ome.logic

Class MetadataImpl

java.lang.Object

ome.logic.AbstractLevel2Service

ome.logic.MetadataImpl

All Implemented Interfaces:

IMetadata, ServiceInterface, SelfConfigurableService

public class MetadataImpl
extends AbstractLevel2Service
implements IMetadata

Implement the IMetadata I/F.

Since:

3.0-Beta4

Author:

Jean-Marie Burel j.burel@dundee.ac.uk, Donald MacDonald donald@lifesci.dundee.ac.uk

Field Summary

Fields inherited from class ome.logic.AbstractLevel2Service

iQuery, iUpdate, metadata, queryFactory, sec

Fields inherited from interface ome.api.IMetadata

MOVIE_MPEG_NS, MOVIE_QT_NS, MOVIE_WMV_NS, NS_IMPORTER_ARCHIVED, NS_INSIGHT_RATING, NS_INSIGHT_TAG_SET

Constructor Summary

Constructors

Constructor and Description
MetadataImpl()

Method Summary

Modifier and Type	Method and Description
java.lang.Long	countAnnotationsUsedNotOwned(java.lang.Class annotationType, long userID) Counts the number of annotation of a given type used by the specified user but not owned by the user.
java.lang.Long	countSpecifiedAnnotations(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, Parameters options) Counts the number of annotation of a given type.
java.lang.Class<? extends ServiceInterface>	getServiceInterface() Returns the Interface implemented by this class.
java.util.Map	getTaggedObjectsCount(java.util.Set<java.lang.Long> tagIds, Parameters options) Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
<A extends Annotation> java.util.Set<A>	loadAnnotation(java.util.Set<java.lang.Long> annotationIds) Loads the specified annotations.
<T extends IObject,A extends Annotation> java.util.Map<java.lang.Long,java.util.Set<A>>	loadAnnotations(java.lang.Class<T> rootNodeType, java.util.Set<java.lang.Long> rootNodeIds, java.util.Set<java.lang.String> annotationTypes, java.util.Set<java.lang.Long> annotatorIds, Parameters options) Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
java.util.Set<IObject>	loadAnnotationsUsedNotOwned(java.lang.Class annotationType, long userID) Loads the annotations of a given type used by the specified user but not owned by the user.
java.util.Set	loadChannelAcquisitionData(java.util.Set<java.lang.Long> ids) Loads the logical channels and the acquisition metadata related to them.
Instrument	loadInstrument(long id) Loads the instrument and its components i.e. detectors, objectives, etc.
java.util.Map<java.lang.Long,java.util.Set<IObject>>	loadLogFiles(java.lang.Class<? extends IObject> rootNodeType, java.util.Set<java.lang.Long> ids) Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
<A extends Annotation> java.util.Set<A>	loadSpecifiedAnnotations(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, Parameters options) Loads all the annotations of a given type.
<A extends Annotation> java.util.Map<java.lang.Long,java.util.Set<A>>	loadSpecifiedAnnotationsLinkedTo(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, java.lang.Class rootNodeType, java.util.Set<java.lang.Long> rootNodeIds, Parameters options) Loads the annotations of a given type linked to the specified objects.
java.util.Map<java.lang.Long,java.util.Set<IObject>>	loadTagContent(java.util.Set<java.lang.Long> tagIds, Parameters options) Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
java.util.Set<IObject>	loadTagSets(Parameters options) Loads all the tag Sets.
void	setIContainer(IContainer iContainer) IContainer bean injector.

Methods inherited from class ome.logic.AbstractLevel2Service

getBeanHelper, getExtendedMetadata, getQueryFactory, getSecuritySystem, selfConfigure, setExtendedMetadata, setQueryFactory, setQueryService, setSecuritySystem, setUpdateService

Methods inherited from class java.lang.Object

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

Constructor Detail

MetadataImpl

public MetadataImpl()

Method Detail

getServiceInterface

public final java.lang.Class<? extends ServiceInterface> getServiceInterface()

Returns the Interface implemented by this class.

Specified by:

getServiceInterface in interface SelfConfigurableService

Returns:

See above.

setIContainer

public final void setIContainer(IContainer iContainer)

IContainer bean injector. For use during configuration. Can only be called once.

