Package ca.corefacility.bioinformatics.irida.service.impl.analysis.submission

Class AnalysisSubmissionServiceImpl

java.lang.Object

ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

ca.corefacility.bioinformatics.irida.service.impl.analysis.submission.AnalysisSubmissionServiceImpl

All Implemented Interfaces:

AnalysisSubmissionService, CRUDService<java.lang.Long,AnalysisSubmission>

@Service
public class AnalysisSubmissionServiceImpl
extends CRUDServiceImpl<java.lang.Long,AnalysisSubmission>
implements AnalysisSubmissionService

Implementation of an AnalysisSubmissionService.

Nested Class Summary

Nested classes/interfaces inherited from interface ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService

AnalysisSubmissionService.AnalysisServiceStatus

Field Summary

Fields

Modifier and Type	Field	Description
static java.util.Map<AnalysisState,java.lang.Float>	STATE_PERCENTAGE	A Map defining the progress transitions points for each state in an AnalysisSubmission.

Fields inherited from class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

CREATED_DATE_SORT_PROPERTY, repository, validator, valueType

Constructor Summary

Constructors

Constructor

Description

AnalysisSubmissionServiceImpl(AnalysisSubmissionRepository analysisSubmissionRepository, AnalysisSubmissionTemplateRepository analysisTemplateRepository, UserRepository userRepository, ReferenceFileRepository referenceFileRepository, SequencingObjectService sequencingObjectService, GalaxyHistoriesService galaxyHistoriesService, ProjectAnalysisSubmissionJoinRepository pasRepository, JobErrorRepository jobErrorRepository, IridaWorkflowsService iridaWorkflowsService, javax.validation.Validator validator)

Builds a new AnalysisSubmissionServiceImpl with the given information.

