajax requests made to the cart that have to do with Galaxy.
CartProjectModel	Model for UI to represent a project and its sample within the cart.
CartProjectSample	Data transfer object for getting the samples that are in the cart and their relevant project identifier
CartSampleModel	Used to represent a Sample on the UI Cart Page.
CartSampleRequest	Object to handle samples that have been sent to the server to be added to the cart.
CartSamplesByUserPermissions	Data transfer object for getting the samples that are in the cart.
CartUpdateResponse	Return value for adding samples to the samples cart.
ChecksumFileProcessor	FileProcessor used to calculate a checksum using sha256 for uploaded SequenceFiles
CleanupAnalysisSubmissionCondition	Defines an interface for a condition on whether or not to clean up an AnalysisSubmission.
CleanupAnalysisSubmissionConditionAge	A condition used to cleanup an AnalysisSubmission if it is too old.
ClientsAjaxController	Controller to handle ajax request for IRIDA Clients.
ClientTableModel	Used to represent an IridaClientDetails in an ant.design table on the Clients page.
ClientTableRequest	UI request for client details for the clients table.
ConcatenateException	Exception thrown when there's an issue with a SequencingObjectConcatenator
ControllerExceptionHandler	Globally handles exceptions thrown by controllers.
Coverage	UI Model for the minimum and maximum coverage and genome size for a project
CoverageFileProcessor	FileProcessor used to calculate coverage of a SequencingObject for a Projects
CoverageQCEntry	a QCEntry relating to the coverage of a sequence
CreateLibraryException	When there is an issue building a new data library.
CreateNamedParameterSetAjaxResponse	Response for creating a new set of named parameters on the pipeline launch page.
CreateProjectRequest	Data transfer object for creating a new project.
CreateRemoteProjectRequest	Used to capture details about creating a new remote project through the UI
CreateSampleRequest	UI Request to create a new sample
CreateUpdateClientDetails	Used by the UI to send details for a new client.
CRUDService<IdentifierType extends java.io.Serializable,Type extends Timestamped<IdentifierType>>	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>>	A universal CRUD service for all types.
CSVView	Write out CSV files to the client.
CurrentUser	Details about the currently logged in user for use by the UI.
CurrentUserAjaxController	UI Controller to get information about the current user
DashboardController	User Login Page Controller
DataAddedToSampleProjectEvent	Event shown when SequenceFile data is added to a Sample for a Project
DatasetCollectionType	The different types for a dataset collection.
DataStorage	Defines the location of data to upload on a filesystem.
DataTable	Static string used in the ResponseBody for DataTables calls.
DataTablesColumnDefinitions	Responsible for extracting and representing DataTables Columns
DataTablesExportable	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	Used to export datatables to either excel or csv formatted files.
DataTablesExportTypes	This class represents the types of files that can be exported from a datatable.
DataTablesParams	Represents all parameters within a DataTables request.
DataTablesRequest	Annotation for DataTablesParams This is used to handle an ajax request from a client for a DataTables response.
DataTablesRequestResolver	Request resolver for DataTablesParams
DataTablesResponse	This is returned to client in an HttpServletResponse in the format the can be consumed by jQuery DataTables.
DataTablesResponseModel	Responsible for adding a DataTables rowId property to the response.
DateJson	Class containing custom JSON serializers/deserializers for Dates.
DateJson.DateDeserializer	Custom JSON deserializer date from format yyyy-MM-DD.
DateJson.DateSerializer	Custom JSON serializer to format date as yyyy-MM-DD.
DateUtilities	Utilities class to help with date conversions.
DefaultFileProcessingChain	Default implementation of FileProcessingChain.
DeleteGalaxyObjectFailedException	Exception when there is a failure to delete a Galaxy object.
DownloadRequest	Request information to download samples from the project samples table
DTProject	User interface model for DataTables for Project
DTProjectSamples	DataTables response object for ProjectSampleJoin
DuplicateSampleException	If there is more than one SequenceFile from a Sample for a IridaWorkflow.
EmailController	Interface describing methods for emailing information to the user
EmailControllerImpl	This class is responsible for all email sent to the server that are templated with Thymeleaf.
EmailScheduledTaskConfig	Scheduled taks configuration for sending digest emails
EntityExistsException	When an entity to be created in the database shares an identifier with an existing entity.
EntityNotFoundException	When an entity cannot be found in the database.
EntriesResponse	Response for linelist to include total count
ErrorNotification	Consumed by the UI to display an error notification.
ErrorResponse	Error message response class to be serialzed to Json and returned from the ControllerExceptionHandler
ExcelCol	Used as a response for encapsulating excel column data
ExcelData	Used as a response for encapsulating parsed excel file data
ExcelHeader	Used as a response for encapsulating excel header column data
ExcelRow	Used as a response for encapsulating excel parsed row data
ExceptionPropertyAndMessage	Class storing a property name and a message name to display if the property is in error.
ExceptionUtilities	Utilities class for Exception handling.
ExecutionManager	Defines an ExecutionManager for executing a workflow.
ExecutionManagerConfig	Configuration for connections to an ExecutionManager in IRIDA.
ExecutionManagerConfigurationException	An exception that gets thrown for an invalid configuration option for an execution manager.
ExecutionManagerDownloadException	Thrown when there is an issue downloading data from an execution manager.
ExecutionManagerException	Exception that gets thrown when dealing with data or workflows from an external execution manager (e.g.
ExecutionManagerGalaxy	Defines an ExecutionManager Galaxy implementation for interacting with Galaxy.
ExecutionManagerObjectNotFoundException	Exception thrown if an object is not found by the execution manager
ExecutorConfig	Configuration for a task executor for running scheduled tasks.
ExistingSampleNameException	Exception thrown when trying to add a Sample to a Project with a duplicate sample name
ExportFormatException	Exception thrown when attempting to export a table with an unknown format.
ExportToFileModel	Used the get the form details submitted via a post to export samples to a CSV.
ExportUploadService	Class which handles uploading a NcbiExportSubmission to NCBI
ExportUploadState	Status of an NcbiExportSubmission.
Fast5Object	SequencingObject implementation for storing .fast5 files.
Fast5Object.Fast5Type	Type of file stored buy this fast5 object
Fast5ObjectRemoteRepository	Repository for synchronizing Fast5Object from a RemoteAPI
Fast5ObjectRemoteRepositoryImpl	A repository implementaion for reading Fast5Object from remote locations using a OAuthTokenRestTemplate
Fast5ObjectRemoteService	A service for reading Fast5Objects from a remote location
Fast5ObjectRemoteServiceImpl	An implementation of Fast5ObjectRemoteService using a Fast5ObjectRemoteRepository to read remote Fast5Object
FastaView	Write out FASTA formatted sequence files to the client.
FastQCDetailsResponse	Used by UI to encapsulate fastqc details.
FastqcFileProcessor	Executes FastQC on a SequenceFile and stores the report in the database.
FastQCImagesResponse	Used by UI to encapsulate fastqc images data.
FastqcToFilesystem	Liquibase update class for moving the fastqc analysis results off the AnalysisFastQC class (and out of the database).
FastqView	Write out FASTQ formatted sequence files to the client.
FieldUpdate	Used by UI when any field needs to have its value updated.
FileProcessingChain	A collection of FileProcessor that are executed, in order, on a specific SequencingObject.
FileProcessingScheduledTaskConfig	Scheduled task configuration for running file processors
FileProcessor	Responsible for processing a SequenceFile after the file has been uploaded to the server.
FileProcessorErrorQCEntry	QCEntry for a failed FileProcessor
FileProcessorException	Exception thrown when a FileProcessor fails to complete execution.
