fr.igred.omero.client

Interface Browser

All Known Subinterfaces:

Client

All Known Implementing Classes:

GatewayWrapper

public interface Browser

Interface to browse data on an OMERO server in a given SecurityContext.

Method Summary

Modifier and Type	Method and Description
default List<IObject>	findByQuery(String query) Finds objects on OMERO through a database query.
BrowseFacility	getBrowseFacility() Gets the BrowseFacility used to access the data from OMERO.
SecurityContext	getCtx() Returns the current SecurityContext.
default Dataset	getDataset(Long id) Gets the dataset with the specified id from OMERO.
default List<Dataset>	getDatasets() Gets all datasets available from OMERO.
default List<Dataset>	getDatasets(Experimenter experimenter) Gets all datasets available from OMERO owned by a given user.
default List<Dataset>	getDatasets(Long... ids) Gets the datasets with the specified ids from OMERO.
default List<Dataset>	getDatasets(String name) Gets all datasets with a certain name from OMERO.
default Folder	getFolder(long id) Gets the folder with the specified ID from OMERO, fully loaded.
default List<Folder>	getFolders() Gets all folders available from OMERO.
default List<Folder>	getFolders(Experimenter experimenter) Gets all the folders owned by a given user from OMERO.
default Image	getImage(Long id) Returns the image with the specified ID from OMERO.
default List<Image>	getImages() Gets all images owned by the current user.
default List<Image>	getImages(Annotation annotation) Gets all images with the specified annotation from OMERO.
default List<Image>	getImages(Long... ids) Gets the images with the specified ids from OMERO
default List<Image>	getImages(String name) Gets all images with a certain name from OMERO.
default List<Image>	getImages(String projectName, String datasetName, String imageName) Gets all images with the name specified inside projects and datasets with the given names.
default List<Image>	getImagesLike(String motif) Gets all images with a certain motif in their name from OMERO.
default List<Image>	getImagesWithKey(String key) Gets all images with a certain key.
default List<Image>	getImagesWithKeyValuePair(String key, String value) Gets all images with a certain key value pair from OMERO
default MapAnnotation	getMapAnnotation(Long id) Gets a specific map annotation (key/value pairs) from the OMERO database.
default List<MapAnnotation>	getMapAnnotations() Gets the list of map annotations available to the user.
default List<MapAnnotation>	getMapAnnotations(String key) Gets the list of map annotations with the specified key available to the user.
default List<MapAnnotation>	getMapAnnotations(String key, String value) Gets the list of map annotations with the specified key and value available to the user.
MetadataFacility	getMetadataFacility() Gets the MetadataFacility used to retrieve annotations from OMERO.
default Plate	getPlate(Long id) Gets the plate with the specified id from OMERO.
default List<Plate>	getPlates() Gets all plates available from OMERO.
default List<Plate>	getPlates(Experimenter experimenter) Gets all plates available from OMERO owned by a given user.
default List<Plate>	getPlates(Long... ids) Gets the plates with the specified ids from OMERO.
default Project	getProject(Long id) Gets the project with the specified id from OMERO.
default List<Project>	getProjects() Gets all projects available from OMERO.
default List<Project>	getProjects(Experimenter experimenter) Gets all projects available from OMERO owned by a given user.
default List<Project>	getProjects(Long... ids) Gets the projects with the specified ids from OMERO.
default List<Project>	getProjects(String name) Gets all projects with a certain name from OMERO.
omero.api.IQueryPrx	getQueryService() Returns the IQueryPrx used to find objects on OMERO.
default Screen	getScreen(Long id) Gets the screen with the specified id from OMERO.
default List<Screen>	getScreens() Gets all screens available from OMERO.
default List<Screen>	getScreens(Experimenter experimenter) Gets all screens available from OMERO owned by a given user.
default List<Screen>	getScreens(Long... ids) Gets the screens with the specified ids from OMERO.
default TagAnnotation	getTag(Long id) Gets a specific tag from the OMERO database.
default List<TagAnnotation>	getTags() Gets the list of tag annotations available to the user.
default List<TagAnnotation>	getTags(String name) Gets the list of tag annotations with the specified name available to the user.
default Well	getWell(Long id) Gets the well with the specified id from OMERO.
default List<Well>	getWells() Gets all wells available from OMERO.
default List<Well>	getWells(Experimenter experimenter) Gets all wells available from OMERO owned by a given user.
default List<Well>	getWells(Long... ids) Gets the wells with the specified ids from OMERO.
default List<Folder>	loadFolders(Long... ids) Gets the folders with the specified IDs from OMERO (fully loaded).

