Package fr.igred.omero.client
Interface Browser
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- All Known Subinterfaces:
Client
- All Known Implementing Classes:
GatewayWrapper
public interface Browser
Interface to browse data on an OMERO server in a givenSecurityContext
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Method Summary
All Methods Instance Methods Abstract Methods Default Methods Modifier and Type Method Description default java.util.List<IObject>
findByQuery(java.lang.String query)
Finds objects on OMERO through a database query.BrowseFacility
getBrowseFacility()
Gets theBrowseFacility
used to access the data from OMERO.SecurityContext
getCtx()
Returns the currentSecurityContext
.default Dataset
getDataset(java.lang.Long id)
Gets the dataset with the specified id from OMERO.default java.util.List<Dataset>
getDatasets()
Gets all datasets available from OMERO.default java.util.List<Dataset>
getDatasets(Experimenter experimenter)
Gets all datasets available from OMERO owned by a given user.default java.util.List<Dataset>
getDatasets(java.lang.Long... ids)
Gets the datasets with the specified ids from OMERO.default java.util.List<Dataset>
getDatasets(java.lang.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 java.util.List<Folder>
getFolders()
Gets all folders available from OMERO.default java.util.List<Folder>
getFolders(Experimenter experimenter)
Gets all the folders owned by a given user from OMERO.default Image
getImage(java.lang.Long id)
Returns the image with the specified ID from OMERO.default java.util.List<Image>
getImages()
Gets all images owned by the current user.default java.util.List<Image>
getImages(Annotation annotation)
Gets all images with the specified annotation from OMERO.default java.util.List<Image>
getImages(java.lang.Long... ids)
Gets the images with the specified ids from OMEROdefault java.util.List<Image>
getImages(java.lang.String name)
Gets all images with a certain name from OMERO.default java.util.List<Image>
getImages(java.lang.String projectName, java.lang.String datasetName, java.lang.String imageName)
Gets all images with the name specified inside projects and datasets with the given names.default java.util.List<Image>
getImagesLike(java.lang.String motif)
Gets all images with a certain motif in their name from OMERO.default java.util.List<Image>
getImagesWithKey(java.lang.String key)
Gets all images with a certain key.default java.util.List<Image>
getImagesWithKeyValuePair(java.lang.String key, java.lang.String value)
Gets all images with a certain key value pair from OMEROdefault MapAnnotation
getMapAnnotation(java.lang.Long id)
Gets a specific map annotation (key/value pairs) from the OMERO database.default java.util.List<MapAnnotation>
getMapAnnotations()
Gets the list of map annotations available to the user.default java.util.List<MapAnnotation>
getMapAnnotations(java.lang.String key)
Gets the list of map annotations with the specified key available to the user.default java.util.List<MapAnnotation>
getMapAnnotations(java.lang.String key, java.lang.String value)
Gets the list of map annotations with the specified key and value available to the user.MetadataFacility
getMetadataFacility()
Gets theMetadataFacility
used to retrieve annotations from OMERO.default Plate
getPlate(java.lang.Long id)
Gets the plate with the specified id from OMERO.default java.util.List<Plate>
getPlates()
Gets all plates available from OMERO.default java.util.List<Plate>
getPlates(Experimenter experimenter)
Gets all plates available from OMERO owned by a given user.default java.util.List<Plate>
getPlates(java.lang.Long... ids)
Gets the plates with the specified ids from OMERO.default Project
getProject(java.lang.Long id)
Gets the project with the specified id from OMERO.default java.util.List<Project>
getProjects()
Gets all projects available from OMERO.default java.util.List<Project>
getProjects(Experimenter experimenter)
Gets all projects available from OMERO owned by a given user.default java.util.List<Project>
getProjects(java.lang.Long... ids)
Gets the projects with the specified ids from OMERO.default java.util.List<Project>
getProjects(java.lang.String name)
Gets all projects with a certain name from OMERO.omero.api.IQueryPrx
getQueryService()
Returns theIQueryPrx
used to find objects on OMERO.default Screen
getScreen(java.lang.Long id)
Gets the screen with the specified id from OMERO.default java.util.List<Screen>
getScreens()
Gets all screens available from OMERO.default java.util.List<Screen>
getScreens(Experimenter experimenter)
Gets all screens available from OMERO owned by a given user.default java.util.List<Screen>
getScreens(java.lang.Long... ids)
Gets the screens with the specified ids from OMERO.default TagAnnotation
getTag(java.lang.Long id)
Gets a specific tag from the OMERO database.default java.util.List<TagAnnotation>
getTags()
Gets the list of tag annotations available to the user.default java.util.List<TagAnnotation>
getTags(java.lang.String name)
Gets the list of tag annotations with the specified name available to the user.default Well
getWell(java.lang.Long id)
Gets the well with the specified id from OMERO.default java.util.List<Well>
getWells()
Gets all wells available from OMERO.default java.util.List<Well>
getWells(Experimenter experimenter)
Gets all wells available from OMERO owned by a given user.default java.util.List<Well>
getWells(java.lang.Long... ids)
Gets the wells with the specified ids from OMERO.default java.util.List<Folder>
loadFolders(java.lang.Long... ids)
Gets the folders with the specified IDs from OMERO (fully loaded).
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Method Detail
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getCtx
SecurityContext getCtx()
Returns the currentSecurityContext
.- Returns:
- See above
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getBrowseFacility
BrowseFacility getBrowseFacility() throws java.util.concurrent.ExecutionException
Gets theBrowseFacility
used to access the data from OMERO.- Returns:
- See above.
- Throws:
java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getQueryService
omero.api.IQueryPrx getQueryService() throws ServiceException
Returns theIQueryPrx
used to find objects on OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.
