omero.gateway.facility

Class BrowseFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.BrowseFacility

public class BrowseFacility
extends Facility

A Facility for browsing the data hierarchy and retrieving ProjectData, DatasetData, etc.

Since:

5.1

Method Summary

Modifier and Type	Method and Description
omero.model.IObject	findIObject(SecurityContext ctx, omero.model.IObject o) Retrieves an updated version of the specified object.
omero.model.IObject	findIObject(SecurityContext ctx, java.lang.String klassName, long id) Retrieves an updated version of the specified object.
omero.model.IObject	findIObject(SecurityContext ctx, java.lang.String klassName, long id, boolean allGroups) Retrieves an updated version of the specified object.
<T extends DataObject> T	findObject(SecurityContext ctx, java.lang.Class<T> klass, long id) Retrieves an updated version of the specified object.
<T extends DataObject> T	findObject(SecurityContext ctx, java.lang.Class<T> klass, long id, boolean allGroups) Retrieves an updated version of the specified object.
DataObject	findObject(SecurityContext ctx, java.lang.String pojoName, long id) Retrieves an updated version of the specified object.
DataObject	findObject(SecurityContext ctx, java.lang.String pojoName, long id, boolean allGroups) Retrieves an updated version of the specified object.
java.util.Set<GroupData>	getAvailableGroups(SecurityContext ctx, ExperimenterData user) Retrieves the groups visible by the current experimenter.
java.util.Collection<DatasetData>	getDatasets(SecurityContext ctx) Loads all datasets
java.util.Collection<DatasetData>	getDatasets(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Loads the datasets with the given ids
java.util.Collection<DatasetData>	getDatasets(SecurityContext ctx, long ownerId) Loads the datasets for a particular user
java.util.Collection<DatasetData>	getDatasets(SecurityContext ctx, long ownerId, java.util.Collection<java.lang.Long> ids) Loads the datasets with the given ids which belong to a particular user
java.util.Collection<DatasetData>	getDatasets(SecurityContext ctx, java.lang.String name) Load dataset by name
java.util.Collection<FolderData>	getFolders(SecurityContext ctx) Get all folders the logged in user has access to.
java.util.Collection<FolderData>	getFolders(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Get the folders for the given folder ids.
java.util.Collection<FolderData>	getFolders(SecurityContext ctx, long userId) Get the folders which belong to the given user.
java.util.Collection<DataObject>	getHierarchy(SecurityContext ctx, java.lang.Class rootType, java.util.List<java.lang.Long> rootIDs, omero.sys.Parameters options) Retrieves hierarchy trees rooted by a given node i.e.
java.util.Collection<DataObject>	getHierarchy(SecurityContext ctx, java.lang.Class rootType, long userId) Retrieves hierarchy trees rooted by a given node.
ImageData	getImage(SecurityContext ctx, long id) Loads a image
ImageData	getImage(SecurityContext ctx, long id, omero.sys.ParametersI params) Loads a image
java.util.Collection<ImageData>	getImages(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Loads the images with the given ids
java.util.Collection<ImageData>	getImages(SecurityContext ctx, java.util.Collection<java.lang.Long> ids, omero.sys.ParametersI params) Loads the images with the given ids
java.util.Collection<ImageData>	getImages(SecurityContext ctx, long ownerId, java.util.Collection<java.lang.Long> ids) Loads the images for a particular user
java.util.Collection<ImageData>	getImages(SecurityContext ctx, java.lang.String name) Load image by name
java.util.Collection<ImageData>	getImagesForDatasets(SecurityContext ctx, java.util.Collection<java.lang.Long> datasetIds) Load all images belonging to particular datasets
java.util.Collection<ImageData>	getImagesForProjects(SecurityContext ctx, java.util.Collection<java.lang.Long> projectIds) Load all images belonging to particular projects
java.util.Collection<java.lang.String>	getLookupTables(SecurityContext ctx) Get the available lookup tables
java.util.Collection<ImageData>	getOrphanedImages(SecurityContext ctx, long userID) Get orphaned images for a certain user
java.util.Collection<PlateData>	getPlates(SecurityContext ctx) Loads all plates
java.util.Collection<PlateData>	getPlates(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Loads the plates with the given ids
java.util.Collection<PlateData>	getPlates(SecurityContext ctx, long ownerId) Loads the plates for a particular user
java.util.Collection<PlateData>	getPlates(SecurityContext ctx, long ownerId, java.util.Collection<java.lang.Long> ids) Loads the plates with the given ids which belong to a particular user
java.util.Collection<PlateData>	getPlates(SecurityContext ctx, java.lang.String name) Load plate by name
java.util.Collection<ProjectData>	getProjects(SecurityContext ctx) Get all projects
java.util.Collection<ProjectData>	getProjects(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Get the projects for the given project ids
java.util.Collection<ProjectData>	getProjects(SecurityContext ctx, long ownerId) Get the projects of a certain user
java.util.Collection<ProjectData>	getProjects(SecurityContext ctx, long ownerId, java.util.Collection<java.lang.Long> ids) Get the projects for the given project ids which belong to a certain user
java.util.Collection<ProjectData>	getProjects(SecurityContext ctx, java.lang.String name) Load project by name
java.util.Collection<ScreenData>	getScreens(SecurityContext ctx) Loads all screens
java.util.Collection<ScreenData>	getScreens(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Loads the screens with the given ids
java.util.Collection<ScreenData>	getScreens(SecurityContext ctx, long ownerId) Loads the screens for a particular user
java.util.Collection<ScreenData>	getScreens(SecurityContext ctx, long ownerId, java.util.Collection<java.lang.Long> ids) Loads the screens with the given ids which belong to a particular user
java.util.Collection<ScreenData>	getScreens(SecurityContext ctx, java.lang.String name) Load screen by name
java.util.Collection<ImageData>	getUserImages(SecurityContext ctx) Loads all images of the logged in user
java.util.Collection<WellData>	getWells(SecurityContext ctx, java.util.Collection<java.lang.Long> wellIds) Loads the wells
java.util.Collection<WellData>	getWells(SecurityContext ctx, long plateId) Loads the wells for a given plate
java.util.Collection<FolderData>	loadFolders(SecurityContext ctx, java.util.Collection<java.lang.Long> ids) Loads the folders for the given Ids.

