omero.api

Class _IContainerDisp

java.lang.Object

Ice.ObjectImpl

omero.api._IContainerDisp

All Implemented Interfaces:

Ice.Object, java.io.Serializable, java.lang.Cloneable, _IContainerOperations, _IContainerOperationsNC, _ServiceInterfaceOperations, _ServiceInterfaceOperationsNC, IContainer, ServiceInterface

Direct Known Subclasses:

_IContainerTie

public abstract class _IContainerDisp
extends Ice.ObjectImpl
implements IContainer

Provides methods for dealing with the core Pojos of OME. Included are: Projects, Datasets, Images.

Read API

The names of the methods correlate to how the function operates:

• load: start at container objects and work down toward the leaves, returning hierarchy (Project->Dataset->Image
• find: start at leaf objects and work up to containers, returning hierarchy
• get: retrieves only leaves in the hierarchy (currently only Images)

Options Mechanism

The options are used to add some constraints to the generic method e.g. load hierarchy trees images for a given user. This mechanism should give us enough flexibility to extend the API if necessary, e.g. in some cases we might want to retrieve the images with or without annotations

Most methods take such an options map which is built on the client-side using the Parameters class. The currently supported options are:

• annotator(Integer): If key exists but value null, annotations are retrieved for all objects in the hierarchy where they exist; if a valid experimenterID, annotations are only retrieved for that user. May not be used be all methods. Default: all annotations
• leaves(Boolean): if FALSE omits images from the returned hierarchy. May not be used by all methods. Default: true
• experimenter(Integer): enables filtering on a per-experimenter basis. This option has a method-specific (and possibly context-specific) meaning. Please see the individual methods.
• group(Integer): enables filtering on a per-group basis. The experimenter value is ignored if present and instead a similar filtering is done using all experimenters in the given group.

Write API

As outlined in TODO, the semantics of the Omero write API are based on three rules:

1. IObject-valued fields for which isLoaded() returns false are assumed filtered
2. Collection-valued fields that are null are assumed filtered
3. Collection-valued fields for which getDetails().isFiltered(String collectionName) returns true are assumed filtered. TODO: should we accept isFiltered for all fields?

In each of these cases, the server will reload that given field before attempting to save the graph.

For all write calls, the options map (see below) must contain the userId and the userGroupId for the newly created objects. TODO umask.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	__ids
static long	serialVersionUID

Fields inherited from interface omero.api.IContainer

ice_staticId

Constructor Summary

Constructors

Constructor and Description
_IContainerDisp()

Method Summary

Modifier and Type	Method and Description
static Ice.DispatchStatus	___createDataObject(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___createDataObjects(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___findContainerHierarchies(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___getCollectionCount(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___getImages(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___getImagesByOptions(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___getImagesBySplitFilesets(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___getUserImages(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___link(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___loadContainerHierarchy(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___retrieveCollection(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___unlink(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___updateDataObject(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___updateDataObjects(IContainer __obj, IceInternal.Incoming __inS, Ice.Current __current)
Ice.DispatchStatus	__dispatch(IceInternal.Incoming in, Ice.Current __current)
protected void	__readImpl(IceInternal.BasicStream __is)
protected void	__writeImpl(IceInternal.BasicStream __os)
void	createDataObject_async(AMD_IContainer_createDataObject __cb, IObject obj, Parameters options) Creates the specified data object.
void	createDataObjects_async(AMD_IContainer_createDataObjects __cb, java.util.List<IObject> dataObjects, Parameters options) Convenience method to save network calls.
void	findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies __cb, java.lang.String rootType, java.util.List<java.lang.Long> imageIds, Parameters options) Retrieves hierarchy trees in various hierarchies that contain the specified Images.
void	getCollectionCount_async(AMD_IContainer_getCollectionCount __cb, java.lang.String type, java.lang.String property, java.util.List<java.lang.Long> ids, Parameters options) Counts the number of members in a collection for a given object.
void	getImages_async(AMD_IContainer_getImages __cb, java.lang.String rootType, java.util.List<java.lang.Long> rootIds, Parameters options) Retrieve a user's (or all users') images within any given container.
void	getImagesByOptions_async(AMD_IContainer_getImagesByOptions __cb, Parameters options) Retrieves images by options.
void	getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets __cb, java.util.Map<java.lang.String,java.util.List<java.lang.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.
void	getUserImages_async(AMD_IContainer_getUserImages __cb, Parameters options) Retrieves a user's images.
protected void	ice_copyStateFrom(Ice.Object __obj)
java.lang.String	ice_id()
java.lang.String	ice_id(Ice.Current __current)
java.lang.String[]	ice_ids()
java.lang.String[]	ice_ids(Ice.Current __current)
boolean	ice_isA(java.lang.String s)
boolean	ice_isA(java.lang.String s, Ice.Current __current)
static java.lang.String	ice_staticId()
void	link_async(AMD_IContainer_link __cb, java.util.List<IObject> links, Parameters options) Convenience method for creating links.
void	loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy __cb, java.lang.String rootType, java.util.List<java.lang.Long> rootIds, Parameters options) Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below)
void	retrieveCollection_async(AMD_IContainer_retrieveCollection __cb, IObject obj, java.lang.String collectionName, Parameters options) Retrieves a collection with all members initialized (loaded).
void	unlink_async(AMD_IContainer_unlink __cb, java.util.List<IObject> links, Parameters options) Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.
void	updateDataObject_async(AMD_IContainer_updateDataObject __cb, IObject obj, Parameters options) Updates a data object.
void	updateDataObjects_async(AMD_IContainer_updateDataObjects __cb, java.util.List<IObject> objs, Parameters options) Convenience method to save network calls.

