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

Class SequencingObjectServiceImpl

java.lang.Object

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

ca.corefacility.bioinformatics.irida.service.impl.SequencingObjectServiceImpl

All Implemented Interfaces:

CRUDService<java.lang.Long,SequencingObject>, SequencingObjectService

@Service
public class SequencingObjectServiceImpl
extends CRUDServiceImpl<java.lang.Long,SequencingObject>
implements SequencingObjectService

Implementation of SequencingObjectService using a SequencingObjectRepository and SampleSequencingObjectJoinRepository to persist and load objects.

Field Summary

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

CREATED_DATE_SORT_PROPERTY, validator, valueType

Constructor Summary

Constructors

Constructor	Description
SequencingObjectServiceImpl(SequencingObjectRepository repository, SequenceFileRepository sequenceFileRepository, SampleSequencingObjectJoinRepository ssoRepository, SequenceConcatenationRepository concatenationRepository, javax.validation.Validator validator)

Method Summary

Modifier and Type	Method	Description
SampleSequencingObjectJoin	concatenateSequences(java.util.List<SequencingObject> toJoin, java.lang.String filename, Sample targetSample, boolean removeOriginals)	Concatenate a collection of SequencingObjects and save back to a Sample
SequencingObject	create(SequencingObject object)	Create a new object in the persistence store.
SampleSequencingObjectJoin	createSequencingObjectInSample(SequencingObject seqObject, Sample sample)	Create a new SequencingObject associated with a Sample
java.lang.Boolean	exists(java.lang.Long id)	Check to see if an identifier for Type exists in the database.
java.util.Collection<SampleSequencingObjectJoin>	getSequencesForSampleOfType(Sample sample, java.lang.Class<? extends SequencingObject> type)	Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type
java.util.Set<SequencingObject>	getSequencingObjectsForAnalysisSubmission(AnalysisSubmission submission)	Get the set of SequencingObjects associated with a given AnalysisSubmission
java.util.Collection<SampleSequencingObjectJoin>	getSequencingObjectsForSample(Sample sample)	Get all the SequencingObjects associate with a given Sample
java.util.Set<SequencingObject>	getSequencingObjectsForSequencingRun(SequencingRun sequencingRun)	Get all the SequencingObjects associated with a given SequencingRun
<Type extends SequencingObject> java.util.Set<Type>	getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission submission, java.lang.Class<Type> type)	Get all SequencingObjects of a given type associated with an AnalysisSubmission
<T extends SequencingObject> java.util.Map<Sample,T>	getUniqueSamplesForSequencingObjects(java.util.Set<T> sequenceFiles)	Gets a map of SequencingObjects and corresponding Sample s.
SequencingObject	read(java.lang.Long id)	Read the object type by unique identifier.
java.lang.Iterable<SequencingObject>	readMultiple(java.lang.Iterable<java.lang.Long> idents)	Read multiple objects by the given collection of identifiers
SequencingObject	readSequencingObjectForSample(Sample sample, java.lang.Long objectId)	Read a SequencingObject and verify that it belongs to a given Sample.
SequencingObject	updateRemoteStatus(java.lang.Long id, RemoteStatus remoteStatus)	Update the RemoteStatus for a SequencingObject

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

count, delete, findAll, findRevisions, findRevisions, list, list, list, 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, delete, findAll, findRevisions, findRevisions, list, list, list, search, search, update, updateFields, updateMultiple

Constructor Detail

SequencingObjectServiceImpl

@Autowired
public SequencingObjectServiceImpl(SequencingObjectRepository repository,
                                   SequenceFileRepository sequenceFileRepository,
                                   SampleSequencingObjectJoinRepository ssoRepository,
                                   SequenceConcatenationRepository concatenationRepository,
                                   javax.validation.Validator validator)

Method Detail

read

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\',\'ROLE_SEQUENCER\', \'ROLE_TECHNICIAN\') or hasPermission(#id, \'canReadSequencingObject\')")
public SequencingObject read(java.lang.Long id)
                      throws EntityNotFoundException

Read the object type by unique identifier.

