Package ca.corefacility.bioinformatics.irida.service.remote

Class ProjectSynchronizationService

java.lang.Object

ca.corefacility.bioinformatics.irida.service.remote.ProjectSynchronizationService

@Service
public class ProjectSynchronizationService
extends java.lang.Object

Service class to run a project synchornization task. Ths class will be responsible for communicating with Remote IRIDA installations and pulling metadata and sequencing data into the local installation.

Constructor Summary

Constructors

Constructor

Description

ProjectSynchronizationService(ProjectService projectService, SampleService sampleService, SequencingObjectService objectService, MetadataTemplateService metadataTemplateService, GenomeAssemblyService assemblyService, ProjectRemoteService projectRemoteService, SampleRemoteService sampleRemoteService, SingleEndSequenceFileRemoteService singleEndRemoteService, SequenceFilePairRemoteService pairRemoteService, GenomeAssemblyRemoteService assemblyRemoteService, Fast5ObjectRemoteService fast5ObjectRemoteService, RemoteAPITokenService tokenService, EmailController emailController)

Method Summary

Modifier and Type	Method	Description
void	findMarkedProjectsToSync()	Find projects which should be synchronized and launch a synchornization task.
void	findProjectsToMark()	Method checking for remote projects that have passed their frequency time.
void	syncAssembly(UploadedAssembly assembly, Sample sample)	Synchronize a given UploadedAssembly to the local installation
void	syncFast5File(Fast5Object fast5Object, Sample sample)	Synchronize a given Fast5Object to the local installation
java.util.List<ProjectSynchronizationException>	syncSample(Sample sample, Project project, java.util.Map<java.lang.String,Sample> existingSamples)	Synchronize a given Sample to the local installation.
void	syncSampleMetadata(Sample remoteSample, Sample localSample)	Synchronize the given sample's metadata
void	syncSequenceFilePair(SequenceFilePair pair, Sample sample)	Synchronize a given SequenceFilePair to the local installation.
void	syncSingleEndSequenceFile(SingleEndSequenceFile file, Sample sample)	Synchronize a given SingleEndSequenceFile to the local installation

Methods inherited from class java.lang.Object

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

Constructor Detail

ProjectSynchronizationService

@Autowired
public ProjectSynchronizationService(ProjectService projectService,
                                     SampleService sampleService,
                                     SequencingObjectService objectService,
                                     MetadataTemplateService metadataTemplateService,
                                     GenomeAssemblyService assemblyService,
                                     ProjectRemoteService projectRemoteService,
                                     SampleRemoteService sampleRemoteService,
                                     SingleEndSequenceFileRemoteService singleEndRemoteService,
                                     SequenceFilePairRemoteService pairRemoteService,
                                     GenomeAssemblyRemoteService assemblyRemoteService,
                                     Fast5ObjectRemoteService fast5ObjectRemoteService,
                                     RemoteAPITokenService tokenService,
                                     EmailController emailController)

Method Detail

findProjectsToMark

public void findProjectsToMark()

Method checking for remote projects that have passed their frequency time. It will mark them as RemoteStatus.SyncStatus.MARKED

findMarkedProjectsToSync

public void findMarkedProjectsToSync()

Find projects which should be synchronized and launch a synchornization task.

syncSample

public java.util.List<ProjectSynchronizationException> syncSample(Sample sample,
                                                                  Project project,
                                                                  java.util.Map<java.lang.String,Sample> existingSamples)

Synchronize a given Sample to the local installation.

Parameters:

sample - the Sample to synchronize. This should have been read from a remote api.

project - The Project the Sample belongs in.

existingSamples - A map of samples that have already been synchronized. These will be checked to see if they've been updated

Returns:

A list of ProjectSynchronizationExceptions, empty if no errors.

syncSampleMetadata

public void syncSampleMetadata(Sample remoteSample,
                               Sample localSample)

Synchronize the given sample's metadata

Parameters:

remoteSample - the sample read from the remote api

localSample - the local sample being saved

syncSingleEndSequenceFile

public void syncSingleEndSequenceFile(SingleEndSequenceFile file,
                                      Sample sample)

Synchronize a given SingleEndSequenceFile to the local installation

Parameters:

file - the SingleEndSequenceFile to sync

sample - the Sample to add the file to

syncFast5File

public void syncFast5File(Fast5Object fast5Object,
                          Sample sample)

Synchronize a given Fast5Object to the local installation

Parameters:

fast5Object - the Fast5Object to sync

sample - the Sample to add the file to

syncAssembly

public void syncAssembly(UploadedAssembly assembly,
                         Sample sample)

Synchronize a given UploadedAssembly to the local installation

Parameters:

assembly - the UploadedAssembly to sync

sample - the Sample to add the assembly to

syncSequenceFilePair

public void syncSequenceFilePair(SequenceFilePair pair,
                                 Sample sample)

Synchronize a given SequenceFilePair to the local installation.

Parameters:

pair - the SequenceFilePair to sync. This should have been read from a remote api.

sample - The Sample to add the pair to.