Method Summary

Modifier and Type	Method	Description
long	count()	How many entities of Type exist in the database?
AnalysisSubmission	create(AnalysisSubmission analysisSubmission)	Create a new object in the persistence store.
AnalysisSubmission	createMultipleSampleSubmission(IridaWorkflow workflow, java.lang.Long ref, java.util.List<SingleEndSequenceFile> sequenceFiles, java.util.List<SequenceFilePair> sequenceFilePairs, java.util.Map<java.lang.String,java.lang.String> params, IridaWorkflowNamedParameters namedParameters, java.lang.String name, java.lang.String newAnalysisDescription, java.util.List<Project> projectsToShare, boolean writeResultsToSamples, boolean emailPipelineResultCompleted, boolean emailPipelineResultError)	Submit AnalysisSubmission for workflows allowing multiple one SequenceFile or SequenceFilePair
java.util.Collection<AnalysisSubmission>	createSingleSampleSubmission(IridaWorkflow workflow, java.lang.Long ref, java.util.List<SingleEndSequenceFile> sequenceFiles, java.util.List<SequenceFilePair> sequenceFilePairs, java.util.Map<java.lang.String,java.lang.String> params, IridaWorkflowNamedParameters namedParameters, java.lang.String name, java.lang.String analysisDescription, java.util.List<Project> projectsToShare, boolean writeResultsToSamples, boolean emailPipelineResultCompleted, boolean emailPipelineResultError)	Submit AnalysisSubmission for workflows requiring only one SequenceFile or SequenceFilePair
AnalysisSubmissionTemplate	createSingleSampleSubmissionTemplate(IridaWorkflow workflow, java.lang.Long referenceFileId, java.util.Map<java.lang.String,java.lang.String> params, IridaWorkflowNamedParameters namedParameters, java.lang.String submissionName, java.lang.String statusMessage, java.lang.String analysisDescription, Project projectsToShare, boolean writeResultsToSamples, boolean emailPipelineResultCompleted, boolean emailPipelineResultError)	Create a new AnalysisSubmissionTemplate for a project with the given settings
void	delete(java.lang.Long id)	Delete the object with the specified identifier from the database.
void	deleteAnalysisSubmissionTemplateForProject(java.lang.Long id, Project project)	Delete an AnalysisSubmissionTemplate from the given Project
void	deleteMultiple(java.util.Collection<java.lang.Long> ids)	Delete multiple AnalysisSubmissions
java.lang.Boolean	exists(java.lang.Long id)	Check to see if an identifier for Type exists in the database.
java.lang.Iterable<AnalysisSubmission>	findAll()	List all objects of Type in the database.
java.util.Collection<AnalysisSubmission>	findAnalysesByState(java.util.Collection<AnalysisState> states)	Get a list of all AnalysisSubmissions with a given AnalysisState
org.springframework.data.history.Revisions<java.lang.Integer,AnalysisSubmission>	findRevisions(java.lang.Long id)	Find all of the revisions for the specified identifier.
org.springframework.data.domain.Page<org.springframework.data.history.Revision<java.lang.Integer,AnalysisSubmission>>	findRevisions(java.lang.Long id, org.springframework.data.domain.Pageable pageable)	Returns a Page of revisions for the entity with the given id.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllAnalysisOutputInfoSharedWithProject(java.lang.Long projectId)	Get all ProjectSampleAnalysisOutputInfo for a Project.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllAutomatedAnalysisOutputInfoForAProject(java.lang.Long projectId)	Get all automated ProjectSampleAnalysisOutputInfo for a Project.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllUserAnalysisOutputInfo(User user)	Get all User generated AnalysisOutputFile info
java.util.List<GenericStatModel>	getAnalysesRanGrouped(java.util.Date createdDate, StatisticTimePeriod statisticTimePeriod)	Get list of GenericStatModel of analyses run in the past n time period grouped by the format provided.
java.lang.Long	getAnalysesRanInTimePeriod(java.util.Date createdDate)	Get count of analyses run in the time period
AnalysisSubmissionService.AnalysisServiceStatus	getAnalysisServiceStatus()	Get the status of the analysis service.
java.util.List<AnalysisSubmission>	getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds(java.util.Collection<java.util.UUID> workflowIds)	Gets all AnalysisSubmissionServices accessible by the current user matching one of the workflow ids.
java.util.Set<AnalysisSubmission>	getAnalysisSubmissionsForCurrentUser()	Gets a Set of AnalysisSubmissions for the current User.
java.util.Set<AnalysisSubmission>	getAnalysisSubmissionsForUser(User user)	Gets a Set of AnalysisSubmissions for a User.
java.util.Collection<AnalysisSubmission>	getAnalysisSubmissionsSharedToProject(Project project)	Get a collection of all AnalysisSubmissions shared with a Project.
java.util.List<AnalysisSubmissionTemplate>	getAnalysisTemplatesForProject(Project project)	Get all the AnalysisSubmissionTemplates for a given Project
JobError	getFirstJobError(java.lang.Long id)	Get first JobError for a AnalysisSubmission id
java.util.List<JobError>	getJobErrors(java.lang.Long id)	Get the JobError objects for a AnalysisSubmission id
int	getNumberAnalysesByUser(User user)	Get count of AnalysisSubmission for the user grouped by the format provided.
float	getPercentCompleteForAnalysisSubmission(java.lang.Long id)	Given the id of an AnalysisSubmission gets the percentage complete.
AnalysisState	getStateForAnalysisSubmission(java.lang.Long analysisSubmissionId)	Given an analysis submission id, gets the state of this analysis.
org.springframework.data.domain.Page<AnalysisSubmission>	list(int page, int size, org.springframework.data.domain.Sort.Direction order)	List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.
org.springframework.data.domain.Page<AnalysisSubmission>	list(int page, int size, org.springframework.data.domain.Sort.Direction order, java.lang.String... sortProperties)	List objects of Type in the database, limited to some specific page.
org.springframework.data.domain.Page<AnalysisSubmission>	listAllSubmissions(java.lang.String search, java.lang.String name, java.util.Set<AnalysisState> states, java.util.Set<java.util.UUID> workflowIds, org.springframework.data.domain.PageRequest pageRequest)	Get a page of all AnalysisSubmissions in the system
org.springframework.data.domain.Page<AnalysisSubmission>	listSubmissionsForProject(java.lang.String search, java.lang.String name, java.util.Set<AnalysisState> states, java.util.Set<java.util.UUID> workflowIds, Project project, org.springframework.data.domain.PageRequest pageRequest)	Get a page of the AnalysisSubmissions shared with a project.
org.springframework.data.domain.Page<AnalysisSubmission>	listSubmissionsForUser(java.lang.String search, java.lang.String name, java.util.Set<AnalysisState> states, User user, java.util.Set<java.util.UUID> workflowIds, org.springframework.data.domain.PageRequest pageRequest)	Get a page of AnalysisSubmissions the given user has submitted.
AnalysisSubmission	read(java.lang.Long id)	Read the object type by unique identifier.
AnalysisSubmissionTemplate	readAnalysisSubmissionTemplateForProject(java.lang.Long id, Project project)	Get an AnalysisSubmissionTemplate on the given Project
java.lang.Iterable<AnalysisSubmission>	readMultiple(java.lang.Iterable<java.lang.Long> idents)	Read multiple objects by the given collection of identifiers
void	removeAnalysisProjectShare(AnalysisSubmission submission, Project project)	Cancel the share of an AnalysisSubmission with a given Project
void	setAnalysisExecutionService(AnalysisExecutionServiceGalaxyCleanupAsync analysisExecutionService)
ProjectAnalysisSubmissionJoin	shareAnalysisSubmissionWithProject(AnalysisSubmission submission, Project project)	Share an AnalysisSubmission with a given Project
AnalysisSubmission	update(AnalysisSubmission object)	Update an object
AnalysisSubmission	updatePriority(AnalysisSubmission submission, AnalysisSubmission.Priority priority)	Update the priority of an AnalysisSubmission