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

getHierarchy

public java.util.Collection<DataObject> getHierarchy(SecurityContext ctx,
                                                     java.lang.Class rootType,
                                                     long userId)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Retrieves hierarchy trees rooted by a given node. i.e. the requested node as root and all of its descendants.

Parameters:

ctx - The security context.

rootType - The type of node to handle.

userId - The user's to retrieve the data to handle.

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.

getHierarchy

public java.util.Collection<DataObject> getHierarchy(SecurityContext ctx,
                                                     java.lang.Class rootType,
                                                     java.util.List<java.lang.Long> rootIDs,
                                                     omero.sys.Parameters options)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Retrieves hierarchy trees rooted by a given node i.e. the requested node as root and all of its descendants.

Parameters:

ctx - The security context.

rootType - The type of node to handle.

rootIDs - The ids of the root nodes. Can be null or empty, in which case all root nodes the user has access to are loaded.

options - The retrieval options.

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.

findObject

public <T extends DataObject> T findObject(SecurityContext ctx,
                                           java.lang.Class<T> klass,
                                           long id)
                                    throws DSOutOfServiceException,
                                           DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

klass - The type of object to retrieve.

id - The object's id.

Returns:

The last version of the 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.

findObject

public <T extends DataObject> T findObject(SecurityContext ctx,
                                           java.lang.Class<T> klass,
                                           long id,
                                           boolean allGroups)
                                    throws DSOutOfServiceException,
                                           DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

klass - The type of object to retrieve.

id - The object's id.

allGroups - Pass true to take all groups into account, false to only use ctx's group

Returns:

The last version of the object (or null it doesn't exist).

Throws:

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

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

findIObject

public omero.model.IObject findIObject(SecurityContext ctx,
                                       java.lang.String klassName,
                                       long id)
                                throws DSOutOfServiceException,
                                       DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

klassName - The type of object to retrieve.

id - The object's id.

Returns:

The last version of the 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.

findObject

public DataObject findObject(SecurityContext ctx,
                             java.lang.String pojoName,
                             long id)
                      throws DSOutOfServiceException,
                             DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

pojoName - The type of object to retrieve. (Either the simple or the full class name, e. g. omero.gateway.model.DatasetData or DatasetData)

id - The object's id.

