Package fr.igred.omero

Class AnnotatableWrapper<T extends DataObject>

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

Type Parameters:

T - Subclass of DataObject

Direct Known Subclasses:

GenericRepositoryObjectWrapper, GenericShapeWrapper, ROIWrapper

public abstract class AnnotatableWrapper<T extends DataObject>
extends GenericObjectWrapper<T>

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

Field Summary

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
long	addAndReplaceFile(Client client, File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
long	addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	addAndReplaceTable(Client client, TableWrapper table)	Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
void	addAndReplaceTable(Client client, TableWrapper table, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
long	addFile(Client client, File file)	Uploads a file and links it to the object
void	addFileAnnotation(Client client, FileAnnotationWrapper annotation)	Deprecated. Links a file annotation to the object.
void	addKeyValuePair(Client client, String key, String value)	Adds a single Key-Value pair to the object.
void	addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)	Deprecated. Adds a List of Key-Value pair to the object.
void	addPairKeyValue(Client client, String key, String value)	Deprecated. Adds a single Key-Value pair to the object.
void	addTable(Client client, TableWrapper table)	Adds a table to the object in OMERO.
void	addTag(Client client, TagAnnotationWrapper tag)	Deprecated. Adds a tag to the object in OMERO, if possible.
void	addTag(Client client, Long id)	Adds a tag to the object in OMERO, if possible.
void	addTag(Client client, String name, String description)	Adds a newly created tag to the object in OMERO, if possible.
void	addTags(Client client, TagAnnotationWrapper... tags)	Deprecated. Adds multiple tag to the object in OMERO, if possible.
void	addTags(Client client, Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
protected abstract String	annotationLinkType()	Returns the type of annotation link for this object.
void	copyAnnotationLinks(Client client, AnnotatableWrapper<?> object)	Copies annotation links from some other object to this one.
AnnotationList	getAnnotations(Client client)	Retrieves annotations linked to the object (of known types).
List<FileAnnotationWrapper>	getFileAnnotations(Client client)	Returns the file annotations
Map<String,String>	getKeyValuePairs(Client client)	Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).
List<MapAnnotationWrapper>	getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
int	getMyRating(Client client)	Returns the user rating for this object (averaged if multiple ratings are linked).
List<RatingAnnotationWrapper>	getRatings(Client client)	Returns all the ratings from all users for this object.
TableWrapper	getTable(Client client, Long fileId)	Gets a certain table linked to the object in OMERO.
List<TableWrapper>	getTables(Client client)	Gets all tables linked to the object in OMERO.
List<TagAnnotationWrapper>	getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
String	getValue(Client client, String key)	Gets the value from a Key-Value pair associated to the object.
<A extends GenericAnnotationWrapper<?>> boolean	isLinked(Client client, A annotation)	Checks if a specific annotation is linked to the object.
protected <A extends AnnotationData> void	link(Client client, A annotation)	Attach an AnnotationData to this object.
void	link(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO, if possible.
void	linkIfNotLinked(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO if they are not already linked.
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.
protected void	removeLinks(Client client, String linkType, Collection<Long> childIds)	Removes the link of the given type with the given child IDs.
<A extends GenericAnnotationWrapper<?>> void	unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
<A extends GenericAnnotationWrapper<?>> void	unlink(Client client, Collection<A> annotations)	Unlinks the given annotations from the current object.

Methods inherited from class fr.igred.omero.GenericObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, distinct, flatten, 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

Constructor Detail

AnnotatableWrapper

protected AnnotatableWrapper(T o)

Constructor of the class GenericRepositoryObjectWrapper.

Parameters:

o - The annotatable DataObject to wrap in the GenericRepositoryObjectWrapper.

Method Detail

annotationLinkType

protected abstract String annotationLinkType()

Returns the type of annotation link for this object.

Returns:

See above.

isLinked

public <A extends GenericAnnotationWrapper<?>> boolean isLinked(Client client,
                                                                A annotation)
                                                         throws ServiceException,
                                                                AccessException,
                                                                ExecutionException

Checks if a specific annotation is linked to the object.

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - Annotation to be checked.