Methods inherited from class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

list, search, search, updateFields, updateMultiple

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ca.corefacility.bioinformatics.irida.service.CRUDService

list, search, search, updateFields, updateMultiple

Field Detail

STATE_PERCENTAGE

public static final java.util.Map<AnalysisState,java.lang.Float> STATE_PERCENTAGE

A Map defining the progress transitions points for each state in an AnalysisSubmission.

Constructor Detail

AnalysisSubmissionServiceImpl

@Autowired
public AnalysisSubmissionServiceImpl(AnalysisSubmissionRepository analysisSubmissionRepository,
                                     AnalysisSubmissionTemplateRepository analysisTemplateRepository,
                                     UserRepository userRepository,
                                     ReferenceFileRepository referenceFileRepository,
                                     SequencingObjectService sequencingObjectService,
                                     GalaxyHistoriesService galaxyHistoriesService,
                                     ProjectAnalysisSubmissionJoinRepository pasRepository,
                                     JobErrorRepository jobErrorRepository,
                                     IridaWorkflowsService iridaWorkflowsService,
                                     javax.validation.Validator validator)

Builds a new AnalysisSubmissionServiceImpl with the given information.

Parameters:

analysisSubmissionRepository - A repository for accessing analysis submissions.

analysisTemplateRepository - repository for AnalysisSubmissionTemplates

userRepository - A repository for accessing user information.

referenceFileRepository - the reference file repository

sequencingObjectService - the SequencingObject service.

galaxyHistoriesService - The GalaxyHistoriesService.

pasRepository - The ProjectAnalysisSubmissionJoinRepository

jobErrorRepository - A repository for accessing JobError

iridaWorkflowsService - The IridaWorkflowsService

validator - A validator.

Method Detail

setAnalysisExecutionService

public void setAnalysisExecutionService(AnalysisExecutionServiceGalaxyCleanupAsync analysisExecutionService)

listSubmissionsForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public org.springframework.data.domain.Page<AnalysisSubmission> listSubmissionsForProject(java.lang.String search,
                                                                                          java.lang.String name,
                                                                                          java.util.Set<AnalysisState> states,
                                                                                          java.util.Set<java.util.UUID> workflowIds,
                                                                                          Project project,
                                                                                          org.springframework.data.domain.PageRequest pageRequest)

Get a page of the AnalysisSubmissions shared with a project.

Specified by:

listSubmissionsForProject in interface AnalysisSubmissionService

Parameters:

search - basic search string

name - analysis submission name

states - Set of AnalysisState of the submission to search

workflowIds - set of workflow UUIDs to search

project - Project to search in

pageRequest - a PageRequest for the results to show

Returns:

a page of AnalysisSubmission

listAllSubmissions

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public org.springframework.data.domain.Page<AnalysisSubmission> listAllSubmissions(java.lang.String search,
                                                                                   java.lang.String name,
                                                                                   java.util.Set<AnalysisState> states,
                                                                                   java.util.Set<java.util.UUID> workflowIds,
                                                                                   org.springframework.data.domain.PageRequest pageRequest)

