Package fr.igred.omero

Class GatewayWrapper

java.lang.Object

fr.igred.omero.GatewayWrapper

Direct Known Subclasses:

Browser

public abstract class GatewayWrapper
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

Modifier	Constructor	Description
protected	GatewayWrapper(Gateway gateway, SecurityContext ctx, ExperimenterWrapper user)	Abstract constructor of the GatewayWrapper class.

Method Summary

Modifier and Type	Method	Description
void	closeImport()	Closes the import store.
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	deleteFile(Long id)	Deletes a file from OMERO
void	deleteFiles(Long... ids)	Deletes files 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 to use admin specific function.
BrowseFacility	getBrowseFacility()	Gets the BrowseFacility used to access the data from OMERO.
SecurityContext	getCtx()	Contains the permissions of the user in the group.
long	getCurrentGroupId()	Gets the current group ID.
DataManagerFacility	getDm()	Gets the DataManagerFacility to handle/write data on OMERO.
Gateway	getGateway()	Returns the Gateway.
long	getId()	Gets the user id.
OMEROMetadataStoreClient	getImportStore()	Creates or recycles the import store.
MetadataFacility	getMetadata()	Gets the MetadataFacility used to retrieve annotations from OMERO.
omero.api.IQueryPrx	getQueryService()	Returns the IQueryPrx used to find objects on OMERO.
ROIFacility	getRoiFacility()	Gets the ROIFacility used to manipulate ROIs from OMERO.
String	getSessionId()	Get the ID of the current session
TablesFacility	getTablesFacility()	Gets the TablesFacility used to manipulate tables on OMERO.
ExperimenterWrapper	getUser()	Returns the current user.
boolean	isConnected()	Check if the client is still connected to the server
IObject	save(IObject object)	Saves an object on OMERO.
void	switchGroup(long groupId)	Change the current group used by the current user;
String	toString()	Overridden to return the host name, the group ID, the username and the connection status.

Methods inherited from class java.lang.Object

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

Constructor Details

GatewayWrapper

protected GatewayWrapper(Gateway gateway,
 SecurityContext ctx,
 ExperimenterWrapper user)

Abstract constructor of the GatewayWrapper class.

Null arguments will be replaced with default empty objects.

Parameters:

gateway - The Gateway.

ctx - The Security Context.

user - The connected user.

Method Details

getGateway

public Gateway getGateway()

Returns the Gateway.

Returns:

The Gateway.

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.

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 ServiceException

Get the ID of the current session

Returns:

See above

Throws:

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

isConnected

public boolean isConnected()

Check if the client is still connected to the server

Returns:

See above.

connect

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

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.

connect

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

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.

connect

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

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.

connect

public void connect(LoginCredentials cred)
             throws ServiceException

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

Parameters:

cred - User credential.

Throws:

ServiceException - Cannot connect to OMERO.

disconnect

public void disconnect()

Disconnects the user

switchGroup

public void switchGroup(long groupId)

Change the current group used by the current user;

Parameters:

groupId - The group ID.

getBrowseFacility

public BrowseFacility getBrowseFacility()
                                 throws ExecutionException

Gets the BrowseFacility used to access the data from OMERO.

Returns:

See above.

Throws:

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

getQueryService

public omero.api.IQueryPrx getQueryService()
                                    throws ServiceException

Returns the IQueryPrx used to find objects on OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

getMetadata

public MetadataFacility getMetadata()
                             throws ExecutionException

Gets the MetadataFacility used to retrieve annotations from OMERO.

Returns:

See above.

Throws:

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

getDm

public DataManagerFacility getDm()
                          throws ExecutionException

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

Returns:

See above.

Throws:

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

getRoiFacility

public ROIFacility getRoiFacility()
                           throws ExecutionException

Gets the ROIFacility used to manipulate ROIs from OMERO.

Returns:

See above.

Throws:

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

getTablesFacility

public TablesFacility getTablesFacility()
                                 throws ExecutionException

Gets the TablesFacility used to manipulate tables on OMERO.

Returns:

See above.

Throws:

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

getAdminFacility

public AdminFacility getAdminFacility()
                               throws ExecutionException

Gets the AdminFacility to use admin specific function.

Returns:

See above.

Throws:

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

getImportStore

public OMEROMetadataStoreClient getImportStore()
                                        throws ServiceException

Creates or recycles the import store.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

closeImport

public void closeImport()

Closes the import store.

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.

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.

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 - Server error.

InterruptedException - If block(long) does not return.

deleteFiles

public void deleteFiles(Long... ids)
                 throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError,
InterruptedException

Deletes files from OMERO.

Parameters:

ids - List of files IDs to delete.

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.

toString

public String toString()

Overridden to return the host name, the group ID, the username and the connection status.

Overrides:

toString in class Object

Returns:

See above.