Package ca.corefacility.bioinformatics.irida.repositories.analysis.submission

Interface AnalysisSubmissionRepository

All Superinterfaces:

org.springframework.data.repository.CrudRepository<AnalysisSubmission,java.lang.Long>, IridaJpaRepository<AnalysisSubmission,java.lang.Long>, org.springframework.data.jpa.repository.JpaSpecificationExecutor<AnalysisSubmission>, org.springframework.data.repository.PagingAndSortingRepository<AnalysisSubmission,java.lang.Long>, org.springframework.data.repository.Repository<AnalysisSubmission,java.lang.Long>, org.springframework.data.repository.history.RevisionRepository<AnalysisSubmission,java.lang.Long,java.lang.Integer>

public interface AnalysisSubmissionRepository
extends IridaJpaRepository<AnalysisSubmission,java.lang.Long>

A repository for managing AnalysisSubmission objects.

Method Summary

Modifier and Type	Method	Description
int	countAnalysesRanByUser(User user)	Get the count of AnalysisSubmissions ran by user
java.util.List<GenericStatModel>	countAnalysesRanGrouped(java.util.Date createdDate, java.lang.String groupByFormat)	Get a list of GenericStatModels for analyses ran in past n time period grouped by format provided.
java.lang.Long	countAnalysesRanInTimePeriod(java.util.Date createdDate)	Get the count of AnalysisSubmissions run in time period
java.lang.Long	countByAnalysisState(java.util.Collection<AnalysisState> state)	Get the analysis submissions that are currently in the given list of states
java.util.Set<AnalysisSubmission>	findAnalysisSubmissionsForSequencingObject(SequencingObject object)	Get the Set of AnalysisSubmissions which use a given SequencingObject
java.util.Set<AnalysisSubmission>	findAnalysisSubmissionsForSequencingObjectBySubmitter(SequencingObject object, User user)	Get the Set of AnalysisSubmissions which use a given SequencingObject for a given User
AnalysisSubmission	findByAnalysis(Analysis analysis)	Finds the AnalysisSubmission that caused the passed Analysis to be created.
java.util.List<AnalysisSubmission>	findByAnalysisState(AnalysisState state)	Loads up a list of AnalysisSubmissions with the given state.
java.util.List<AnalysisSubmission>	findByAnalysisState(AnalysisState analysisState, AnalysisCleanedState analysisCleanedState)	Loads up a list of AnalysisSubmissions with the given states.
java.util.List<AnalysisSubmission>	findByAnalysisState(java.util.Collection<AnalysisState> state)	Loads up a list of AnalysisSubmissions with the given state.
java.util.Set<AnalysisSubmission>	findByReferenceFile(ReferenceFile file)	Get the Set of AnalysisSubmissions making use of the given ReferenceFile.
java.util.Set<AnalysisSubmission>	findBySubmitter(User submitter)	Loads up all AnalysisSubmissions by the submitted User.
java.util.List<AnalysisSubmission>	findByWorkflowIds(java.util.Collection<java.util.UUID> workflowIds)	Finds all AnalysisSubmissions corresponding to the given workflow ids.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllAnalysisOutputInfoSharedWithProject(java.lang.Long projectId, java.util.Set<java.util.UUID> workflowIds)	Get all ProjectSampleAnalysisOutputInfo shared with a Project.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllAutomatedAnalysisOutputInfoForAProject(java.lang.Long projectId, java.util.Set<java.util.UUID> workflowIds)	Get all automated ProjectSampleAnalysisOutputInfo for a Project.
java.util.List<ProjectSampleAnalysisOutputInfo>	getAllUserAnalysisOutputInfo(java.lang.Long userId)	Get all User generated analysis output information.

Methods inherited from interface org.springframework.data.repository.CrudRepository

count, delete, deleteAll, deleteAll, deleteAllById, deleteById, existsById, findAll, findAllById, findById, save, saveAll

Methods inherited from interface org.springframework.data.jpa.repository.JpaSpecificationExecutor

count, exists, findAll, findAll, findAll, findOne

Methods inherited from interface org.springframework.data.repository.PagingAndSortingRepository

findAll, findAll

Methods inherited from interface org.springframework.data.repository.history.RevisionRepository

findLastChangeRevision, findRevision, findRevisions, findRevisions

Method Detail

findByAnalysisState

@Query("select s from AnalysisSubmission s where s.analysisState = ?1")
java.util.List<AnalysisSubmission> findByAnalysisState(AnalysisState state)

Loads up a list of AnalysisSubmissions with the given state.

Parameters:

state - The state of the analyses to search for.

Returns:

A List of AnalysisSubmission objects with the given state.

findByAnalysisState

@Query("select s from AnalysisSubmission s where s.analysisState in ?1")
java.util.List<AnalysisSubmission> findByAnalysisState(java.util.Collection<AnalysisState> state)

Loads up a list of AnalysisSubmissions with the given state.

Parameters:

state - A collection of states to search for.

Returns:

A List of AnalysisSubmission objects with the given state.

countByAnalysisState

@Query("select count(s.id) from AnalysisSubmission s where s.analysisState in ?1")
java.lang.Long countByAnalysisState(java.util.Collection<AnalysisState> state)

Get the analysis submissions that are currently in the given list of states

Parameters:

state - the list of states to get analyses fro

Returns:

the number of analyses with that state

findByAnalysisState

@Query("select s from AnalysisSubmission s where s.analysisState = ?1 and s.analysisCleanedState = ?2")
java.util.List<AnalysisSubmission> findByAnalysisState(AnalysisState analysisState,
                                                       AnalysisCleanedState analysisCleanedState)

Loads up a list of AnalysisSubmissions with the given states.