Get a page of all AnalysisSubmissions in the system

Specified by:

listAllSubmissions in interface AnalysisSubmissionService

Parameters:

search - basic search string

name - analysis submission name

states - Set of AnalysisState of the submission to search

workflowIds - set of workflow UUIDs to search

pageRequest - a PageRequest for the results to show

Returns:

a page of AnalysisSubmission

listSubmissionsForUser

@PreAuthorize("hasRole(\'ROLE_USER\')")
public org.springframework.data.domain.Page<AnalysisSubmission> listSubmissionsForUser(java.lang.String search,
                                                                                       java.lang.String name,
                                                                                       java.util.Set<AnalysisState> states,
                                                                                       User user,
                                                                                       java.util.Set<java.util.UUID> workflowIds,
                                                                                       org.springframework.data.domain.PageRequest pageRequest)

Get a page of AnalysisSubmissions the given user has submitted.

Specified by:

listSubmissionsForUser in interface AnalysisSubmissionService

Parameters:

search - basic search string

name - analysis submission name

states - Set of AnalysisState of the submission to search

user - the User to get submissions for

workflowIds - set of workflow UUIDs to search

pageRequest - a PageRequest for the restults to show

Returns:

a page of AnalysisSubmissions for the given user

getStateForAnalysisSubmission

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#analysisSubmissionId, \'canReadAnalysisSubmission\')")
public AnalysisState getStateForAnalysisSubmission(java.lang.Long analysisSubmissionId)
                                            throws EntityNotFoundException

Given an analysis submission id, gets the state of this analysis.

Specified by:

getStateForAnalysisSubmission in interface AnalysisSubmissionService

Parameters:

analysisSubmissionId - The id of this analysis.

Returns:

The state of this analysis.

Throws:

EntityNotFoundException - If the corresponding analysis cannot be found.

read

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public AnalysisSubmission read(java.lang.Long id)
                        throws EntityNotFoundException

Read the object type by unique identifier.

Specified by:

read in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

read in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

id - The unique identifier for this object.

Returns:

The object corresponding to the unique identifier.

Throws:

EntityNotFoundException - If the identifier does not exist in the database.

readMultiple

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#idents, \'canReadAnalysisSubmission\')")
public java.lang.Iterable<AnalysisSubmission> readMultiple(java.lang.Iterable<java.lang.Long> idents)

Read multiple objects by the given collection of identifiers

Specified by:

readMultiple in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

readMultiple in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

idents - The unique identifiers of the objects to read

Returns:

A collection of the requested objects

findAll

@PreAuthorize("hasRole(\'ROLE_USER\')")
@PostFilter("hasPermission(filterObject, \'canReadAnalysisSubmission\')")
public java.lang.Iterable<AnalysisSubmission> findAll()

List all objects of Type in the database.

Specified by:

findAll in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

findAll in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Returns:

All objects of the specified Type in the database.

exists

@PreAuthorize("hasRole(\'ROLE_USER\')")
public java.lang.Boolean exists(java.lang.Long id)

Check to see if an identifier for Type exists in the database.

Specified by:

exists in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

exists in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

id - The identifier to check for.

Returns:

true if the identifier exists, false otherwise.

findRevisions

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public org.springframework.data.history.Revisions<java.lang.Integer,AnalysisSubmission> findRevisions(java.lang.Long id)

Find all of the revisions for the specified identifier.

Specified by:

findRevisions in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

findRevisions in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

id - the identifier to find revisions for.

Returns:

the collection of revisions for the identifier.

findRevisions

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public org.springframework.data.domain.Page<org.springframework.data.history.Revision<java.lang.Integer,AnalysisSubmission>> findRevisions(java.lang.Long id,
                                                                                                                                                 org.springframework.data.domain.Pageable pageable)

Returns a Page of revisions for the entity with the given id.

Specified by:

findRevisions in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

findRevisions in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

id - the identifier to find revisions for.

pageable - the page specification.

Returns:

the page of revisions for the specified resource.

list

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public org.springframework.data.domain.Page<AnalysisSubmission> list(int page,
                                                                     int size,
                                                                     org.springframework.data.domain.Sort.Direction order,
                                                                     java.lang.String... sortProperties)
                                                              throws java.lang.IllegalArgumentException

List objects of Type in the database, limited to some specific page.

Specified by:

list in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

list in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

page - the specific page to use.

size - the size of the pages used to compute the number of pages.

order - the order of the sort.

sortProperties - the properties used to sort the collection.

