omero.gateway.facility

Class DataManagerFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.DataManagerFacility

public class DataManagerFacility
extends Facility

A Facility for saving, deleting and updating data objects

Since:

5.1

Method Summary

Modifier and Type	Method and Description
void	addImagesToDataset(SecurityContext ctx, java.util.Collection<ImageData> images, DatasetData ds) Adds the ImageDatas to the given DatasetData
void	addImageToDataset(SecurityContext ctx, ImageData image, DatasetData ds) Adds the ImageData to the given DatasetData
<T extends AnnotationData> T	attachAnnotation(SecurityContext ctx, T annotation, DataObject target) Create/attach an AnnotationData to a given DataObject
java.util.concurrent.Future<FileAnnotationData>	attachFile(SecurityContext ctx, java.io.File file, java.lang.String mimetype, java.lang.String description, java.lang.String namespace, DataObject target) Attaches a File to a DataObject
void	changeGroup(SecurityContext ctx, java.util.List<? extends DataObject> objects, long groupId) Move the given objects into another group
DatasetData	createDataset(SecurityContext ctx, DatasetData dataset, ProjectData project) Creates the DatasetData on the server and attaches it to the ProjectData (if not null) (if the project doesn't exist on the server yet, it will be created, too)
omero.cmd.CmdCallbackI	delete(SecurityContext ctx, omero.model.IObject object) Deletes the specified object asynchronously
omero.cmd.CmdCallbackI	delete(SecurityContext ctx, java.util.List<omero.model.IObject> objects) Deletes the specified objects asynchronously
omero.cmd.CmdCallbackI	deleteFolders(SecurityContext ctx, java.util.Collection<FolderData> folders, boolean includeSubFolders, boolean includeContent) Delete Folders (asynchronous)
void	move(SecurityContext ctx, java.util.List<? extends DataObject> objects, DataObject from, DataObject to) Moves DataObjects from one object to another, i.e.
DataObject	saveAndReturnObject(SecurityContext ctx, DataObject object) Updates the specified object.
DataObject	saveAndReturnObject(SecurityContext ctx, DataObject object, java.lang.String userName) Updates the specified object.
omero.model.IObject	saveAndReturnObject(SecurityContext ctx, omero.model.IObject object) Updates the specified object.
omero.model.IObject	saveAndReturnObject(SecurityContext ctx, omero.model.IObject object, java.util.Map options) Updates the specified object.
omero.model.IObject	saveAndReturnObject(SecurityContext ctx, omero.model.IObject object, java.util.Map options, java.lang.String userName) Updates the specified object.
omero.model.IObject	saveAndReturnObject(SecurityContext ctx, omero.model.IObject object, java.lang.String userName) Updates the specified object.
java.util.List<omero.model.IObject>	saveAndReturnObject(SecurityContext ctx, java.util.List<omero.model.IObject> objects, java.util.Map options, java.lang.String userName) Updates the specified object.
omero.model.IObject	updateObject(SecurityContext ctx, omero.model.IObject object, omero.sys.Parameters options) Updates the specified object.
java.util.List<omero.model.IObject>	updateObjects(SecurityContext ctx, java.util.List<omero.model.IObject> objects, omero.sys.Parameters options) Updates the specified IObjects and returned the updated IObjects.

Methods inherited from class omero.gateway.facility.Facility

addPropertyChangeListener, clear, firePropertyChanged, firePropertyChanged, getFacility, logDebug, logError, logInfo, logWarn, removePropertyChangeListener

Methods inherited from class java.lang.Object

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

Method Detail

delete

public omero.cmd.CmdCallbackI delete(SecurityContext ctx,
                                     omero.model.IObject object)
                              throws DSOutOfServiceException,
                                     DSAccessException

Deletes the specified object asynchronously

Parameters:

ctx - The security context.

object - The object to delete.

Returns:

The CmdCallbackI

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

deleteFolders

public omero.cmd.CmdCallbackI deleteFolders(SecurityContext ctx,
                                            java.util.Collection<FolderData> folders,
                                            boolean includeSubFolders,
                                            boolean includeContent)
                                     throws DSOutOfServiceException,
                                            DSAccessException

Delete Folders (asynchronous)

Parameters:

ctx - The SecurityContext

folders - The Folder to delete

includeSubFolders - Pass true to recursively delete sub folders

includeContent - Pass true to also delete content of the folders, otherwise content (ROIs, Images) will be orphaned

Returns:

The Callback reference

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

delete

public omero.cmd.CmdCallbackI delete(SecurityContext ctx,
                                     java.util.List<omero.model.IObject> objects)
                              throws DSOutOfServiceException,
                                     DSAccessException

Deletes the specified objects asynchronously

Parameters:

ctx - The security context.

objects - The objects to delete.

