Merge pull request ome#5779 from kouichi-c-nakamura/unlinkAnnotation_m

unlinkAnnotation.m components\tools\OmeroM\src\annotations

components/tools/OmeroM/src/annotations/unlinkAnnotations.m

@@ -0,0 +1,161 @@
+function unlinkAnnotations(session,parentType,parentID,varargin)
+% unlinkAnnotations allows you to unlink all or specified
+% omero.model.Annotation objects from parent in OMERO server.
+%
+% SYNTAX
+% unlinkAnnotations(session,parentType,parentID)
+% unlinkAnnotations(session,parentType,parentID,annt)
+%
+%
+% BEFORE USE
+% 
+%   client = loadOmero('demo.openmicroscopy.org', 4064)
+%   username = 'xxxxxxx'
+%   password = 'xxxxxxx'
+%   session = client.createSession(username, password)
+%
+%
+% AFTER USE
+%
+%   clear
+%   unloadOmero
+%
+% REQUIREMENTS
+%
+% OMERO.matlab toolbox
+% https://docs.openmicroscopy.org/latest/omero/developers/Matlab.html
+% 
+%
+% INPUT ARGUMENTS
+% session     omero.api.ServiceFactoryPrxHelper object
+%
+%               client = loadOmero('demo.openmicroscopy.org', 4064)
+%               session = client.createSession(username, password)
+%
+% parentType  'project' | 'dataset' | 'image' | 'screen' | 'plate' | 
+%             'plateacquisition' | 'roi'
+%
+% parentID    vector of non-negative integers
+%             parentID can be found via OMERO GUI
+%
+%
+% annt        omero.model.Annotation object or its array | [] (default)
+%
+%             (Optional) omero.model.Annotation object (supports
+%             omero.model.MapAnnotationI, omero.model.TagAnnotationI,
+%             omero.model.CommentAnnotationI, and
+%             omero.model.FileAnnotationI at the moment) to be unlinked
+%             from parent If empty or not specified, all linked
+%             MapAnnotation objects will be unlinked.
+%            
+%             For example, to obtain MapAnnotationI object(s) from an image:
+%
+%               annt = getObjectAnnotations(session, 'map', 'image', parentID);
+%
+%             or
+%
+%               annt = getImageTagAnnotations(session, ids)
+% 
+%             annt can be empty, scalar or a vector.
+%
+%             Also you can use following functions or similar.
+%
+%               annt = getAnnotations(session,ids,'tags')
+%               annt = getTagAnnotations(session,tagID)
+%
+%
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% [email protected]
+% 09-Jun-2018 03:27:05
+%
+% See also
+% linkAnnotation
+
+objects = getObjectTypes();
+
+p = inputParser;
+p.addRequired('session',@(x) isjava(x));
+p.addRequired('parentType',@(x) ischar(x) && ismember(x, {objects.name}));
+p.addRequired('parentID',@(x) isnumeric(x) && isvector(x));
+
+p.addOptional('annt',[],@(x) isempty(x) || all(isa(x, 'omero.model.Annotation')));
+p.parse(session,parentType,parentID,varargin{:});
+
+annt = p.Results.annt;
+
+
+% https://docs.openmicroscopy.org/omero/5.4.6/developers/Model/StructuredAnnotations.html
+% Project
+% Dataset
+% Pixels
+% OriginalFile
+% PlaneInfo
+% Roi
+% Channel
+% Folder
+
+% https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/matlab/ReadData.m#L334
+
+
+switch parentType
+
+    case 'project'
+        ParentType = 'Project';
+    case 'dataset'
+        ParentType = 'Dataset';
+    case 'image'
+        ParentType = 'Image';
+    case 'screen'
+        ParentType = 'Screen';
+    case 'plate'
+        ParentType = 'Plate';
+    case 'plateacquisition'
+        ParentType = 'PlateAcquisition';
+    case 'roi'
+        ParentType = 'Roi';
+end
+
+for m = 1:length(parentID)
+
+    parents = session.getQueryService().findAllByQuery(...
+        [sprintf('select obj from %s as obj left outer join fetch obj.annotationLinks as link join fetch link.child as annotation where obj.id =  ',ParentType), ...
+        num2str(parentID(m))], []);
+
+    n = size(parents);
+    for k = 1:n
+
+        prt = parents.get(k-1);
+
+        al = prt.copyAnnotationLinks();
+
+        if ~isempty(annt)
+
+            for j = 1:numel(annt)
+
+                for i = (1:size(al))-1
+                    if al.get(i).getChild().getId().equals(annt(j).getId())
+
+                        prt.unlinkAnnotation(al.get(i).getChild());
+
+                    end
+                end
+
+            end
+
+        else
+
+            prt.clearAnnotationLinks % did work (clear all the AnnotationLinks at once)
+
+        end
+
+        prt = session.getUpdateService().saveAndReturnObject(prt);
+
+    end
+
+end
+
+
+end

examples/Training/matlab/WriteData.m

@@ -672,6 +672,31 @@
     xas = getScreenXmlAnnotations(session, screenId1, 'include', ns);
     assert(hasAnnotation(xa, xas), 'WriteData: Could not find annotation');
 
+   % Unlink Annotations
+   % ==================
+
+   % Unlink single annotation
+   fprintf(1, 'Unlinking file annotation from project %g\n', projectId1);
+   unlinkAnnotations(session, 'project', projectId1, fa);
+   assert(isempty(getProjectFileAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+
+   % Unlink all annotations linked to a project
+   fprintf(1, 'Unlinking all annotations from project %g\n', projectId1);
+   unlinkAnnotations(session, 'project', projectId1);
+   assert(isempty(getProjectFileAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+   assert(isempty(getProjectTagAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+   assert(isempty(getProjectCommentAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+   assert(isempty(getProjectDoubleAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+   assert(isempty(getProjectLongAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');
+   assert(isempty(getProjectDoubleAnnotations(session, projectId1)),...
+       'WriteData: Annotation not deleted');    
+
 %%
 % end-code
 %%