ome.api

Interface IMetadata

All Superinterfaces:

ServiceInterface

All Known Implementing Classes:

MetadataImpl

public interface IMetadata
extends ServiceInterface

Provides method to interact with acquisition metadata and annotations.

Since:

3.0-Beta4

Version:

3.0

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
static String	MOVIE_MPEG_NS The name space used to indicate that the FileAnnotation is an MPEG file.
static String	MOVIE_QT_NS The name space used to indicate that the FileAnnotation is an QT file.
static String	MOVIE_WMV_NS The name space used to indicate that the FileAnnotation is an WMV file.
static String	NS_IMPORTER_ARCHIVED The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
static String	NS_INSIGHT_RATING The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].
static String	NS_INSIGHT_TAG_SET The name space indicating that the tag is used a tag set.

Method Summary

Modifier and Type	Method and Description
Long	countAnnotationsUsedNotOwned(Class annotationType, long userID) Counts the number of annotation of a given type used by the specified user but not owned by the user.
Long	countSpecifiedAnnotations(Class type, Set<String> include, Set<String> exclude, Parameters options) Counts the number of annotation of a given type.
Map<Long,Long>	getTaggedObjectsCount(Set<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> Set<A>	loadAnnotation(Set<Long> annotationIds) Loads the specified annotations.
<T extends IObject,A extends Annotation> Map<Long,Set<A>>	loadAnnotations(Class<T> nodeType, Set<Long> rootNodeIds, Set<String> annotationType, Set<Long> annotatorIds, Parameters options) Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
Set<IObject>	loadAnnotationsUsedNotOwned(Class annotationType, long userID) Loads the annotations of a given type used by the specified user but not owned by the user.
Set<LogicalChannel>	loadChannelAcquisitionData(Set<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.
Map<Long,Set<IObject>>	loadLogFiles(Class<? extends IObject> rootNodeType, Set<Long> ids) Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
<A extends Annotation> Set<A>	loadSpecifiedAnnotations(Class type, Set<String> include, Set<String> exclude, Parameters options) Loads all the annotations of a given type.
<A extends Annotation> Map<Long,Set<A>>	loadSpecifiedAnnotationsLinkedTo(Class type, Set<String> include, Set<String> exclude, Class rootNodeType, Set<Long> rootNodeIds, Parameters options) Loads the annotations of a given type linked to the specified objects.
Map<Long,Set<IObject>>	loadTagContent(Set<Long> tagIds, Parameters options) Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
Set<IObject>	loadTagSets(Parameters options) Loads all the tag Sets.

Field Detail

NS_INSIGHT_TAG_SET

static final String NS_INSIGHT_TAG_SET

The name space indicating that the tag is used a tag set.

See Also:

Constant Field Values

NS_INSIGHT_RATING

static final String NS_INSIGHT_RATING

The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].

See Also:

Constant Field Values

NS_IMPORTER_ARCHIVED

static final String NS_IMPORTER_ARCHIVED

The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.

See Also:

Constant Field Values

MOVIE_MPEG_NS

static final String MOVIE_MPEG_NS

The name space used to indicate that the FileAnnotation is an MPEG file.

See Also:

Constant Field Values

MOVIE_QT_NS

static final String MOVIE_QT_NS

The name space used to indicate that the FileAnnotation is an QT file.

See Also:

Constant Field Values

MOVIE_WMV_NS

static final String MOVIE_WMV_NS

The name space used to indicate that the FileAnnotation is an WMV file.

See Also:

Constant Field Values

Method Detail

loadChannelAcquisitionData

Set<LogicalChannel> loadChannelAcquisitionData(Set<Long> ids)

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

Parameters:

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

Returns:

The collection of loaded logical channels.

loadAnnotations

<T extends IObject,A extends Annotation> Map<Long,Set<A>> loadAnnotations(Class<T> nodeType,
                                                                          Set<Long> rootNodeIds,
                                                                          Set<String> annotationType,
                                                                          Set<Long> annotatorIds,
                                                                          Parameters options)

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.

Parameters:

nodeType - 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.

annotationType - 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.

options -

Returns:

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

loadSpecifiedAnnotations

<A extends Annotation> Set<A> loadSpecifiedAnnotations(Class type,
                                                       Set<String> include,
                                                       Set<String> exclude,
                                                       Parameters options)

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.

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.

loadTagContent

Map<Long,Set<IObject>> loadTagContent(Set<Long> tagIds,
                                      Parameters options)

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

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

Set<IObject> loadTagSets(Parameters options)

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 NS_INSIGHT_TAG_SET.

Parameters:

options - The POJO options.

Returns:

See above.

getTaggedObjectsCount

Map<Long,Long> getTaggedObjectsCount(Set<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.

Parameters:

tagIds - The collection of ids.

options - The POJO options.

Returns:

See above.

countSpecifiedAnnotations

Long countSpecifiedAnnotations(Class type,
                               Set<String> include,
                               Set<String> exclude,
                               Parameters options)

Counts the number of annotation of a given type.

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

<A extends Annotation> Set<A> loadAnnotation(Set<Long> annotationIds)

Loads the specified annotations.

Parameters:

annotationIds - The collection of annotation's ids.

Returns:

See above.

loadInstrument

Instrument loadInstrument(long id)

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

Parameters:

id - The id of the instrument to load.

Returns:

See above

countAnnotationsUsedNotOwned

Long countAnnotationsUsedNotOwned(Class annotationType,
                                  long userID)

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

Parameters:

annotationType - The type of annotations to load.

userID - The identifier of the user.

Returns:

See above.

loadAnnotationsUsedNotOwned

Set<IObject> loadAnnotationsUsedNotOwned(Class annotationType,
                                         long userID)

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

Parameters:

annotationType - The type of annotations to load.

userID - The identifier of the user.

Returns:

See above.

loadSpecifiedAnnotationsLinkedTo

<A extends Annotation> Map<Long,Set<A>> loadSpecifiedAnnotationsLinkedTo(Class type,
                                                                         Set<String> include,
                                                                         Set<String> exclude,
                                                                         Class rootNodeType,
                                                                         Set<Long> rootNodeIds,
                                                                         Parameters options)

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.

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

Map<Long,Set<IObject>> loadLogFiles(Class<? extends IObject> rootNodeType,
                                    Set<Long> ids)

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

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