Package | Description |
---|---|
ome.api |
Contains the central verbs of the Omero System.
|
ome.logic |
The central repository of implementations which will be accessible through this server.
|
ome.parameters |
Contains necessary parameters for various API methods throughout OMERO.
|
ome.services |
Base services package for OMERO API services
This includes classes that implement OMERO API services described as interfaces in the
OMERO Common component.
|
ome.services.query |
facilitates the creation of Hibernate Queries and Criteria.
|
ome.services.scripts | |
ome.services.search |
Internal search implementation classes.
|
ome.tools.hibernate |
Hibernate specific tools for the OMERO Server
Classes/Interfaces that implement Hibernate method mechanics for the OMERO server
Related Documentation
For more information, please see:
TODO
|
omero.util |
Modifier and Type | Method and Description |
---|---|
void |
Search.byHqlQuery(String query,
Parameters p)
Delegates to
IQuery.findAllByQuery(String, Parameters) method to
take advantage of the Search.and() , Search.or() , and
Search.not() methods, or queue-semantics. |
Long |
IMetadata.countSpecifiedAnnotations(Class type,
Set<String> include,
Set<String> exclude,
Parameters options)
Counts the number of annotation of a given type.
|
<T extends IObject> |
IContainer.createDataObject(T object,
Parameters options)
Creates the specified data object.
|
IObject[] |
IContainer.createDataObjects(IObject[] dataObjects,
Parameters options)
convenience method to save network calls.
|
<T extends IObject> |
IQuery.findAllByFullText(Class<T> type,
String query,
Parameters parameters)
executes a full text search based on Lucene.
|
<T extends IObject> |
IQuery.findAllByQuery(String queryName,
Parameters parameters)
executes the stored query with the given name.
|
<T extends IObject> |
IQuery.findByQuery(String queryName,
Parameters parameters)
executes the stored query with the given name.
|
<T extends IObject> |
IContainer.findContainerHierarchies(Class<T> rootNodeType,
Set<Long> imagesIds,
Parameters options)
Retrieves hierarchy trees in various hierarchies that contain the
specified Images.
|
Map |
IContainer.getCollectionCount(String type,
String property,
Set<Long> ids,
Parameters options)
Counts the number of members in a collection for a given object.
|
<T extends IObject> |
IContainer.getImages(Class<T> rootNodeType,
Set<Long> rootNodeIds,
Parameters options)
Retrieve a user's (or all users') images within any given container.
|
Set<Image> |
IContainer.getImagesByOptions(Parameters options)
Retrieve images by options.
|
Map<Long,Map<Boolean,List<Long>>> |
IContainer.getImagesBySplitFilesets(Map<Class<? extends IObject>,List<Long>> included,
Parameters options)
Given a list of IDs of certain entity types, calculates which filesets are split such that
a non-empty proper subset of their images are referenced, directly or indirectly, as being
included.
|
Map<Long,Long> |
IMetadata.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.
|
Set<Image> |
IContainer.getUserImages(Parameters options)
Retrieve a user's images.
|
ILink[] |
IContainer.link(ILink[] dataObjectLinks,
Parameters options)
Convenience method for creating links.
|
<T extends IObject,A extends Annotation> |
IMetadata.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 . |
<T extends IObject> |
IContainer.loadContainerHierarchy(Class<T> rootNodeType,
Set<Long> rootNodeIds,
Parameters options)
Retrieves hierarchy trees rooted by a given node (unless orphan is
specified -- See below)
This method also retrieves the Experimenters linked to the objects in the
tree.
|
<A extends Annotation> |
IMetadata.loadSpecifiedAnnotations(Class type,
Set<String> include,
Set<String> exclude,
Parameters options)
Loads all the annotations of a given type.
|
<A extends Annotation> |
IMetadata.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>> |
IMetadata.loadTagContent(Set<Long> tagIds,
Parameters options)
Loads the Tag Set if the id is specified otherwise loads all the Tag
Set.
|
Set<IObject> |
IMetadata.loadTagSets(Parameters options)
Loads all the tag Sets.