FileProcessorTimeoutException	Thrown when the FileProcessingChain waits longer than a specified timeout for the SequencingObjectService to finish executing its transaction.
FileSizeConverter	Converts a files size (originally in bytes) to Kilobytes
FilesystemSupplementedRepository<Type extends VersionedFileFields<java.lang.Long> & IridaThing>	Custom implementation interface for writing the Path part of a SequenceFile to disk.
FilesystemSupplementedRepositoryImpl<Type extends VersionedFileFields<java.lang.Long> & IridaThing>	Custom implementation of a repository that writes the Path part of an entity to disk.
FilesystemSupplementedRepositoryImpl.RelativePathTranslatorListener	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.
FileUtilities	Download a zip archive of all output files within an AnalysisSubmission
FileUtils	A class containing a number of utilities for dealing with files.
ForbidJpqlUpdateDeletePostProcessor	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.
Formats	This class is responsible for holding the formats of different Strings (e.g.
GalaxyAccountEmail	A GalaxyAccount object for storing credentials for an account in Galaxy.
GalaxyDatasetException	This exception is thrown when there is an error obtaining a Galaxy dataset.
GalaxyDatasetNotFoundException	Exception thrown if a given dataset is not found in galaxy
GalaxyExportAuthentication	UI Model to hold whether the current galaxy client has a valid security token.
GalaxyExportSample	UI Model to return sample links in the format that galaxy expects:
GalaxyHistoriesService	Class for working with Galaxy Histories.
GalaxyJobErrorsService	Class to create new JobError objects using a Galaxy HistoriesClient, ToolsClient and JobsClient if an error occurred during an Galaxy pipeline AnalysisSubmission.
GalaxyLibrariesService	A service class for dealing with Galaxy libraries.
GalaxyOutputsForWorkflowException	An exception in getting outputs from Galaxy for a workflow.
GalaxyProjectName	A name for a Galaxy project (Library) used for checking the validity of the name.
GalaxyRedirectionEndpointController	Controller for handling OAuth2 authorization codes for the Galaxy exporter
GalaxySessionInterceptor	Interceptor to determine if the HttpServletRequest is from a Galaxy Instance.
GalaxyToolDataService	A service class for dealing with Galaxy Tool Data Tables.
GalaxyToolDataTableException	An exception that gets thrown when there a problem accessing a Galaxy Tool Data Table.
GalaxyWorkflowService	Handles operating with workflows in Galaxy.
GalaxyWorkflowState	Defines the state of a workflow.
GalaxyWorkflowStatus	Defines the status of a workflow.
GalaxyWorkflowStatus.GalaxyWorkflowStatusBuilder	Used to build a GalaxyWorkflowStatus from the underlying Galaxy objects.
GenbankView	Write out GenBank formatted sequence files to the client.
GenericsException	An exception that can be used when the RESTGenericController fails to construct a resource.
GenericStatModel	Used to represent the time period and counts for statistics.
GenomeAssembly	Defines a genome assembly which can be associated with a sample.
GenomeAssemblyFromAnalysis	Defines a genome assembly from an IRIDA-based analysis.
GenomeAssemblyRemoteRepository	Repository for synchronizing GenomeAssembly from a RemoteAPI
GenomeAssemblyRemoteRepositoryImpl	A repository implementaion for reading GenomeAssembly from remote locations using a OAuthTokenRestTemplate
GenomeAssemblyRemoteService	A service for reading UploadedAssemblys from a remote location
GenomeAssemblyRemoteServiceImpl	An implementation of GenomeAssemblyRemoteService using a GenomeAssemblyRemoteRepository to read remote GenomeAssembly
GenomeAssemblyRepository	A repository for storing and retrieving GenomeAssembly entities
GenomeAssemblyRepositoryImpl	A FilesystemSupplementedRepositoryImpl implementation for GenomeAssembly
GenomeAssemblyService	A service for storing and retrieving GenomeAssembly entities.
GenomeAssemblyServiceImpl	Service implementation for storing and retrieving GenomeAssembly
GzipFileProcessor	Handle gzip-ed files (if necessary).
HttpHeadFilter	Servlet filter that presents a HEAD request as a GET.
InfoNotification	Consumed by the UI to display an information notification.
InMemoryTaxonomyService	A TaxonomyService leveraging Apache Jena's in memory storage service and Apache Lucene's text searching abilities.
Input	Used in the UI to render a Irida Workflow Pipeline Parameter option
InputFileType	Defines acceptable file types for input to a workflow.
InputWithOptions	Represents a IRIDA Workflow Pipeline Parameter that has specific options to be rendered within the UI.
InvalidPropertyException	Thrown when a property cannot be set or retrieved by a service class.
IridaAccountDisabledException	Thrown when a password reset is requested by a user whose account is disabled
IridaAnalysisTypesServiceConfig	Class to load up AnalysisTypesService.
IridaApiAspectsConfig	Configures the aspects in IRIDA
IridaApiFilesystemRepositoryConfig	Configuration for filesystem repositories in IRIDA
IridaApiJdbcDataSourceConfig	Configuration for IRIDA's JDBC Datasource
IridaApiJdbcDataSourceConfig.ApplicationContextAwareSpringLiquibase	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.
IridaApiPropertyPlaceholderConfig	Configuration class for loading properties files.
IridaApiRepositoriesConfig	Configuration for repository/data storage classes.
IridaApiSecurityConfig	Configuration for IRIDA's spring security modules
IridaApiServicesConfig	Configuration for the IRIDA platform.
IridaApiServicesConfig.IridaLocaleList	Inner class storing the enabled locales for IRIDA
IridaApplication	Entry point to Spring Boot application
IridaClientDetails	Object representing a client that has been registered to communicate with this API via OAuth2
IridaClientDetailsRepository	Repository for storing and retriving IridaClientDetails.
IridaClientDetailsService	Service for storing and reading IridaClientDetails objects
IridaClientDetailsServiceImpl	Service for storing and retrieving IridaClientDetails object.
IridaClientDetailsSpecification	Specification class for IridaClientDetails
IridaCustomExceptionHandler	Exception Handler for when a user is navigating around in the web interface.
IridaEnvironmentPostProcessor	EnvironmentPostProcessor to translate deprecated properties into valid properties.
IridaJpaRepository<Type,Identifier extends java.io.Serializable>	Repository type that extends PagingAndSortingRepository, JpaSpecificationExecutor, and RevisionRepository.
IridaOAuth2AuthorizationService	A customized version of JdbcOAuth2AuthorizationService that adds a method to find OAuth2Authorizations with OAuth2AccessTokens for a specific RegisteredClient.
IridaOAuthErrorHandler	Error handler for use in OAuthTokenRestTemplate.
IridaOAuthException	Exception thrown when attempting to read from a remote API via OAuth2 fails.
IridaOauthSecurityConfig	Configuration for REST API security using OAuth2
IridaOauthSecurityConfig.AuthorizationServerConfig	Class for configuring the OAuth authorization server
IridaOauthSecurityConfig.JWKConfig	Class for configuring the JSON Web Key for JSON Web Tokens used in OAuth2
IridaOauthSecurityConfig.ResourceServerConfig	Class for configuring the OAuth resource server security
IridaPermissionEvaluator	Custom permission evaluator to determine whether or not an authenticated user has authorization to view or modify a resource.
IridaPlugin	Interface describing the methods which must be exposed by an IRIDA pipeline plugin
IridaPluginConfig	Configuration file for loading IRIDA plugins
IridaPluginException	An exception thrown when initializing IRIDA pipelines
IridaPluginMessageSource	A MessageSource used to store and search through MessageSources for IRIDA Plugins.