Returns:

the list of users within the specified range.

Throws:

java.lang.IllegalArgumentException - If the Type has no public property sortProperty.

list

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public org.springframework.data.domain.Page<AnalysisSubmission> list(int page,
                                                                     int size,
                                                                     org.springframework.data.domain.Sort.Direction order)

List objects of Type in the database, limited to some specific page, ordered by calling the compareTo method on the class.

Specified by:

list in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

list in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

page - the specific page to use.

size - the size of the pages used to compute the number of pages.

order - the order of the sort.

Returns:

the list of users within the specified range.

count

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public long count()

How many entities of Type exist in the database?

Specified by:

count in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

count in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Returns:

the number of entities in the database.

delete

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canUpdateAnalysisSubmission\')")
public void delete(java.lang.Long id)
            throws EntityNotFoundException

Delete the object with the specified identifier from the database.

Specified by:

delete in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

delete in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

id - The identifier of the object to delete.

Throws:

EntityNotFoundException - If no object with the specified identifier exists in the database.

deleteMultiple

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#ids, \'canUpdateAnalysisSubmission\')")
public void deleteMultiple(java.util.Collection<java.lang.Long> ids)

Delete multiple AnalysisSubmissions

Specified by:

deleteMultiple in interface AnalysisSubmissionService

Parameters:

ids - the collection of IDs to delete

update

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#object, \'canUpdateAnalysisSubmission\')")
public AnalysisSubmission update(AnalysisSubmission object)

Update an object

Specified by:

update in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

update in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

object - The object to update

Returns:

The updated object

updatePriority

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public AnalysisSubmission updatePriority(AnalysisSubmission submission,
                                         AnalysisSubmission.Priority priority)

Update the priority of an AnalysisSubmission

Specified by:

updatePriority in interface AnalysisSubmissionService

Parameters:

submission - the submission to update

priority - the new priority

Returns:

the updated submission

getAllUserAnalysisOutputInfo

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or authentication.name == #user.username")
public java.util.List<ProjectSampleAnalysisOutputInfo> getAllUserAnalysisOutputInfo(User user)

Description copied from interface: AnalysisSubmissionService

Get all User generated AnalysisOutputFile info

Specified by:

getAllUserAnalysisOutputInfo in interface AnalysisSubmissionService

Parameters:

user - User

Returns:

List of AnalysisOutputFile info

getAllAnalysisOutputInfoSharedWithProject

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\') or hasPermission(#projectId, \'canReadProject\')")
public java.util.List<ProjectSampleAnalysisOutputInfo> getAllAnalysisOutputInfoSharedWithProject(java.lang.Long projectId)

Get all ProjectSampleAnalysisOutputInfo for a Project.

Specified by:

getAllAnalysisOutputInfoSharedWithProject in interface AnalysisSubmissionService

Parameters:

projectId - Project id

Returns:

a list of ProjectSampleAnalysisOutputInfo

getAllAutomatedAnalysisOutputInfoForAProject

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\') or hasPermission(#projectId, \'canReadProject\')")
public java.util.List<ProjectSampleAnalysisOutputInfo> getAllAutomatedAnalysisOutputInfoForAProject(java.lang.Long projectId)

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

Specified by:

getAllAutomatedAnalysisOutputInfoForAProject in interface AnalysisSubmissionService

Parameters:

projectId - Project id

Returns:

a list of ProjectSampleAnalysisOutputInfo

create

@PreAuthorize("hasRole(\'ROLE_USER\')")
public AnalysisSubmission create(AnalysisSubmission analysisSubmission)
                          throws javax.validation.ConstraintViolationException,
                                 EntityExistsException

Create a new object in the persistence store.

Specified by:

create in interface CRUDService<java.lang.Long,AnalysisSubmission>

Overrides:

create in class CRUDServiceImpl<java.lang.Long,AnalysisSubmission>

Parameters:

analysisSubmission - The object to persist.

Returns:

The object as it was persisted in the database. May modify the identifier of the object when returned.

Throws:

javax.validation.ConstraintViolationException - If the object being persisted cannot be validated by validation rules associated with the object.

EntityExistsException - If the object being persisted violates uniqueness constraints in the database.

getAnalysisSubmissionsForUser

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or authentication.name == #user.username")
public java.util.Set<AnalysisSubmission> getAnalysisSubmissionsForUser(User user)

Gets a Set of AnalysisSubmissions for a User.