Parameters:

analysisState - The AnalysisState of the analyses to search for.

analysisCleanedState - The AnalysisCleanedState of the analyses to search for.

Returns:

A List of AnalysisSubmission objects with the given states.

findByWorkflowIds

@Query("select s from AnalysisSubmission s where s.workflowId in ?1")
java.util.List<AnalysisSubmission> findByWorkflowIds(java.util.Collection<java.util.UUID> workflowIds)

Finds all AnalysisSubmissions corresponding to the given workflow ids.

Parameters:

workflowIds - The workflow ids to match.

Returns:

A list of AnalysisSubmissions matching one of the workflow ids.

findBySubmitter

@Query("select s from AnalysisSubmission s where s.submitter = ?1")
java.util.Set<AnalysisSubmission> findBySubmitter(User submitter)

Loads up all AnalysisSubmissions by the submitted User.

Parameters:

submitter - The User who submitted the analysis.

Returns:

A List of AnalysisSubmissions by the User .

findByAnalysis

@Query("select s from AnalysisSubmission s where s.analysis = ?1")
AnalysisSubmission findByAnalysis(Analysis analysis)

Finds the AnalysisSubmission that caused the passed Analysis to be created.

Parameters:

analysis - the analysis to find the submission for

Returns:

the submission for the analysis

findAnalysisSubmissionsForSequencingObject

@Query("FROM AnalysisSubmission s WHERE ?1 IN elements(s.inputFiles)")
java.util.Set<AnalysisSubmission> findAnalysisSubmissionsForSequencingObject(SequencingObject object)

Get the Set of AnalysisSubmissions which use a given SequencingObject

Parameters:

object - The SequencingObject to get submissions for

Returns:

Set of AnalysisSubmission

findAnalysisSubmissionsForSequencingObjectBySubmitter

@Query("FROM AnalysisSubmission s WHERE ?1 IN elements(s.inputFiles) AND s.submitter = ?2")
java.util.Set<AnalysisSubmission> findAnalysisSubmissionsForSequencingObjectBySubmitter(SequencingObject object,
                                                                                        User user)

Get the Set of AnalysisSubmissions which use a given SequencingObject for a given User

Parameters:

object - The SequencingObject to get submissions for

user - The user to get submissions for

Returns:

Set of AnalysisSubmission

findByReferenceFile

@Query("FROM AnalysisSubmission s WHERE ?1 = referenceFile")
java.util.Set<AnalysisSubmission> findByReferenceFile(ReferenceFile file)

Get the Set of AnalysisSubmissions making use of the given ReferenceFile.

Parameters:

file - The ReferenceFile.

Returns:

A Set of AnalysisSubmissions.

getAllUserAnalysisOutputInfo

java.util.List<ProjectSampleAnalysisOutputInfo> getAllUserAnalysisOutputInfo(java.lang.Long userId)

Get all User generated analysis output information.

Parameters:

userId - User id

Returns:

a list of ProjectSampleAnalysisOutputInfo

getAllAnalysisOutputInfoSharedWithProject

java.util.List<ProjectSampleAnalysisOutputInfo> getAllAnalysisOutputInfoSharedWithProject(java.lang.Long projectId,
                                                                                          java.util.Set<java.util.UUID> workflowIds)

Get all ProjectSampleAnalysisOutputInfo shared with a Project.

Parameters:

projectId - Project id

workflowIds - Workflow UUIDs of workflow pipelines to get output files for

Returns:

a list of ProjectSampleAnalysisOutputInfo

getAllAutomatedAnalysisOutputInfoForAProject

java.util.List<ProjectSampleAnalysisOutputInfo> getAllAutomatedAnalysisOutputInfoForAProject(java.lang.Long projectId,
                                                                                             java.util.Set<java.util.UUID> workflowIds)

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

Parameters:

projectId - Project id

workflowIds - Workflow UUIDs of workflow pipelines to get output files for

Returns:

a list of ProjectSampleAnalysisOutputInfo

countAnalysesRanInTimePeriod

@Query("select count(s.id) from AnalysisSubmission s where s.createdDate >= ?1")
java.lang.Long countAnalysesRanInTimePeriod(java.util.Date createdDate)

Get the count of AnalysisSubmissions run in time period

Parameters:

createdDate - The minimum created date for the analysis submission

Returns:

A count of AnalysisSubmissions run in time period.

countAnalysesRanGrouped

@Query("select new ca.corefacility.bioinformatics.irida.ria.web.admin.dto.statistics.GenericStatModel(function(\'date_format\', s.createdDate, ?2), count(s.id))from AnalysisSubmission s where s.createdDate >= ?1 group by function(\'date_format\', s.createdDate, ?2) order by function(\'date_format\', s.createdDate, ?2) asc")
java.util.List<GenericStatModel> countAnalysesRanGrouped(java.util.Date createdDate,
                                                         java.lang.String groupByFormat)

Get a list of GenericStatModels for analyses ran in past n time period grouped by format provided.

Parameters:

createdDate - The minimum created date for the analysis submission

groupByFormat - The format to use for grouping the results.

Returns:

A list of GenericStatModels

countAnalysesRanByUser

@Query("select count(s.id) from AnalysisSubmission s where s.submitter = ?1")
int countAnalysesRanByUser(User user)

Get the count of AnalysisSubmissions ran by user

Parameters:

user - The user to get the count of analyses for

Returns:

count of analyses ran by user