IridaPostAuthenicationChecker	Expired credentials should be ignored when a user is trying to change their password.
IridaPostAuthenticationFailureHandler	AuthenticationFailureHandler used to handle specific AuthenticationException's.
IridaRegisteredClientsRepository	A converter implementation of RegisteredClientRepository, that transforms IridaClientDetails to/from RegisteredClient.
IridaRepresentationModel	Adds a collection of Links to extending objects.
IridaRestApiWebConfig	Configuration for IRIDA REST API.
IridaScheduledTasksConfig	Config for only activating scheduled tasks in certain profiles.
IridaSequenceFile	Describes fields that must be made available for a Sequence File in IRIDA
IRIDASettingsAjaxController	Handles asynchronous requests for IRIDA settings.
IridaThing	An interface for all model classes in the IRIDA system.
IridaToolParameter	A parameter for a particular tool in a workflow.
IridaUIWebConfig
IridaWebSecurityConfig	Configuration for web security using OAuth2
IridaWebSecurityConfig.UISecurityConfig	UI security config for IRIDA
IridaWorkflow	Describes a workflow for IRIDA.
IridaWorkflowAnalysisTypeException	Exception for when there is an issue building a particular Analysis type.
IridaWorkflowDefaultException	Exception that gets thrown when attempting to set a default workflow for an analysis type that already has a default workflow set.
IridaWorkflowDescription	Class providing access to generic information about a workflow.
IridaWorkflowDynamicSourceGalaxy	Class providing access to information about a Dynamic Parameter Source that is supplied by Galaxy.
IridaWorkflowException	Exception that gets thrown for any Irida workflows.
IridaWorkflowIdSet	A class wrapping around a Set of UUIDs for IRIDA workflows.
IridaWorkflowInput	Defines the input labels for a workflow.
IridaWorkflowLoaderService	Used to load up IRIDA workflows.
IridaWorkflowLoadException	An exception that gets thrown when attempting to load a workflow.
IridaWorkflowNamedParameters	Users can create, save, and re-use named parameters in their workflow submissions.
IridaWorkflowNoParameterException	Defines an exception in cases of no parameters within an IRIDA workflow.
IridaWorkflowNotDisplayableException	Exception that gets thrown if a workflow is not displayable.
IridaWorkflowNotFoundException	Exception that gets thrown if a workflow is not found.
IridaWorkflowOutput	Defines the output files and file names for a workflow.
IridaWorkflowParameter	Defines input parameters for a workflow which can be adjusted.
IridaWorkflowParameterChoice	Defines a valid choice for a parameter of a workflow.
IridaWorkflowParameterException	Defines an exception for parameters within an IRIDA workflow.
IridaWorkflowsConfig	Class used to load up test workflows.
IridaWorkflowSet	Wraps around a Set of IridaWorkflows to allow it to be handled as a spring managed bean.
IridaWorkflowsService	Class used to load up installed workflows in IRIDA.
IridaWorkflowStructure	Defines the structure of a workflow for IRIDA.
IridaWorkflowToolRepository	Defines a Galaxy ToolShed repository containing dependency tools for a workflow.
JobError	Galaxy Job failure information when a tool in a IRIDA workflow produces an error state for an AnalysisSubmission
JobErrorRepository	A repository for managing JobError objects
Join<SubjectType extends IridaThing,ObjectType extends IridaThing>	Interface that the join classes should extend.
LabelledRelationshipResource<Owner extends IridaThing,Child extends IridaThing>	An implementation of a resource that only has a label and an identifier.
Latitude	Validates geographic latitude coordinate values.
LatitudeValidator	Validator for validating latitude portion of a geographic coordinate.
LaunchAjaxController	Controller to handle AJAX requests from the UI for Workflow Pipelines
LaunchController	Controller for workflow launch pages.
LaunchesProjectEvent	Annotation to be put on methods which should create a ProjectEvent.
LaunchRequest	Information required to launch a IRIDA Workflow Pipeline
LaunchSample	Represents a sample within the cart on the pipeline launch page.
LineListController	This controller is responsible for AJAX handling for the line list page, which displays sample metadata.
LinkNotFoundException	Exception thrown when there is no link for a given rel when reading from an API
ListItem	Generic List item for UI responses.
ListResourceWrapper<Type extends IridaRepresentationModel>	Object wrapping a list of returned resources from a remote IRIDA API.
Locale	Stores locale info.
LoginController
LoginSuccessHandler	Handles actions for when a user is successfully logged in.
Longitude	Validates geographic longitude coordinate values.
LongitudeValidator	Validator for validating longitude portion of a geographic coordinate.
ManageLocalProjectSettingsPermission	Permission checking if a user can update local project settings
MergeRequest	DTO to handle merging 2 samples
MetadataAjaxController	Ajax controller for project metadata templates.
MetadataEntry	Class for storing generic metadata for a Sample
MetadataEntryRepository	Repository for saving and reading MetadataEntry
MetadataEntryRepositoryCustom	Custom repository methods for retrieving MetadataEntrys
MetadataEntryRepositoryImpl	Implementation of the custom methods for retrieving MetadataEntry
MetadataFieldRepository	A repository for storing and reading MetadataTemplateFields
MetadataFieldRepositoryCustom	Custom repository methods for getting MetadataTemplateFields
MetadataFieldRepositoryImpl	Custom repository methods for getting MetadataTemplateFields
MetadataImportFileTypeNotSupportedError	Exception to be thrown if the upload metadata file does not match any of the predetermined formats.
MetadataRestriction	A class to define restrictions on which metadata fields can be viewed by a ProjectRole on a Project
MetadataRestrictionRepository	Interface for storing and retrieving MetadataRestriction
MetadataRoleValidate	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	Stores a collection of MetadataTemplateFields that will often used together
MetadataTemplateField	Describes an individual field in a MetadataTemplate.
MetadataTemplateRepository	A repository for storing and reading MetadataTemplates
MetadataTemplateService	Service for managing MetadataTemplates and related Projects
MetadataTemplateServiceImpl	Service for storing and reading MetadataTemplates
MethodEvent	Captures the arguments and return value of a method call.
MinimalModel	Basic implementation for items that want to return a smaller model to the UI Usually should stay as just name and id.
MissingRequiredParametersException	This exception is thrown if a pipeline is attempted to be launched that has required parameters that haven't been provided
ModelKeys	Use as prefixes when generating UI model keys.
ModifyProjectPermission	Superclass permission whether a user can modify project settings.
MutableIridaThing	An object that can be modified
NCBIAjaxController	Spring Ajax Controller to handle NCBI requests.
NcbiBioSampleFiles	SequenceFiles and SequenceFilePairs associated with a NcbiExportSubmission.
NcbiBioSampleFiles.Builder	Builder class for NcbiBioSampleFiles
NcbiBioSampleModel	Describes an NCBI SRA Submission's BioSample's files for the UI.
NcbiExportSubmission	Class storing a request to upload sequence data to NCBI.
NcbiExportSubmissionAdminTableModel	Represents a NcbiExportSubmission for viewing by an Administrator.
NcbiExportSubmissionRepository	Repository for storing and reading NcbiExportSubmissions
NcbiExportSubmissionService	Service for exporting SequenceFile data to NCBI
NcbiExportSubmissionServiceImpl	Service impl for submitting data to NCBI
NcbiExportSubmissionTableModel	Represents a NcbiExportSubmission for use within the UI.
NcbiInstrumentModel	 * Instrument model for NCBI Upload.