Specified by:

read in interface CRUDService<java.lang.Long,SequencingObject>

Overrides:

read in class CRUDServiceImpl<java.lang.Long,SequencingObject>

Parameters:

id - The unique identifier for this object.

Returns:

The object corresponding to the unique identifier.

Throws:

EntityNotFoundException - If the identifier does not exist in the database.

create

@Transactional
@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\', \'ROLE_USER\')")
public SequencingObject create(SequencingObject object)
                        throws javax.validation.ConstraintViolationException,
                               EntityExistsException

Create a new object in the persistence store.

Specified by:

create in interface CRUDService<java.lang.Long,SequencingObject>

Overrides:

create in class CRUDServiceImpl<java.lang.Long,SequencingObject>

Parameters:

object - The object to persist.

Returns:

The object as it was persisted in the database. May modify the identifier of the object when returned.

Throws:

javax.validation.ConstraintViolationException - If the object being persisted cannot be validated by validation rules associated with the object.

EntityExistsException - If the object being persisted violates uniqueness constraints in the database.

createSequencingObjectInSample

@Transactional
@PreAuthorize("hasPermission(#sample, \'canUpdateSample\')")
public SampleSequencingObjectJoin createSequencingObjectInSample(SequencingObject seqObject,
                                                                 Sample sample)

Create a new SequencingObject associated with a Sample

Specified by:

createSequencingObjectInSample in interface SequencingObjectService

Parameters:

seqObject - The SequencingObject to create

sample - the Sample to associate it with

Returns:

a new SampleSequencingObjectJoin describing the relationship

getSequencingObjectsForSample

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\') or hasPermission(#sample, \'canReadSample\')")
public java.util.Collection<SampleSequencingObjectJoin> getSequencingObjectsForSample(Sample sample)

Get all the SequencingObjects associate with a given Sample

Specified by:

getSequencingObjectsForSample in interface SequencingObjectService

Parameters:

sample - The Sample to get sequences for

Returns:

A collection of SampleSequencingObjectJoin

getSequencesForSampleOfType

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\') or hasPermission(#sample, \'canReadSample\')")
public java.util.Collection<SampleSequencingObjectJoin> getSequencesForSampleOfType(Sample sample,
                                                                                    java.lang.Class<? extends SequencingObject> type)

Get a collection of SampleSequencingObjectJoins assocaited with a given Sample and of the given class type

Specified by:

getSequencesForSampleOfType in interface SequencingObjectService

Parameters:

sample - the Sample used in the join

type - The type of SequencingObject that must be in the join

Returns:

a Collection of SampleSequencingObjectJoin

readSequencingObjectForSample

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\') or hasPermission(#sample, \'canReadSample\')")
public SequencingObject readSequencingObjectForSample(Sample sample,
                                                      java.lang.Long objectId)

Read a SequencingObject and verify that it belongs to a given Sample.

Specified by:

readSequencingObjectForSample in interface SequencingObjectService

Parameters:

sample - the Sample to get the SequencingObject for

objectId - The SequencingObject ID

Returns:

A SequencingObject object

getUniqueSamplesForSequencingObjects

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\') or hasPermission(#sequenceFiles, \'canReadSequencingObject\')")
public <T extends SequencingObject> java.util.Map<Sample,T> getUniqueSamplesForSequencingObjects(java.util.Set<T> sequenceFiles)
                                                                                                throws DuplicateSampleException

Gets a map of SequencingObjects and corresponding Sample s.

Specified by:

getUniqueSamplesForSequencingObjects in interface SequencingObjectService

Type Parameters:

T - The type of sequencing object which should be returned

Parameters:

sequenceFiles - A Set of SequencingObjects.

Returns:

A Map of between Sample and SequencingObject.

