Package fr.igred.omero

Class Client

java.lang.Object

fr.igred.omero.GatewayWrapper

fr.igred.omero.Client

public class Client
extends GatewayWrapper

Basic class, contains the gateway, the security context, and multiple facilities.

Allows the user to connect to OMERO and browse through all the data accessible to the user.

Constructor Summary

Constructors

Constructor	Description
Client()	Constructor of the Client class.

Method Summary

Modifier and Type	Method	Description
void	delete(TableWrapper table)	Deletes a table from OMERO
void	delete(GenericObjectWrapper<?> object)	Deletes an object from OMERO.
void	delete(Collection<? extends GenericObjectWrapper<?>> objects)	Deletes multiple objects from OMERO.
DatasetWrapper	getDataset(Long id)	Gets the dataset with the specified id from OMERO.
List<DatasetWrapper>	getDatasets()	Gets all datasets available from OMERO.
List<DatasetWrapper>	getDatasets(Long... ids)	Gets the datasets with the specified ids from OMERO.
List<DatasetWrapper>	getDatasets(String name)	Gets all datasets with a certain name from OMERO.
GroupWrapper	getGroup(String groupName)	Returns the group which matches the name.
ImageWrapper	getImage(Long id)	Returns an ImageWrapper that contains the image with the specified id from OMERO.
List<ImageWrapper>	getImages()	Gets all images owned by the current user.
List<ImageWrapper>	getImages(Long... ids)	Gets the images with the specified ids from OMERO
List<ImageWrapper>	getImages(String name)	Gets all images with a certain name from OMERO.
List<ImageWrapper>	getImages(String projectName, String datasetName, String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
List<ImageWrapper>	getImagesKey(String key)	Gets all images with a certain key
List<ImageWrapper>	getImagesLike(String motif)	Gets all images with a certain motif in their name from OMERO.
List<ImageWrapper>	getImagesPairKeyValue(String key, String value)	Gets all images with a certain key value pair from OMERO
List<ImageWrapper>	getImagesTagged(TagAnnotationWrapper tag)	Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesTagged(Long tagId)	Gets all images tagged with a specified tag from OMERO.
PlateWrapper	getPlate(Long id)	Gets the plate with the specified id from OMERO.
List<PlateWrapper>	getPlates()	Gets all plates available from OMERO.
List<PlateWrapper>	getPlates(Long... ids)	Gets the plates with the specified ids from OMERO.
ProjectWrapper	getProject(Long id)	Gets the project with the specified id from OMERO.
List<ProjectWrapper>	getProjects()	Gets all projects available from OMERO.
List<ProjectWrapper>	getProjects(Long... ids)	Gets the projects with the specified ids from OMERO.
List<ProjectWrapper>	getProjects(String name)	Gets all projects with a certain name from OMERO.
ScreenWrapper	getScreen(Long id)	Gets the screen with the specified id from OMERO.
List<ScreenWrapper>	getScreens()	Gets all screens available from OMERO.
List<ScreenWrapper>	getScreens(Long... ids)	Gets the screens with the specified ids from OMERO.
TagAnnotationWrapper	getTag(Long id)	Gets a specific tag from the OMERO database
List<TagAnnotationWrapper>	getTags()	Gets the list of TagAnnotationWrapper available to the user
List<TagAnnotationWrapper>	getTags(String name)	Gets the list of TagAnnotationWrapper with the specified name available to the user
ExperimenterWrapper	getUser(String username)	Returns the user which matches the username.
WellWrapper	getWell(Long id)	Gets the well with the specified id from OMERO.
List<WellWrapper>	getWells()	Gets all wells available from OMERO.
List<WellWrapper>	getWells(Long... ids)	Gets the wells with the specified ids from OMERO.
Client	sudoGetUser(String username)	Gets the client associated with the username in the parameters.

Methods inherited from class fr.igred.omero.GatewayWrapper

connect, connect, connect, connect, deleteFile, disconnect, findByQuery, getAdminFacility, getBrowseFacility, getCtx, getCurrentGroupId, getDm, getGateway, getId, getImportStore, getMetadata, getRoiFacility, getSessionId, getTablesFacility, getUser, isConnected, save, switchGroup

Methods inherited from class java.lang.Object

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

Constructor Detail

Client

public Client()

Constructor of the Client class. Initializes the gateway.