Methods inherited from class Ice.ObjectImpl

___ice_id, ___ice_ids, ___ice_isA, ___ice_ping, __checkMode, __read, __read, __readImpl, __write, __write, __writeImpl, clone, ice_dispatch, ice_dispatch, ice_operationAttributes, ice_ping, ice_ping, ice_postUnmarshal, ice_preMarshal

Methods inherited from class java.lang.Object

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

Methods inherited from interface omero.api._IContainerOperations

createDataObject_async, createDataObjects_async, findContainerHierarchies_async, getCollectionCount_async, getImages_async, getImagesByOptions_async, getImagesBySplitFilesets_async, getUserImages_async, link_async, loadContainerHierarchy_async, retrieveCollection_async, unlink_async, updateDataObject_async, updateDataObjects_async

Methods inherited from interface Ice.Object

__read, __read, __write, __write, clone, ice_dispatch, ice_dispatch, ice_operationAttributes, ice_ping, ice_ping, ice_postUnmarshal, ice_preMarshal

Field Detail

__ids

public static final java.lang.String[] __ids

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

_IContainerDisp

public _IContainerDisp()

Method Detail

ice_copyStateFrom

protected void ice_copyStateFrom(Ice.Object __obj)
                          throws java.lang.CloneNotSupportedException

Throws:

java.lang.CloneNotSupportedException

ice_isA

public boolean ice_isA(java.lang.String s)

Specified by:

ice_isA in interface Ice.Object

Overrides:

ice_isA in class Ice.ObjectImpl

ice_isA

public boolean ice_isA(java.lang.String s,
                       Ice.Current __current)

Specified by:

ice_isA in interface Ice.Object

Overrides:

ice_isA in class Ice.ObjectImpl

ice_ids

public java.lang.String[] ice_ids()

Specified by:

ice_ids in interface Ice.Object

Overrides:

ice_ids in class Ice.ObjectImpl

ice_ids

public java.lang.String[] ice_ids(Ice.Current __current)

Specified by:

ice_ids in interface Ice.Object

Overrides:

ice_ids in class Ice.ObjectImpl

ice_id

public java.lang.String ice_id()

Specified by:

ice_id in interface Ice.Object

Overrides:

ice_id in class Ice.ObjectImpl

ice_id

public java.lang.String ice_id(Ice.Current __current)

Specified by:

ice_id in interface Ice.Object

Overrides:

ice_id in class Ice.ObjectImpl

ice_staticId

public static java.lang.String ice_staticId()

createDataObject_async

public final void createDataObject_async(AMD_IContainer_createDataObject __cb,
                                         IObject obj,
                                         Parameters options)
                                  throws ServerError

Creates the specified data object.

