Package fr.igred.omero

Class Browser

java.lang.Object

fr.igred.omero.GatewayWrapper

fr.igred.omero.Browser

Direct Known Subclasses:

Client

public abstract class Browser
extends GatewayWrapper

Abstract class to browse data on an OMERO server in a given SecurityContext and wrap DataObjects.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
DatasetWrapper	getDataset(Long id)	Gets the dataset with the specified id from OMERO.
List<DatasetWrapper>	getDatasets()	Gets all datasets available from OMERO.
List<DatasetWrapper>	getDatasets(ExperimenterWrapper experimenter)	Gets all datasets available from OMERO owned by a given user.
List<DatasetWrapper>	getDatasets(Long... ids)	Gets the datasets with the specified ids from OMERO.
List<DatasetWrapper>	getDatasets(String name)	Gets all datasets with a certain name from OMERO.
FolderWrapper	getFolder(long id)	Gets the folder with the specified ID from OMERO, fully loaded.
List<FolderWrapper>	getFolders()	Gets all folders available from OMERO.
List<FolderWrapper>	getFolders(ExperimenterWrapper experimenter)	Gets all the folders owned by a given user from OMERO.
ImageWrapper	getImage(Long id)	Returns the image with the specified ID from OMERO.
List<ImageWrapper>	getImages()	Gets all images owned by the current user.
abstract List<ImageWrapper>	getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation from OMERO.
List<ImageWrapper>	getImages(Long... ids)	Gets the images with the specified ids from OMERO
List<ImageWrapper>	getImages(String name)	Gets all images with a certain name from OMERO.
abstract List<ImageWrapper>	getImages(String projectName, String datasetName, String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
abstract List<ImageWrapper>	getImagesKey(String key)	Deprecated. Gets all images with a certain key
List<ImageWrapper>	getImagesLike(String motif)	Gets all images with a certain motif in their name from OMERO.
abstract List<ImageWrapper>	getImagesPairKeyValue(String key, String value)	Deprecated. Gets all images with a certain key value pair from OMERO
List<ImageWrapper>	getImagesTagged(TagAnnotationWrapper tag)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesTagged(Long tagId)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesWithKey(String key)	Gets all images with a certain key.
List<ImageWrapper>	getImagesWithKeyValuePair(String key, String value)	Gets all images with a certain key value pair from OMERO
MapAnnotationWrapper	getMapAnnotation(Long id)	Gets a specific map annotation (key/value pairs) from the OMERO database.
List<MapAnnotationWrapper>	getMapAnnotations()	Gets the list of map annotations available to the user.
List<MapAnnotationWrapper>	getMapAnnotations(String key)	Gets the list of map annotations with the specified key available to the user.
List<MapAnnotationWrapper>	getMapAnnotations(String key, String value)	Gets the list of map annotations with the specified key and value available to the user.
PlateWrapper	getPlate(Long id)	Gets the plate with the specified id from OMERO.
List<PlateWrapper>	getPlates()	Gets all plates available from OMERO.
List<PlateWrapper>	getPlates(ExperimenterWrapper experimenter)	Gets all plates available from OMERO owned by a given user.
List<PlateWrapper>	getPlates(Long... ids)	Gets the plates with the specified ids 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(ExperimenterWrapper experimenter)	Gets all projects available from OMERO owned by a given user.
List<ProjectWrapper>	getProjects(Long... ids)	Gets the projects with the specified ids from OMERO.
List<ProjectWrapper>	getProjects(String name)	Gets all projects with a certain name from OMERO.
ScreenWrapper	getScreen(Long id)	Gets the screen with the specified id from OMERO.
List<ScreenWrapper>	getScreens()	Gets all screens available from OMERO.
List<ScreenWrapper>	getScreens(ExperimenterWrapper experimenter)	Gets all screens available from OMERO owned by a given user.
List<ScreenWrapper>	getScreens(Long... ids)	Gets the screens with the specified ids from OMERO.
TagAnnotationWrapper	getTag(Long id)	Gets a specific tag from the OMERO database.
List<TagAnnotationWrapper>	getTags()	Gets the list of tag annotations available to the user.
List<TagAnnotationWrapper>	getTags(String name)	Gets the list of tag annotations with the specified name available to the user.
WellWrapper	getWell(Long id)	Gets the well with the specified id from OMERO.
List<WellWrapper>	getWells()	Gets all wells available from OMERO.
List<WellWrapper>	getWells(ExperimenterWrapper experimenter)	Gets all wells available from OMERO owned by a given user.
List<WellWrapper>	getWells(Long... ids)	Gets the wells with the specified ids from OMERO.
List<FolderWrapper>	loadFolders(Long... ids)	Gets the folders with the specified IDs from OMERO (fully loaded).

