fr.igred.omero

Class AnnotatableWrapper<T extends DataObject>

java.lang.Object

fr.igred.omero.ObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

Type Parameters:

T - Subclass of DataObject

All Implemented Interfaces:

Annotatable, RemoteObject

Direct Known Subclasses:

FolderWrapper, ImageWrapper, ImportWrapper, PlateAcquisitionWrapper, PlateWrapper, ProjectWrapper, ROIWrapper, ShapeWrapper, WellWrapper

public abstract class AnnotatableWrapper<T extends DataObject>
extends ObjectWrapper<T>
implements Annotatable

Generic class containing an annotatable DataObject (or a subclass) object.

Field Summary

Fields inherited from class fr.igred.omero.ObjectWrapper

data

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AnnotatableWrapper(T o) Constructor of the class AnnotatableWrapper.

Method Summary

Modifier and Type	Method and Description
long	addAndReplaceFile(Client client, File file, ReplacePolicy policy) Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	addAndReplaceTable(Client client, Table table, ReplacePolicy policy) Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	addKeyValuePair(DataManager dm, String key, String value) Adds a single Key-Value pair to the object.
void	addTag(DataManager dm, Long id) Adds a tag to the object in OMERO, if possible.
void	addTag(DataManager dm, String name, String description) Adds a newly created tag to the object in OMERO, if possible.
protected abstract String	annotationLinkType() Returns the type of annotation link for this object.
List<Annotation>	getAnnotations(Browser browser) Retrieves annotations linked to the object (of known types).
List<FileAnnotation>	getFileAnnotations(Browser browser) Returns the file annotations
List<MapAnnotation>	getMapAnnotations(Browser browser) Gets all map annotations linked to an object in OMERO, if possible.
int	getMyRating(Browser browser) Returns the user rating for this object (averaged if multiple ratings are linked).
Table	getTable(DataManager dm, Long fileId) Gets a certain table linked to the object in OMERO.
List<TagAnnotation>	getTags(Browser browser) Gets all tags linked to an object in OMERO, if possible.
void	rate(Client client, int rating) Rates the object (using a rating annotation).
protected void	removeLink(Client client, String linkType, long childId) Removes the link of the given type with the given child ID.
<A extends Annotation> void	unlink(Client client, A annotation) Unlinks the given annotation from the current object.

Methods inherited from class fr.igred.omero.ObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, getCreated, getGroupId, getId, getOwner, getUpdated, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.igred.omero.Annotatable

addAndReplaceFile, addAndReplaceTable, addFile, addTable, addTags, copyAnnotationLinks, getAnnotationData, getKeyValuePairs, getTables, getValues, isLinked, link, link, link, linkIfNotLinked

Methods inherited from interface fr.igred.omero.RemoteObject

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, distinct, flatten, getCreated, getElementsOf, getGroupId, getId, getOwner, getUpdated, saveAndUpdate

Constructor Detail

AnnotatableWrapper

protected AnnotatableWrapper(T o)

Constructor of the class AnnotatableWrapper.

Parameters:

o - The annotatable DataObject to wrap in the AnnotatableWrapper.

Method Detail

annotationLinkType

protected abstract String annotationLinkType()

Returns the type of annotation link for this object.

Returns:

See above.

addTag

public void addTag(DataManager dm,
                   String name,
                   String description)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Adds a newly created tag to the object in OMERO, if possible.

Specified by:

addTag in interface Annotatable

Parameters:

dm - The data manager.

name - Tag Name.

description - Tag description.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTag

public void addTag(DataManager dm,
                   Long id)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Adds a tag to the object in OMERO, if possible.

Specified by:

addTag in interface Annotatable

Parameters:

dm - The data manager.

id - ID of the tag to add to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getTags

public List<TagAnnotation> getTags(Browser browser)
                            throws ServiceException,
                                   AccessException,
                                   ExecutionException

Gets all tags linked to an object in OMERO, if possible.

Specified by:

getTags in interface Annotatable

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getMapAnnotations

public List<MapAnnotation> getMapAnnotations(Browser browser)
                                      throws ServiceException,
                                             AccessException,
                                             ExecutionException

Gets all map annotations linked to an object in OMERO, if possible.

Specified by:

getMapAnnotations in interface Annotatable

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addKeyValuePair

public void addKeyValuePair(DataManager dm,
                            String key,
                            String value)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

Adds a single Key-Value pair to the object.

Specified by:

addKeyValuePair in interface Annotatable

Parameters:

dm - The data manager.

key - Name of the key.

value - Value associated to the key.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

rate

public void rate(Client client,
                 int rating)
          throws ServiceException,
                 AccessException,
                 ExecutionException,
                 InterruptedException

Rates the object (using a rating annotation).

If multiple ratings are present, only one will be kept and updated.

Specified by:

rate in interface Annotatable

Parameters:

client - The client handling the connection.

rating - The rating.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

getMyRating

public int getMyRating(Browser browser)
                throws ServiceException,
                       AccessException,
                       ExecutionException

Returns the user rating for this object (averaged if multiple ratings are linked).

Specified by:

getMyRating in interface Annotatable

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addAndReplaceTable

public void addAndReplaceTable(Client client,
                               Table table,
                               ReplacePolicy policy)
                        throws ServiceException,
                               AccessException,
                               ExecutionException,
                               InterruptedException

Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.

Specified by:

addAndReplaceTable in interface Annotatable

Parameters:

client - The client handling the connection.

table - Table to add to the object.

policy - Whether older tables should be unlinked, deleted or deleted only if they become orphaned.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

getTable

public Table getTable(DataManager dm,
                      Long fileId)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Gets a certain table linked to the object in OMERO.

Specified by:

getTable in interface Annotatable

Parameters:

dm - The data manager.

fileId - FileId of the table researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addAndReplaceFile

public long addAndReplaceFile(Client client,
                              File file,
                              ReplacePolicy policy)
                       throws ExecutionException,
                              InterruptedException,
                              AccessException,
                              ServiceException

Uploads a file, links it to the object and unlinks or deletes previous files with the same name.

Specified by:

addAndReplaceFile in interface Annotatable

Parameters:

client - The client handling the connection.

file - File to add.

policy - Whether older files should be unlinked, deleted or deleted only if they become orphaned.

Returns:

ID of the file created in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

getFileAnnotations

public List<FileAnnotation> getFileAnnotations(Browser browser)
                                        throws ExecutionException,
                                               ServiceException,
                                               AccessException

Returns the file annotations

Specified by:

getFileAnnotations in interface Annotatable

Parameters:

browser - The data browser.

Returns:

The list of tile annotations.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

unlink

public <A extends Annotation> void unlink(Client client,
                                          A annotation)
                                   throws ServiceException,
                                          AccessException,
                                          ExecutionException,
                                          InterruptedException

Unlinks the given annotation from the current object.

Specified by:

unlink in interface Annotatable

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - An annotation.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

removeLink

protected void removeLink(Client client,
                          String linkType,
                          long childId)
                   throws ServiceException,
                          AccessException,
                          ExecutionException,
                          InterruptedException

Removes the link of the given type with the given child ID.

Parameters:

client - The client handling the connection.

linkType - The link type.

childId - Link child ID.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

getAnnotations

public List<Annotation> getAnnotations(Browser browser)
                                throws AccessException,
                                       ServiceException,
                                       ExecutionException

Retrieves annotations linked to the object (of known types).

Specified by:

getAnnotations in interface Annotatable

Parameters:

browser - The data browser.

Returns:

A list of annotations.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.