|
List<Object[]> |
IQuery.projection(String query,
Parameters parameters)
|
Collection |
IContainer.retrieveCollection(IObject dataObject,
String collectionName,
Parameters options)
Retrieves a collection with all members initialized ("loaded").
|
void |
IContainer.unlink(ILink[] dataObjectLinks,
Parameters options)
Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image
Note that the objects themselves aren't deleted, only the Link objects.
|
<T extends IObject> |
IContainer.updateDataObject(T dataObject,
Parameters options)
Updates a data object.
|
IObject[] |
IContainer.updateDataObjects(IObject[] dataObjects,
Parameters options)
convenience method to save network calls.
|
Modifier and Type | Method and Description |
---|---|
Long |
QueryImpl.aggByQuery(String agg,
String field,
String query,
Parameters params) |
Map<String,Long> |
QueryImpl.aggMapByQuery(String agg,
String mapKey,
String field,
String query,
Parameters params) |
Long |
MetadataImpl.countSpecifiedAnnotations(Class type,
Set<String> include,
Set<String> exclude,
Parameters options) |
IObject |
PojosImpl.createDataObject(IObject arg0,
Parameters arg1) |
IObject[] |
PojosImpl.createDataObjects(IObject[] arg0,
Parameters arg1) |
<T extends IObject> |
QueryImpl.findAllByFullText(Class<T> type,
String query,
Parameters params) |
<T extends IObject> |
QueryImpl.findAllByQuery(String queryName,
Parameters params) |
<T extends IObject> |
QueryImpl.findByQuery(String queryName,
Parameters params) |
Set |
PojosImpl.findContainerHierarchies(Class rootNodeType,
Set imageIds,
Parameters options) |
Map |
PojosImpl.getCollectionCount(String type,
String property,
Set ids,
Parameters options) |
Set |
PojosImpl.getImages(Class rootNodeType,
Set rootNodeIds,
Parameters options) |
Set |
PojosImpl.getImagesByOptions(Parameters options) |
Map<Long,Map<Boolean,List<Long>>> |
PojosImpl.getImagesBySplitFilesets(Map<Class<? extends IObject>,List<Long>> included,
Parameters options) |
Map |
MetadataImpl.getTaggedObjectsCount(Set<Long> tagIds,
Parameters options) |
Set |
PojosImpl.getUserImages(Parameters options) |
ILink[] |
PojosImpl.link(ILink[] arg0,
Parameters arg1) |
<T extends IObject,A extends Annotation> |
MetadataImpl.loadAnnotations(Class<T> rootNodeType,
Set<Long> rootNodeIds,
Set<String> annotationTypes,
Set<Long> annotatorIds,
Parameters options) |
Set |
PojosImpl.loadContainerHierarchy(Class rootNodeType,
Set rootNodeIds,
Parameters options) |
<A extends Annotation> |
MetadataImpl.loadSpecifiedAnnotations(Class type,
Set<String> include,
Set<String> exclude,
Parameters options) |
<A extends Annotation> |
MetadataImpl.loadSpecifiedAnnotationsLinkedTo(Class type,
Set<String> include,
Set<String> exclude,
Class rootNodeType,
Set<Long> rootNodeIds,
Parameters options) |
Map<Long,Set<IObject>> |
MetadataImpl.loadTagContent(Set<Long> tagIds,
Parameters options) |
Set<IObject> |
MetadataImpl.loadTagSets(Parameters options) |
List<Object[]> |
QueryImpl.projection(String query,
Parameters p) |
Collection |
PojosImpl.retrieveCollection(IObject arg0,
String arg1,
Parameters arg2) |
void |
PojosImpl.unlink(ILink[] arg0,
Parameters arg1) |
IObject |
PojosImpl.updateDataObject(IObject arg0,
Parameters arg1) |
IObject[] |
PojosImpl.updateDataObjects(IObject[] arg0,
Parameters arg1) |
Modifier and Type | Method and Description |
---|---|
Parameters |
Parameters.add(QueryParameter parameter) |
Parameters |
Parameters.addAlgorithm(String algo) |
Parameters |
Parameters.addAll(Parameters old)
adds all the information from the passed in Parameters instance to this
instance.
|
Parameters |
Parameters.addAll(QueryParameter[] queryParameters)
adds all the information from the passed in Parameters instance to this
instance.
