Package fr.igred.omero

Class Client

java.lang.Object

fr.igred.omero.GatewayWrapper

fr.igred.omero.Browser

fr.igred.omero.Client

public class Client
extends Browser

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.
Client(Gateway gateway, SecurityContext ctx, ExperimenterWrapper user)	Constructor of the Client class.

Method Summary

Modifier and Type	Method	Description
void	delete(TableWrapper table)	Deprecated. 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.
void	deleteTable(TableWrapper table)	Deletes a table from OMERO.
void	deleteTables(Collection<? extends TableWrapper> tables)	Deletes tables from OMERO.
GroupWrapper	getGroup(long groupId)	Returns the group which matches the group ID.
GroupWrapper	getGroup(String groupName)	Returns the group which matches the name.
List<ImageWrapper>	getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation 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)	Deprecated. Gets all images with a certain key
List<ImageWrapper>	getImagesPairKeyValue(String key, String value)	Deprecated. Gets all images with a certain key value pair from OMERO
ExperimenterWrapper	getUser(long userId)	Returns the user which matches the user ID.
ExperimenterWrapper	getUser(String username)	Returns the user which matches the username.
Client	sudoGetUser(String username)	Gets the client associated with the username in the parameters.

Methods inherited from class fr.igred.omero.Browser

getDataset, getDatasets, getDatasets, getDatasets, getDatasets, getFolder, getFolders, getFolders, getImage, getImages, getImages, getImages, getImagesLike, getImagesTagged, getImagesTagged, getImagesWithKey, getImagesWithKeyValuePair, getMapAnnotation, getMapAnnotations, getMapAnnotations, getMapAnnotations, getPlate, getPlates, getPlates, getPlates, getProject, getProjects, getProjects, getProjects, getProjects, getScreen, getScreens, getScreens, getScreens, getTag, getTags, getTags, getWell, getWells, getWells, getWells, loadFolders

Methods inherited from class fr.igred.omero.GatewayWrapper

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

Methods inherited from class java.lang.Object

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

Constructor Details

Client

public Client()

Constructor of the Client class. Initializes the gateway.

Client

public Client(Gateway gateway,
 SecurityContext ctx,
 ExperimenterWrapper user)

Constructor of the Client class.

Parameters:

gateway - The gateway

ctx - The security context

user - The user

Method Details

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.

Specified by:

getImages in class Browser

Parameters:

projectName - Expected project name.

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.

getImages

public List<ImageWrapper> getImages(GenericAnnotationWrapper<?> annotation)
                             throws ServiceException,
AccessException,
OMEROServerError,
ExecutionException

Gets all images with the specified annotation from OMERO.

Specified by:

getImages in class Browser

Parameters:

annotation - TagAnnotation containing the tag researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getImagesKey

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

Deprecated.

Gets all images with a certain key

Specified by:

getImagesKey in class Browser

Parameters:

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.

getImagesPairKeyValue

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

Deprecated.

Gets all images with a certain key value pair from OMERO

Specified by:

getImagesPairKeyValue in class Browser

Parameters:

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.

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 - Server error.

InterruptedException - If block(long) does not return.

delete

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

Deletes an object from OMERO.

Make sure a folder is loaded before deleting it.

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 - Server error.

InterruptedException - If block(long) does not return.

delete

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

Deprecated.

Deletes a table from OMERO.

Parameters:

table - 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 - Server error.

InterruptedException - If block(long) does not return.

deleteTable

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

Deletes a table from OMERO.

Parameters:

table - 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 - Server error.

InterruptedException - If block(long) does not return.

deleteTables

public void deleteTables(Collection<? extends TableWrapper> tables)
                  throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError,
InterruptedException

Deletes tables from OMERO.

Parameters:

tables - List of tables 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 - Server error.

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 cannot be found.

getUser

public ExperimenterWrapper getUser(long userId)
                            throws ServiceException,
OMEROServerError

Returns the user which matches the user ID.

Parameters:

userId - The ID of the user.

Returns:

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

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

NoSuchElementException - The requested user cannot be found.

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 cannot be found.

getGroup

public GroupWrapper getGroup(long groupId)
                      throws ServiceException,
OMEROServerError

Returns the group which matches the group ID.

Parameters:

groupId - The ID of the group.

Returns:

The group with the appropriate group ID, if it exists.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

NoSuchElementException - The requested group cannot be found.

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.