NcbiLibrarySelection	Library selection of an ncbi export
NcbiLibrarySource	Library source of an NCBI export
NcbiLibraryStrategy	Library strategy of an ncbi export
NcbiPlatform	List of all available NCBI Platforms
NcbiPlatformInstrumentModel	Represents the relationship between sequencing platforms and instruments allowed by NCBI
NCBISubmission	A group definition for fields that are required when submitting to NCBI repositories.
NcbiSubmissionModel	Describes an NCBI SRA Submission for the UI
NCBISubmissionOneOf	NCBI defines some attributes as a "one-of" must not be null.
NcbiSubmissionRequest	Request for submitting to the NCBI SRA
NcbiSubmissionSample	Represents a sample in a NcbiSubmissionRequest
NcbiUploadScheduledTaskConfig	Scheduled task configuration for uploading to NCBI
NcbiXmlParseException	Exception thrown when there's an error parsing NCBI responses
NewickFileView	Write out Newick formatted tree files to the client.
NewMemberRequest	Used to send information to the server about a user to be added as a project member
NewProjectMetadataRestriction	Helper class when creating a project with samples from the cart to indicate which restriction level the metadata attached should have.
NGSLinkerAjaxController	Controller to handle asynchronous request for the ngs-linker
NGSLinkerCmdRequest	Data transfer object for creating a command for the ngs-linker.pl
NGSLinkerService	Service for converting data for creating the ngs-linker command.
NoGalaxyHistoryException	An exception that gets thrown when there is no history in Galaxy that can be found.
NoPercentageCompleteException	An exception that gets thrown when no percentage complete exists for an AnalysisSubmission.
NoSuchValueException	Exception thrown when attempting to access a value that does not currently exist.
Notification	Abstract class to represent an Ant Design UI notification.
NotificationType	Different types of notification found in Ant Design
OAuth2ResourceOwnerPasswordAuthenticationConverter	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.
OAuth2ResourceOwnerPasswordAuthenticationProvider	An AuthenticationProvider impementation for the OAuth 2.0 Resource Owner Password Credentials Grant.
OAuth2ResourceOwnerPasswordAuthenticationToken	An Authentication implementation used for the OAuth 2.0 Resource Owner Password Credentials Grant.
OAuthTokenRestTemplate	Rest Template used to communicate with OAuth2 enabled REST APIs.
OltuAuthorizationController	Controller for handling OAuth2 authorizations
OpenAPIConfig	Configuration for IRIDA REST API documentation.
OverrepresentedSequence	A SequenceFile may have 0 or more over-represented sequences.
PagedListResponse	UI Response for returning a paged list to the UI.
PairedEndSequenceFileModel	Describes a SequenceFilePair for the UI
ParameterBuilderGalaxy	A class used to build up the parameter data structures used for Galaxy.
ParameterBuilderGalaxy.ParameterId	An id for a particular parameter.
PasswordExpiryChecker	Checks whether a user's password has changed within the configured expiry time.
PasswordReset	A password reset object.
PasswordResetAjaxController	Handles asynchronous requests for password resets.
PasswordResetController	Controller for handling password reset flow
PasswordResetRepository	A repository to store password resets for a user.
PasswordResetService	Service for managing PasswordReset entities.
PasswordResetServiceImpl	Implementation for managing PasswordReset
PasswordReusedException	Thrown when a user attempts to update a password with one they've already used.
PathConverter	Converts a Path to a String before persisting a value to a column in a database.
PathJson	Serialization class for java Path objects.
PathJson.PathSerializer	Serializer for Java Path objects.
Pipeline	Analysis Workflow pipeline for consumption by the UI.
PipelineController	Controller for pipeline related views
PipelineProvidedMetadataEntry	MetadataEntry that has been created by an analysis pipeline
PostProcessingException	Exception thrown when a AnalysisSampleUpdater fails during post processing
PreparedWorkflow<WorkflowInputsType extends WorkflowInputsGeneric>	A Workflow that has been prepared for execution.
PreparedWorkflowGalaxy	A Galaxy workflow that has been prepared for execution.
Priorities	UI model for the priority and available priorities for a projects automated pipelines
Project	A project object.
ProjectAnalysisSubmissionJoin	Join connection between an AnalysisSubmission and Project
ProjectAnalysisSubmissionJoinRepository	repository for storing and reading ProjectAnalysisSubmissionJoins
ProjectAssociatedProjectsAjaxController	Ajax Controller for handling associated projects
ProjectCartSample	This class is USED ONLY for when a user selects all sample to be added to the cart from the project samples page.
ProjectControllerUtils	Common functions for project related controllers
ProjectCurrentUserModel	Details about how the current user can interact with a specific project
ProjectDetailsAjaxController	Handle asynchronous requests for the UI project details page.
ProjectDetailsResponse	Encapsulates information about the project as well as permissions.
ProjectEvent	Class storing events that happen on a Project.
ProjectEventAspect	Aspect used to create project events for methods annotated with event annotations
ProjectEventEmailScheduledTask	Scheduled task for emailing new ProjectEvents to Users
ProjectEventEmailScheduledTaskImpl	Implementation of ProjectEventEmailScheduledTask which sends emails to users when they have new events
ProjectEventHandler	Handles the creation of ProjectEvents from methods annotated with LaunchesProjectEvent
ProjectEventRepository	Repository for storing events that occurred on a project
ProjectEventService	Service for reading and managing ProjectEvents
ProjectEventServiceImpl	Implementation of ProjectEventService using a ProjectEventRepository
ProjectHashingService	Component used to compute a deep hashcode of a full project.
ProjectHashResource	Resource class for storing a full project hash for the REST API
ProjectLineListController	Handles requests for the metadata in a project
ProjectMembersAjaxController	Controller for all asynchronous request from the UI for Project Members
ProjectMemberTableModel	Represents a Project member in the UI.
ProjectMetadataField	A representation of a MetadataTemplateField specifically for a project.
ProjectMetadataResponse	Object grouping a project and all the metadata for samples within that project.
ProjectMetadataRole	Role for a user's level of metadata access for a project.
ProjectMetadataRoleValidator	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.
ProjectMetadataTemplate	Used to represent a project metadata template in the UI.
ProjectMinimalModel	Minimal model for a Project in the UI
ProjectModel	Representation of a Project used in the UI Projects listing table.
ProjectObject	Representation of a Project used in the Project Samples table.
ProjectOwnerPermission	Confirms that a given user is the owner of a project
ProjectReferenceFileController	Controller for ajax request dealing with project reference files.
ProjectReferenceFileJoin	Join-type relating Project to ReferenceFile.
ProjectReferenceFileJoinRepository	Repository for interacting with ProjectReferenceFileJoin.
ProjectRemoteRepository	Service for reading Project objects from a remote IRIDA API
ProjectRemoteRepositoryImpl	Remote repository for retrieving Projects from RemoteAPIs
ProjectRemoteService	Service for reading Project objects from a remote IRIDA API
ProjectRemoteServiceImpl	Remote service for retrieving Projects
ProjectRepository	Specialized repository for Project.
ProjectRepositoryCustom	Custom repository methods for Projects
ProjectRepositoryImpl	Implementation of custom repository methods for Projects
ProjectRole	Roles for users accessing projects.
ProjectsAjaxController	Controller for handling all ajax requests for Projects.
ProjectSampleAnalysisOutputInfo	Class to store basic AnalysisOutputFile and associated Sample, Project and AnalysisSubmission information from a native SQL query.
ProjectSampleJoin
ProjectSampleJoinRepository	Repository for managing ProjectUserJoin.