|
Parameters |
Parameters.addBoolean(String name,
Boolean value) |
Parameters |
Parameters.addClass(Class klass) |
Parameters |
Parameters.addClass(String name,
Class value) |
Parameters |
Parameters.addId(Long id) |
Parameters |
Parameters.addIds(Collection ids) |
Parameters |
Parameters.addInteger(String name,
Integer value) |
Parameters |
Parameters.addList(String name,
List value) |
Parameters |
Parameters.addLong(String name,
Long value) |
Parameters |
Parameters.addMap(String name,
Map value) |
Parameters |
Parameters.addSet(String name,
Set value) |
Parameters |
Parameters.addString(String name,
String value) |
Parameters |
Parameters.allExps() |
Parameters |
Parameters.endTime(Timestamp timestamp) |
Parameters |
Parameters.exp(long id) |
Parameters |
Parameters.grp(long id) |
Parameters |
Parameters.leaves() |
Parameters |
Parameters.noLeaves() |
Parameters |
Parameters.noOrphan() |
Parameters |
Parameters.orphan() |
Parameters |
Parameters.page(Integer offset,
Integer limit) |
Parameters |
Parameters.paginate(Integer offset,
Integer limit) |
Parameters |
Parameters.setFilter(Filter filter) |
Parameters |
Parameters.setOptions(Options options) |
Parameters |
Parameters.startTime(Timestamp timestamp) |
Parameters |
Parameters.unique() |
Modifier and Type | Method and Description |
---|---|
Parameters |
Parameters.addAll(Parameters old)
adds all the information from the passed in Parameters instance to this
instance.
|
Constructor and Description |
---|
Parameters(Parameters old)
copy constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchBean.addParameters(Parameters params) |
void |
SearchBean.byHqlQuery(String query,
Parameters p) |
Modifier and Type | Field and Description |
---|---|
protected Parameters |
Query.params
container of
QueryParameter instances. |
Modifier and Type | Method and Description |
---|---|
Query |
ClassQuerySource.lookup(String queryID,
Parameters parameters) |
Query |
NullQuerySource.lookup(String queryID,
Parameters parameters) |
Query |
StringQuerySource.lookup(String queryID,
Parameters parameters) |
<T> Query<T> |
QueryFactory.lookup(String queryID,
Parameters params) |
abstract <T> Query<T> |
QuerySource.lookup(String queryID,
Parameters parameters)
map the queryID argument to some Query instance (including null).
|
Constructor and Description |
---|
AbstractClassIdsOptionsQuery(Parameters parameters) |
CollectionCountQueryDefinition(Parameters parameters) |
IObjectClassQuery(Parameters parameters) |
PojosFindAnnotationsQueryDefinition(Parameters parameters) |
PojosFindHierarchiesQueryDefinition(Parameters p) |
PojosGetImagesByOptionsQueryDefinition(Parameters parameters) |
PojosGetImagesQueryDefinition(Parameters parameters) |
PojosGetUserImagesQueryDefinition(Parameters parameters) |
PojosLoadHierarchyQueryDefinition(Parameters parameters) |
Query(Definitions definitions,
Parameters parameters)
main constructor used by subclasses.
|
StringQuery(Parameters parameters)
Default constructor, used primarily for testing.
|
StringQuery(SqlAction sql,
Parameters parameters) |
Modifier and Type | Method and Description |
---|---|
protected List<OriginalFile> |
ScriptFinder.loadScripts(ServiceFactory sf,
Parameters p)
Load all scripts that match the name, hash, and format for script
|
Modifier and Type | Method and Description |
---|---|
void |
SearchValues.copy(Parameters params)
Copies all known values from Parameters
|
Constructor and Description |
---|
HqlQuery(SearchValues values,
String query,
Parameters p) |
Modifier and Type | Method and Description |
---|---|
void |
QueryBuilder.params(Parameters params2) |
Modifier and Type | Method and Description |
---|---|
Parameters |
IceMapper.convert(omero.sys.Parameters params) |
Version: 5.3.5-ice35-b73
Copyright © 2017 The University of Dundee & Open Microscopy Environment. All Rights Reserved.