Returns:

The CmdCallbackI

Throws:

DSOutOfServiceException - If the connection is broken, or logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

saveAndReturnObject

public omero.model.IObject saveAndReturnObject(SecurityContext ctx,
                                               omero.model.IObject object,
                                               java.util.Map options)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

options - Options to update the data.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public DataObject saveAndReturnObject(SecurityContext ctx,
                                      DataObject object)
                               throws DSOutOfServiceException,
                                      DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public omero.model.IObject saveAndReturnObject(SecurityContext ctx,
                                               omero.model.IObject object)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public omero.model.IObject saveAndReturnObject(SecurityContext ctx,
                                               omero.model.IObject object,
                                               java.util.Map options,
                                               java.lang.String userName)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

options - Options to update the data.

userName - The name of the user to create the data for.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public DataObject saveAndReturnObject(SecurityContext ctx,
                                      DataObject object,
                                      java.lang.String userName)
                               throws DSOutOfServiceException,
                                      DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

userName - The name of the user to create the data for.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public omero.model.IObject saveAndReturnObject(SecurityContext ctx,
                                               omero.model.IObject object,
                                               java.lang.String userName)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

userName - The name of the user to create the data for.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

saveAndReturnObject

public java.util.List<omero.model.IObject> saveAndReturnObject(SecurityContext ctx,
                                                               java.util.List<omero.model.IObject> objects,
                                                               java.util.Map options,
                                                               java.lang.String userName)
                                                        throws DSOutOfServiceException,
                                                               DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

objects - The objects to update.

options - Options to update the data.

userName - The username

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

updateObject

public omero.model.IObject updateObject(SecurityContext ctx,
                                        omero.model.IObject object,
                                        omero.sys.Parameters options)
                                 throws DSOutOfServiceException,
                                        DSAccessException

Updates the specified object.

Parameters:

ctx - The security context.

object - The object to update.

options - Options to update the data.

Returns:

The updated object.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObject(IObject, Parameters)

updateObjects

public java.util.List<omero.model.IObject> updateObjects(SecurityContext ctx,
                                                         java.util.List<omero.model.IObject> objects,
                                                         omero.sys.Parameters options)
                                                  throws DSOutOfServiceException,
                                                         DSAccessException

Updates the specified IObjects and returned the updated IObjects.

Parameters:

ctx - The security context.

objects - The array of objects to update.

options - Options to update the data.

Returns:

See above.

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

See Also:

IContainerPrx.updateDataObjects(List, Parameters)

addImageToDataset

public void addImageToDataset(SecurityContext ctx,
                              ImageData image,
                              DatasetData ds)
                       throws DSOutOfServiceException,
                              DSAccessException

Adds the ImageData to the given DatasetData

Parameters:

ctx - The security context.

image - The image to add to the dataset

ds - The dataset to add the image to

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

addImagesToDataset

public void addImagesToDataset(SecurityContext ctx,
                               java.util.Collection<ImageData> images,
                               DatasetData ds)
                        throws DSOutOfServiceException,
                               DSAccessException

Adds the ImageDatas to the given DatasetData

Parameters:

ctx - The security context.

images - The images to add to the dataset

ds - The dataset to add the images to

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

createDataset

public DatasetData createDataset(SecurityContext ctx,
                                 DatasetData dataset,
                                 ProjectData project)
                          throws DSOutOfServiceException,
                                 DSAccessException

Creates the DatasetData on the server and attaches it to the ProjectData (if not null) (if the project doesn't exist on the server yet, it will be created, too)

Parameters:

ctx - The SecurityContext

dataset - The DatasetData

project - The ProjectData

Returns:

The DatasetData

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

attachFile

public java.util.concurrent.Future<FileAnnotationData> attachFile(SecurityContext ctx,
                                                                  java.io.File file,
                                                                  java.lang.String mimetype,
                                                                  java.lang.String description,
                                                                  java.lang.String namespace,
                                                                  DataObject target)

Attaches a File to a DataObject

Parameters:

ctx - The SecurityContext

file - The File to attach

mimetype - The mimetype of the file (can be null)

description - A description (can be null)

namespace - The namespace (can be null)

target - The DataObject to attach the file to

Returns:

The Future FileAnnotationData

attachAnnotation

public <T extends AnnotationData> T attachAnnotation(SecurityContext ctx,
                                                     T annotation,
                                                     DataObject target)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Create/attach an AnnotationData to a given DataObject

Parameters:

ctx - The SecurityContext

annotation - The AnnotationData

target - The DataObject to attach to

Returns:

The AnnotationData

Throws:

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

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

move

public void move(SecurityContext ctx,
                 java.util.List<? extends DataObject> objects,
                 DataObject from,
                 DataObject to)
          throws DSOutOfServiceException,
                 DSAccessException

Moves DataObjects from one object to another, i.e. Annotations from one Image to another, or Images from one Dataset to another.

Parameters:

ctx - The SecurityContext

objects - The objects to move

from - The object to which the objects are attached now

to - The object to which the objects should be attached

Throws:

DSOutOfServiceException

DSAccessException

changeGroup

public void changeGroup(SecurityContext ctx,
                        java.util.List<? extends DataObject> objects,
                        long groupId)
                 throws DSAccessException,
                        DSOutOfServiceException

Move the given objects into another group

Parameters:

ctx - The SecurityContext

objects - The objects to move into another group

groupId - The group to move the objects into

Throws:

DSAccessException

DSOutOfServiceException