Returns:

True if the object is linked to the given annotation, false otherwise.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

link

protected <A extends AnnotationData> void link(Client client,
                                               A annotation)
                                        throws ServiceException,
                                               AccessException,
                                               ExecutionException

Attach an AnnotationData to this object.

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - The AnnotationData.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

link

public <A extends GenericAnnotationWrapper<?>> void link(Client client,
                                                         A annotation)
                                                  throws ServiceException,
                                                         AccessException,
                                                         ExecutionException

Adds an annotation to the object in OMERO, if possible (and if it's not a TagSet).

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - Annotation to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

link

public void link(Client client,
                 GenericAnnotationWrapper<?>... annotations)
          throws ServiceException,
                 AccessException,
                 ExecutionException

Adds multiple annotations to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

annotations - Annotations to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

linkIfNotLinked

public void linkIfNotLinked(Client client,
                            GenericAnnotationWrapper<?>... annotations)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

Adds multiple annotations to the object in OMERO if they are not already linked.

Parameters:

client - The client handling the connection.

annotations - Annotations to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addTag

public void addTag(Client client,
                   String name,
                   String description)
            throws ServiceException,
                   AccessException,
                   ExecutionException

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

Parameters:

client - The client handling the connection.

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

@Deprecated
public void addTag(Client client,
                   TagAnnotationWrapper tag)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Deprecated.

Adds a tag to the object in OMERO, if possible. Use link(fr.igred.omero.Client, A) instead.

Parameters:

client - The client handling the connection.

tag - Tag to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addTag

public void addTag(Client client,
                   Long id)
            throws ServiceException,
                   AccessException,
                   ExecutionException

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

Parameters:

client - The client handling the connection.

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.

addTags

@Deprecated
public void addTags(Client client,
                    TagAnnotationWrapper... tags)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Deprecated.

Adds multiple tag to the object in OMERO, if possible. Use link(Client, GenericAnnotationWrapper[]) instead.

Parameters:

client - The client handling the connection.

tags - Array of tag annotations to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addTags

public void addTags(Client client,
                    Long... ids)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Adds multiple tags by ID to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

ids - Array of tag id in OMERO to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getTags

public List<TagAnnotationWrapper> getTags(Client client)
                                   throws ServiceException,
                                          AccessException,
                                          ExecutionException

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

Parameters:

client - The client handling the connection.

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<MapAnnotationWrapper> getMapAnnotations(Client client)
                                             throws ServiceException,
                                                    AccessException,
                                                    ExecutionException

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

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addPairKeyValue

@Deprecated
public void addPairKeyValue(Client client,
                            String key,
                            String value)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

Deprecated.

Adds a single Key-Value pair to the object.

Parameters:

client - The client handling the connection.

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.

addKeyValuePair

public void addKeyValuePair(Client client,
                            String key,
                            String value)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

Adds a single Key-Value pair to the object.

Parameters:

client - The client handling the connection.

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.

getKeyValuePairs

public Map<String,String> getKeyValuePairs(Client client)
                                          throws ServiceException,
                                                 AccessException,
                                                 ExecutionException

Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getValue

public String getValue(Client client,
                       String key)
                throws ServiceException,
                       AccessException,
                       ExecutionException

Gets the value from a Key-Value pair associated to the object.

Parameters:

client - The client handling the connection.

key - Key researched.

Returns:

Value associated to the key.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - Key not found.

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

getRatings

public List<RatingAnnotationWrapper> getRatings(Client client)
                                         throws ServiceException,
                                                AccessException,
                                                ExecutionException

Returns all the ratings from all users for this object.

Parameters:

client - The client handling the connection.

Returns:

See above.

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,
                 OMEROServerError,
                 InterruptedException

Rates the object (using a rating annotation).

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.

OMEROServerError - Server error.

InterruptedException - The thread was interrupted.

getMyRating

public int getMyRating(Client client)
                throws ServiceException,
                       AccessException,
                       ExecutionException

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

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addMapAnnotation

@Deprecated
public void addMapAnnotation(Client client,
                             MapAnnotationWrapper mapAnnotation)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Deprecated.

Adds a List of Key-Value pair to the object. Use link(fr.igred.omero.Client, A) instead.

