omero.api

Interface _IContainerOperations

All Superinterfaces:

_ServiceInterfaceOperations

All Known Subinterfaces:

IContainer

All Known Implementing Classes:

_IContainerDisp, _IContainerTie, ContainerI

public interface _IContainerOperations
extends _ServiceInterfaceOperations

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.

Method Summary

Modifier and Type	Method and Description
void	createDataObject_async(AMD_IContainer_createDataObject __cb, IObject obj, Parameters options, Ice.Current __current) Creates the specified data object.
void	createDataObjects_async(AMD_IContainer_createDataObjects __cb, java.util.List<IObject> dataObjects, Parameters options, Ice.Current __current) 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, Ice.Current __current) 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, Ice.Current __current) 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, Ice.Current __current) Retrieve a user's (or all users') images within any given container.
void	getImagesByOptions_async(AMD_IContainer_getImagesByOptions __cb, Parameters options, Ice.Current __current) 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, Ice.Current __current) 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, Ice.Current __current) Retrieves a user's images.
void	link_async(AMD_IContainer_link __cb, java.util.List<IObject> links, Parameters options, Ice.Current __current) 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, Ice.Current __current) 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, Ice.Current __current) Retrieves a collection with all members initialized (loaded).
void	unlink_async(AMD_IContainer_unlink __cb, java.util.List<IObject> links, Parameters options, Ice.Current __current) 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, Ice.Current __current) Updates a data object.
void	updateDataObjects_async(AMD_IContainer_updateDataObjects __cb, java.util.List<IObject> objs, Parameters options, Ice.Current __current) Convenience method to save network calls.

Method Detail

loadContainerHierarchy_async

void loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy __cb,
                                  java.lang.String rootType,
                                  java.util.List<java.lang.Long> rootIds,
                                  Parameters options,
                                  Ice.Current __current)
                           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.

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.

__current - The Current object for the invocation.

Throws:

ServerError

findContainerHierarchies_async

void findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies __cb,
                                    java.lang.String rootType,
                                    java.util.List<java.lang.Long> imageIds,
                                    Parameters options,
                                    Ice.Current __current)
                             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.

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.

__current - The Current object for the invocation.

Throws:

ServerError

getImages_async

void getImages_async(AMD_IContainer_getImages __cb,
                     java.lang.String rootType,
                     java.util.List<java.lang.Long> rootIds,
                     Parameters options,
                     Ice.Current __current)
              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.

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.

__current - The Current object for the invocation.

Throws:

ServerError

getUserImages_async

void getUserImages_async(AMD_IContainer_getUserImages __cb,
                         Parameters options,
                         Ice.Current __current)
                  throws ServerError

Retrieves a user's images.

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.

__current - The Current object for the invocation.

Throws:

ServerError

getImagesByOptions_async

void getImagesByOptions_async(AMD_IContainer_getImagesByOptions __cb,
                              Parameters options,
                              Ice.Current __current)
                       throws ServerError

Retrieves images by options.

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.

__current - The Current object for the invocation.

Throws:

ServerError

getImagesBySplitFilesets_async

void getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets __cb,
                                    java.util.Map<java.lang.String,java.util.List<java.lang.Long>> included,
                                    Parameters options,
                                    Ice.Current __current)
                             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.

Parameters:

__cb - The callback object for the operation.

included - the entities included

__current - The Current object for the invocation.

Throws:

ServerError

getCollectionCount_async

void getCollectionCount_async(AMD_IContainer_getCollectionCount __cb,
                              java.lang.String type,
                              java.lang.String property,
                              java.util.List<java.lang.Long> ids,
                              Parameters options,
                              Ice.Current __current)
                       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.

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.

__current - The Current object for the invocation.

Throws:

ServerError

retrieveCollection_async

void retrieveCollection_async(AMD_IContainer_retrieveCollection __cb,
                              IObject obj,
                              java.lang.String collectionName,
                              Parameters options,
                              Ice.Current __current)
                       throws ServerError

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

Parameters:

__cb - The callback object for the operation.

obj - Can be unloaded.

options - Parameters. Unused.

__current - The Current object for the invocation.

Throws:

ServerError

createDataObject_async

void createDataObject_async(AMD_IContainer_createDataObject __cb,
                            IObject obj,
                            Parameters options,
                            Ice.Current __current)
                     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.

Parameters:

__cb - The callback object for the operation.

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

options - Parameters as above.

__current - The Current object for the invocation.

Throws:

ServerError

createDataObjects_async

void createDataObjects_async(AMD_IContainer_createDataObjects __cb,
                             java.util.List<IObject> dataObjects,
                             Parameters options,
                             Ice.Current __current)
                      throws ServerError

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

Parameters:

__cb - The callback object for the operation.

dataObjects - Array of Omero IObjects

options - Parameters as above.

__current - The Current object for the invocation.

Throws:

ServerError

unlink_async

void unlink_async(AMD_IContainer_unlink __cb,
                  java.util.List<IObject> links,
                  Parameters options,
                  Ice.Current __current)
           throws ServerError

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

Parameters:

__cb - The callback object for the operation.

links - Not null.

__current - The Current object for the invocation.

Throws:

ServerError

link_async

void link_async(AMD_IContainer_link __cb,
                java.util.List<IObject> links,
                Parameters options,
                Ice.Current __current)
         throws ServerError

Convenience method for creating links. Functionality also available from createDataObject

Parameters:

__cb - The callback object for the operation.

links - Array of links to be created.

__current - The Current object for the invocation.

Throws:

ServerError

updateDataObject_async

void updateDataObject_async(AMD_IContainer_updateDataObject __cb,
                            IObject obj,
                            Parameters options,
                            Ice.Current __current)
                     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

Parameters:

__cb - The callback object for the operation.

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

options - Parameters as above.

__current - The Current object for the invocation.

Throws:

ServerError

updateDataObjects_async

void updateDataObjects_async(AMD_IContainer_updateDataObjects __cb,
                             java.util.List<IObject> objs,
                             Parameters options,
                             Ice.Current __current)
                      throws ServerError

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

Parameters:

__cb - The callback object for the operation.

objs -

__current - The Current object for the invocation.

Throws:

ServerError