Specified by:

getAnalysisSubmissionsForUser in interface AnalysisSubmissionService

Parameters:

user - The User to find all submissions for.

Returns:

A Set of AnalysisSubmissions for a user.

getAnalysisSubmissionsForCurrentUser

@PreAuthorize("hasRole(\'ROLE_USER\')")
public java.util.Set<AnalysisSubmission> getAnalysisSubmissionsForCurrentUser()

Gets a Set of AnalysisSubmissions for the current User.

Specified by:

getAnalysisSubmissionsForCurrentUser in interface AnalysisSubmissionService

Returns:

A Set of AnalysisSubmissions for the current user.

getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds

@PreAuthorize("hasRole(\'ROLE_USER\')")
@PostFilter("hasPermission(filterObject, \'canReadAnalysisSubmission\')")
public java.util.List<AnalysisSubmission> getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds(java.util.Collection<java.util.UUID> workflowIds)

Gets all AnalysisSubmissionServices accessible by the current user matching one of the workflow ids.

Specified by:

getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds in interface AnalysisSubmissionService

Parameters:

workflowIds - The workflow ids to match.

Returns:

A list of AnalysisSubmissions matching one of the workflow ids.

getAnalysisTemplatesForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.List<AnalysisSubmissionTemplate> getAnalysisTemplatesForProject(Project project)

Get all the AnalysisSubmissionTemplates for a given Project

Specified by:

getAnalysisTemplatesForProject in interface AnalysisSubmissionService

Parameters:

project - the Project to get templates for

Returns:

a list of all AnalysisSubmissionTemplates

createSingleSampleSubmissionTemplate

@PreAuthorize("hasPermission(#projectsToShare, \'canManageLocalProjectSettings\')")
public AnalysisSubmissionTemplate createSingleSampleSubmissionTemplate(IridaWorkflow workflow,
                                                                       java.lang.Long referenceFileId,
                                                                       java.util.Map<java.lang.String,java.lang.String> params,
                                                                       IridaWorkflowNamedParameters namedParameters,
                                                                       java.lang.String submissionName,
                                                                       java.lang.String statusMessage,
                                                                       java.lang.String analysisDescription,
                                                                       Project projectsToShare,
                                                                       boolean writeResultsToSamples,
                                                                       boolean emailPipelineResultCompleted,
                                                                       boolean emailPipelineResultError)

Create a new AnalysisSubmissionTemplate for a project with the given settings

Specified by:

createSingleSampleSubmissionTemplate in interface AnalysisSubmissionService

Parameters:

workflow - IridaWorkflow that the files will be run on

referenceFileId - Long id for a ReferenceFile

params - Map of parameters specific for the pipeline

namedParameters - the named parameters to use for the workflow.

submissionName - String the name for the analysis

statusMessage - A status message for the submission template

analysisDescription - String the description of the analysis being submitted

projectsToShare - The Project to save the analysis to

writeResultsToSamples - If true, results of this pipeline will be saved back to the samples on successful completion.

emailPipelineResultCompleted - Whether or not to email the pipeline results that completed to the user

emailPipelineResultError - Whether or not to email the pipeline results that errored to the user

Returns:

the newly created AnalysisSubmissionTemplate

readAnalysisSubmissionTemplateForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public AnalysisSubmissionTemplate readAnalysisSubmissionTemplateForProject(java.lang.Long id,
                                                                           Project project)

Get an AnalysisSubmissionTemplate on the given Project

Specified by:

readAnalysisSubmissionTemplateForProject in interface AnalysisSubmissionService

Parameters:

id - the AnalysisSubmissionTemplate id

project - the Project to get templates for

Returns:

the found AnalysisSubmissionTemplate

deleteAnalysisSubmissionTemplateForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public void deleteAnalysisSubmissionTemplateForProject(java.lang.Long id,
                                                       Project project)

Delete an AnalysisSubmissionTemplate from the given Project

Specified by:

deleteAnalysisSubmissionTemplateForProject in interface AnalysisSubmissionService

Parameters:

id - The id of an AnalysisSubmissionTemplate.

