Package fr.igred.omero

Class 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 Detail

      • 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 Detail

      • getProject

        public ProjectWrapper 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

        public java.util.List<ProjectWrapper> 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

        public java.util.List<ProjectWrapper> 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

        public java.util.List<ProjectWrapper> getProjects​(ExperimenterWrapper 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

        public java.util.List<ProjectWrapper> 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

        public DatasetWrapper 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

        public java.util.List<DatasetWrapper> 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

        public java.util.List<DatasetWrapper> 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

        public ImageWrapper 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

        public java.util.List<ImageWrapper> 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

        public java.util.List<ImageWrapper> 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

        public java.util.List<ImageWrapper> 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

        public abstract java.util.List<ImageWrapper> 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.

      • getImagesLike

        public java.util.List<ImageWrapper> 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.

      • getImagesTagged

        @Deprecated
public java.util.List<ImageWrapper> getImagesTagged​(java.lang.Long tagId)
                                             throws ServiceException,
                                                    AccessException,
                                                    OMEROServerError,
                                                    java.util.concurrent.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.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

      • getImagesKey

        @Deprecated
public abstract java.util.List<ImageWrapper> getImagesKey​(java.lang.String key)
                                                   throws ServiceException,
                                                          AccessException,
                                                          java.util.concurrent.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.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

      • getImagesPairKeyValue

        @Deprecated
public abstract java.util.List<ImageWrapper> getImagesPairKeyValue​(java.lang.String key,
                                                                   java.lang.String value)
                                                            throws ServiceException,
                                                                   AccessException,
                                                                   java.util.concurrent.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.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

      • getImagesWithKeyValuePair

        public java.util.List<ImageWrapper> getImagesWithKeyValuePair​(java.lang.String key,
                                                              java.lang.String value)
                                                       throws ServiceException,
                                                              AccessException,
                                                              java.util.concurrent.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.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

      • getScreen

        public ScreenWrapper 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

        public java.util.List<ScreenWrapper> 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

        public java.util.List<ScreenWrapper> 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

        public java.util.List<ScreenWrapper> getScreens​(ExperimenterWrapper 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

        public PlateWrapper 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

        public java.util.List<PlateWrapper> 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

        public java.util.List<PlateWrapper> 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

        public java.util.List<PlateWrapper> getPlates​(ExperimenterWrapper 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

        public WellWrapper 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

        public java.util.List<WellWrapper> 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

        public FolderWrapper 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

        public java.util.List<FolderWrapper> 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

        public java.util.List<FolderWrapper> getFolders​(ExperimenterWrapper 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

        public java.util.List<FolderWrapper> 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.

      • getMapAnnotations

        public java.util.List<MapAnnotationWrapper> getMapAnnotations​(java.lang.String key,
                                                              java.lang.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​(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.