Package fr.igred.omero

Class Client

java.lang.Object

fr.igred.omero.Client

public class Client
extends Object

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	connect(String hostname, int port, String sessionId)	Connects to OMERO using a session ID.
void	connect(String hostname, int port, String username, char[] password)	Connects the user to OMERO.
void	connect(String hostname, int port, String username, char[] password, Long groupID)	Connects the user to OMERO.
void	connect(LoginCredentials cred)	Connects the user to OMERO.
void	delete(TableWrapper table)	Deletes a table from OMERO
void	delete(GenericObjectWrapper<?> object)	Deletes an object from OMERO.
void	deleteFile(Long id)	Deletes a file from OMERO
void	disconnect()	Disconnects the user
List<IObject>	findByQuery(String query)	Finds objects on OMERO through a database query.
AdminFacility	getAdminFacility()	Gets the AdminFacility linked to the gateway to use admin specific function.
BrowseFacility	getBrowseFacility()	Gets the BrowseFacility used to access the data from OMERO.
ImportConfig	getConfig()	Gets a copy of the importation config for the user.
SecurityContext	getCtx()	Contains the permissions of the user in the group.
long	getCurrentGroupId()	Gets the current group ID.
DatasetWrapper	getDataset(Long id)	Gets the dataset with the specified id from OMERO.
List<DatasetWrapper>	getDatasets()	Gets all the datasets available from OMERO.
List<DatasetWrapper>	getDatasets(String name)	Gets all datasets with a certain name from OMERO.
DataManagerFacility	getDm()	Gets the DataManagerFacility to handle/write data on OMERO.
Gateway	getGateway()
GroupWrapper	getGroup(String groupName)	Returns the group which matches the name.
long	getId()	Gets the user id.
ImageWrapper	getImage(Long id)	Returns an ImageWrapper that contains the image with the specified id from OMERO.
List<ImageWrapper>	getImages()	Gets all images available from OMERO.
List<ImageWrapper>	getImages(String name)	Gets all images with a certain from OMERO.
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.
MetadataFacility	getMetadata()	Gets the MetadataFacility used to manipulate annotations 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(String name)	Gets all projects with a certain name from OMERO.
ROIFacility	getRoiFacility()	Gets the ROIFacility used to manipulate ROI from OMERO.
String	getSessionId()	Get the ID of the current session
TablesFacility	getTablesFacility()	Gets the TablesFacility used to manipulate table 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()	Returns the current user.
ExperimenterWrapper	getUser(String username)	Returns the user which matches the username.
IObject	save(IObject object)	Saves an object on OMERO.
Client	sudoGetUser(String username)	Gets the client associated with the username in the parameters.
void	switchGroup(long groupId)	Change the current group used by the current user;

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

getUser

public ExperimenterWrapper getUser()

Returns the current user.

Returns:

The current user.

getCtx

public SecurityContext getCtx()

Contains the permissions of the user in the group.

Returns:

the SecurityContext of the user.

getBrowseFacility

public BrowseFacility getBrowseFacility()

Gets the BrowseFacility used to access the data from OMERO.

Returns:

the BrowseFacility linked to the gateway.

getDm

public DataManagerFacility getDm()
                          throws ExecutionException

Gets the DataManagerFacility to handle/write data on OMERO. A

Returns:

the DataManagerFacility linked to the gateway.

Throws:

ExecutionException - If the DataManagerFacility can't be retrieved or instantiated.

getMetadata

public MetadataFacility getMetadata()
                             throws ExecutionException

Gets the MetadataFacility used to manipulate annotations from OMERO.

Returns:

the MetadataFacility linked to the gateway.

Throws:

ExecutionException - If the MetadataFacility can't be retrieved or instantiated.

getRoiFacility

public ROIFacility getRoiFacility()
                           throws ExecutionException

Gets the ROIFacility used to manipulate ROI from OMERO.

Returns:

the ROIFacility linked to the gateway.