project - the Project to delete from

createSingleSampleSubmission

@PreAuthorize("hasRole(\'ROLE_USER\')")
public java.util.Collection<AnalysisSubmission> createSingleSampleSubmission(IridaWorkflow workflow,
                                                                             java.lang.Long ref,
                                                                             java.util.List<SingleEndSequenceFile> sequenceFiles,
                                                                             java.util.List<SequenceFilePair> sequenceFilePairs,
                                                                             java.util.Map<java.lang.String,java.lang.String> params,
                                                                             IridaWorkflowNamedParameters namedParameters,
                                                                             java.lang.String name,
                                                                             java.lang.String analysisDescription,
                                                                             java.util.List<Project> projectsToShare,
                                                                             boolean writeResultsToSamples,
                                                                             boolean emailPipelineResultCompleted,
                                                                             boolean emailPipelineResultError)

Submit AnalysisSubmission for workflows requiring only one SequenceFile or SequenceFilePair

Specified by:

createSingleSampleSubmission in interface AnalysisSubmissionService

Parameters:

workflow - IridaWorkflow that the files will be run on

ref - Long id for a ReferenceFile

sequenceFiles - List of SequenceFile to run on the workflow

sequenceFilePairs - List of SequenceFilePair to run on the workflow

params - Map of parameters specific for the pipeline

namedParameters - the named parameters to use for the workflow.

name - String the name for the analysis

analysisDescription - String the description of the analysis being submitted

projectsToShare - A list of Projects to share analysis results with

writeResultsToSamples - If true, results of this pipeline will be saved back to the samples on successful completion.

emailPipelineResultCompleted - If true, user will be emailed if a pipelines successfully completes

emailPipelineResultError - If true, user will be emailed if a pipeline errors

Returns:

the Collection of AnalysisSubmission created for the supplied files.

createMultipleSampleSubmission

@PreAuthorize("hasRole(\'ROLE_USER\')")
public AnalysisSubmission createMultipleSampleSubmission(IridaWorkflow workflow,
                                                         java.lang.Long ref,
                                                         java.util.List<SingleEndSequenceFile> sequenceFiles,
                                                         java.util.List<SequenceFilePair> sequenceFilePairs,
                                                         java.util.Map<java.lang.String,java.lang.String> params,
                                                         IridaWorkflowNamedParameters namedParameters,
                                                         java.lang.String name,
                                                         java.lang.String newAnalysisDescription,
                                                         java.util.List<Project> projectsToShare,
                                                         boolean writeResultsToSamples,
                                                         boolean emailPipelineResultCompleted,
                                                         boolean emailPipelineResultError)

Submit AnalysisSubmission for workflows allowing multiple one SequenceFile or SequenceFilePair

Specified by:

createMultipleSampleSubmission in interface AnalysisSubmissionService

Parameters:

workflow - IridaWorkflow that the files will be run on

ref - Long id for a ReferenceFile

sequenceFiles - List of SequenceFile to run on the workflow

sequenceFilePairs - List of SequenceFilePair to run on the workflow

params - Map of parameters specific for the pipeline

namedParameters - the named parameters to use for the workflow.

name - String the name for the analysis

newAnalysisDescription - String the description of the analysis being submitted

projectsToShare - A list of Projects to share analysis results with

writeResultsToSamples - If true, results of this pipeline will be saved back to the samples on successful completion.

emailPipelineResultCompleted - If true, user will be emailed if a pipeline successfully completes

emailPipelineResultError - If true, user will be emailed if a pipeline errors

Returns:

the AnalysisSubmission created for the files.

getPercentCompleteForAnalysisSubmission

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public float getPercentCompleteForAnalysisSubmission(java.lang.Long id)
                                              throws EntityNotFoundException,
                                                     ExecutionManagerException,
                                                     NoPercentageCompleteException

Given the id of an AnalysisSubmission gets the percentage complete.

Specified by:

getPercentCompleteForAnalysisSubmission in interface AnalysisSubmissionService

Parameters:

id - The id of an AnalysisSubmission.

Returns:

The percentage complete for this AnalysisSubmission.

Throws:

EntityNotFoundException - If no such corresponding submission exists.

NoPercentageCompleteException - An exception that indicates there is no percentage complete for the submission.