Throws:

DuplicateSampleException - If there is a duplicate sample.

getSequencingObjectsForSequencingRun

@Transactional(readOnly=true)
@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\', \'ROLE_TECHNICIAN\')")
public java.util.Set<SequencingObject> getSequencingObjectsForSequencingRun(SequencingRun sequencingRun)

Get all the SequencingObjects associated with a given SequencingRun

Specified by:

getSequencingObjectsForSequencingRun in interface SequencingObjectService

Parameters:

sequencingRun - the run to get objects for

Returns:

a set of SequencingObject

readMultiple

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#idents, \'canReadSequencingObject\')")
public java.lang.Iterable<SequencingObject> readMultiple(java.lang.Iterable<java.lang.Long> idents)

Read multiple objects by the given collection of identifiers

Specified by:

readMultiple in interface CRUDService<java.lang.Long,SequencingObject>

Overrides:

readMultiple in class CRUDServiceImpl<java.lang.Long,SequencingObject>

Parameters:

idents - The unique identifiers of the objects to read

Returns:

A collection of the requested objects

exists

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadSequencingObject\')")
public java.lang.Boolean exists(java.lang.Long id)

Check to see if an identifier for Type exists in the database.

Specified by:

exists in interface CRUDService<java.lang.Long,SequencingObject>

Overrides:

exists in class CRUDServiceImpl<java.lang.Long,SequencingObject>

Parameters:

id - The identifier to check for.

Returns:

true if the identifier exists, false otherwise.

updateRemoteStatus

@PreAuthorize("hasRole(\'ROLE_ADMIN\') or hasPermission(#id, \'canReadSequencingObject\')")
public SequencingObject updateRemoteStatus(java.lang.Long id,
                                           RemoteStatus remoteStatus)
                                    throws javax.validation.ConstraintViolationException,
                                           EntityExistsException,
                                           InvalidPropertyException

Update the RemoteStatus for a SequencingObject

Specified by:

updateRemoteStatus in interface SequencingObjectService

Parameters:

id - ID of the objet to update

remoteStatus - a RemoteStatus to set

Returns:

the updated SequencingObject

Throws:

javax.validation.ConstraintViolationException

EntityExistsException

InvalidPropertyException

getSequencingObjectsForAnalysisSubmission

@PreAuthorize("hasPermission(#submission, \'canReadAnalysisSubmission\')")
public java.util.Set<SequencingObject> getSequencingObjectsForAnalysisSubmission(AnalysisSubmission submission)

Get the set of SequencingObjects associated with a given AnalysisSubmission

Specified by:

getSequencingObjectsForAnalysisSubmission in interface SequencingObjectService

Parameters:

submission - the AnalysisSubmission

Returns:

the associated SequencingObjects

getSequencingObjectsOfTypeForAnalysisSubmission

@PreAuthorize("hasPermission(#submission, \'canReadAnalysisSubmission\')")
public <Type extends SequencingObject> java.util.Set<Type> getSequencingObjectsOfTypeForAnalysisSubmission(AnalysisSubmission submission,
                                                                                                           java.lang.Class<Type> type)

Get all SequencingObjects of a given type associated with an AnalysisSubmission

Specified by:

getSequencingObjectsOfTypeForAnalysisSubmission in interface SequencingObjectService

Type Parameters:

Type - a class type extending SequencingObject

Parameters:

submission - the AnalysisSubmission

type - the class type of SequencingObject to return

Returns:

a set of the requested type

concatenateSequences

@PreAuthorize("hasPermission(#toJoin, \'canReadSequencingObject\') and hasPermission(#targetSample, \'canUpdateSample\')")
@Transactional
public SampleSequencingObjectJoin concatenateSequences(java.util.List<SequencingObject> toJoin,
                                                       java.lang.String filename,
                                                       Sample targetSample,
                                                       boolean removeOriginals)
                                                throws ConcatenateException

Concatenate a collection of SequencingObjects and save back to a Sample

Specified by:

concatenateSequences in interface SequencingObjectService

Parameters:

toJoin - the SequencingObjects to concatenate

filename - The name of the file to create on concatenation

targetSample - the Sample to save to

removeOriginals - Whether to remove the original SequencingObjects from the sample

Returns:

the new SampleSequencingObjectJoin

Throws:

ConcatenateException - if there was an error concatenating the sequences