ProjectSampleJoinSpecification	Specification for searching ProjectSampleJoins
ProjectSampleMetadataAjaxController	This class is designed to be used for bulk actions on MetadataEntry within a Project.
ProjectSampleModel	Used for exporting the project samples table.
ProjectSamplesAjaxController	AJAX Controller for handling asynchronous requests for project samples.
ProjectSamplesFilter	DTO to handle filtering samples in a project
ProjectSamplesMetadataTemplateController	Handles requests for MetadataTemplates in a Project
ProjectSamplesTableRequest	DTO for representing a page request in the Project Samples table
ProjectSampleTableItem	Representation of a row used in the Project Samples table.
ProjectsController	Controller for project related views
ProjectService	A specialized service layer for projects.
ProjectServiceImpl	A specialized service layer for projects.
ProjectSettingsAjaxController	Controller to handle all asynchronous call from the project settings UI.
ProjectSettingsRemoteAjaxController	Controller for managing settings for a remotely sync'd project asynchronously
ProjectSubscription	Class for storing email subscriptions to Projects for Users .
ProjectSubscriptionRepository	Repository for storing, removing, and retrieving ProjectSubscriptions
ProjectSubscriptionsAjaxController	Controller for handling AJAX requests for ProjectSubscription
ProjectSubscriptionService	A specialized service layer for project subscriptions.
ProjectSubscriptionServiceImpl	A specialized service layer for project subscriptions.
ProjectSyncFrequency	Describes how often a project should be synchronized by a remote api
ProjectSynchronizationAuthenticationToken	An authentication token used to identify when an action is being taken during project synchronization.
ProjectSynchronizationException	An exception thrown when there is an error synchronizing a project.
ProjectSynchronizationService	Service class to run a project synchornization task.
ProjectSyncScheduledTaskConfig	Scheduled task configuration for synchronizing projects from other IRIDA installations
ProjectUserGroupsAjaxController	UI Ajax Controller for handling project user groups
ProjectUserGroupsTableModel	UI Model for user groups that are associated with a project
ProjectUserJoin	A join table and class for users and projects.
ProjectUserJoinRepository	A repository for ProjectUserJoin.
ProjectWithoutOwnerException	Exception thrown if role change is not allowed
QCEntry	Abstract class describing quality control entries for a SequencingObject
QCEntry.QCEntryStatus	Status of a QCEntry, whether checks are positive, negative, or can't be calculated.
QCEntry.QCEntryType	The type of QCEntry
QCEntryRepository	Repository for saving and retrieving QCEntry objects
ReadAnalysisPermission	Confirms if a User can read a Analysis.
ReadAnalysisSubmissionPermission	Confirms if a User can read a AnalysisSubmission.
ReadExportSubmissionPermission	Whether or not a User can read a given NcbiExportSubmission
ReadMetadataEntryPermission	Permission for reading individual MetadataEntry for a sample
ReadMetadataTemplatePermission	Permission for reading MetadataTemplate
ReadProjectMetadataResponsePermission	Permission for checking that a user should have access to the given MetadataTemplateFields in a ProjectMetadataResponse.
ReadProjectPermission	Confirms that the authenticated user is allowed to read a project.
ReadReferenceFilePermission	Permission testing if a given user can read a given reference file.
ReadSamplePermission	Confirms that the authenticated user is allowed to read a sample.
ReadSequencingObjectPermission	Evaluate whether or not a user can read a SequencingObject
ReadSequencingRunPermission	Permission allowing a user to read a SequencingRun
RecursiveDeleteVisitor	Delete an entire directory structure recursively.
ReferenceFile	A reference file to be associated with a Project.
ReferenceFileAjaxController	Controller for ajax actions for reference files
ReferenceFileRepository	Repository for interacting with ReferenceFile.
ReferenceFileRepositoryImpl	Custom implementation of FilesystemSupplementedRepositoryImpl for ReferenceFile.
ReferenceFileRequiredException	This exception is thrown if a pipeline is attempted to be launched that requires a reference file, but does not have one.
ReferenceFileService	Interface for interactions with ReferenceFile.
ReferenceFileServiceImpl	Service for storing and reading ReferenceFile objects
RelatedProjectJoin	Relationship between two Projects.
RelatedProjectRepository	Repository for managing RelatedProjectJoins
RemoteAPI	Description of a remote Irida API that this API can communicate with via OAuth2
RemoteAPIAjaxController	Controller for asynchronous requests for remote api functionality.
RemoteAPIController	Controller handling basic operations for listing, viewing, adding, and removing RemoteAPIs
RemoteAPIModel	UI Model to represent the details of a RemoteAPI
RemoteAPIRepository	A repository to store RemoteAPI instances that this IRIDA instance can connect to
RemoteAPIService	Service for storing and retrieving RemoteAPIs that this API can connect to
RemoteAPIServiceImpl	Service implementation for storing and retrieving RemoteAPI objects from a RemoteAPIRepository
RemoteAPISpecification	Specification class for RemoteAPI
RemoteAPITableAdminModel	Represents a RemoteAPI in the Remote API table.
RemoteAPITableModel	Represents a RemoteAPI in the Remote API table.
RemoteAPIToken	OAuth2 token for communicating with a RemoteAPI for a given User
RemoteApiTokenRepository	Repository for storing an reading RemoteAPITokens
RemoteAPITokenService	Service for saving and reading tokens for Remote APIs
RemoteAPITokenServiceImpl	Service implementation for storing and reading remote api tokens
RemoteFileNotCachedException	Exception thrown when a remote file is attempted to be used before it has been cached locally.
RemoteProjectModel	Used to represent a remote project for selecting from available remote projects in the create remote synchronized project form
RemoteProjectSettings	Used as a response for encapsulating a remote synchronized project settings
RemoteProjectSettingsUpdateRequest	Used to handle requests from the UI to update settings for a remote sync'd project.
RemoteRepository<Type extends IridaRepresentationModel>	A repository for storing and retrieving objects from a remote api
RemoteRepositoryImpl<Type extends IridaRepresentationModel>	Remote repository to request from remote IRIDA instances using OAuthTokenRestTemplates
RemoteService<Type extends IridaRepresentationModel & IridaThing>	Service for communicating with a remote IRIDA instance
RemoteServiceImpl<Type extends IridaRepresentationModel & IridaThing>	Remote service to request from remote IRIDA instances using OAuth2
RemoteStatus	Information about an entity that was copied from a remote api.
RemoteStatus.SyncStatus	The status of the synchronized object
RemoteSynchronizable	Marks an object which can be synchronized from a RemoteAPI
RemoveSamplesRequest	DTO for removing samples from a project
RepositoryBackedPermission<DomainObjectType,IdentifierType extends java.io.Serializable>	Superclass for permissions on objects which can be read from a CrudRepository.
ResourceAdditionalProperties<Type extends IridaRepresentationModel>	Class to be used when returning additional properties about a model object via the REST API.
ResourceCollection<Type>	Wraps a collection of ResourceCollection objects to be sent to the client.
ResourceList<Type extends IridaRepresentationModel>	Class to hold a list of resources when being read from a remote Irida API
ResourceWrapper<Type extends IridaRepresentationModel>	Object wrapping a resource read from an Irida API
ResponseDetails	Used as a response for ajax result
ResponseProjectResource<Type>	The resource for displaying the API project response.
ResponseResource<Type>	The resource for displaying the API responses.
RESTAnalysisSubmissionController	REST controller to manage sharing of AnalysisSubmission, Analysis, and AnalysisOutputFile classes.
RESTGenericController<Type extends IridaRepresentationModel & IridaThing & java.lang.Comparable<Type>>	A controller that can serve any model from the database.