ExecutionManagerException - If there was an issue when contacting the execution manager.

getJobErrors

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public java.util.List<JobError> getJobErrors(java.lang.Long id)
                                      throws EntityNotFoundException

Get the JobError objects for a AnalysisSubmission id

Specified by:

getJobErrors in interface AnalysisSubmissionService

Parameters:

id - AnalysisSubmission id

Returns:

JobError objects for a AnalysisSubmission

Throws:

EntityNotFoundException - If no such AnalysisSubmission exists.

getFirstJobError

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadAnalysisSubmission\')")
public JobError getFirstJobError(java.lang.Long id)
                          throws EntityNotFoundException

Get first JobError for a AnalysisSubmission id

Specified by:

getFirstJobError in interface AnalysisSubmissionService

Parameters:

id - AnalysisSubmission id

Returns:

JobError object

Throws:

EntityNotFoundException - If no such AnalysisSubmission exists.

shareAnalysisSubmissionWithProject

@PreAuthorize("hasPermission(#submission, \'canUpdateAnalysisSubmission\') AND hasPermission(#project, \'canReadProject\')")
public ProjectAnalysisSubmissionJoin shareAnalysisSubmissionWithProject(AnalysisSubmission submission,
                                                                        Project project)

Share an AnalysisSubmission with a given Project

Specified by:

shareAnalysisSubmissionWithProject in interface AnalysisSubmissionService

Parameters:

submission - AnalysisSubmission to share

project - Project to share with

Returns:

a ProjectAnalysisSubmissionJoin describing the relationship

removeAnalysisProjectShare

@PreAuthorize("hasPermission(#submission, \'canUpdateAnalysisSubmission\') AND hasPermission(#project, \'canReadProject\')")
public void removeAnalysisProjectShare(AnalysisSubmission submission,
                                       Project project)

Cancel the share of an AnalysisSubmission with a given Project

Specified by:

removeAnalysisProjectShare in interface AnalysisSubmissionService

Parameters:

submission - the AnalysisSubmission to stop sharing

project - the Project to stop sharing with

findAnalysesByState

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public java.util.Collection<AnalysisSubmission> findAnalysesByState(java.util.Collection<AnalysisState> states)

Get a list of all AnalysisSubmissions with a given AnalysisState

Specified by:

findAnalysesByState in interface AnalysisSubmissionService

Parameters:

states - A list of AnalysisState to find AnalysisSubmissions for

Returns:

a Collection of AnalysisSubmission

getAnalysisSubmissionsSharedToProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.Collection<AnalysisSubmission> getAnalysisSubmissionsSharedToProject(Project project)

Get a collection of all AnalysisSubmissions shared with a Project.

Specified by:

getAnalysisSubmissionsSharedToProject in interface AnalysisSubmissionService

Parameters:

project - The Project to search.

Returns:

A collection of AnalysisSubmissions.

getAnalysisServiceStatus

@PreAuthorize("hasRole(\'ROLE_USER\')")
public AnalysisSubmissionService.AnalysisServiceStatus getAnalysisServiceStatus()

Get the status of the analysis service. This will be the number of running and queued analyses

Specified by:

getAnalysisServiceStatus in interface AnalysisSubmissionService

Returns:

An AnalysisSubmissionService.AnalysisServiceStatus object showing the number of running and queued analyses

getAnalysesRanInTimePeriod

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public java.lang.Long getAnalysesRanInTimePeriod(java.util.Date createdDate)

Get count of analyses run in the time period

Specified by:

getAnalysesRanInTimePeriod in interface AnalysisSubmissionService

Parameters:

createdDate - the minimum date for submissions ran

Returns:

An Long count of analyses ran

getAnalysesRanGrouped

@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public java.util.List<GenericStatModel> getAnalysesRanGrouped(java.util.Date createdDate,
                                                              StatisticTimePeriod statisticTimePeriod)

Get list of GenericStatModel of analyses run in the past n time period grouped by the format provided.

Specified by:

getAnalysesRanGrouped in interface AnalysisSubmissionService

Parameters:

createdDate - the minimum date for submissions ran

statisticTimePeriod - the enum containing format for which to group the results by

Returns:

An GenericStatModel list

getNumberAnalysesByUser

@PreAuthorize("hasRole(\'ROLE_USER\')")
public int getNumberAnalysesByUser(User user)

Get count of AnalysisSubmission for the user grouped by the format provided.

Specified by:

getNumberAnalysesByUser in interface AnalysisSubmissionService

Parameters:

user - The user identifier

Returns:

Count of analyses ran by user