fr.igred.omero

Interface Annotatable

All Superinterfaces:

RemoteObject

All Known Subinterfaces:

Dataset, Ellipse, Folder, Image, Line, Mask, Plate, PlateAcquisition, Point, Polygon, Polyline, Project, Rectangle, ROI, Screen, Shape, Text, Well

All Known Implementing Classes:

AnnotatableWrapper, DatasetWrapper, EllipseWrapper, FolderWrapper, ImageWrapper, ImportWrapper, LineWrapper, MaskWrapper, PlateAcquisitionWrapper, PlateWrapper, PointWrapper, PolygonWrapper, PolylineWrapper, ProjectWrapper, RectangleWrapper, ROIWrapper, ScreenWrapper, ShapeWrapper, TextWrapper, WellWrapper

public interface Annotatable
extends RemoteObject

Interface to handle Annotatable Objects on OMERO.

Method Summary

Modifier and Type	Method and Description
default 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, ReplacePolicy policy) Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
default void	addAndReplaceTable(Client client, Table 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, Table table, ReplacePolicy policy) Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
default long	addFile(DataManager dm, File file) Uploads a file and links it to the object
void	addKeyValuePair(DataManager dm, String key, String value) Adds a single Key-Value pair to the object.
default void	addTable(DataManager dm, Table table) Adds a table to the object in OMERO.
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.
default void	addTags(DataManager dm, Long... ids) Adds multiple tags by ID to the object in OMERO, if possible.
default void	copyAnnotationLinks(Client client, Annotatable object) Copies annotation links from some other object to this one.
default List<AnnotationData>	getAnnotationData(Browser browser) Retrieves annotations linked to the object.
List<Annotation>	getAnnotations(Browser browser) Retrieves annotations linked to the object (of known types).
List<FileAnnotation>	getFileAnnotations(Browser browser) Returns the file annotations
default List<Map.Entry<String,String>>	getKeyValuePairs(Browser browser) Gets the List of Key-Value pairs associated to an object.
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.
default List<Table>	getTables(DataManager dm) Gets all tables linked to the object in OMERO.
List<TagAnnotation>	getTags(Browser browser) Gets all tags linked to an object in OMERO, if possible.
default List<String>	getValues(Browser browser, String key) Gets the value from a Key-Value pair associated to the object.
default <A extends Annotation> boolean	isLinked(Browser browser, A annotation) Checks if a specific annotation is linked to the object.
default <A extends Annotation> void	link(DataManager dm, A annotation) Adds an annotation to the object in OMERO, if possible.
default <A extends AnnotationData> void	link(DataManager dm, A annotation) Attach an AnnotationData to this object.
default void	link(DataManager dm, Annotation... annotations) Adds multiple annotations to the object in OMERO, if possible.
default void	linkIfNotLinked(Client client, Annotation... 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).
<A extends Annotation> void	unlink(Client client, A annotation) Unlinks the given annotation from the current object.

Methods inherited from interface fr.igred.omero.RemoteObject

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

Method Detail

isLinked

default <A extends Annotation> boolean isLinked(Browser browser,
                                                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:

browser - The data browser.

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

default <A extends AnnotationData> void link(DataManager dm,
                                             A annotation)
                                      throws ServiceException,
                                             AccessException,
                                             ExecutionException

Attach an AnnotationData to this object.

Type Parameters:

A - The type of the annotation.

Parameters:

dm - The data manager.

annotation - The AnnotationData.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

link

default <A extends Annotation> void link(DataManager dm,
                                         A annotation)
                                  throws ServiceException,
                                         AccessException,
                                         ExecutionException

Adds an annotation to the object in OMERO, if possible.

Type Parameters:

A - The type of the annotation.

Parameters:

dm - 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

default void link(DataManager dm,
                  Annotation... annotations)
           throws ServiceException,
                  AccessException,
                  ExecutionException

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

Parameters:

dm - The data manager.

annotations - Annotations to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

linkIfNotLinked

default void linkIfNotLinked(Client client,
                             Annotation... 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

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

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

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

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

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

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.

addTags

default void addTags(DataManager dm,
                     Long... ids)
              throws ServiceException,
                     AccessException,
                     ExecutionException

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

Parameters:

dm - The data manager.

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

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

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

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

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

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

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

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

Adds a single Key-Value pair to the object.

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.

getKeyValuePairs

default List<Map.Entry<String,String>> getKeyValuePairs(Browser browser)
                                                 throws ServiceException,
                                                        AccessException,
                                                        ExecutionException

Gets the List of Key-Value pairs associated to an object.

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.

getValues

default List<String> getValues(Browser browser,
                               String key)
                        throws ServiceException,
                               AccessException,
                               ExecutionException

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

Parameters:

browser - The data browser.

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.

rate

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.

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

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

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

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.

addTable

default void addTable(DataManager dm,
                      Table table)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Adds a table to the object in OMERO.

Parameters:

dm - The data manager.

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

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.

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.

addAndReplaceTable

default void addAndReplaceTable(Client client,
                                Table table)
                         throws ServiceException,
                                AccessException,
                                ExecutionException,
                                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.

getTable

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

Gets a certain table linked to the object in OMERO.

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.

getTables

default List<Table> getTables(DataManager dm)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

Gets all tables linked to the object in OMERO.

Parameters:

dm - The data manager.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addFile

default long addFile(DataManager dm,
                     File file)
              throws ExecutionException,
                     InterruptedException

Uploads a file and links it to the object

Parameters:

dm - The data manager.

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

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.

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.

addAndReplaceFile

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

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.

getFileAnnotations

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

Returns the file annotations

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

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

InterruptedException - If block(long) does not return.

getAnnotationData

default List<AnnotationData> getAnnotationData(Browser browser)
                                        throws AccessException,
                                               ServiceException,
                                               ExecutionException

Retrieves annotations linked to the object.

Parameters:

browser - The data browser.

Returns:

A list of annotations, as AnnotationData.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getAnnotations

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

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

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.

copyAnnotationLinks

default void copyAnnotationLinks(Client client,
                                 Annotatable 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.