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getMetadataFacility
MetadataFacility getMetadataFacility() throws java.util.concurrent.ExecutionException
Gets theMetadataFacility
used to retrieve annotations from OMERO.- Returns:
- See above.
- Throws:
java.util.concurrent.ExecutionException
- If the MetadataFacility can't be retrieved or instantiated.
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findByQuery
default java.util.List<IObject> findByQuery(java.lang.String query) throws ServiceException, ServerException
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.ServerException
- Server error.
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getProject
default Project getProject(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getProjects
default java.util.List<Project> getProjects(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getProjects
default java.util.List<Project> getProjects() throws ServiceException, AccessException, java.util.concurrent.ExecutionException
Gets all projects available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getProjects
default java.util.List<Project> getProjects(Experimenter experimenter) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getProjects
default java.util.List<Project> getProjects(java.lang.String name) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getDataset
default Dataset getDataset(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getDatasets
default java.util.List<Dataset> getDatasets(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getDatasets
default java.util.List<Dataset> getDatasets() throws ServiceException, AccessException, ServerException, java.util.concurrent.ExecutionException
Gets all datasets available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.ServerException
- Server error.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getDatasets
default java.util.List<Dataset> getDatasets(Experimenter experimenter) throws ServiceException, AccessException, ServerException, java.util.concurrent.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.ServerException
- Server error.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getDatasets
default java.util.List<Dataset> getDatasets(java.lang.String name) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImage
default Image getImage(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImages
default java.util.List<Image> getImages(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImages
default java.util.List<Image> getImages() throws ServiceException, AccessException, java.util.concurrent.ExecutionException
Gets all images owned by the current user.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImages
default java.util.List<Image> getImages(java.lang.String name) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImages
default java.util.List<Image> getImages(java.lang.String projectName, java.lang.String datasetName, java.lang.String imageName) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImages
default java.util.List<Image> getImages(Annotation annotation) throws ServiceException, AccessException, ServerException, java.util.concurrent.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.ServerException
- Server error.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImagesLike
default java.util.List<Image> getImagesLike(java.lang.String motif) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImagesWithKey
default java.util.List<Image> getImagesWithKey(java.lang.String key) throws ServiceException, AccessException, java.util.concurrent.ExecutionException, ServerException
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.ServerException
- Server error.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getImagesWithKeyValuePair
default java.util.List<Image> getImagesWithKeyValuePair(java.lang.String key, java.lang.String value) throws ServiceException, AccessException, java.util.concurrent.ExecutionException, ServerException
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.ServerException
- Server error.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getScreen
default Screen getScreen(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getScreens
default java.util.List<Screen> getScreens(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getScreens
default java.util.List<Screen> getScreens() throws ServiceException, AccessException, java.util.concurrent.ExecutionException
Gets all screens available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getScreens
default java.util.List<Screen> getScreens(Experimenter experimenter) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getPlate
default Plate getPlate(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getPlates
default java.util.List<Plate> getPlates(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getPlates
default java.util.List<Plate> getPlates() throws ServiceException, AccessException, java.util.concurrent.ExecutionException
Gets all plates available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getPlates
default java.util.List<Plate> getPlates(Experimenter experimenter) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getWell
default Well getWell(java.lang.Long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getWells
default java.util.List<Well> getWells(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getWells
default java.util.List<Well> getWells() throws ServiceException, AccessException, java.util.concurrent.ExecutionException, ServerException
Gets all wells available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.ServerException
- Server error.
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getWells
default java.util.List<Well> getWells(Experimenter experimenter) throws ServiceException, AccessException, java.util.concurrent.ExecutionException, ServerException
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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.ServerException
- Server error.
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getFolder
default Folder getFolder(long id) throws ServiceException, AccessException, java.util.concurrent.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.java.util.NoSuchElementException
- No element with such id.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getFolders
default java.util.List<Folder> getFolders() throws java.util.concurrent.ExecutionException, AccessException, ServiceException
Gets all folders available from OMERO.- Returns:
- See above.
- Throws:
ServiceException
- Cannot connect to OMERO.AccessException
- Cannot access data.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getFolders
default java.util.List<Folder> getFolders(Experimenter experimenter) throws java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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loadFolders
default java.util.List<Folder> loadFolders(java.lang.Long... ids) throws ServiceException, AccessException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getTags
default java.util.List<TagAnnotation> getTags() throws ServerException, ServiceException
Gets the list of tag annotations available to the user.- Returns:
- See above.
- Throws:
ServerException
- Server error.ServiceException
- Cannot connect to OMERO.
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getTags
default java.util.List<TagAnnotation> getTags(java.lang.String name) throws ServerException, 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:
ServerException
- Server error.ServiceException
- Cannot connect to OMERO.
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getTag
default TagAnnotation getTag(java.lang.Long id) throws ServiceException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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getMapAnnotations
default java.util.List<MapAnnotation> getMapAnnotations() throws ServerException, ServiceException
Gets the list of map annotations available to the user.- Returns:
- See above.
- Throws:
ServerException
- Server error.ServiceException
- Cannot connect to OMERO.
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getMapAnnotations
default java.util.List<MapAnnotation> getMapAnnotations(java.lang.String key) throws ServerException, 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:
ServerException
- Server error.ServiceException
- Cannot connect to OMERO.
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getMapAnnotations
default java.util.List<MapAnnotation> getMapAnnotations(java.lang.String key, java.lang.String value) throws ServerException, 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:
ServerException
- Server error.ServiceException
- Cannot connect to OMERO.
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getMapAnnotation
default MapAnnotation getMapAnnotation(java.lang.Long id) throws ServiceException, java.util.concurrent.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.java.util.concurrent.ExecutionException
- A Facility can't be retrieved or instantiated.
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