Method Detail

getCtx

SecurityContext getCtx()

Returns the current SecurityContext.

Returns:

See above

getBrowseFacility

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

omero.api.IQueryPrx getQueryService()
                             throws ServiceException,
                                    AccessException

Returns the IQueryPrx used to find objects on OMERO.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getMetadataFacility

MetadataFacility getMetadataFacility()
                              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.

findByQuery

default List<IObject> findByQuery(String query)
                           throws ServiceException,
                                  AccessException

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.

AccessException - Cannot access data.

getProject

default Project 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 such id.

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

getProjects

default List<Project> 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

default List<Project> 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

default List<Project> getProjects(Experimenter 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

default List<Project> 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

default Dataset 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 such id.

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

getDatasets

default List<Dataset> 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

default List<Dataset> getDatasets()
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Gets all datasets 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.

getDatasets

default List<Dataset> getDatasets(Experimenter experimenter)
                           throws ServiceException,
                                  AccessException,
                                  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.

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

getDatasets

default List<Dataset> 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

default Image 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 such id.

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

getImages

default List<Image> 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

default List<Image> 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

default List<Image> 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

default List<Image> 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

default List<Image> getImages(Annotation annotation)
                       throws ServiceException,
                              AccessException,
                              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.

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

getImagesLike

default List<Image> 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.

getImagesWithKey

default List<Image> getImagesWithKey(String key)
                              throws ServiceException,
                                     AccessException,
                                     ExecutionException

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.

getImagesWithKeyValuePair

default List<Image> getImagesWithKeyValuePair(String key,
                                              String value)
                                       throws ServiceException,
                                              AccessException,
                                              ExecutionException

Gets all images with a certain key value pair from OMERO

Parameters:

key - Name of the key researched.

value - Value associated with the key.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreen

default Screen 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 such id.

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

getScreens

default List<Screen> 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

default List<Screen> 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

default List<Screen> getScreens(Experimenter 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

default Plate 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 such id.

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

getPlates

default List<Plate> 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

default List<Plate> 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

default List<Plate> getPlates(Experimenter 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

default Well 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 such id.

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

getWells

default List<Well> 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

default List<Well> getWells()
                     throws ServiceException,
                            AccessException,
                            ExecutionException

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.

getWells

default List<Well> getWells(Experimenter experimenter)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

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.

getFolder

default Folder 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 such id.

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

getFolders

default List<Folder> 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

default List<Folder> getFolders(Experimenter 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

default List<Folder> 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

default List<TagAnnotation> getTags()
                             throws ServiceException,
                                    AccessException

Gets the list of tag annotations available to the user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getTags

default List<TagAnnotation> getTags(String name)
                             throws ServiceException,
                                    AccessException

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:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getTag

default TagAnnotation getTag(Long id)
                      throws ServiceException,
                             ExecutionException,
                             AccessException

Gets a specific tag from the OMERO database.

Parameters:

id - ID of the tag.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getMapAnnotations

default List<MapAnnotation> getMapAnnotations()
                                       throws ServiceException,
                                              AccessException

Gets the list of map annotations available to the user.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getMapAnnotations

default List<MapAnnotation> getMapAnnotations(String key)
                                       throws ServiceException,
                                              AccessException

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:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getMapAnnotations

default List<MapAnnotation> getMapAnnotations(String key,
                                              String value)
                                       throws ServiceException,
                                              AccessException

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:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getMapAnnotation

default MapAnnotation getMapAnnotation(Long id)
                                throws ServiceException,
                                       AccessException,
                                       ExecutionException

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.