A placeholder parent object is created if the data object is to be put in a collection.

For example, if the object is a Dataset, we first create a Project as parent then we set the Dataset parent as follows: //pseudo-code TODO Project p = new Project(id,false); dataset.addProject(p); then for each parent relationship a DataObject ILink is created.

Specified by:

createDataObject_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

obj - IObject. Supported: Project, Dataset, Annotation, Group, Experimenter. Not null.

options - Parameters as above.

Throws:

ServerError

createDataObjects_async

public final void createDataObjects_async(AMD_IContainer_createDataObjects __cb,
                                          java.util.List<IObject> dataObjects,
                                          Parameters options)
                                   throws ServerError

Convenience method to save network calls. Loops over the array of IObjects calling createDataObject.

Specified by:

createDataObjects_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

dataObjects - Array of Omero IObjects

options - Parameters as above.

Throws:

ServerError

findContainerHierarchies_async

public final void findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies __cb,
                                                 java.lang.String rootType,
                                                 java.util.List<java.lang.Long> imageIds,
                                                 Parameters options)
                                          throws ServerError

Retrieves hierarchy trees in various hierarchies that contain the specified Images.

This method will look for all the containers containing the specified Images and then for all containers containing those containers and on up the container hierarchy.

This method returns a Set with all root nodes that were found. Every root node is linked to the found objects and so on until the leaf nodes, which are Image objects. Note that the type of any root node in the returned set can be the given rootNodeType, any of its containees or an Image.

For example, say that you pass in the ids of six Images: i1, i2, i3, i4, i5, i6. If the P/D/I hierarchy in the DB looks like this:

 |                  __p1__                     
 |                 /      \                    
 |               _d1_    _d2_      d3          
 |              /    \  /    \     |           
 |             i1     i2     i3    i4    i5  i6
 

Then the returned set will contain p1, d3, i5, i6. All objects will be properly linked up.

Finally, this method will only retrieve the nodes that are connected in a tree to the specified leaf image nodes. Back to the previous example, if d1 contained image img500, then the returned object would not contain img500. In a similar way, if p1 contained ds300 and this dataset weren't linked to any of the i1, i2, i3, i4, i5, i6 images, then ds300 would not be part of the returned tree rooted by p1.

Specified by:

findContainerHierarchies_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

rootType - top-most type which will be searched for Can be Project. Not null.

imageIds - Contains the ids of the Images that sit at the bottom of the trees. Not null.

options - Parameters as above. annotator used. experimenter|group may be applied at the top-level only or at each level in the hierarchy, but will not apply to the leaf (Image) level.

Throws:

ServerError

getCollectionCount_async

public final void getCollectionCount_async(AMD_IContainer_getCollectionCount __cb,
                                           java.lang.String type,
                                           java.lang.String property,
                                           java.util.List<java.lang.Long> ids,
                                           Parameters options)
                                    throws ServerError

Counts the number of members in a collection for a given object. For example, if you wanted to retrieve the number of Images contained in a Dataset you would pass TODO.

Specified by:

getCollectionCount_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

type - The fully-qualified classname of the object to be tested

property - Name of the property on that class, omitting getters and setters.

ids - Set of Longs, the ids of the objects to test

options - Parameters. Unused.

Throws:

ServerError

getImages_async

public final void getImages_async(AMD_IContainer_getImages __cb,
                                  java.lang.String rootType,
                                  java.util.List<java.lang.Long> rootIds,
                                  Parameters options)
                           throws ServerError

Retrieve a user's (or all users') images within any given container. For example, all images in project, applying temporal filtering or pagination.

Specified by:

getImages_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

rootType - A Class which will have its hierarchy searched for Images. Not null.

rootIds - A set of ids of type rootNodeType Not null.

options - Parameters as above. No notion of leaves. experimenter|group apply at the Image level. OPTIONS: - startTime and/or endTime should be Timestamp.valueOf("YYYY-MM-DD hh:mm:ss.ms");

limit and offset are applied at the Image-level. That is, calling with Dataset.class, limit == 10 and offset == 0 will first perform one query to get an effective set of rootNodeIds, then getImages will be called with an effective rootNodeType of Image.class and the new ids.

acquisition data is only relevant for images.