Method Detail

getProject

public ProjectWrapper getProject(Long id)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

Gets the project with the specified id from OMERO.

Parameters:

id - ID of the project.

Returns:

ProjectWrapper containing the project.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getProjects

public List<ProjectWrapper> getProjects(Long... ids)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets the projects with the specified ids from OMERO.

Parameters:

ids - Project IDs

Returns:

List of ProjectWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getProjects

public List<ProjectWrapper> getProjects()
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets all projects available from OMERO.

Returns:

Collection of ProjectWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getProjects

public List<ProjectWrapper> getProjects(String name)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets all projects with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

Collection of ProjectWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getDataset

public DatasetWrapper getDataset(Long id)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

Gets the dataset with the specified id from OMERO.

Parameters:

id - ID of the dataset.

Returns:

ProjectWrapper containing the project.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getDatasets

public List<DatasetWrapper> getDatasets(Long... ids)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets the datasets with the specified ids from OMERO.

Parameters:

ids - Dataset IDs

Returns:

List of DatasetWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getDatasets

public List<DatasetWrapper> getDatasets()
                                 throws ServiceException,
                                        AccessException,
                                        OMEROServerError,
                                        ExecutionException

Gets all datasets available from OMERO.

Returns:

List of DatasetWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getDatasets

public List<DatasetWrapper> getDatasets(String name)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets all datasets with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

Collection of DatasetWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImage

public ImageWrapper getImage(Long id)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Returns an ImageWrapper that contains the image with the specified id from OMERO.

Parameters:

id - ID of the image.

Returns:

ImageWrapper containing the image.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getImages

public List<ImageWrapper> getImages(Long... ids)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets the images with the specified ids from OMERO

Parameters:

ids - Image IDs

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

public List<ImageWrapper> getImages()
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images owned by the current user.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

public List<ImageWrapper> getImages(String name)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

public List<ImageWrapper> getImages(String projectName,
                                    String datasetName,
                                    String imageName)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images with the name specified inside projects and datasets with the given names.

Parameters:

projectName - Expected project name.

datasetName - Expected dataset name.

imageName - Expected image name.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesLike

public List<ImageWrapper> getImagesLike(String motif)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

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

Parameters:

motif - Motif searched in an image name.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesTagged

public List<ImageWrapper> getImagesTagged(TagAnnotationWrapper tag)
                                   throws ServiceException,
                                          AccessException,
                                          OMEROServerError,
                                          ExecutionException

Gets all images tagged with a specified tag from OMERO.

Parameters:

tag - TagAnnotationWrapper containing the tag researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getImagesTagged

public List<ImageWrapper> getImagesTagged(Long tagId)
                                   throws ServiceException,
                                          AccessException,
                                          OMEROServerError,
                                          ExecutionException

Gets all images tagged with a specified tag from OMERO.

Parameters:

tagId - Id of the tag researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getImagesKey

public List<ImageWrapper> getImagesKey(String key)
                                throws ServiceException,
                                       AccessException,
                                       ExecutionException

Gets all images with a certain key

Parameters:

key - Name of the key researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesPairKeyValue

public List<ImageWrapper> getImagesPairKeyValue(String key,
                                                String value)
                                         throws ServiceException,
                                                AccessException,
                                                ExecutionException

Gets all images with a certain key value pair from OMERO

Parameters:

key - Name of the key researched.

value - Value associated with the key.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreen

public ScreenWrapper getScreen(Long id)
                        throws ServiceException,
                               AccessException,
                               ExecutionException

Gets the screen with the specified id from OMERO.

Parameters:

id - ID of the screen.

Returns:

ScreenWrapper containing the screen.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getScreens

public List<ScreenWrapper> getScreens(Long... ids)
                               throws ServiceException,
                                      AccessException,
                                      ExecutionException

Gets the screens with the specified ids from OMERO.