Returns:

The last version of the 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.

findIObject

public omero.model.IObject findIObject(SecurityContext ctx,
                                       java.lang.String klassName,
                                       long id,
                                       boolean allGroups)
                                throws DSOutOfServiceException,
                                       DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

klassName - The type of object to retrieve.

id - The object's id.

allGroups - Pass true to look for all groups

Returns:

The last version of the 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.

findObject

public DataObject findObject(SecurityContext ctx,
                             java.lang.String pojoName,
                             long id,
                             boolean allGroups)
                      throws DSOutOfServiceException,
                             DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

pojoName - The type of object to retrieve. (Either the simple or the full class name, e. g. omero.gateway.model.DatasetData or DatasetData)

id - The object's id.

allGroups - Pass true to look for all groups

Returns:

The last version of the object (or null it doesn't exist).

Throws:

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

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

findIObject

public omero.model.IObject findIObject(SecurityContext ctx,
                                       omero.model.IObject o)
                                throws DSOutOfServiceException,
                                       DSAccessException

Retrieves an updated version of the specified object.

Parameters:

ctx - The security context.

o - The object to retrieve.

Returns:

The last version of the object or null if the object hasn't been persisted previously

Throws:

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

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

getAvailableGroups

public java.util.Set<GroupData> getAvailableGroups(SecurityContext ctx,
                                                   ExperimenterData user)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Retrieves the groups visible by the current experimenter.

Parameters:

ctx - The security context.

user - The user currently logged in.

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.

getProjects

public java.util.Collection<ProjectData> getProjects(SecurityContext ctx)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get all projects

Parameters:

ctx - The SecurityContext

Returns:

A collection of ProjectDatas

Throws:

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

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

getProjects

public java.util.Collection<ProjectData> getProjects(SecurityContext ctx,
                                                     java.util.Collection<java.lang.Long> ids)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get the projects for the given project ids

Parameters:

ctx - The SecurityContext

ids - The ids of the projects to fetch

Returns:

A collection of ProjectDatas

Throws:

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

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

getProjects

public java.util.Collection<ProjectData> getProjects(SecurityContext ctx,
                                                     long ownerId)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get the projects of a certain user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getProjects(SecurityContext))

Returns:

A collection of ProjectDatas

Throws:

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

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

getProjects

public java.util.Collection<ProjectData> getProjects(SecurityContext ctx,
                                                     long ownerId,
                                                     java.util.Collection<java.lang.Long> ids)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get the projects for the given project ids which belong to a certain user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getProjects(SecurityContext, Collection))

ids - The ids of the projects to fetch

Returns:

A collection of ProjectDatas

Throws:

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

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

getProjects

public java.util.Collection<ProjectData> getProjects(SecurityContext ctx,
                                                     java.lang.String name)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Load project by name

Parameters:

ctx - The SecurityContext

name - The name of the project

Returns:

A collection of ProjectDatas

Throws:

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

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

getDatasets

public java.util.Collection<DatasetData> getDatasets(SecurityContext ctx)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Loads all datasets

Parameters:

ctx - The SecurityContext

Returns:

A collection of DatasetDatas

Throws:

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

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

getDatasets

public java.util.Collection<DatasetData> getDatasets(SecurityContext ctx,
                                                     java.util.Collection<java.lang.Long> ids)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Loads the datasets with the given ids

Parameters:

ctx - The SecurityContext

ids - The ids of the datasets to load

Returns:

A collection of DatasetDatas

Throws:

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

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

getDatasets

public java.util.Collection<DatasetData> getDatasets(SecurityContext ctx,
                                                     long ownerId)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Loads the datasets for a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getDatasets(SecurityContext))

Returns:

A collection of DatasetDatas

Throws:

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

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

getDatasets

public java.util.Collection<DatasetData> getDatasets(SecurityContext ctx,
                                                     long ownerId,
                                                     java.util.Collection<java.lang.Long> ids)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Loads the datasets with the given ids which belong to a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getDatasets(SecurityContext, Collection))

ids - The ids of the datasets to load

Returns:

A collection of DatasetDatas

Throws:

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

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

getDatasets

public java.util.Collection<DatasetData> getDatasets(SecurityContext ctx,
                                                     java.lang.String name)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Load dataset by name

Parameters:

ctx - The SecurityContext

name - The name of the dataset

Returns:

A collection of DatasetDatas

Throws:

