OMERO5DEV__3: fileset image linkage

components/blitz/src/ome/services/blitz/repo/PublicRepositoryI.java

@@ -662,9 +662,9 @@ private CheckedPath checkId(final long id, final Ice.Current curr)
     private void assertFindDir(final CheckedPath checked, final Ice.Current curr)
         throws omero.ServerError {
         if (null == repositoryDao.findRepoFile(repoUuid, checked, null, curr)) {
-            omero.ResourceError re = new omero.ResourceError(null, null,
-                    "Directory exists but is not registered: " + checked);
-            IceMapper.fillServerError(re, new RuntimeException());
+            omero.ResourceError re = new omero.ResourceError();
+            IceMapper.fillServerError(re, new RuntimeException(
+                    "Directory exists but is not registered: " + checked));
             throw re;
         }
     }

components/blitz/src/ome/services/blitz/repo/RepositoryDaoImpl.java

@@ -243,7 +243,9 @@ private void _treeList(RMap rv, String repoUuid, CheckedPath checked,
         rv.put(name, subRv);
         subVal.put("id", omero.rtypes.rlong(id));
         subVal.put("mimetype", omero.rtypes.rstring(mime));
-        subVal.put("size", omero.rtypes.rlong(size));
+        if (size != null) {
+            subVal.put("size", omero.rtypes.rlong(size));
+        }
 
         if (file.getMimetype() != null && // FIXME: should be set!
                 PublicRepositoryI.DIRECTORY_MIMETYPE.equals(file.getMimetype())) {

components/blitz/src/pojos/FilesetData.java

@@ -33,7 +33,7 @@
 //Application-internal dependencies
 import omero.model.Fileset;
 import omero.model.FilesetEntry;
-import omero.model.FilesetImageLink;
+import omero.model.Image;
 import omero.model.OriginalFile;
 
 /** 
@@ -84,21 +84,21 @@ public List<String> getAbsolutePaths()
 		}
 		return paths;
 	}
-	
+
 	/**
 	 * Returns the collection of images related to the file set.
-	 * 
+	 *
 	 * @return See above.
 	 */
 	public List<Long> getImageIds()
 	{
 		List<Long> ids = new ArrayList<Long>();
 		Fileset fs = (Fileset) asIObject();
-		List<FilesetImageLink> links = fs.copyImageLinks();
-		if (links == null || links.size() == 0) return ids;
-		Iterator<FilesetImageLink> i = links.iterator();
+		List<Image> images = fs.copyImages();
+		if (images == null || images.size() == 0) return ids;
+		Iterator<Image> i = images.iterator();
 		while (i.hasNext()) {
-			ids.add(i.next().getChild().getId().getValue());
+			ids.add(i.next().getId().getValue());
 		}
 		return ids;
 	}

components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

@@ -422,8 +422,7 @@ private String createFileSetQuery()
 	{
 		StringBuffer buffer = new StringBuffer();
 		buffer.append("select fs from Fileset as fs ");
-		buffer.append("left outer join fetch fs.imageLinks as fil ");
-		buffer.append("join fetch fil.child as image ");
+		buffer.append("join fetch fs.images as image ");
 		buffer.append("left outer join fetch fs.usedFiles as usedFile ");
 		buffer.append("join fetch usedFile.originalFile ");
 		buffer.append("where image.id in (:imageIds)");

components/model/resources/mappings/acquisition.ome.xml

@@ -38,7 +38,7 @@
 			<zeromany name="rois" type="ome.model.roi.Roi" inverse="image"/>
 			<!-- Containers -->
 			<parent name="datasetLinks" type="ome.model.containers.DatasetImageLink" target="ome.model.containers.Dataset"/>
-			<parent name="filesetLinks" type="ome.model.fs.FilesetImageLink" target="ome.model.fs.Fileset"/>
+			<optional name="fileset" type="ome.model.fs.Fileset"/>
 		</properties>
 	</type>
 	<type id="ome.model.acquisition.ObjectiveSettings">