RESTOAuthAuthorizationConsentController	Controller class for serving custom OAuth2 authorization consent pages
RESTProjectAnalysisController	Controller for managing relationships between Project and AnalysisSubmission.
RESTProjectSamplesController	Controller for managing relationships between Project and Sample.
RESTProjectsController	Controller for managing Projects in the database.
RESTProjectUsersController	Controller for managing relationships between Project and User.
RESTRootController	A basis for clients to begin discovering other URLs in our API.
RESTSampleAssemblyController	Controller for viewing and downloading assemblies for samples
RESTSampleMetadataController	REST controller to handle storing and retrieving metadata from a Sample
RESTSampleSequenceFilesController	Controller for managing relationships between Sample and SequenceFile.
RESTSequencingRunController
RESTSequencingRunSequenceFilesController
RESTUsersController	Controller for managing users.
Role	Roles for authorization in the application.
Role	Represents a ProjectRole in the interface, including it's translation.
Role	Stores role info.
RoleMixin	This mixin class is used to serialize/deserialize Role.
RoleUtilities	Utilities class to help with role access.
RootResource	Resource for sending links back when a client requests the root resource.
RunAsUser	Annotation saying the function should be run as the User identified in the RunAsUser.value().
RunAsUserAspect	Aspect to update the Authentication object in the SecurityContext to be the user specified in the annotation using SpEL.
Sample	A biological sample.
SampleAddedProjectEvent	Event created when a Sample is added to a Project
SampleAnalyses	Used to return analyses ran with Sample sequencing objects back to the user interface.
SampleAnalysisDuplicateException	If there is a duplicate Sample which is being sent for analysis.
SampleDetails	Used to return details of a Sample back to the user interface.
SampleExportFiles
SampleFiles	Collection of different files that can be on a sample
SampleFilesResponse	Response for getting details about the files belonging to multiple samples
SampleGenomeAssemblyFileModel	Used to send genome assembly object information with file size to the UI
SampleGenomeAssemblyJoin	Relationship between a Sample and a GenomeAssembly.
SampleGenomeAssemblyJoinRepository	Repository for storing and retrieving SampleGenomeAssemblyJoins.
SampleMergeException	Error thrown during the samples merge process
SampleMetadata	Used to return Sample metadata back to the user interface.
SampleMetadataFieldEntry	Used to return metadata field and entry back to the user interface.
SampleMetadataResponse	Response class for grouping MetadataEntrys for response in the REST API
SampleMetadataStorage	Used to store information relating to sample metadata during upload.
SampleMetadataStorageRow	Used to store information relating to sample metadata rows during upload.
SampleNameValidationResponse	UI Response to indicate the value of validating a proposed sample name.
SampleObject	Representation of a Sample used in the Project Samples table.
SamplePairer	Utility class for pairing up sequence files with common prefixes and expected characters for forward and reverse sequence files.
SampleRemoteRepository	Repository to read Samples from a RemoteAPI
SampleRemoteRepositoryImpl	An implementation of SampleRemoteRepository
SampleRemoteService	Service for reading Samples
SampleRemoteServiceImpl	Implementation of SampleRemoteService using SampleRemoteRepository
SampleRemovedProjectEvent	Event for when a sample is removed from a project.
SampleRepository	A repository for storing Sample objects
SampleRepositoryCustom	Custom repository methods for Samples
SampleRepositoryImpl	Implementation of custom repository methods for Samples
SamplesAjaxController	Controller for asynchronous requests for a Sample
SampleSequencingObjectFileModel	Used to send sequencing object information with file sizes to the UI
SampleSequencingObjectJoin	Relationship between a Sample and a SequencingObject
SampleSequencingObjectJoinRepository	Repository for storing and retrieving SampleSequencingObjectJoins
SampleSequencingObjectSpecification	Specification for searching through SampleSequencingObjectJoins
SampleService	A service class for working with samples.
SampleServiceImpl	Service class for managing Sample.
SavedMetadataErrorResponse	Returns the SampleMetadataStorage on error.
SavedMetadataException	Returns the SampleMetadataStorage on error.
SavedPipelineParameters	Used by the UI for displaying a named pipeline parameter set.
SavePipelineParametersRequest	Used to save new values for Saved Pipeline Parameters on the Pipeline Launch Page
SchemaExporter	Export the current hibernate-generated schema (with auditing tables).
SearchController	Controller to manage global searching
SearchCriteria	Define a search criteria for a given key and value.
SearchOperation	Search operations available to use in SearchCriteria's
SelectOption	Generically represents a UI Select Option
SequenceConcatenation	Class storing when 2 SequencingObjects are concatenated into a new SequencingObject
SequenceConcatenationRepository	Repository for SequenceConcatenations
SequenceFile	A file that may be stored somewhere on the file system and belongs to a particular Sample.
SequenceFileAjaxController	Ajax controller to get data for the fastqc page.
SequenceFileAnalysisException	Thrown when there is an issue with a SequenceFile analysis.
SequenceFileDetails	Data transfer object for retrieving SequenceFile details from a SequencingRun.
SequenceFileMessageConverter	Message markdownConverter for converting application/fastq HTTP responses to a Java Path temporary file
SequenceFileModel	UI Model for a SequenceFile
SequenceFilePair	A pair of sequence files in forward/reverse orientation.
SequenceFilePairConcatenator	SequencingObjectConcatenator for SequenceFilePairs
SequenceFilePairRemoteRepository	RemoteRepository for reading SequenceFilePair objects
SequenceFilePairRemoteRepositoryImpl	RemoteRepositoryImpl for reading and listing SequenceFilePair objects.
SequenceFilePairRemoteService	Remote service for reading sequence file pairs from a remote api
SequenceFilePairRemoteServiceImpl	Remote service implementation for reading sequence file pairs from a remote api
SequenceFileProcessorLauncher	SequenceFile processor which launches a FileProcessingChain on a collection of SequenceFile ids
SequenceFileRemoteRepository	Repository for reading SequenceFiles from a Remote IRIDA installation
SequenceFileRemoteRepositoryImpl	Implementation of SequenceFileRemoteRepository using OAuthTokenRestTemplate for making requests
SequenceFileRepository	A repository to store information about sequence files.
SequenceFileRepositoryImpl	Custom implementation of FilesystemSupplementedRepositoryImpl for SequenceFile.
SequenceFileResource	Resource wrapper for SequenceFile.
SequenceFileUtilities	Utility class for executing common functions on sequence files
SequencerUILoginException	Thrown if an authentication request is rejected because the account's role is ROLE_SEQUENCER.
SequencingObject	Objects that were obtained from some sequencing platform.
SequencingObject.ProcessingState	The status of the file processing upon upload
SequencingObjectConcatenator<Type extends SequencingObject>	Class to concatenate multiple SequencingObjects and return a single new SequencingObject.
SequencingObjectConcatenatorFactory	Factory class for returning an instance of SequencingObjectConcatenator for a given filetype
SequencingObjectProcessingService	Service used to run a FileProcessingChain on incoming SequencingObjects.
SequencingObjectRemoteService<Type extends SequencingObject>	Service for reading SequencingObjects from remote sources
SequencingObjectRemoteServiceImpl<Type extends SequencingObject>	Service to read SequencingObjects from a remote api.
SequencingObjectRepository	Repository for storing and retrieving SequencingObjects
SequencingObjectService	Service for managing SequencingObjects and relationships with related objects
SequencingObjectServiceImpl	Implementation of SequencingObjectService using a SequencingObjectRepository and SampleSequencingObjectJoinRepository to persist and load objects.