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

Browser

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

Constructor of the Browser class.

Parameters:

gateway - The gateway

ctx - The security context

user - The user

Method Details

getProject

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

Gets the project with the specified id from OMERO.

Parameters:

id - ID of the project.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getProjects

public List<ProjectWrapper> getProjects(Long... ids)
                                 throws ServiceException,
AccessException,
ExecutionException

Gets the projects with the specified ids from OMERO.

Parameters:

ids - Project IDs

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getProjects

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

Gets all projects available from OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getProjects

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

Gets all projects available from OMERO owned by a given user.

Parameters:

experimenter - The user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getProjects

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

Gets all projects with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getDataset

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

Gets the dataset with the specified id from OMERO.

Parameters:

id - ID of the dataset.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getDatasets

public List<DatasetWrapper> getDatasets(Long... ids)
                                 throws ServiceException,
AccessException,
ExecutionException

Gets the datasets with the specified ids from OMERO.

Parameters:

ids - Dataset IDs

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getDatasets

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

Gets all datasets available from OMERO.

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.

getDatasets

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

Gets all datasets available from OMERO owned by a given user.

Parameters:

experimenter - The user.

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.

getDatasets

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

Gets all datasets with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImage

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

Returns the image with the specified ID from OMERO.

Parameters:

id - ID of the image.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getImages

public List<ImageWrapper> getImages(Long... ids)
                             throws ServiceException,
AccessException,
ExecutionException

Gets the images with the specified ids from OMERO

Parameters:

ids - Image IDs

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()
                             throws ServiceException,
AccessException,
ExecutionException

Gets all images owned by the current user.

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(String name)
                             throws ServiceException,
AccessException,
ExecutionException

Gets all images with a certain name from OMERO.

Parameters:

name - Name searched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

public abstract 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.

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

Gets all images with the specified annotation from OMERO.

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.

getImagesLike

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

Gets all images with a certain motif in their name from OMERO.

Parameters:

motif - Motif searched in an image name.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesTagged

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

Deprecated.

Gets all images tagged with a specified tag from OMERO.

Parameters:

tag - The tag annotation.

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.

getImagesTagged

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

Deprecated.

Gets all images tagged with a specified tag from OMERO.

Parameters:

tagId - Id of 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 abstract List<ImageWrapper> getImagesKey(String key)
                                         throws ServiceException,
AccessException,
ExecutionException

Deprecated.

Gets all images with a certain key

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.

getImagesWithKey

public List<ImageWrapper> getImagesWithKey(String key)
                                    throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError

Gets all images with a certain key.

Parameters:

key - Name of the key 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.

getImagesPairKeyValue

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

Deprecated.

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:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesWithKeyValuePair

public List<ImageWrapper> getImagesWithKeyValuePair(String key,
 String value)
                                             throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError

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:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getScreen

public ScreenWrapper getScreen(Long id)
                        throws ServiceException,
AccessException,
ExecutionException

Gets the screen with the specified id from OMERO.

Parameters:

id - ID of the screen.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getScreens

public List<ScreenWrapper> getScreens(Long... ids)
                               throws ServiceException,
AccessException,
ExecutionException

Gets the screens with the specified ids from OMERO.

