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

Class SequencingRunServiceImpl

java.lang.Object

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

ca.corefacility.bioinformatics.irida.service.impl.SequencingRunServiceImpl

All Implemented Interfaces:

CRUDService<java.lang.Long,SequencingRun>, SequencingRunService

@Service
public class SequencingRunServiceImpl
extends CRUDServiceImpl<java.lang.Long,SequencingRun>
implements SequencingRunService

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
SequencingRunServiceImpl(SequencingRunRepository repository, SequenceFileRepository sequenceFileRepository, SequencingObjectRepository objectRepository, SampleSequencingObjectJoinRepository ssoRepository, SampleRepository sampleRepository, AnalysisSubmissionRepository submissionRepository, UserRepository userRepository, javax.validation.Validator validator)

Method Summary

Modifier and Type	Method	Description
void	addSequencingObjectToSequencingRun(SequencingRun run, SequencingObject seqobject)	Create a join between a SequencingObject to a SequencingRun
SequencingRun	create(SequencingRun o)	Create a new object in the persistence store.
void	delete(java.lang.Long id)	Delete the object with the specified identifier from the database.
java.lang.Iterable<SequencingRun>	findAll()	List all objects of Type in the database.
org.springframework.data.domain.Page<SequencingRun>	list(int page, int size, org.springframework.data.domain.Sort sort)	List objects of Type in the database, limited to some specific page
org.springframework.data.domain.Page<SequencingRun>	list(int page, int size, org.springframework.data.domain.Sort.Direction order, java.lang.String... sortProperties)	List objects of Type in the database, limited to some specific page.
SequencingRun	read(java.lang.Long id)	Read the object type by unique identifier.
SequencingRun	update(SequencingRun object)	Update an object
SequencingRun	updateFields(java.lang.Long id, java.util.Map<java.lang.String,java.lang.Object> updatedFields)	Update properties of the given object by given fields.

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

count, exists, findRevisions, findRevisions, list, readMultiple, search, search, 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, exists, findRevisions, findRevisions, list, readMultiple, search, search, updateMultiple

Constructor Detail

SequencingRunServiceImpl

@Autowired
public SequencingRunServiceImpl(SequencingRunRepository repository,
                                SequenceFileRepository sequenceFileRepository,
                                SequencingObjectRepository objectRepository,
                                SampleSequencingObjectJoinRepository ssoRepository,
                                SampleRepository sampleRepository,
                                AnalysisSubmissionRepository submissionRepository,
                                UserRepository userRepository,
                                javax.validation.Validator validator)

Method Detail

read

@Transactional(readOnly=true)
@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\', \'ROLE_USER\', \'ROLE_TECHNICIAN\')")
public SequencingRun read(java.lang.Long id)

Read the object type by unique identifier.

Specified by:

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

Overrides:

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

Parameters:

id - The unique identifier for this object.

Returns:

The object corresponding to the unique identifier.

findAll

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\', \'ROLE_USER\', \'ROLE_TECHNICIAN\')")
@PostFilter("hasPermission(filterObject, \'canReadSequencingRun\')")
public java.lang.Iterable<SequencingRun> findAll()

List all objects of Type in the database.

Specified by:

findAll in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

findAll in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Returns:

All objects of the specified Type in the database.

addSequencingObjectToSequencingRun

@Transactional
@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\',\'ROLE_ADMIN\')")
public void addSequencingObjectToSequencingRun(SequencingRun run,
                                               SequencingObject seqobject)

Create a join between a SequencingObject to a SequencingRun

Specified by:

addSequencingObjectToSequencingRun in interface SequencingRunService

Parameters:

run - The SequencingRun

seqobject - The SequencingObject

create

@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\',\'ROLE_ADMIN\', \'ROLE_USER\')")
public SequencingRun create(SequencingRun o)

Description copied from class: CRUDServiceImpl

Create a new object in the persistence store.

Specified by:

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

Overrides:

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

Parameters:

o - The object to persist.

Returns:

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

delete

@Transactional
@PreAuthorize("hasRole(\'ROLE_ADMIN\')")
public void delete(java.lang.Long id)

Delete the object with the specified identifier from the database.

Specified by:

delete in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

delete in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Parameters:

id - The identifier of the object to delete.

updateFields

@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\',\'ROLE_ADMIN\') or hasPermission(#id, \'canUpdateSequencingRun\')")
public SequencingRun updateFields(java.lang.Long id,
                                  java.util.Map<java.lang.String,java.lang.Object> updatedFields)
                           throws javax.validation.ConstraintViolationException,
                                  EntityExistsException,
                                  InvalidPropertyException

Update properties of the given object by given fields. The object must have a valid identifier prior to being passed to this method.

Specified by:

updateFields in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

updateFields in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Parameters:

id - The identifier of the object to update.

updatedFields - the object properties that should be updated.

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.

InvalidPropertyException - If the updated properties map contains a property name that does not exist on the domain model.

update

@PreAuthorize("hasAnyRole(\'ROLE_SEQUENCER\',\'ROLE_ADMIN\') or hasPermission(#object, \'canUpdateSequencingRun\')")
public SequencingRun update(SequencingRun object)

Update an object

Specified by:

update in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

update in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Parameters:

object - The object to update

Returns:

The updated object

list

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\', \'ROLE_TECHNICIAN\')")
public org.springframework.data.domain.Page<SequencingRun> list(int page,
                                                                int size,
                                                                org.springframework.data.domain.Sort.Direction order,
                                                                java.lang.String... sortProperties)
                                                         throws java.lang.IllegalArgumentException

List objects of Type in the database, limited to some specific page.

Specified by:

list in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

list in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Parameters:

page - the specific page to use.

size - the size of the pages used to compute the number of pages.

order - the order of the sort.

sortProperties - the properties used to sort the collection.

Returns:

the list of users within the specified range.

Throws:

java.lang.IllegalArgumentException - If the Type has no public property sortProperty.

list

@PreAuthorize("hasAnyRole(\'ROLE_ADMIN\', \'ROLE_SEQUENCER\', \'ROLE_TECHNICIAN\')")
public org.springframework.data.domain.Page<SequencingRun> list(int page,
                                                                int size,
                                                                org.springframework.data.domain.Sort sort)
                                                         throws java.lang.IllegalArgumentException

List objects of Type in the database, limited to some specific page

Specified by:

list in interface CRUDService<java.lang.Long,SequencingRun>

Overrides:

list in class CRUDServiceImpl<java.lang.Long,SequencingRun>

Parameters:

page - the specific page to use

size - the size of the pages

sort - A Sort object for ordering the results

Returns:

a list of objects in the given range

Throws:

java.lang.IllegalArgumentException