SequencingRun	This class represents a collection of sequence files that have come off one run of a sequencer.
SequencingRun.LayoutType	The type of layout for the run.
SequencingRunAjaxController	Controller to handle AJAX requests for sequencing run data
SequencingRunController	Controller for displaying and interacting with SequencingRun objects
SequencingRunDetails	Data transfer object for retrieving sequencing run details from a sql query.
SequencingRunModel	Model to format a SequencingRun into a format that can be used in the UI Table.
SequencingRunRepository
SequencingRunService	Service layer for SequencingRun objects
SequencingRunServiceImpl
SequencingRunsListRequest	Request for data for the sequencing run listing page.
SequencingRunUploadStatus	Encodes the status of an uploaded SequencingRun.
ServletInitializer	Servlet Initializer for Spring Boot application
SessionFilter	Filter to be used to add constants to the session for templating
ShareMetadataRestriction	Helper class used when sharing / moving samples to indicate, which restriction level the metadata attached should have.
ShareSamplesRequest	Handles data transfer for sharing samples between projects
SingleEndSequenceFile	SequencingObject from a single ended sequence run.
SingleEndSequenceFileConcatenator	SequenceFilePairConcatenator for SingleEndSequenceFiles
SingleEndSequenceFileModel	IRIDA UI model to represent SingleEndSequenceFile
SingleEndSequenceFileRemoteRepository	RemoteRepository for storing and reading SingleEndSequenceFiles
SingleEndSequenceFileRemoteRepositoryImpl	Implementation of a SingleEndSequenceFileRemoteRepository extending RemoteRepositoryImpl
SingleEndSequenceFileRemoteService	Service for storing and retrieving SingleEndSequenceFiles from a RemoteAPI
SingleEndSequenceFileRemoteServiceImpl	Implementation of SingleEndSequenceFileRemoteService using a SingleEndSequenceFileRemoteRepository
SistrResult	Used as a response for encapsulating a SISTR result object
SISTRSampleUpdater	AnalysisSampleUpdater that adds a number of results from a SISTR run to the metadata of a Sample
SlashFilter	A simple filter that wraps HttpServletRequest to replace any incoming requests with two or more slashes with a single slash.
StateFilter	Class for conversion from JSON.
StaticMetadataTemplateField	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.
StatisticsResponse	UI Response to to encapsulate statistics.
StatisticTimePeriod	Defines a arrays of time periods and group by formats used for getting statistics for the Admin Panel.
StorageException	When a database error occurs
SubmissionIds	This class is used to store workflow submission ids in the session.
SuccessNotification	Consumed by the UI to display a success notification.
TableModel	Used as the base class of any item to be represented in an ant.design Table.
TableModel	Used as the base class of any item to be represented in an ant.design Table.
TableRequest	Handles the conversion of the HttpRequestBody into an object.
TableRequest	Default for request for table contents.
TableResponse	Contains information needed for listing of items in an ag-grid table
TableResponse<T extends TableModel>	Response sent when items are requested for a table.
TaxonomyAjaxController	Handle asynchronous request related to the taxonomy ontology.
TaxonomyEntry	Used by the UI to generate a select input based on a search within the taxonomy.
TaxonomyService	Service for reading taxonomy information
TestEmailController	Email controller used for testing.
Timestamped<Identifier>	An object with a timestamp and ID
TimestampJson	Serialization class for java Date objects.
TimestampJson.TimestampSerializer	Default serializer for Date objects.
TimestampMixin	This mixin class is used to serialize/deserialize Timestamp.
ToolExecution	A historical record of how a tool was executed by a workflow execution manager to produce some set of outputs.
ToolsListExporter	Exports a YAML configuration file containing the list of all tools necessary in Galaxy to run this IRIDA instance.
TreeNode<ValueType>	Simple generic tree node with links to parent and a list of children
UIActivitiesService	UI service for converting events into UI activities.
UIAddAssociatedProjectException	Error to throw if there is an error adding an associated project to a project
UIAdminStatisticsService	A utility class for formatting responses for the admin statistics page UI.
UIAnalysesOutputsService	UI Service for all things related to project single sample analysis outputs.
UIAnalysesService	UI Service for analyses
UIAnnouncementsService	A utility class for formatting responses for the announcements page UI.
UIAssociatedProjectsService	Service for handling associated projects
UICartService	Service for handling all aspects of interaction with the Cart.
UIClientService	UI Service to handle IRIDA Clients
UIConstraintViolationException	Used by UI to contain internationalized constraint violations.
UIEmailSendException	Exception to be thrown by the UI when an email failed to send.
UIEntityNotFoundException	Exception to be thrown by the UI when the entity does not exist.
UIMetadataField	This is a generic class to represent all possible headers (MetadataFields) in a line list.
UIMetadataFieldDefault	Represents metadata fields that are not part of the sample metadata, but are included on the line list page.
UIMetadataFileImportService	UI service to handle parsing metadata files so they can be saved to the session.
UIMetadataImportService	UI service to handle importing metadata files, so they can be saved to the session.
UIMetadataService	Service for Metadata Templates in the user interface
UIMetadataTemplate	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.
UINcbiService	Utility class for formatting responses for NCBI Export Listing page UI.
UIPasswordResetService	Handles service calls for password resets.
UIPipelineDetailsResponse	Model class to send details about a workflow pipeline to the UI Used on the launch pipeline page.
UIPipelineSampleService	UI Service for all things related to samples within the pipeline
UIPipelineService	UI Service for all things related to workflow pipelines.
UIPipelineStartService	Service to handle starting of IridaWorkflows through the UI.
UIProjectMembersService	Service class for the UI for handling project members actions.
UIProjectReferenceFileService	A utility class for formatting responses for the project reference files page UI.
UIProjectSampleService	UI Service to handle samples within a project.
UIProjectsService	A utility class for formatting responses for the project members page UI.
UIProjectSubscriptionService	A utility class for formatting responses for the project subscriptions page UI.
UIProjectUserGroupsService	UI Service to handle requests for project user groups.
UIProjectWithoutOwnerException	Exception to be thrown by the UI when the member being removed from the project, would leave the project without a manager.
UIReferenceFile	Represents a reference file in the UI.
UIRemoteAPIService	UI Service to handle request for Remote APIs
UIRemoteProjectService	A utility class for doing operations on remote project sync settings.
UIRemoveAssociatedProjectException	Exception to through if there is an error removing an associated project from a project
UISampleFilter	User Interface model for available field to filter the Project Samples by.
UISampleMetadata	Represents Sample metadata in the linelist table.
UISampleService	UI Service for samples
UISequenceFileService	UI Service for handling requests related to SequenceFiles
UISequencingRunService	UI Service for handling requests related to SequencingRuns
UISettingsService	Handles service calls for settings in IRIDA.
UIShareSamplesException	Exception to through if there is an error sharing samples between projects
UIUserFormException	Exception to be thrown by the UI when a user cannot be created or updated.
UIUserGroupsService	Service class for the UI for handling UserGroups
UIUsersService	Handles service call for the administration of the IRIDA users.
UIUserStatisticsService	UI Service for handling requests related to user statistics
UIUserStatusException	Exception to throw if there is an error updating the user status
UnauthenticatedAnonymousAuthenticationFilter	Anonymous authentication filter that sets anonymous tokens as being unauthenticated
UndefinedPermissionException	Thrown when the IridaPermissionEvaluator is asked to test a permission that it doesn't know about.
UnsupportedReferenceFileContentError	Error that's thrown when BioJava can't parse an uploaded reference file.