Throws:

ServerError

getImagesByOptions_async

public final void getImagesByOptions_async(AMD_IContainer_getImagesByOptions __cb,
                                           Parameters options)
                                    throws ServerError

Retrieves images by options.

Specified by:

getImagesByOptions_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

options - Parameters as above. No notion of leaves. experimenter|group apply at the Image level and must be present. OPTIONS: - startTime and/or endTime should be Timestamp.valueOf("YYYY-MM-DD hh:mm:ss.ms"). acquisition data is only relevant for images.

Throws:

ServerError

getImagesBySplitFilesets_async

public final void getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets __cb,
                                                 java.util.Map<java.lang.String,java.util.List<java.lang.Long>> included,
                                                 Parameters options)
                                          throws ServerError

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. The return value lists both the fileset IDs and the image IDs in ascending order, the image ID lists separated by if they were included. Warning: following discussion in trac ticket 11019 the return type may be changed.

Specified by:

getImagesBySplitFilesets_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

included - the entities included

Throws:

ServerError

getUserImages_async

public final void getUserImages_async(AMD_IContainer_getUserImages __cb,
                                      Parameters options)
                               throws ServerError

Retrieves a user's images.

Specified by:

getUserImages_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

options - Parameters as above. No notion of leaves. experimenter|group apply at the Image level and must be present.

Throws:

ServerError

link_async

public final void link_async(AMD_IContainer_link __cb,
                             java.util.List<IObject> links,
                             Parameters options)
                      throws ServerError

Convenience method for creating links. Functionality also available from createDataObject

Specified by:

link_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

links - Array of links to be created.

Throws:

ServerError

loadContainerHierarchy_async

public final void loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy __cb,
                                               java.lang.String rootType,
                                               java.util.List<java.lang.Long> rootIds,
                                               Parameters options)
                                        throws ServerError

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. Similarly, all Images will be linked to their Pixel objects if included.

Note that objects are never duplicated. For example, if an Experimenter owns all the objects in the retrieved tree, then those objects will be linked to the same instance of Experimenter. Or if an Image is contained in more than one Dataset in the retrieved tree, then all enclosing Dataset objects will point to the same Image object. And so on.

Specified by:

loadContainerHierarchy_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

rootType - The type of the root node. Can be Project, Dataset, Screen or Plate. Cannot be null.

rootIds - The ids of the root nodes. Can be null if an Experimenter is specified in options, otherwise an Exception is thrown to prevent all images in the entire database from being downloaded.

options - Parameters as above. annotator, leaves, orphan, acquisition data used. acquisition data is only relevant for images and taken into account if the images are loaded. If rootNodeIds==null, experimenter|group must be set and filtering will be applied at the Class-level; e.g. to retrieve a user's Projects, or user's Datasets. If rootNodeIds!=null, the result will be filtered by the experimenter|group at the Image and intermediate levels if available. Due to the amount of data potentially linked a Screen/Plate, the leaves option is not taken into account when the root node is a Screen. orphan implies that objects which are not contained in an object of rootNodeType should also be returned.

Throws:

ServerError

retrieveCollection_async

public final void retrieveCollection_async(AMD_IContainer_retrieveCollection __cb,
                                           IObject obj,
                                           java.lang.String collectionName,
                                           Parameters options)
                                    throws ServerError

Retrieves a collection with all members initialized (loaded). This is useful when a collection has been nulled in a previous query.

Specified by:

retrieveCollection_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

obj - Can be unloaded.

options - Parameters. Unused.

Throws:

ServerError

unlink_async

public final void unlink_async(AMD_IContainer_unlink __cb,
                               java.util.List<IObject> links,
                               Parameters options)
                        throws ServerError

Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.

Specified by:

unlink_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

links - Not null.

Throws:

ServerError

updateDataObject_async

public final void updateDataObject_async(AMD_IContainer_updateDataObject __cb,
                                         IObject obj,
                                         Parameters options)
                                  throws ServerError

Updates a data object.

