fr.igred.omero.containers

Interface Project

All Superinterfaces:

Annotatable, RemoteObject, RepositoryObject

All Known Implementing Classes:

ProjectWrapper

public interface Project
extends RepositoryObject, Annotatable

Interface to handle Projects on OMERO.

Method Summary

Modifier and Type	Method and Description
default Dataset	addDataset(DataManager dm, Dataset dataset) Adds a dataset to the project in OMERO.
Dataset	addDataset(DataManager dm, String name, String description) Creates a dataset and adds it to the project in OMERO. .
ProjectData	asDataObject() Returns a ProjectData corresponding to the handled object.
default List<RepositoryObject>	getChildren(Browser browser) Gets the object children.
List<Dataset>	getDatasets() Gets all the datasets in the project available from OMERO.
default List<Dataset>	getDatasets(Browser browser) Reloads this project and retrieves the updated list of datasets contained in this project.
default List<Dataset>	getDatasets(String name) Gets the dataset with the specified name from OMERO
List<Image>	getImages(Browser browser) Gets all images in the project available from OMERO.
default List<Image>	getImages(Browser browser, String name) Gets all images in the project with a certain name from OMERO.
default List<Image>	getImages(Browser browser, String datasetName, String imageName) Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
default List<Image>	getImagesLike(Browser browser, String motif) Gets all images in the project with a certain motif in their name from OMERO.
default List<Image>	getImagesTagged(Browser browser, Long tagId) Gets all images in the project tagged with a specified tag from OMERO.
default List<Image>	getImagesTagged(Browser browser, TagAnnotation tag) Gets all images in the project tagged with a specified tag from OMERO.
default List<Image>	getImagesWithKey(Browser browser, String key) Gets all images in the project with a certain key
default List<Image>	getImagesWithKeyValuePair(Browser browser, String key, String value) Gets all images in the project with a certain key value pair from OMERO.
default List<RepositoryObject>	getParents(Browser browser) Returns an empty list as projects do not have parents.
void	reload(Browser browser) Reloads the project from OMERO.
void	removeDataset(Client client, Dataset dataset) Removes a dataset from the project in OMERO.
void	setDescription(String description) Sets the description of the project.
void	setName(String name) Sets the name of the project.

Methods inherited from interface fr.igred.omero.RepositoryObject

getDescription, getName

Methods inherited from interface fr.igred.omero.Annotatable

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addKeyValuePair, addTable, addTag, addTag, addTags, copyAnnotationLinks, getAnnotationData, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValues, isLinked, link, link, link, linkIfNotLinked, rate, unlink

Methods inherited from interface fr.igred.omero.RemoteObject

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

Method Detail

asDataObject

ProjectData asDataObject()

Returns a ProjectData corresponding to the handled object.

Specified by:

asDataObject in interface RemoteObject

Returns:

See above.

setName

void setName(String name)

Sets the name of the project.

Parameters:

name - The name of the project. Mustn't be null.

Throws:

IllegalArgumentException - If the name is null.

setDescription

void setDescription(String description)

Sets the description of the project.

Parameters:

description - The description of the project.

getParents

default List<RepositoryObject> getParents(Browser browser)

Returns an empty list as projects do not have parents.

Specified by:

getParents in interface RepositoryObject

Parameters:

browser - The data browser.

Returns:

See above.

getChildren

default List<RepositoryObject> getChildren(Browser browser)
                                    throws AccessException,
                                           ServiceException,
                                           ExecutionException

Gets the object children.

Specified by:

getChildren in interface RepositoryObject

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

AccessException - Cannot access data.

ServiceException - Cannot connect to OMERO.

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

getDatasets

List<Dataset> getDatasets()

Gets all the datasets in the project available from OMERO.

Returns:

Collection of Dataset.

getDatasets

default List<Dataset> getDatasets(Browser browser)
                           throws AccessException,
                                  ServiceException,
                                  ExecutionException

Reloads this project and retrieves the updated list of datasets contained in this project.

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.

getDatasets

default List<Dataset> getDatasets(String name)

Gets the dataset with the specified name from OMERO

Parameters:

name - Name of the dataset searched.

Returns:

List of dataset with the given name.

addDataset

Dataset addDataset(DataManager dm,
                   String name,
                   String description)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Creates a dataset and adds it to the project in OMERO. .

The project needs to be reloaded afterwards to list the new dataset.

Parameters:

dm - The client handling the connection.

name - Dataset name.

description - Dataset description.

Returns:

The object saved in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addDataset

default Dataset addDataset(DataManager dm,
                           Dataset dataset)
                    throws ServiceException,
                           AccessException,
                           ExecutionException

Adds a dataset to the project in OMERO.

The project needs to be reloaded afterwards to list the new dataset.

Parameters:

dm - The data manager.

dataset - Dataset to be added.

Returns:

The object saved in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

removeDataset

void removeDataset(Client client,
                   Dataset dataset)
            throws ServiceException,
                   AccessException,
                   ExecutionException,
                   InterruptedException

Removes a dataset from the project in OMERO.

Parameters:

client - The client handling the connection.

dataset - Dataset to remove.

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.

getImages

List<Image> getImages(Browser browser)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Gets all images in the project available from OMERO.

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.

getImages

default List<Image> getImages(Browser browser,
                              String name)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

Gets all images in the project with a certain name from OMERO.

Parameters:

browser - The data browser.

name - Name searched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

default List<Image> getImages(Browser browser,
                              String datasetName,
                              String imageName)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

Gets all images with a certain name from datasets with the specified name inside this project on OMERO.

Parameters:

browser - The data browser.

datasetName - Expected dataset name.

imageName - Expected image name.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesLike

default List<Image> getImagesLike(Browser browser,
                                  String motif)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Gets all images in the project with a certain motif in their name from OMERO.

Parameters:

browser - The data browser.

motif - Motif searched in an image name.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesTagged

default List<Image> getImagesTagged(Browser browser,
                                    TagAnnotation tag)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images in the project tagged with a specified tag from OMERO.

Parameters:

browser - The data browser.

tag - TagAnnotation containing the tag researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesTagged

default List<Image> getImagesTagged(Browser browser,
                                    Long tagId)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images in the project tagged with a specified tag from OMERO.

Parameters:

browser - The data browser.

tagId - Id of the tag researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesWithKey

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

Gets all images in the project with a certain key

Parameters:

browser - The data browser.

key - Name of the key researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesWithKeyValuePair

default List<Image> getImagesWithKeyValuePair(Browser browser,
                                              String key,
                                              String value)
                                       throws ServiceException,
                                              AccessException,
                                              ExecutionException

Gets all images in the project with a certain key value pair from OMERO.

Parameters:

browser - The data browser.

key - Name of the key researched.

value - Value associated with the key.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

reload

void reload(Browser browser)
     throws ServiceException,
            AccessException,
            ExecutionException

Reloads the project from OMERO.

Specified by:

reload in interface RepositoryObject

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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