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

Class GenomeAssemblyRemoteServiceImpl

java.lang.Object

ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl<UploadedAssembly>

ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

All Implemented Interfaces:

GenomeAssemblyRemoteService, RemoteService<UploadedAssembly>

@Service
public class GenomeAssemblyRemoteServiceImpl
extends RemoteServiceImpl<UploadedAssembly>
implements GenomeAssemblyRemoteService

An implementation of GenomeAssemblyRemoteService using a GenomeAssemblyRemoteRepository to read remote GenomeAssembly

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	SAMPLE_ASSEMBLY_REL

Constructor Summary

Constructors

Constructor	Description
GenomeAssemblyRemoteServiceImpl(GenomeAssemblyRemoteRepository repository, RemoteAPIRepository remoteAPIRepository)	Create a new remote service that interacts with the given repository

Method Summary

Modifier and Type	Method	Description
java.util.List<UploadedAssembly>	getGenomeAssembliesForSample(Sample sample)	List the GenomeAssembly for a given Sample
UploadedAssembly	mirrorAssembly(UploadedAssembly seqObject)	Download the given UploadedAssembly to the local server

Methods inherited from class ca.corefacility.bioinformatics.irida.service.remote.impl.RemoteServiceImpl

getRemoteApiForURI, getServiceStatus, list, read, read

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.remote.RemoteService

getServiceStatus, list, read, read

Field Detail

SAMPLE_ASSEMBLY_REL

public static final java.lang.String SAMPLE_ASSEMBLY_REL

See Also:

Constant Field Values

Constructor Detail

GenomeAssemblyRemoteServiceImpl

public GenomeAssemblyRemoteServiceImpl(GenomeAssemblyRemoteRepository repository,
                                       RemoteAPIRepository remoteAPIRepository)

Create a new remote service that interacts with the given repository

Parameters:

repository - The GenomeAssemblyRemoteRepository to interact with remote apis

remoteAPIRepository - repository for storing and retrieving RemoteAPIs

Method Detail

getGenomeAssembliesForSample

public java.util.List<UploadedAssembly> getGenomeAssembliesForSample(Sample sample)
                                                              throws LinkNotFoundException

List the GenomeAssembly for a given Sample

Specified by:

getGenomeAssembliesForSample in interface GenomeAssemblyRemoteService

Parameters:

sample - the Sample to get assemblies for

Returns:

a list of UploadedAssembly

Throws:

LinkNotFoundException - if the targeted API does not support assemblies

mirrorAssembly

public UploadedAssembly mirrorAssembly(UploadedAssembly seqObject)

Download the given UploadedAssembly to the local server

Specified by:

mirrorAssembly in interface GenomeAssemblyRemoteService

Parameters:

seqObject - the UploadedAssembly to download

Returns:

a local copy of the UploadedAssembly