UpdateAnalysisSubmissionPermission	Confirms if a User can update a AnalysisSubmission.
UpdatedAnalysisProgress	Used by the UI to to update the state and duration of an analysis.
UpdatedAnalysisTableProgress	Used by the UI to to update the state and duration of an analysis.
UpdateException	Thrown if there was an error during the update.
UpdateMetadataTemplatePermission	Permission for updating a MetadataTemplate
UpdateProjectAttributeRequest	Used to handle requests from the UI to update a specific attribute on a project.
UpdateReferenceFilePermission	Confirms that the authenticated user is allowed to modify a reference file.
UpdateSampleAttributeRequest	Used to handle requests from the UI to update a specific attribute on a sample.
UpdateSampleMetadataRequest	Used to handle requests from the UI to update a sample metadata field/entry/restriction.
UpdateSamplePermission	Custom permission implementation for updating Sample.
UpdateSampleRequest	UI Request to update an existing sample
UpdateSamplesFromAnalysisSubmissionPermission	Permission for whether a user can update samples in a given analysis submission.
UpdateSequencingRunPermission	Permission checking if a user is the owner of a SequencingRun or if they are ROLE_SEQUENCER
UpdateUserGroupPermission	Confirms that the authenticated user is allowed to modify a user group.
UpdateUserPermission	Confirms that the authenticated user is allowed to modify another (or their own) user account.
UploadConnectionException	Thrown when a connection to a remote site for uploading data fails.
UploadedAssembly	A GenomeAssembly implementation that was uploaded by a user or service
UploaderAccountName	An account name for setting up permissions of uploaded files to a remote endpoint.
UploadErrorException	Exception that gets thrown when there is an error while uploading data to a separate data management system (e.g.
UploadException	Exception that gets thrown when uploading data to a separate data management system (e.g.
UploadProjectName	Defines the name of a project to be uploaded to a remote site.
UploadReferenceFilesResponse	Used by UI to handle the return of a successful upload on one or more reference files.
UploadTimeoutException	Exception that gets thrown when there is a timeout while uploading data to a separate data management system (e.g.
User	A user object.
UserCreateRequest	Data transfer object for creating a new user account.
UserDetailsModel	Describes a User in a ant.design table.
UserDetailsResponse	Returns an AjaxResponse with user details.
UserEditRequest	Data transfer object for editing user details.
UserGroup	A collection of User accounts is a UserGroup.
UserGroupDetails	Used to return details about a user group to the UI.
UserGroupJoin	A relationship between an individual User account and a UserGroup.
UserGroupJoin.UserGroupRole	The role of a user in the group
UserGroupJoinRepository	Repository for working with UserGroupJoin.
UserGroupMember	Used to send information about a user group member to the UI.
UserGroupProjectJoin	A relationship between a UserGroup and Project.
UserGroupProjectJoinRepository	Repository for UserGroupProjectJoin.
UserGroupProjectTableModel	Used to send information about a project in a user group to the UI.
UserGroupRemovedProjectEvent	Event created when a UserGroup is removed from a Project.
UserGroupRepository	A repository for UserGroup.
UserGroupRole	Represents a user group role in the UI.
UserGroupRoleSetProjectEvent	Event created when a UserGroup is added or has role changed on a Project.
UserGroupsAjaxController	Controller for asynchronous request for User Groups
UserGroupsController	Controller for interacting with UserGroup.
UserGroupService	Service for working with UserGroups.
UserGroupServiceImpl	Implementation of UserGroupService.
UserGroupSpecification	Search specification for UserGroup.
UserGroupTableModel	Represent a UserGroup in the UI
UserGroupWithoutOwnerException	Exception thrown when a change to membership of a UserGroup causes that group to have no owner.
UserMinimalModel	Minimal model for a User in the UI.
UserMixin	This mixin class is used to serialize/deserialize User.
UserPasswordResetDetails	Data transfer object for user's password reset details
UserProjectDetailsModel	Used to represent user Projects on the UI user account projects page.
UserRemovedProjectEvent	Event for when a User is removed from a Project
UserRepository	Specialized repository for User.
UserRepositoryCustom	Custom repository methods for UserRepository
UserRepositoryImpl	Custom implementation of UserRepository that throws UsernameNotFoundException.
UserRevEntity	Envers Revision class storing the timestamp, user, and oauth client used to make a change.
UserRevListener
UserRoleSetProjectEvent	Event created when a User is added to or has a role changed on a Project.
UsersAjaxController	Handles asynchronous requests for the administration users table.
UsersController	Controller for all User related views
UserSecurityInterceptor	Interceptor Adaptor to add the user to the Model each server call.
UserService	Customized service for accessing user objects.
UserServiceImpl	Implementation of the UserService.
UserSpecification	Specification for searching a User
UserStatisticsAjaxController	Controller for user statistics
UserStatisticsResponse	UI Response to to encapsulate user statistics.
ValidateSampleNameModel	Model for UI to represent a sample.
ValidateSampleNamesRequest	UI request to validate sample names.
ValidateSampleNamesResponse	Return a list of sample names.
ValidMethodParametersAspect	This aspect automatically invokes a Validator for method parameters annotated with the Valid annotation.
ValidProjectName	Custom validation annotation that implements a block-list of unacceptable characters in resources that can be named.
ValidProjectName.ValidProjectNameBlocklist	Invalid characters in a project name
ValidSampleName	A collection of patterns that validate the name of a sample.
ValidSampleName.ValidSampleNameBlocklist	Characters not allowed in a sample name
VersionedFileFields<VersionType extends java.io.Serializable>	An instance of a class may have a property with Version or may have an internally managed version representation.
WarnNotification	Consumed by the UI to display a warning notification.
WebEmailConfig	Configuration class for loading properties files.
WebEmailConfig.ConfigurableJavaMailSender	An extension of JavaMailSender that allows checking to see if it's configured.
WebEmailConfig.ConfigurableJavaMailSenderImpl	Implementation of WebEmailConfig.ConfigurableJavaMailSender.
WebpackAssetsManifest	Container for the assets manifest file deserialization
WebpackAssetsManifestDeserializer	Deserializer for the webpack assets-manifest file
WebpackEntry	Each webpack entry with have at least one JavaScript file, and possibly css files and html (translatons)
WebpackEntryDeserializer	Deserializer for the webpack manifest file entry.
WebpackerCSSElementTagProcessor	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.
WebpackerDialect	Webpacker Dialect.
WebpackerJavascriptElementTagProcessor	Thymeleaf Tag Processor for webpacker elements.
WebpackerManifestParser	Responsible for parsing the webpack manifest file and passing along the chunks for js, css, and html resources.
WebpackerScriptAttributeTagProcessor	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.
WebpackerTagType	Enum for available webpacker tag types
WebpackParserException	Thrown web there is an error parsing the webpack assets-manifest file.
WebStylesConfig	Configuration for Ant Design theme styles from properties file.
WorkflowException	Exception that gets thrown when there is an issue running a workflow.
WorkflowInputsGalaxy	Describes a set of workflow inputs for a Galaxy workflow.
WorkflowInputsGeneric	Describes a generic set of inputs to a workflow.
WorkflowInvalidException	An exception thrown if a workflow is invalid.
WorkflowNamedParametersRepository	Repository for working with named parameter sets.
WorkflowNamedParametersService	Service for interacting with named parameter sets.
WorkflowNamedParametersServiceImpl	Service for interacting with named parameter sets.
WorkflowPreprationException	An exception that gets thrown during the preparation of a workflow.
WorkflowUploadException	Exception that gets thrown when there is an error uploading a workflow to Galaxy.