Parameters:

iContainer - The value to set.

loadInstrument

@Transactional(readOnly=true)
public Instrument loadInstrument(long id)

Description copied from interface: IMetadata

Loads the instrument and its components i.e. detectors, objectives, etc.

Specified by:

loadInstrument in interface IMetadata

Parameters:

id - The id of the instrument to load.

Returns:

See above

loadChannelAcquisitionData

@Transactional(readOnly=true)
public java.util.Set loadChannelAcquisitionData(java.util.Set<java.lang.Long> ids)

Description copied from interface: IMetadata

Loads the logical channels and the acquisition metadata related to them.

Specified by:

loadChannelAcquisitionData in interface IMetadata

Parameters:

ids - The collection of logical channel's ids. Mustn't be null.

Returns:

The collection of loaded logical channels.

loadAnnotations

@Transactional(readOnly=true)
public <T extends IObject,A extends Annotation> java.util.Map<java.lang.Long,java.util.Set<A>> loadAnnotations(java.lang.Class<T> rootNodeType,
                                                                                                                                             java.util.Set<java.lang.Long> rootNodeIds,
                                                                                                                                             java.util.Set<java.lang.String> annotationTypes,
                                                                                                                                             java.util.Set<java.lang.Long> annotatorIds,
                                                                                                                                             Parameters options)

Description copied from interface: IMetadata

Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds. If no types specified, all annotations will be loaded. This method looks for the annotations that have been attached to each of the specified objects. It then maps each rootNodeId onto the set of annotations that were found for that node. If no annotations were found for that node, then the entry will be null. Otherwise it will be a Set containing Annotation objects.

Specified by:

loadAnnotations in interface IMetadata

Parameters:

rootNodeType - The type of the nodes the annotations are linked to. Mustn't be null.

rootNodeIds - Ids of the objects of type rootNodeType. Mustn't be null.

annotationTypes - The types of annotation to retrieve. If null all annotations will be loaded. String of the type ome.model.annotations.*.

annotatorIds - Ids of the users for whom annotations should be retrieved. If null, all annotations returned.

Returns:

A map whose key is rootNodeId and value the Set of all annotations for that node or null.

loadSpecifiedAnnotations

@Transactional(readOnly=true)
public <A extends Annotation> java.util.Set<A> loadSpecifiedAnnotations(java.lang.Class type,
                                                                                                      java.util.Set<java.lang.String> include,
                                                                                                      java.util.Set<java.lang.String> exclude,
                                                                                                      Parameters options)

Description copied from interface: IMetadata

Loads all the annotations of a given type. It is possible to filter the annotations by including or excluding name spaces set on the annotations.

Specified by:

loadSpecifiedAnnotations in interface IMetadata

Parameters:

type - The type of annotations to load.

include - Include the annotations with the specified name spaces.

exclude - Exclude the annotations with the specified name spaces.

options - The POJO options.

Returns:

A collection of found annotations.

countSpecifiedAnnotations

@Transactional(readOnly=true)
public java.lang.Long countSpecifiedAnnotations(java.lang.Class type,
                                                                              java.util.Set<java.lang.String> include,
                                                                              java.util.Set<java.lang.String> exclude,
                                                                              Parameters options)

Description copied from interface: IMetadata

Counts the number of annotation of a given type.

Specified by:

countSpecifiedAnnotations in interface IMetadata

Parameters:

type - The type of annotations to load.

include - The collection of name space, one of the constants defined by this class.

exclude - The collection of name space, one of the constants defined by this class.

options - The POJO options.

Returns:

See above.

loadAnnotation

@Transactional(readOnly=true)
public <A extends Annotation> java.util.Set<A> loadAnnotation(java.util.Set<java.lang.Long> annotationIds)

Description copied from interface: IMetadata

Loads the specified annotations.

Specified by:

loadAnnotation in interface IMetadata

Parameters:

annotationIds - The collection of annotation's ids.

Returns:

See above.

loadTagContent

@Transactional(readOnly=true)
public java.util.Map<java.lang.Long,java.util.Set<IObject>> loadTagContent(java.util.Set<java.lang.Long> tagIds,
                                                                                                         Parameters options)

Description copied from interface: IMetadata

Loads the Tag Set if the id is specified otherwise loads all the Tag Set.