components/model/resources/mappings/fs.ome.xml

@@ -42,25 +42,11 @@ with this program; if not, write to the Free Software Foundation, Inc.,
             <to_child type="ome.model.jobs.Job"/>
         </properties>
     </link>
-    <link id="ome.model.fs.FilesetImageLink">
-        <properties>
-            <from_parent type="ome.model.fs.Fileset"/>
-            <to_child type="ome.model.core.Image"/>
-        </properties>
-    </link>
-    <link id="ome.model.fs.FilesetPlateLink">
-        <properties>
-            <from_parent type="ome.model.fs.Fileset"/>
-            <to_child type="ome.model.screen.Plate"/>
-        </properties>
-    </link>
     <type id="ome.model.fs.Fileset" annotated="true">
         <properties>
             <onemany name="usedFiles" type="ome.model.fs.FilesetEntry" inverse="fileset" ordered="true"/>
+            <onemany name="images" type="ome.model.core.Image" inverse="fileset"/>
             <child name="jobLinks" type="ome.model.fs.FilesetJobLink" target="ome.model.jobs.Job" ordered="true"/>
-            <!-- TODO: Perhaps use annotation links? -->
-            <child name="imageLinks" type="ome.model.fs.FilesetImageLink" target="ome.model.core.Image"/>
-            <child name="plateLinks" type="ome.model.fs.FilesetPlateLink" target="ome.model.screen.Plate"/>"
         </properties>
     </type>
 </types>

components/model/resources/mappings/screen.ome.xml

@@ -48,7 +48,6 @@
 			<optional name="status" type="string"/>
 			<optional name="externalIdentifier" type="string"/>
 			<parent name="screenLinks" type="ome.model.screen.ScreenPlateLink" target="ome.model.screen.Screen"/>
-			<parent name="filesetLinks" type="ome.model.fs.FilesetPlateLink" target="ome.model.fs.Fileset"/>
 			<zeromany name="wells" type="ome.model.screen.Well" inverse="plate"/>
 			<zeromany name="plateAcquisitions" type="ome.model.screen.PlateAcquisition" inverse="plate"/>
 		</properties>

components/server/resources/ome/services/spec.xml

@@ -208,9 +208,8 @@
         <constructor-arg>
             <list>
                 <value>/Image/DatasetImageLink;FORCE</value>
-                <value>/Image/FilesetImageLink;HARD</value>
                 <value>/Image+Only</value>
-                <value>/Fileset;HARD;/Image/FilesetImageLink</value>
+                <value>/Fileset;HARD;/Image</value>
             </list>
         </constructor-arg>
     </bean>
@@ -227,9 +226,7 @@
         <constructor-arg>
             <list>
                 <value>/Image/DatasetImageLink;FORCE</value>
-                <value>/Image/FilesetImageLink;HARD</value>
                 <value>/Image+Only</value>
-                <!-- Missing /Fileset here -->
             </list>
         </constructor-arg>
     </bean>
@@ -243,7 +240,6 @@
         <constructor-arg>
             <list>
                 <value>/Image/DatasetImageLink;FORCE</value>
-                <value>/Image/FilesetImageLink;HARD</value>
                 <value>/Image+Only</value>
                 <!-- Missing /Fileset here -->
             </list>
@@ -336,20 +332,8 @@
         <constructor-arg>
             <list>
                 <value>/Plate/ScreenPlateLink;FORCE</value>
-                <value>/Plate/FilesetPlateLink;HARD</value>
-                <value>/Plate+Only</value>
-                <value>/Fileset;HARD;/Plate/FilesetPlateLink</value>
-            </list>
-        </constructor-arg>
-    </bean>
-
-    <bean parent="delSpec" name="/Plate+FS">
-        <constructor-arg>
-            <list>
-                <value>/Plate/ScreenPlateLink;FORCE</value>
-                <value>/Plate/FilesetPlateLink;HARD</value>
                 <value>/Plate+Only</value>
-                <!-- No fileset here. See /Image+FS for an explanation -->
+                <!-- Accessing fileset? -->
             </list>
         </constructor-arg>
     </bean>
@@ -424,10 +408,8 @@
     <bean parent="delSpec" name="/Fileset">
         <constructor-arg>
             <list>
-                <value>/Fileset/FilesetImageLink</value>
-                <value>/Image+FS;HARD;/Fileset/FilesetImageLink</value>
-                <value>/Fileset/FilesetPlateLink</value>
-                <value>/Plate+FS;HARD;/Fileset/FilesetPlateLink</value>
+                <value>/Image+FS;HARD;/Fileset</value>
+                <!-- How to delete Plate -->
                 <value>/Fileset/FilesetEntry</value>
                 <value>/OriginalFile+Only;HARD;/Fileset/FilesetEntry</value><!-- and hope it's not double linked -->
                 <value>/Fileset/FilesetJobLink</value>

