ome.logic

Class PojosImpl

java.lang.Object

ome.logic.AbstractLevel2Service

ome.logic.PojosImpl

All Implemented Interfaces:

IContainer, ServiceInterface, SelfConfigurableService

@Transactional
public class PojosImpl
extends AbstractLevel2Service
implements IContainer

implementation of the Pojos service interface.

Since:

OMERO 2.0

Author:

Josh Moore, josh.moore@gmx.de

Field Summary

Fields inherited from class ome.logic.AbstractLevel2Service

iQuery, iUpdate, metadata, queryFactory, sec

Constructor Summary

Constructors

Constructor and Description
PojosImpl()

Method Summary

Modifier and Type	Method and Description
protected void	checkProperty(String type, String property)
protected void	checkType(String type)
IObject	createDataObject(IObject arg0, Parameters arg1) Creates the specified data object.
IObject[]	createDataObjects(IObject[] arg0, Parameters arg1) convenience method to save network calls.
Set	findContainerHierarchies(Class rootNodeType, Set imageIds, Parameters options) Retrieves hierarchy trees in various hierarchies that contain the specified Images.
Map	getCollectionCount(String type, String property, Set ids, Parameters options) Counts the number of members in a collection for a given object.
Set	getImages(Class rootNodeType, Set rootNodeIds, Parameters options) Retrieve a user's (or all users') images within any given container.
Set	getImagesByOptions(Parameters options) Retrieve images by options.
Map<Long,Map<Boolean,List<Long>>>	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.
Class<? extends ServiceInterface>	getServiceInterface() Returns the Interface implemented by this class.
Set	getUserImages(Parameters options) Retrieve a user's images.
ILink[]	link(ILink[] arg0, Parameters arg1) Convenience method for creating links.
Set	loadContainerHierarchy(Class rootNodeType, Set 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.
Collection	retrieveCollection(IObject arg0, String arg1, Parameters arg2) Retrieves a collection with all members initialized ("loaded").
void	unlink(ILink[] arg0, Parameters arg1) Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.
IObject	updateDataObject(IObject arg0, Parameters arg1) Updates a data object.
IObject[]	updateDataObjects(IObject[] arg0, Parameters arg1) convenience method to save network calls.

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

PojosImpl

public PojosImpl()

Method Detail

getServiceInterface

public final Class<? extends ServiceInterface> getServiceInterface()

Returns the Interface implemented by this class.

Specified by:

getServiceInterface in interface SelfConfigurableService

Returns:

See above.

loadContainerHierarchy

@Transactional(readOnly=true)
public Set loadContainerHierarchy(Class rootNodeType,
                                                                Set rootNodeIds,
                                                                Parameters options)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

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

rootNodeIds - 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. TODO should it be applied at all levels?

Returns:

a set of hierarchy trees. The requested node as root and all of its descendants. The type of the returned value will be rootNodeType, unless orphan is specified in which case objects of type rootNodeType and below may be returned.

findContainerHierarchies

@Transactional(readOnly=true)
public Set findContainerHierarchies(Class rootNodeType,
                                                                  Set imageIds,
                                                                  Parameters options)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

rootNodeType - 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.

Returns:

A Set with all root nodes that were found. TODO decide on use of experimenter option

getImages

@Transactional(readOnly=true)
public Set getImages(Class rootNodeType,
                                                   Set rootNodeIds,
                                                   Parameters options)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

rootNodeType - A Class which will have its hierarchy searched for Images. Not null. TODO types?

rootNodeIds - 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.

Returns:

A set of images.

See Also:

Parameters.paginate(Integer, Integer), Parameters.startTime(java.sql.Timestamp), Parameters.endTime(java.sql.Timestamp)

getImagesByOptions

@Transactional(readOnly=true)
public Set getImagesByOptions(Parameters options)

Description copied from interface: IContainer

Retrieve images by options.

Specified by:

getImagesByOptions in interface IContainer

Parameters:

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.

Returns:

A set of images.

getImagesBySplitFilesets

@Transactional(readOnly=true)
public Map<Long,Map<Boolean,List<Long>>> getImagesBySplitFilesets(Map<Class<? extends IObject>,List<Long>> included,
                                                                                                Parameters options)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

included - the entities included

options - parameters, presently ignored

Returns:

the partially included filesets

getUserImages

@Transactional(readOnly=true)
public Set getUserImages(Parameters options)

Description copied from interface: IContainer

Retrieve a user's images.

Specified by:

getUserImages in interface IContainer

Parameters:

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

Returns:

A set of images.

getCollectionCount

@Transactional(readOnly=true)
public Map getCollectionCount(String type,
                                                            String property,
                                                            Set ids,
                                                            Parameters options)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

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.

Returns:

A map from id integer to count integer

retrieveCollection

@Transactional(readOnly=true)
public Collection retrieveCollection(IObject arg0,
                                                                   String arg1,
                                                                   Parameters arg2)

Description copied from interface: IContainer

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

Specified by:

retrieveCollection in interface IContainer

Parameters:

arg0 - Can be "unloaded".

arg1 - public final static String from the IObject.class

arg2 - Parameters. Unused.

Returns:

An initialized collection.

createDataObject

@Transactional(readOnly=false)
public IObject createDataObject(IObject arg0,
                                                               Parameters arg1)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

arg0 - IObject. Supported: Project, Dataset, Annotation, Group, Experimenter. Not null.

arg1 - Parameters as above.

Returns:

the created object

createDataObjects

@Transactional(readOnly=false)
public IObject[] createDataObjects(IObject[] arg0,
                                                                  Parameters arg1)

Description copied from interface: IContainer

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

Specified by:

createDataObjects in interface IContainer

Parameters:

arg0 - Array of Omero IObjects

arg1 - Parameters as above.

See Also:

IContainer.createDataObject(IObject, Parameters)

unlink

@Transactional(readOnly=false)
public void unlink(ILink[] arg0,
                                                  Parameters arg1)

Description copied from interface: IContainer

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 in interface IContainer

Parameters:

arg0 - Not null.

arg1 - Parameters as above.

link

@Transactional(readOnly=false)
public ILink[] link(ILink[] arg0,
                                                   Parameters arg1)

Description copied from interface: IContainer

Convenience method for creating links. Functionality also availeble from IContainer.createDataObject(IObject, Parameters)

Specified by:

link in interface IContainer

Parameters:

arg0 - Array of links to be created.

arg1 - Parameters as above.

Returns:

the created links

updateDataObject

@Transactional(readOnly=false)
public IObject updateDataObject(IObject arg0,
                                                               Parameters arg1)

Description copied from interface: IContainer

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. Tink 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 in interface IContainer

Parameters:

arg0 - Pojos-based IObject. Supported: supported: Project, Dataset, Annotation, Group, Experimenter.

arg1 - Parameters as above.

Returns:

created data object

updateDataObjects

@Transactional(readOnly=false)
public IObject[] updateDataObjects(IObject[] arg0,
                                                                  Parameters arg1)

Description copied from interface: IContainer

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

Specified by:

updateDataObjects in interface IContainer

arg1 - Parameters as above.

Returns:

created data objects.

See Also:

IContainer.updateDataObject(IObject, Parameters)

checkType

protected void checkType(String type)

checkProperty

protected void checkProperty(String type,
                             String property)