Specified by:

loadTagContent in interface IMetadata

Parameters:

tagIds - The id of the tag to load or -1.

options - The POJO options.

Returns:

Map whose key is a Tag/Tag Set and the value either a Map or a list of related DataObject.

loadTagSets

@Transactional(readOnly=true)
public java.util.Set<IObject> loadTagSets(Parameters options)

Description copied from interface: IMetadata

Loads all the tag Sets. Returns a collection of AnnotationAnnotatioLink objects and, if the orphan parameters is true, the TagAnnotation object. Note that the difference between a Tag Set and a Tag is made using the name space IMetadata.NS_INSIGHT_TAG_SET.

Specified by:

loadTagSets in interface IMetadata

Parameters:

options - The POJO options.

Returns:

See above.

getTaggedObjectsCount

@Transactional(readOnly=true)
public java.util.Map getTaggedObjectsCount(java.util.Set<java.lang.Long> tagIds,
                                                                         Parameters options)

Description copied from interface: IMetadata

Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.

Specified by:

getTaggedObjectsCount in interface IMetadata

Parameters:

tagIds - The collection of ids.

options - The POJO options.

Returns:

See above.

loadAnnotationsUsedNotOwned

@Transactional(readOnly=true)
public java.util.Set<IObject> loadAnnotationsUsedNotOwned(java.lang.Class annotationType,
                                                                                        long userID)

Description copied from interface: IMetadata

Loads the annotations of a given type used by the specified user but not owned by the user.

Specified by:

loadAnnotationsUsedNotOwned in interface IMetadata

Parameters:

annotationType - The type of annotations to load.

userID - The identifier of the user.

Returns:

See above.

countAnnotationsUsedNotOwned

@Transactional(readOnly=true)
public java.lang.Long countAnnotationsUsedNotOwned(java.lang.Class annotationType,
                                                                                 long userID)

Description copied from interface: IMetadata

Counts the number of annotation of a given type used by the specified user but not owned by the user.

Specified by:

countAnnotationsUsedNotOwned in interface IMetadata

Parameters:

annotationType - The type of annotations to load.

userID - The identifier of the user.

Returns:

See above.

loadSpecifiedAnnotationsLinkedTo

@Transactional(readOnly=true)
public <A extends Annotation> java.util.Map<java.lang.Long,java.util.Set<A>> loadSpecifiedAnnotationsLinkedTo(java.lang.Class type,
                                                                                                                                            java.util.Set<java.lang.String> include,
                                                                                                                                            java.util.Set<java.lang.String> exclude,
                                                                                                                                            java.lang.Class rootNodeType,
                                                                                                                                            java.util.Set<java.lang.Long> rootNodeIds,
                                                                                                                                            Parameters options)

Description copied from interface: IMetadata

Loads the annotations of a given type linked to the specified objects. It is possible to filter the annotations by including or excluding name spaces set on the annotations. This method looks for the annotations that have been attached to each of the specified objects. It then maps each rootNodeId onto the set of annotations that were found for that node. If no annotations were found for that node, the map will not contain an entry for that node. Otherwise it will be a Set containing Annotation objects. The rootNodeType supported are: Project, Dataset, Image, Pixels, Screen, Plate, PlateAcquisition, Well, Fileset.

Specified by:

loadSpecifiedAnnotationsLinkedTo in interface IMetadata

Parameters:

type - The type of annotations to load.

include - Include the annotations with the specified name spaces.

exclude - Exclude the annotations with the specified name spaces.

rootNodeType - The type of objects the annotations are linked to.

rootNodeIds - The identifiers of the objects.

options - The POJO options.

Returns:

A collection of found annotations.

loadLogFiles

@Transactional(readOnly=true)
public java.util.Map<java.lang.Long,java.util.Set<IObject>> loadLogFiles(java.lang.Class<? extends IObject> rootNodeType,
                                                                                                       java.util.Set<java.lang.Long> ids)

Description copied from interface: IMetadata

Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.

Specified by:

loadLogFiles in interface IMetadata

Parameters:

rootNodeType - the root node type, may be Image or Fileset

ids - the IDs of the entities for which the import log original file IDs are required

Returns:

the original file IDs of the import logs