Package ca.corefacility.bioinformatics.irida.service

Interface AnalysisSubmissionService

All Superinterfaces:

CRUDService<java.lang.Long,AnalysisSubmission>

All Known Implementing Classes:

AnalysisSubmissionServiceImpl

public interface AnalysisSubmissionService
extends CRUDService<java.lang.Long,AnalysisSubmission>

A service for AnalysisSubmissions.

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	AnalysisSubmissionService.AnalysisServiceStatus	Class to store the number of running and queued analyses

Method Summary

Modifier and Type	Method	Description
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> unnamedParameters, 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 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> unnamedParameters, 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	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.util.Collection<AnalysisSubmission>	findAnalysesByState(java.util.Collection<AnalysisState> states)	Get a list of all AnalysisSubmissions with a given AnalysisState
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>	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.
AnalysisSubmissionTemplate	readAnalysisSubmissionTemplateForProject(java.lang.Long id, Project project)	Get an AnalysisSubmissionTemplate on the given Project
void	removeAnalysisProjectShare(AnalysisSubmission submission, Project project)	Cancel the share of an AnalysisSubmission with a given Project
ProjectAnalysisSubmissionJoin	shareAnalysisSubmissionWithProject(AnalysisSubmission submission, Project project)	Share an AnalysisSubmission with a given Project
AnalysisSubmission	updatePriority(AnalysisSubmission submission, AnalysisSubmission.Priority priority)	Update the priority of an AnalysisSubmission

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

count, create, delete, exists, findAll, findRevisions, findRevisions, list, list, list, read, readMultiple, search, search, update, updateFields, updateMultiple

Method Detail

getStateForAnalysisSubmission

AnalysisState getStateForAnalysisSubmission(java.lang.Long analysisSubmissionId)
                                     throws EntityNotFoundException

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

Parameters:

analysisSubmissionId - The id of this analysis.

Returns:

The state of this analysis.

Throws:

EntityNotFoundException - If the corresponding analysis cannot be found.

getAnalysisSubmissionsForUser

java.util.Set<AnalysisSubmission> getAnalysisSubmissionsForUser(User user)

Gets a Set of AnalysisSubmissions for a User.

Parameters:

user - The User to find all submissions for.

Returns:

A Set of AnalysisSubmissions for a user.

getAnalysisSubmissionsForCurrentUser

java.util.Set<AnalysisSubmission> getAnalysisSubmissionsForCurrentUser()

Gets a Set of AnalysisSubmissions for the current User.

Returns:

A Set of AnalysisSubmissions for the current user.

getAnalysisSubmissionsAccessibleByCurrentUserByWorkflowIds

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.

Parameters:

workflowIds - The workflow ids to match.

Returns:

A list of AnalysisSubmissions matching one of the workflow ids.

deleteMultiple

void deleteMultiple(java.util.Collection<java.lang.Long> ids)

Delete multiple AnalysisSubmissions

Parameters:

ids - the collection of IDs to delete

createMultipleSampleSubmission

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> unnamedParameters,
                                                  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 allowing multiple one SequenceFile or SequenceFilePair

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

unnamedParameters - 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 pipeline successfully completes

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

Returns:

the AnalysisSubmission created for the files.

createSingleSampleSubmission

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> unnamedParameters,
                                                                      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

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

unnamedParameters - 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.

createSingleSampleSubmissionTemplate

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

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

getAnalysisTemplatesForProject

java.util.List<AnalysisSubmissionTemplate> getAnalysisTemplatesForProject(Project project)

Get all the AnalysisSubmissionTemplates for a given Project

Parameters:

project - the Project to get templates for

Returns:

a list of all AnalysisSubmissionTemplates

readAnalysisSubmissionTemplateForProject

AnalysisSubmissionTemplate readAnalysisSubmissionTemplateForProject(java.lang.Long id,
                                                                    Project project)

Get an AnalysisSubmissionTemplate on the given Project

Parameters:

id - the AnalysisSubmissionTemplate id

project - the Project to get templates for

Returns:

the found AnalysisSubmissionTemplate

deleteAnalysisSubmissionTemplateForProject

void deleteAnalysisSubmissionTemplateForProject(java.lang.Long id,
                                                Project project)

Delete an AnalysisSubmissionTemplate from the given Project

Parameters:

id - The id of an AnalysisSubmissionTemplate.

project - the Project to delete from

getPercentCompleteForAnalysisSubmission

float getPercentCompleteForAnalysisSubmission(java.lang.Long id)
                                       throws EntityNotFoundException,
                                              NoPercentageCompleteException,
                                              ExecutionManagerException

Given the id of an AnalysisSubmission gets the percentage complete.