components/server/src/ome/formats/OMEROMetadataStore.java

@@ -1710,17 +1710,10 @@ private void checkAndCollapseGraph()
     private void linkFileset(FilesetJobLink link)
     {
         final Fileset fs = link.parent().proxy(); // Unloaded
-        for (Plate plate : plateList.values())
-        {
-            plate.linkFileset(fs);
-        }
 
         for (Image image : imageList.values())
         {
-            if (image.sizeOfWellSamples() < 1)
-            {
-                image.linkFileset(fs.proxy());
-            }
+            image.setFileset(fs.proxy());
         }
     }
 

components/tools/OmeroPy/src/omero/gateway/__init__.py

@@ -3264,15 +3264,14 @@ def deleteObjects(self, graph_spec, obj_ids, deleteAnns=False,
             if len(imgsWithFs) > 0:
                 params = omero.sys.Parameters()
                 params.map = {'imageIds': wrap(imgsWithFs)}
-                query = "select fs from Fileset as fs "\
-                        "left outer join fetch fs.imageLinks as fil "\
-                        "join fetch fil.child as image " \
+                query = "select fs from Fileset fs "\
+                        "left outer join fetch fs.images as image "\
                         "where image.id in (:imageIds)"
                 queryService = self.getQueryService()
                 filesets = queryService.findAllByQuery(query, params, self.SERVICE_OPTS)
                 for fs in filesets:
-                    for fsImgLink in fs.copyImageLinks():
-                        imgsToDelete.append(fsImgLink.child.id.val)
+                    for fsImg in fs.copyImages():
+                        imgsToDelete.append(fsImg.id.val)
                         break
             obj_ids = imgsToDelete
 
@@ -7415,7 +7414,7 @@ def countFilesetFiles (self):
             params = omero.sys.Parameters()
             params.map = {'imageId': rlong(self.getId())}
             query = "select count(fse.id) from FilesetEntry as fse join fse.fileset as fs "\
-                    "left outer join fs.imageLinks as imageLink where imageLink.child.id=:imageId"
+                    "left outer join fs.images as image where image.id=:imageId"
             queryService = self._conn.getQueryService()
             fscount = queryService.projection(query, params, self._conn.SERVICE_OPTS)
             self._filesetFileCount = fscount[0][0]._val
@@ -7449,8 +7448,7 @@ def getImportedImageFiles (self):
             params = omero.sys.Parameters()
             params.map = {'imageId': rlong(self.getId())}
             query = "select fs from Fileset as fs "\
-                    "left outer join fetch fs.imageLinks as fil "\
-                    "join fetch fil.child as image " \
+                    "left outer join fetch fs.images as image "\
                     "left outer join fetch fs.usedFiles as usedFile " \
                     "join fetch usedFile.originalFile where image.id=:imageId"
             queryService = self._conn.getQueryService()

components/tools/OmeroPy/test/integration/repository.py

@@ -337,8 +337,7 @@ def testDirPrivateGroup(self):
         self.assertWrite(f1.repo, filename, ofile)
 
         self.assertNoRead(f2.repo, filename, ofile)
-        self.assertRaises(omero.SecurityViolation,
-                          f2.repo.listFiles, dirname)
+        self.assertEquals(0, len(f2.repo.listFiles(dirname)))
 
