Class DatasetWrapper

    • Field Detail

      • ANNOTATION_LINK

        public static final java.lang.String ANNOTATION_LINK
        Annotation link name for this type of object
        See Also:
        Constant Field Values
    • Constructor Detail

      • DatasetWrapper

        public DatasetWrapper​(java.lang.String name,
                              java.lang.String description)
        Constructor of the DatasetWrapper class
        Parameters:
        name - Name of the dataset.
        description - Description of the dataset.
      • DatasetWrapper

        public DatasetWrapper​(DatasetData dataset)
        Constructor of the DatasetWrapper class
        Parameters:
        dataset - Dataset to be contained.
    • Method Detail

      • setName

        public void setName​(java.lang.String name)
        Sets the name of the dataset.
        Parameters:
        name - The name of the dataset. Mustn't be null.
        Throws:
        java.lang.IllegalArgumentException - If the name is null.
      • setDescription

        public void setDescription​(java.lang.String description)
        Sets the description of the dataset.
        Parameters:
        description - The description of the dataset.
      • getImages

        public java.util.List<ImageWrapper> getImages​(Client client)
                                               throws ServiceException,
                                                      AccessException,
                                                      java.util.concurrent.ExecutionException
        Gets all images in the dataset available from OMERO.
        Parameters:
        client - The client handling the connection.
        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​(Client client,
                                                      java.lang.String name)
                                               throws ServiceException,
                                                      AccessException,
                                                      java.util.concurrent.ExecutionException
        Gets all images in the dataset with a certain name from OMERO.
        Parameters:
        client - The client handling the connection.
        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.
      • getImagesLike

        public java.util.List<ImageWrapper> getImagesLike​(Client client,
                                                          java.lang.String motif)
                                                   throws ServiceException,
                                                          AccessException,
                                                          java.util.concurrent.ExecutionException
        Gets all images in the dataset with a certain motif in their name from OMERO.
        Parameters:
        client - The client handling the connection.
        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

        public java.util.List<ImageWrapper> getImagesTagged​(Client client,
                                                            java.lang.Long tagId)
                                                     throws ServiceException,
                                                            AccessException,
                                                            OMEROServerError,
                                                            java.util.concurrent.ExecutionException
        Gets all images in the dataset tagged with a specified tag from OMERO.
        Parameters:
        client - The client handling the connection.
        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 java.util.List<ImageWrapper> getImagesKey​(Client client,
                                                         java.lang.String key)
                                                  throws ServiceException,
                                                         AccessException,
                                                         java.util.concurrent.ExecutionException
        Deprecated.
        Gets all images in the dataset with a certain key
        Parameters:
        client - The client handling the connection.
        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.
      • getImagesWithKey

        public java.util.List<ImageWrapper> getImagesWithKey​(Client client,
                                                             java.lang.String key)
                                                      throws ServiceException,
                                                             AccessException,
                                                             java.util.concurrent.ExecutionException
        Gets all images in the dataset with a certain key
        Parameters:
        client - The client handling the connection.
        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 java.util.List<ImageWrapper> getImagesPairKeyValue​(Client client,
                                                                  java.lang.String key,
                                                                  java.lang.String value)
                                                           throws ServiceException,
                                                                  AccessException,
                                                                  java.util.concurrent.ExecutionException
        Deprecated.
        Gets all images in the dataset with a certain key value pair from OMERO
        Parameters:
        client - The client handling the connection.
        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​(Client client,
                                                                      java.lang.String key,
                                                                      java.lang.String value)
                                                               throws ServiceException,
                                                                      AccessException,
                                                                      java.util.concurrent.ExecutionException
        Gets all images in the dataset with a certain key value pair from OMERO
        Parameters:
        client - The client handling the connection.
        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.
      • addImages

        public void addImages​(Client client,
                              java.util.List<? extends ImageWrapper> images)
                       throws ServiceException,
                              AccessException,
                              java.util.concurrent.ExecutionException
        Adds a list of image to the dataset in OMERO.
        Parameters:
        client - The client handling the connection.
        images - Image to add to the dataset.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • addImage