Parameters:

id - The id of an AnalysisSubmission.

Returns:

The percentage complete for this AnalysisSubmission.

Throws:

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

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

EntityNotFoundException - If no such corresponding submission exists.

getJobErrors

java.util.List<JobError> getJobErrors(java.lang.Long id)
                               throws EntityNotFoundException,
                                      ExecutionManagerException

Get the JobError objects for a AnalysisSubmission id

Parameters:

id - AnalysisSubmission id

Returns:

JobError objects for a AnalysisSubmission

Throws:

EntityNotFoundException - If no such AnalysisSubmission exists.

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

getFirstJobError

JobError getFirstJobError(java.lang.Long id)
                   throws EntityNotFoundException,
                          ExecutionManagerException

Get first JobError for a AnalysisSubmission id

Parameters:

id - AnalysisSubmission id

Returns:

JobError object

Throws:

EntityNotFoundException - If no such AnalysisSubmission exists.

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

shareAnalysisSubmissionWithProject

ProjectAnalysisSubmissionJoin shareAnalysisSubmissionWithProject(AnalysisSubmission submission,
                                                                 Project project)

Share an AnalysisSubmission with a given Project

Parameters:

submission - AnalysisSubmission to share

project - Project to share with

Returns:

a ProjectAnalysisSubmissionJoin describing the relationship

removeAnalysisProjectShare

void removeAnalysisProjectShare(AnalysisSubmission submission,
                                Project project)

Cancel the share of an AnalysisSubmission with a given Project

Parameters:

submission - the AnalysisSubmission to stop sharing

project - the Project to stop sharing with

findAnalysesByState

java.util.Collection<AnalysisSubmission> findAnalysesByState(java.util.Collection<AnalysisState> states)

Get a list of all AnalysisSubmissions with a given AnalysisState

Parameters:

states - A list of AnalysisState to find AnalysisSubmissions for

Returns:

a Collection of AnalysisSubmission

getAnalysisSubmissionsSharedToProject

java.util.Collection<AnalysisSubmission> getAnalysisSubmissionsSharedToProject(Project project)

Get a collection of all AnalysisSubmissions shared with a Project.

Parameters:

project - The Project to search.

Returns:

A collection of AnalysisSubmissions.

listSubmissionsForProject

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.

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

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

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

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.

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

updatePriority

AnalysisSubmission updatePriority(AnalysisSubmission submission,
                                  AnalysisSubmission.Priority priority)

Update the priority of an AnalysisSubmission

Parameters:

submission - the submission to update

priority - the new priority

Returns:

the updated submission

getAllUserAnalysisOutputInfo

java.util.List<ProjectSampleAnalysisOutputInfo> getAllUserAnalysisOutputInfo(User user)

Get all User generated AnalysisOutputFile info

Parameters:

user - User

Returns:

List of AnalysisOutputFile info

getAllAnalysisOutputInfoSharedWithProject

java.util.List<ProjectSampleAnalysisOutputInfo> getAllAnalysisOutputInfoSharedWithProject(java.lang.Long projectId)

Get all ProjectSampleAnalysisOutputInfo for a Project.

Parameters:

projectId - Project id

Returns:

a list of ProjectSampleAnalysisOutputInfo

getAllAutomatedAnalysisOutputInfoForAProject

java.util.List<ProjectSampleAnalysisOutputInfo> getAllAutomatedAnalysisOutputInfoForAProject(java.lang.Long projectId)

Get all automated ProjectSampleAnalysisOutputInfo for a Project.

Parameters:

projectId - Project id

Returns:

a list of ProjectSampleAnalysisOutputInfo

getAnalysisServiceStatus

AnalysisSubmissionService.AnalysisServiceStatus getAnalysisServiceStatus()

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

Returns:

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

getAnalysesRanInTimePeriod

java.lang.Long getAnalysesRanInTimePeriod(java.util.Date createdDate)

Get count of analyses run in the time period

Parameters:

createdDate - the minimum date for submissions ran

Returns:

An Long count of analyses ran

getAnalysesRanGrouped

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.

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

int getNumberAnalysesByUser(User user)

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

Parameters:

user - The user identifier

Returns:

Count of analyses ran by user