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

Class GenomeAssemblyServiceImpl

java.lang.Object

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

ca.corefacility.bioinformatics.irida.service.impl.GenomeAssemblyServiceImpl

All Implemented Interfaces:

CRUDService<java.lang.Long,GenomeAssembly>, GenomeAssemblyService

@Service
public class GenomeAssemblyServiceImpl
extends CRUDServiceImpl<java.lang.Long,GenomeAssembly>
implements GenomeAssemblyService

Service implementation for storing and retrieving GenomeAssembly

Field Summary

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

CREATED_DATE_SORT_PROPERTY, repository, validator, valueType

Constructor Summary

Constructors

Constructor	Description
GenomeAssemblyServiceImpl(GenomeAssemblyRepository repository, SampleGenomeAssemblyJoinRepository sampleGenomeAssemblyJoinRepository, javax.validation.Validator validator)

Method Summary

Modifier and Type	Method	Description
SampleGenomeAssemblyJoin	createAssemblyInSample(Sample sample, GenomeAssembly assembly)	Create a new GenomeAssembly in the given Sample
java.util.Collection<SampleGenomeAssemblyJoin>	getAssembliesForSample(Sample sample)	Get all GenomeAssembly for the given Sample
GenomeAssembly	getGenomeAssemblyForSample(Sample sample, java.lang.Long genomeAssemblyId)	Gets the genome assembly for a sample.
void	removeGenomeAssemblyFromSample(Sample sample, java.lang.Long genomeAssemblyId)	Deletes the given genome assembly from the given sample.

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

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

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

Constructor Detail

GenomeAssemblyServiceImpl

@Autowired
public GenomeAssemblyServiceImpl(GenomeAssemblyRepository repository,
                                 SampleGenomeAssemblyJoinRepository sampleGenomeAssemblyJoinRepository,
                                 javax.validation.Validator validator)

Method Detail

createAssemblyInSample

@Transactional
@PreAuthorize("hasPermission(#sample, \'canUpdateSample\')")
public SampleGenomeAssemblyJoin createAssemblyInSample(Sample sample,
                                                       GenomeAssembly assembly)

Create a new GenomeAssembly in the given Sample

Specified by:

createAssemblyInSample in interface GenomeAssemblyService

Parameters:

sample - the sample to add a new assembly

assembly - the assembly to create

Returns:

a new SampleGenomeAssemblyJoin

getAssembliesForSample

@PreAuthorize("hasPermission(#sample, \'canReadSample\')")
public java.util.Collection<SampleGenomeAssemblyJoin> getAssembliesForSample(Sample sample)

Get all GenomeAssembly for the given Sample

Specified by:

getAssembliesForSample in interface GenomeAssemblyService

Parameters:

sample - the sample to get assemblies for

Returns:

a collection of SampleGenomeAssemblyJoin

getGenomeAssemblyForSample

@PreAuthorize("hasPermission(#sample, \'canReadSample\')")
public GenomeAssembly getGenomeAssemblyForSample(Sample sample,
                                                 java.lang.Long genomeAssemblyId)

Gets the genome assembly for a sample.

Specified by:

getGenomeAssemblyForSample in interface GenomeAssemblyService

Parameters:

sample - The sample.

genomeAssemblyId - The id of the genome assembly.

Returns:

The GenomeAssembly with the given information.

removeGenomeAssemblyFromSample

@Transactional
@PreAuthorize("hasPermission(#sample, \'canUpdateSample\')")
public void removeGenomeAssemblyFromSample(Sample sample,
                                           java.lang.Long genomeAssemblyId)

Deletes the given genome assembly from the given sample.

Specified by:

removeGenomeAssemblyFromSample in interface GenomeAssemblyService

Parameters:

sample - The sample.

genomeAssemblyId - The genome assembly.