     def testDirReadOnlyGroup(self):
         f1, f2 = self.setup2RepoUsers("rwr---")
@@ -662,8 +661,8 @@ def testRecursiveDeleteMethodAvailable(self):
     # to delete more. Muahahaha...
     def testDoubleDot(self):
         naughty = self.unique_dir + "/" + ".." + ".." + ".."
-        handle = self.mrepo.deletePaths([naughty], True, True)
-        self.waitOnCmd(self.client, handle, passes=True)
+        self.assertRaises(omero.ValidationException,
+                          self.mrepo.deletePaths, [naughty], True, True)
 
 
 class TestDeleteLog(AbstractRepoTest):
@@ -746,5 +745,36 @@ def testUserDirShouldBeGloballyWriteable(self):
         mrepo.makeDir(bDir, True)
         self.createFile(mrepo, bFile)
 
+
+class TestFilesetQueries(AbstractRepoTest):
+
+    def project(self, *args, **kwargs):
+        self.client.sf.getQueryService().projection(*args, **kwargs)
+
+    def testDeleteQuery(self):
+        query = "select fs from Fileset fs "\
+                "left outer join fetch fs.images as image "\
+                "where image.id in (:imageIds)"
+        params = omero.sys.Parameters()
+        params.map = {'imageIds': omero.rtypes.wrap([omero.rtypes.rlong(-1)])}
+        self.project(query, params)
+
+    def testCountFilesetFiles(self):
+        params = omero.sys.Parameters()
+        params.map = {'imageId': omero.rtypes.rlong(-1)}
+        query = "select count(fse.id) from FilesetEntry as fse join fse.fileset as fs "\
+                "left outer join fs.images as image where image.id=:imageId"
+        self.project(query, params)
+
+    def testImportedImageFiles(self):
+        params = omero.sys.Parameters()
+        params.map = {'imageId': omero.rtypes.rlong(-1)}
+        query = "select fs from Fileset as fs "\
+                "left outer join fetch fs.images as image "\
+                "left outer join fetch fs.usedFiles as usedFile " \
+                "join fetch usedFile.originalFile where image.id=:imageId"
+        self.project(query, params)
+
+
 if __name__ == '__main__':
     unittest.main()

etc/omero.properties

@@ -16,7 +16,7 @@ omero.data.cron=* * 0 * * ?
 
 omero.db.authority=export.openmicroscopy.org
 omero.db.version=OMERO5.0DEV
-omero.db.patch=1
+omero.db.patch=3
 omero.db.host=localhost
 omero.db.name=omero
 omero.db.user=omero

sql/psql/OMERO5.0DEV__1/enums_update.sql → sql/psql/OMERO5.0DEV__3/enums_update.sql

@@ -1396,4 +1396,3 @@ insert into renderingmodel (id,permissions,value)
 insert into renderingmodel (id,permissions,value)
     select ome_nextval('seq_renderingmodel'),-35,'greyscale' from renderingmodel where not exists(
         select 1 from renderingmodel where value = 'greyscale') limit 1;
-

sql/psql/OMERO5.0DEV__1/psql-footer.sql → sql/psql/OMERO5.0DEV__3/psql-footer.sql

