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

      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 the BrowseFacility used to access the data from OMERO.
      SecurityContext getCtx()
      Returns the current SecurityContext.
      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 OMERO
      default 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 OMERO
      default 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 the MetadataFacility 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 the IQueryPrx 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).
    • Method Detail

      • getBrowseFacility

        BrowseFacility getBrowseFacility()
                                  throws java.util.concurrent.ExecutionException
        Gets the BrowseFacility used to access the data from OMERO.
        Returns:
        See above.
        Throws:
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • getQueryService

        omero.api.IQueryPrx getQueryService()
                                     throws ServiceException
        Returns the IQueryPrx used to find objects on OMERO.
        Returns:
        See above.
        Throws:
        ServiceException - Cannot connect to OMERO.
      • getMetadataFacility

        MetadataFacility getMetadataFacility()
                                      throws java.util.concurrent.ExecutionException
        Gets the MetadataFacility used to retrieve annotations from OMERO.
        Returns:
        See above.
        Throws:
        java.util.concurrent.ExecutionException - If the MetadataFacility can't be retrieved or instantiated.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.