        public void addImage​(Client client,
                             ImageWrapper image)
                      throws ServiceException,
                             AccessException,
                             java.util.concurrent.ExecutionException
        Adds a single image to the dataset in OMERO
        Parameters:
        client - The client handling the connection.
        image - Image to add.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • removeImage

        public void removeImage​(Client client,
                                ImageWrapper image)
                         throws ServiceException,
                                AccessException,
                                java.util.concurrent.ExecutionException,
                                OMEROServerError,
                                java.lang.InterruptedException
        Removes an image from the dataset in OMERO.
        Parameters:
        client - The client handling the connection.
        image - Image to remove.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
        OMEROServerError - Server error.
        java.lang.InterruptedException - If block(long) does not return.
      • importImages

        public boolean importImages​(Client client,
                                    java.lang.String... paths)
                             throws ServiceException,
                                    OMEROServerError,
                                    AccessException,
                                    java.io.IOException,
                                    java.util.concurrent.ExecutionException
        Imports all images candidates in the paths to the dataset in OMERO.
        Parameters:
        client - The client handling the connection.
        paths - Paths to the image files on the computer.
        Returns:
        If the import did not exit because of an error.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        OMEROServerError - Server error.
        java.io.IOException - Cannot read file.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • importImage

        public java.util.List<java.lang.Long> importImage​(Client client,
                                                          java.lang.String path)
                                                   throws ServiceException,
                                                          AccessException,
                                                          OMEROServerError,
                                                          java.util.concurrent.ExecutionException
        Imports one image file to the dataset in OMERO.
        Parameters:
        client - The client handling the connection.
        path - Path to the image file on the computer.
        Returns:
        The list of IDs of the newly imported images.
        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.
      • replaceImages

        public java.util.List<ImageWrapper> replaceImages​(Client client,
                                                          java.util.Collection<? extends ImageWrapper> oldImages,
                                                          ImageWrapper newImage)
                                                   throws AccessException,
                                                          ServiceException,
                                                          java.util.concurrent.ExecutionException,
                                                          OMEROServerError,
                                                          java.lang.InterruptedException
        Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations and ROIs, and concatenating the descriptions (on new lines).
        Parameters:
        client - The client handling the connection.
        oldImages - The list of old images to replace.
        newImage - The new image.
        Returns:
        The list of images that became orphaned once replaced.
        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.
        java.lang.InterruptedException - If block(long) does not return.
      • importAndReplaceImages

        public java.util.List<java.lang.Long> importAndReplaceImages​(Client client,
                                                                     java.lang.String path,
                                                                     GenericRepositoryObjectWrapper.ReplacePolicy policy)
                                                              throws ServiceException,
                                                                     AccessException,
                                                                     OMEROServerError,
                                                                     java.util.concurrent.ExecutionException,
                                                                     java.lang.InterruptedException
        Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.
        Parameters:
        client - The client handling the connection.
        path - Path to the image on the computer.
        policy - Whether older images should be unlinked, deleted or deleted only if they become orphaned.
        Returns:
        The list of IDs of the newly imported images.
        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.
        java.lang.InterruptedException - If block(long) does not return.
      • importAndReplaceImages

        public java.util.List<java.lang.Long> importAndReplaceImages​(Client client,
                                                                     java.lang.String path)
                                                              throws ServiceException,
                                                                     AccessException,
                                                                     OMEROServerError,
                                                                     java.util.concurrent.ExecutionException,
                                                                     java.lang.InterruptedException
        Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.
        Parameters:
        client - The client handling the connection.
        path - Path to the image on the computer.
        Returns:
        The list of IDs of the newly imported images.
        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.
        java.lang.InterruptedException - If block(long) does not return.
      • refresh

        public void refresh​(Client client)
                     throws ServiceException,
                            AccessException,
                            java.util.concurrent.ExecutionException
        Refreshes the dataset.
        Parameters:
        client - The client handling the connection.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.