@@ -379,18 +379,10 @@
   CREATE INDEX i_filesetentry_group ON filesetentry(group_id);
   CREATE INDEX i_FilesetEntry_fileset ON filesetentry(fileset);
   CREATE INDEX i_FilesetEntry_originalFile ON filesetentry(originalFile);
-  CREATE INDEX i_filesetimagelink_owner ON filesetimagelink(owner_id);
-  CREATE INDEX i_filesetimagelink_group ON filesetimagelink(group_id);
-  CREATE INDEX i_FilesetImageLink_parent ON filesetimagelink(parent);
-  CREATE INDEX i_FilesetImageLink_child ON filesetimagelink(child);
   CREATE INDEX i_filesetjoblink_owner ON filesetjoblink(owner_id);
   CREATE INDEX i_filesetjoblink_group ON filesetjoblink(group_id);
   CREATE INDEX i_FilesetJobLink_parent ON filesetjoblink(parent);
   CREATE INDEX i_FilesetJobLink_child ON filesetjoblink(child);
-  CREATE INDEX i_filesetplatelink_owner ON filesetplatelink(owner_id);
-  CREATE INDEX i_filesetplatelink_group ON filesetplatelink(group_id);
-  CREATE INDEX i_FilesetPlateLink_parent ON filesetplatelink(parent);
-  CREATE INDEX i_FilesetPlateLink_child ON filesetplatelink(child);
   CREATE INDEX i_filesetversioninfo_owner ON filesetversioninfo(owner_id);
   CREATE INDEX i_filesetversioninfo_group ON filesetversioninfo(group_id);
   CREATE INDEX i_filter_owner ON filter(owner_id);
@@ -420,6 +412,7 @@
   CREATE INDEX i_Image_instrument ON image(instrument);
   CREATE INDEX i_Image_stageLabel ON image(stageLabel);
   CREATE INDEX i_Image_experiment ON image(experiment);
+  CREATE INDEX i_Image_fileset ON image(fileset);
   CREATE INDEX i_imageannotationlink_owner ON imageannotationlink(owner_id);
   CREATE INDEX i_imageannotationlink_group ON imageannotationlink(group_id);
   CREATE INDEX i_ImageAnnotationLink_parent ON imageannotationlink(parent);
@@ -775,9 +768,7 @@ CREATE SEQUENCE seq_filamenttype; INSERT INTO _lock_ids (name, id) SELECT 'seq_f
 CREATE SEQUENCE seq_fileset; INSERT INTO _lock_ids (name, id) SELECT 'seq_fileset', nextval('_lock_seq');
 CREATE SEQUENCE seq_filesetannotationlink; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetannotationlink', nextval('_lock_seq');
 CREATE SEQUENCE seq_filesetentry; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetentry', nextval('_lock_seq');
-CREATE SEQUENCE seq_filesetimagelink; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetimagelink', nextval('_lock_seq');
 CREATE SEQUENCE seq_filesetjoblink; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetjoblink', nextval('_lock_seq');
-CREATE SEQUENCE seq_filesetplatelink; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetplatelink', nextval('_lock_seq');
 CREATE SEQUENCE seq_filesetversioninfo; INSERT INTO _lock_ids (name, id) SELECT 'seq_filesetversioninfo', nextval('_lock_seq');
 CREATE SEQUENCE seq_filter; INSERT INTO _lock_ids (name, id) SELECT 'seq_filter', nextval('_lock_seq');
 CREATE SEQUENCE seq_filterset; INSERT INTO _lock_ids (name, id) SELECT 'seq_filterset', nextval('_lock_seq');
@@ -1256,7 +1247,7 @@ alter table dbpatch alter message set default 'Updating';
 -- running so that if anything goes wrong, we'll have some record.
 --
 insert into dbpatch (currentVersion, currentPatch, previousVersion, previousPatch, message)
-             values ('OMERO5.0DEV',  1,    'OMERO5.0DEV',   0,             'Initializing');
+             values ('OMERO5.0DEV',  3,    'OMERO5.0DEV',   0,             'Initializing');
 
 --
 -- Here we will create the root account and the necessary groups
@@ -2139,9 +2130,8 @@ after delete on originalfile
 -- Here we have finished initializing this database.
 update dbpatch set message = 'Database ready.', finished = clock_timestamp()
   where currentVersion = 'OMERO5.0DEV' and
-        currentPatch = 1 and
+        currentPatch = 3 and
         previousVersion = 'OMERO5.0DEV' and
         previousPatch = 0;
 
 COMMIT;
-

sql/psql/OMERO5.0DEV__1/psql-header.sql → sql/psql/OMERO5.0DEV__3/psql-header.sql

@@ -14,4 +14,3 @@
 --
 --
 BEGIN;
-