Parameters:

ids - A list of screen ids

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreens

public List<ScreenWrapper> getScreens()
                               throws ServiceException,
AccessException,
ExecutionException

Gets all screens available from OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreens

public List<ScreenWrapper> getScreens(ExperimenterWrapper experimenter)
                               throws ServiceException,
AccessException,
ExecutionException

Gets all screens available from OMERO owned by a given user.

Parameters:

experimenter - The user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlate

public PlateWrapper getPlate(Long id)
                      throws ServiceException,
AccessException,
ExecutionException

Gets the plate with the specified id from OMERO.

Parameters:

id - ID of the plate.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getPlates

public List<PlateWrapper> getPlates(Long... ids)
                             throws ServiceException,
AccessException,
ExecutionException

Gets the plates with the specified ids from OMERO.

Parameters:

ids - A list of plate ids

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlates

public List<PlateWrapper> getPlates()
                             throws ServiceException,
AccessException,
ExecutionException

Gets all plates available from OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlates

public List<PlateWrapper> getPlates(ExperimenterWrapper experimenter)
                             throws ServiceException,
AccessException,
ExecutionException

Gets all plates available from OMERO owned by a given user.

Parameters:

experimenter - The user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getWell

public WellWrapper getWell(Long id)
                    throws ServiceException,
AccessException,
ExecutionException

Gets the well with the specified id from OMERO.

Parameters:

id - ID of the well.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getWells

public List<WellWrapper> getWells(Long... ids)
                           throws ServiceException,
AccessException,
ExecutionException

Gets the wells with the specified ids from OMERO.

Parameters:

ids - A list of well ids

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getWells

public List<WellWrapper> getWells()
                           throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError

Gets all wells available from OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

getWells

public List<WellWrapper> getWells(ExperimenterWrapper experimenter)
                           throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError

Gets all wells available from OMERO owned by a given user.

Parameters:

experimenter - The user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

getFolder

public FolderWrapper getFolder(long id)
                        throws ServiceException,
AccessException,
ExecutionException

Gets the folder with the specified ID from OMERO, fully loaded.

Parameters:

id - ID of the folder.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - No element with this ID.

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

getFolders

public List<FolderWrapper> getFolders()
                               throws ExecutionException,
AccessException,
ServiceException

Gets all folders available from OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getFolders

public List<FolderWrapper> getFolders(ExperimenterWrapper experimenter)
                               throws ExecutionException,
AccessException,
ServiceException

Gets all the folders owned by a given user from OMERO.

Parameters:

experimenter - The user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

loadFolders

public List<FolderWrapper> loadFolders(Long... ids)
                                throws ServiceException,
AccessException,
ExecutionException

Gets the folders with the specified IDs from OMERO (fully loaded).

Parameters:

ids - Project IDs

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getTags

public List<TagAnnotationWrapper> getTags()
                                   throws OMEROServerError,
ServiceException

Gets the list of tag annotations available to the user.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getTags

public List<TagAnnotationWrapper> getTags(String name)
                                   throws OMEROServerError,
ServiceException

Gets the list of tag annotations with the specified name available to the user.

Parameters:

name - Name of the tag searched.

Returns:

See above.

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:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

NoSuchElementException - No element with this ID.

getMapAnnotations

public List<MapAnnotationWrapper> getMapAnnotations()
                                             throws OMEROServerError,
ServiceException

Gets the list of map annotations available to the user.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getMapAnnotations

public List<MapAnnotationWrapper> getMapAnnotations(String key)
                                             throws OMEROServerError,
ServiceException

Gets the list of map annotations with the specified key available to the user.

Parameters:

key - Name of the tag searched.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getMapAnnotations

public List<MapAnnotationWrapper> getMapAnnotations(String key,
 String value)
                                             throws OMEROServerError,
ServiceException

Gets the list of map annotations with the specified key and value available to the user.

Parameters:

key - The required key.

value - The required value.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

getMapAnnotation

public MapAnnotationWrapper getMapAnnotation(Long id)
                                      throws ServiceException,
ExecutionException,
AccessException

Gets a specific map annotation (key/value pairs) from the OMERO database.

Parameters:

id - ID of the map annotation.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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