The list is contained in the map annotation.

Parameters:

client - The client handling the connection.

mapAnnotation - The map annotation.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addTable

public void addTable(Client client,
                     TableWrapper table)
              throws ServiceException,
                     AccessException,
                     ExecutionException

Adds a table to the object in OMERO.

Parameters:

client - The client handling the connection.

table - Table to add to the object.

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,
                               TableWrapper table,
                               GenericRepositoryObjectWrapper.ReplacePolicy policy)
                        throws ServiceException,
                               AccessException,
                               ExecutionException,
                               OMEROServerError,
                               InterruptedException

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

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.

OMEROServerError - Server error.

addAndReplaceTable

public void addAndReplaceTable(Client client,
                               TableWrapper table)
                        throws ServiceException,
                               AccessException,
                               ExecutionException,
                               OMEROServerError,
                               InterruptedException

Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.

Parameters:

client - The client handling the connection.

table - Table to add to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

InterruptedException - The thread was interrupted.

OMEROServerError - Server error.

getTable

public TableWrapper getTable(Client client,
                             Long fileId)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets a certain table linked to the object in OMERO.

Parameters:

client - The client handling the connection.

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.

getTables

public List<TableWrapper> getTables(Client client)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all tables linked to the object in OMERO.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addFile

public long addFile(Client client,
                    File file)
             throws ExecutionException,
                    InterruptedException

Uploads a file and links it to the object

Parameters:

client - The client handling the connection.

file - File to add.

Returns:

ID of the file created in OMERO.

Throws:

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

InterruptedException - The thread was interrupted.

addAndReplaceFile

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

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

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.

OMEROServerError - Server error.

addAndReplaceFile

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

Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.

Parameters:

client - The client handling the connection.

file - File to add.

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.

OMEROServerError - Server error.

addFileAnnotation

@Deprecated
public void addFileAnnotation(Client client,
                              FileAnnotationWrapper annotation)
                       throws AccessException,
                              ServiceException,
                              ExecutionException

Deprecated.

Links a file annotation to the object. Use link(fr.igred.omero.Client, A) instead.

Parameters:

client - The client handling the connection.

annotation - FileAnnotationWrapper to link.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getFileAnnotations

public List<FileAnnotationWrapper> getFileAnnotations(Client client)
                                               throws ExecutionException,
                                                      ServiceException,
                                                      AccessException

Returns the file annotations

Parameters:

client - The client handling the connection.

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 GenericAnnotationWrapper<?>> void unlink(Client client,
                                                           A annotation)
                                                    throws ServiceException,
                                                           AccessException,
                                                           ExecutionException,
                                                           OMEROServerError,
                                                           InterruptedException

Unlinks the given annotation from the current object.

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.

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

unlink

public <A extends GenericAnnotationWrapper<?>> void unlink(Client client,
                                                           Collection<A> annotations)
                                                    throws ServiceException,
                                                           AccessException,
                                                           ExecutionException,
                                                           OMEROServerError,
                                                           InterruptedException

Unlinks the given annotations from the current object.

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotations - List of annotations

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

removeLinks

protected void removeLinks(Client client,
                           String linkType,
                           Collection<Long> childIds)
                    throws ServiceException,
                           OMEROServerError,
                           AccessException,
                           ExecutionException,
                           InterruptedException

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

Parameters:

client - The client handling the connection.

linkType - The link type.

childIds - List of link child IDs.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

removeLink

protected void removeLink(Client client,
                          String linkType,
                          long childId)
                   throws ServiceException,
                          OMEROServerError,
                          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.

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

getAnnotations

public AnnotationList getAnnotations(Client client)
                              throws AccessException,
                                     ServiceException,
                                     ExecutionException

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

Parameters:

client - The client handling the connection.

Returns:

A list of annotations.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

copyAnnotationLinks

public void copyAnnotationLinks(Client client,
                                AnnotatableWrapper<?> object)
                         throws AccessException,
                                ServiceException,
                                ExecutionException

Copies annotation links from some other object to this one.

Parameters:

client - The client handling the connection.

object - Other repository object to copy annotations from.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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