Parameters:

ids - A list of screen ids

Returns:

List of ScreenWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreens

public List<ScreenWrapper> getScreens()
                               throws ServiceException,
                                      AccessException,
                                      ExecutionException

Gets all screens available from OMERO.

Returns:

List of ScreenWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlate

public PlateWrapper getPlate(Long id)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets the plate with the specified id from OMERO.

Parameters:

id - ID of the plate.

Returns:

PlateWrapper containing the plate.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getPlates

public List<PlateWrapper> getPlates(Long... ids)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets the plates with the specified ids from OMERO.

Parameters:

ids - A list of plate ids

Returns:

List of PlateWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlates

public List<PlateWrapper> getPlates()
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all plates available from OMERO.

Returns:

List of PlateWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getWell

public WellWrapper getWell(Long id)
                    throws ServiceException,
                           AccessException,
                           ExecutionException

Gets the well with the specified id from OMERO.

Parameters:

id - ID of the well.

Returns:

WellWrapper containing the well.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with such id.

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

getWells

public List<WellWrapper> getWells(Long... ids)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Gets the wells with the specified ids from OMERO.

Parameters:

ids - A list of well ids

Returns:

List of WellWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getWells

public List<WellWrapper> getWells()
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException,
                                  OMEROServerError

Gets all wells available from OMERO.

Returns:

List of WellWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

getTags

public List<TagAnnotationWrapper> getTags()
                                   throws OMEROServerError,
                                          ServiceException

Gets the list of TagAnnotationWrapper available to the user

Returns:

list of TagAnnotationWrapper.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getTags

public List<TagAnnotationWrapper> getTags(String name)
                                   throws OMEROServerError,
                                          ServiceException

Gets the list of TagAnnotationWrapper with the specified name available to the user

Parameters:

name - Name of the tag searched.

Returns:

list of TagAnnotationWrapper.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getTag

public TagAnnotationWrapper getTag(Long id)
                            throws OMEROServerError,
                                   ServiceException

Gets a specific tag from the OMERO database

Parameters:

id - Id of the tag.

Returns:

TagAnnotationWrapper containing the specified tag.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

delete

public void delete(Collection<? extends GenericObjectWrapper<?>> objects)
            throws ServiceException,
                   AccessException,
                   ExecutionException,
                   OMEROServerError,
                   InterruptedException

Deletes multiple objects from OMERO.

Parameters:

objects - The OMERO object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - If the thread was interrupted.

InterruptedException - If block(long) does not return.

delete

public void delete(GenericObjectWrapper<?> object)
            throws ServiceException,
                   AccessException,
                   ExecutionException,
                   OMEROServerError,
                   InterruptedException

Deletes an object from OMERO.

Parameters:

object - The OMERO object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - If the thread was interrupted.

InterruptedException - If block(long) does not return.

delete

public void delete(TableWrapper table)
            throws ServiceException,
                   AccessException,
                   ExecutionException,
                   OMEROServerError,
                   InterruptedException

Deletes a table from OMERO

Parameters:

table - TableWrapper containing the table to delete.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

IllegalArgumentException - Id not defined.

OMEROServerError - If the thread was interrupted.

InterruptedException - If block(long) does not return.

getUser

public ExperimenterWrapper getUser(String username)
                            throws ExecutionException,
                                   ServiceException,
                                   AccessException

Returns the user which matches the username.

Parameters:

username - The name of the user.

Returns:

The user matching the username, or null if it does not exist.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

NoSuchElementException - The requested user does not exist.

getGroup

public GroupWrapper getGroup(String groupName)
                      throws ExecutionException,
                             ServiceException,
                             AccessException

Returns the group which matches the name.

Parameters:

groupName - The name of the group.

Returns:

The group with the appropriate name, if it exists.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

NoSuchElementException - The requested group does not exist.

sudoGetUser

public Client sudoGetUser(String username)
                   throws ServiceException,
                          AccessException,
                          ExecutionException

Gets the client associated with the username in the parameters. The user calling this function needs to have administrator rights. All action realized with the client returned will be considered as his.

Parameters:

username - Username of user.

Returns:

The client corresponding to the new user.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

NoSuchElementException - The requested user does not exist.