To link or unlink objects to the specified object, we should call the methods link or unlink. TODO Or do we use for example dataset.setProjects(set of projects) to add. Link has to be set as follows dataset→project and project→dataset. Alternatively, you can make sure that the collection is exactly how it should be in the database. If you can't guarantee this, it's best to send all your collections back as null

Specified by:

updateDataObject_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

obj - Pojos-based IObject. Supported: Project, Dataset, Annotation, Group, Experimenter.

options - Parameters as above.

Throws:

ServerError

updateDataObjects_async

public final void updateDataObjects_async(AMD_IContainer_updateDataObjects __cb,
                                          java.util.List<IObject> objs,
                                          Parameters options)
                                   throws ServerError

Convenience method to save network calls. Loops over the array of IObjects calling updateDataObject.

Specified by:

updateDataObjects_async in interface _IContainerOperationsNC

Parameters:

__cb - The callback object for the operation.

objs -

Throws:

ServerError

___loadContainerHierarchy

public static Ice.DispatchStatus ___loadContainerHierarchy(IContainer __obj,
                                                           IceInternal.Incoming __inS,
                                                           Ice.Current __current)

___findContainerHierarchies

public static Ice.DispatchStatus ___findContainerHierarchies(IContainer __obj,
                                                             IceInternal.Incoming __inS,
                                                             Ice.Current __current)

___getImages

public static Ice.DispatchStatus ___getImages(IContainer __obj,
                                              IceInternal.Incoming __inS,
                                              Ice.Current __current)

___getUserImages

public static Ice.DispatchStatus ___getUserImages(IContainer __obj,
                                                  IceInternal.Incoming __inS,
                                                  Ice.Current __current)

___getImagesByOptions

public static Ice.DispatchStatus ___getImagesByOptions(IContainer __obj,
                                                       IceInternal.Incoming __inS,
                                                       Ice.Current __current)

___getImagesBySplitFilesets

public static Ice.DispatchStatus ___getImagesBySplitFilesets(IContainer __obj,
                                                             IceInternal.Incoming __inS,
                                                             Ice.Current __current)

___getCollectionCount

public static Ice.DispatchStatus ___getCollectionCount(IContainer __obj,
                                                       IceInternal.Incoming __inS,
                                                       Ice.Current __current)

___retrieveCollection

public static Ice.DispatchStatus ___retrieveCollection(IContainer __obj,
                                                       IceInternal.Incoming __inS,
                                                       Ice.Current __current)

___createDataObject

public static Ice.DispatchStatus ___createDataObject(IContainer __obj,
                                                     IceInternal.Incoming __inS,
                                                     Ice.Current __current)

___createDataObjects

public static Ice.DispatchStatus ___createDataObjects(IContainer __obj,
                                                      IceInternal.Incoming __inS,
                                                      Ice.Current __current)

___unlink

public static Ice.DispatchStatus ___unlink(IContainer __obj,
                                           IceInternal.Incoming __inS,
                                           Ice.Current __current)

___link

public static Ice.DispatchStatus ___link(IContainer __obj,
                                         IceInternal.Incoming __inS,
                                         Ice.Current __current)

___updateDataObject

public static Ice.DispatchStatus ___updateDataObject(IContainer __obj,
                                                     IceInternal.Incoming __inS,
                                                     Ice.Current __current)

___updateDataObjects

public static Ice.DispatchStatus ___updateDataObjects(IContainer __obj,
                                                      IceInternal.Incoming __inS,
                                                      Ice.Current __current)

__dispatch

public Ice.DispatchStatus __dispatch(IceInternal.Incoming in,
                                     Ice.Current __current)

Specified by:

__dispatch in interface Ice.Object

Overrides:

__dispatch in class Ice.ObjectImpl

__writeImpl

protected void __writeImpl(IceInternal.BasicStream __os)

Overrides:

__writeImpl in class Ice.ObjectImpl

__readImpl

protected void __readImpl(IceInternal.BasicStream __is)

Overrides:

__readImpl in class Ice.ObjectImpl