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

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

getScreens

public java.util.Collection<ScreenData> getScreens(SecurityContext ctx)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Loads all screens

Parameters:

ctx - The SecurityContext

Returns:

A collection of ScreenDatas

Throws:

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

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

getScreens

public java.util.Collection<ScreenData> getScreens(SecurityContext ctx,
                                                   java.util.Collection<java.lang.Long> ids)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Loads the screens with the given ids

Parameters:

ctx - The SecurityContext

ids - The ids of the screens to load

Returns:

A collection of ScreenDatas

Throws:

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

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

getScreens

public java.util.Collection<ScreenData> getScreens(SecurityContext ctx,
                                                   long ownerId)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Loads the screens for a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getScreens(SecurityContext))

Returns:

A collection of ScreenDatas

Throws:

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

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

getScreens

public java.util.Collection<ScreenData> getScreens(SecurityContext ctx,
                                                   long ownerId,
                                                   java.util.Collection<java.lang.Long> ids)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Loads the screens with the given ids which belong to a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getScreens(SecurityContext, Collection))

ids - The ids of the screens to load

Returns:

A collection of ScreenDatas

Throws:

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

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

getScreens

public java.util.Collection<ScreenData> getScreens(SecurityContext ctx,
                                                   java.lang.String name)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Load screen by name

Parameters:

ctx - The SecurityContext

name - The name of the screen

Returns:

A collection of ScreenDatas

Throws:

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

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

getPlates

public java.util.Collection<PlateData> getPlates(SecurityContext ctx)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads all plates

Parameters:

ctx - The SecurityContext

Returns:

A collection of PlateDatas

Throws:

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

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

getPlates

public java.util.Collection<PlateData> getPlates(SecurityContext ctx,
                                                 java.util.Collection<java.lang.Long> ids)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the plates with the given ids

Parameters:

ctx - The SecurityContext

ids - The ids of the screens to load

Returns:

A collection of PlateDatas

Throws:

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

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

getPlates

public java.util.Collection<PlateData> getPlates(SecurityContext ctx,
                                                 long ownerId)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the plates for a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getPlates(SecurityContext))

Returns:

A collection of PlateDatas

Throws:

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

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

getPlates

public java.util.Collection<PlateData> getPlates(SecurityContext ctx,
                                                 long ownerId,
                                                 java.util.Collection<java.lang.Long> ids)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the plates with the given ids which belong to a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user (if 0 see getPlates(SecurityContext, Collection))

ids - The ids of the plates to load

Returns:

A collection of PlateDatas

Throws:

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

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

getPlates

public java.util.Collection<PlateData> getPlates(SecurityContext ctx,
                                                 java.lang.String name)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Load plate by name

Parameters:

ctx - The SecurityContext

name - The name of the plate

Returns:

A collection of PlateDatas

Throws:

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

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

getWells

public java.util.Collection<WellData> getWells(SecurityContext ctx,
                                               java.util.Collection<java.lang.Long> wellIds)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Loads the wells

Parameters:

ctx - The SecurityContext

wellIds - The ids of the wells to load

Returns:

A collection of WellDatas

Throws:

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

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

getWells

public java.util.Collection<WellData> getWells(SecurityContext ctx,
                                               long plateId)
                                        throws DSOutOfServiceException,
                                               DSAccessException

Loads the wells for a given plate

Parameters:

ctx - The SecurityContext

plateId - The ID of the plate

Returns:

A collection of WellDatas

Throws:

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

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

getUserImages

public java.util.Collection<ImageData> getUserImages(SecurityContext ctx)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Loads all images of the logged in user

Parameters:

ctx - The SecurityContext

Returns:

A collection of ImageDatas

Throws:

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

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

getImage

public ImageData getImage(SecurityContext ctx,
                          long id)
                   throws DSOutOfServiceException,
                          DSAccessException

Loads a image

Parameters:

ctx - The SecurityContext

id - The ids of the image to load

Returns:

The ImageData

Throws:

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

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

getImage

public ImageData getImage(SecurityContext ctx,
                          long id,
                          omero.sys.ParametersI params)
                   throws DSOutOfServiceException,
                          DSAccessException

Loads a image

Parameters:

ctx - The SecurityContext

id - The ids of the image to load

params - Custom parameters, can be null

Returns:

The ImageData

Throws:

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

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

getImages

public java.util.Collection<ImageData> getImages(SecurityContext ctx,
                                                 java.util.Collection<java.lang.Long> ids)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the images with the given ids

Parameters:

ctx - The SecurityContext

ids - The ids of the images to load

Returns:

A collection of ImageDatas

Throws:

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

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

getImages

public java.util.Collection<ImageData> getImages(SecurityContext ctx,
                                                 java.util.Collection<java.lang.Long> ids,
                                                 omero.sys.ParametersI params)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the images with the given ids

Parameters:

ctx - The SecurityContext

ids - The ids of the images to load

params - Custom parameters, can be null

Returns:

A collection of ImageDatas

Throws:

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

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

getOrphanedImages

public java.util.Collection<ImageData> getOrphanedImages(SecurityContext ctx,
                                                         long userID)

Get orphaned images for a certain user

Parameters:

ctx - The SecurityContext

userID - The id of the user

Returns:

See above.

getImages

public java.util.Collection<ImageData> getImages(SecurityContext ctx,
                                                 long ownerId,
                                                 java.util.Collection<java.lang.Long> ids)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the images for a particular user

Parameters:

ctx - The SecurityContext

ownerId - The id of the user

ids - The image ids

Returns:

A collection of ImageDatas

Throws:

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

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

getImagesForDatasets

public java.util.Collection<ImageData> getImagesForDatasets(SecurityContext ctx,
                                                            java.util.Collection<java.lang.Long> datasetIds)
                                                     throws DSOutOfServiceException,
                                                            DSAccessException

Load all images belonging to particular datasets

Parameters:

ctx - The SecurityContext

datasetIds - The ids of the datasets

Returns:

A collection of ImageDatas

Throws:

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

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

getImagesForProjects

public java.util.Collection<ImageData> getImagesForProjects(SecurityContext ctx,
                                                            java.util.Collection<java.lang.Long> projectIds)
                                                     throws DSOutOfServiceException,
                                                            DSAccessException

Load all images belonging to particular projects

Parameters:

ctx - The SecurityContext

projectIds - The ids of the projects

Returns:

A collection of ImageDatas

Throws:

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

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

getImages

public java.util.Collection<ImageData> getImages(SecurityContext ctx,
                                                 java.lang.String name)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Load image by name

Parameters:

ctx - The SecurityContext

name - The name of the image

Returns:

A collection of ImageDatas

Throws:

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

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

loadFolders

public java.util.Collection<FolderData> loadFolders(SecurityContext ctx,
                                                    java.util.Collection<java.lang.Long> ids)
                                             throws DSOutOfServiceException,
                                                    DSAccessException

Loads the folders for the given Ids. FolderData objects will be fully initialized. (See getFolders(SecurityContext, Collection) for a faster but not fully initialized method)

Parameters:

ctx - The SecurityContext

ids - The folder Ids

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.

getFolders

public java.util.Collection<FolderData> getFolders(SecurityContext ctx)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Get all folders the logged in user has access to. Note: FolderData objects won't be fully initialized (i. e. sub folder, roi, etc. collections will be unloaded!). If you need fully initialized objects see loadFolders(SecurityContext, Collection).

Parameters:

ctx - The SecurityContext

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.

getFolders

public java.util.Collection<FolderData> getFolders(SecurityContext ctx,
                                                   java.util.Collection<java.lang.Long> ids)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Get the folders for the given folder ids. Note: FolderData objects won't be fully initialized (i. e. sub folder, roi, etc. collections will be unloaded!). If you need fully initialized objects see loadFolders(SecurityContext, Collection).

Parameters:

ctx - The SecurityContext

ids - The folder ids

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.

getFolders

public java.util.Collection<FolderData> getFolders(SecurityContext ctx,
                                                   long userId)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Get the folders which belong to the given user. Note: FolderData objects won't be fully initialized (i. e. sub folder, roi, etc. collections will be unloaded!). If you need fully initialized objects see loadFolders(SecurityContext, Collection).

Parameters:

ctx - The SecurityContext

userId - The user id

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.

getLookupTables

public java.util.Collection<java.lang.String> getLookupTables(SecurityContext ctx)
                                                       throws DSOutOfServiceException,
                                                              DSAccessException

Get the available lookup tables

Parameters:

ctx - The SecurityContext

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.