Throws:

ExecutionException - If the ROIFacility can't be retrieved or instantiated.

getTablesFacility

public TablesFacility getTablesFacility()
                                 throws ExecutionException

Gets the TablesFacility used to manipulate table from OMERO.

Returns:

the TablesFacility linked to the gateway.

Throws:

ExecutionException - If the TablesFacility can't be retrieved or instantiated.

getAdminFacility

public AdminFacility getAdminFacility()
                               throws ExecutionException

Gets the AdminFacility linked to the gateway to use admin specific function.

Returns:

the AdminFacility linked to the gateway.

Throws:

ExecutionException - If the AdminFacility can't be retrieved or instantiated.

findByQuery

public List<IObject> findByQuery(String query)
                          throws ServiceException,
                                 OMEROServerError

Finds objects on OMERO through a database query.

Parameters:

query - The database query.

Returns:

A list of OMERO objects.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

getConfig

public ImportConfig getConfig()

Gets a copy of the importation config for the user.

Returns:

config.

getId

public long getId()

Gets the user id.

Returns:

The user ID.

getCurrentGroupId

public long getCurrentGroupId()

Gets the current group ID.

Returns:

The group ID.

getSessionId

public String getSessionId()
                    throws DSOutOfServiceException

Get the ID of the current session

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

getGateway

public Gateway getGateway()

connect

public void connect(String hostname,
                    int port,
                    String sessionId)
             throws ServiceException,
                    ExecutionException

Connects to OMERO using a session ID.

Parameters:

hostname - Name of the host.

port - Port used by OMERO.

sessionId - The session ID.

Throws:

ServiceException - Cannot connect to OMERO.

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

connect

public void connect(String hostname,
                    int port,
                    String username,
                    char[] password,
                    Long groupID)
             throws ServiceException,
                    ExecutionException

Connects the user to OMERO.

Uses the argument to connect to the gateway.

Connects to the group specified in the argument.

Parameters:

hostname - Name of the host.

port - Port used by OMERO.

username - Username of the user.

password - Password of the user.

groupID - Id of the group to connect.

Throws:

ServiceException - Cannot connect to OMERO.

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

connect

public void connect(String hostname,
                    int port,
                    String username,
                    char[] password)
             throws ServiceException,
                    ExecutionException

Connects the user to OMERO.

Uses the argument to connect to the gateway.

Connects to the default group of the user.

Parameters:

hostname - Name of the host.

port - Port used by OMERO.

username - Username of the user.

password - Password of the user.

Throws:

ServiceException - Cannot connect to OMERO.

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

connect

public void connect(LoginCredentials cred)
             throws ServiceException,
                    ExecutionException

Connects the user to OMERO. Gets the SecurityContext and the BrowseFacility.

Parameters:

cred - User credential.

Throws:

ServiceException - Cannot connect to OMERO.

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

disconnect

public void disconnect()

Disconnects the user

getProject

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

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.

getProjects

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

Gets all projects available from OMERO.

Returns:

Collection of ProjectWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getProjects

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

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.

getDataset

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

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.

getDatasets

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

Gets all the datasets available from OMERO.

Returns:

Collection of DatasetWrapper.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

getDatasets

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

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.

getImage

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

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.

getImages

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

Gets all images available from OMERO.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getImages

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

Gets all images with a certain from OMERO.

Parameters:

name - Name searched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getImagesLike

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

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.

getImagesTagged

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

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.

getImagesTagged

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

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.

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.

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.

switchGroup

public void switchGroup(long groupId)

Change the current group used by the current user;

Parameters:

groupId - The group ID.

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.

save

public IObject save(IObject object)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Saves an object on OMERO.

Parameters:

object - The OMERO object.

Returns:

The saved OMERO object

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

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.

deleteFile

public void deleteFile(Long id)
                throws ServiceException,
                       AccessException,
                       ExecutionException,
                       OMEROServerError,
                       InterruptedException

Deletes a file from OMERO

Parameters:

id - Id of the file to delete.

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.

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.

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, 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.