pushing plate acquisition wrapper to omero.gateway, refactoring getNu…

…mberOfFields, close #7111

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

@@ -947,7 +947,7 @@ def __getattr__ (self, attr):
         @return:        The named attribute.
         @rtype:         method, value (string, long etc)
         """
-
+        
         # handle lookup of 'get' methods, using '_attrs' dict to define how we wrap returned objects. 
         if attr != 'get' and attr.startswith('get') and hasattr(self, '_attrs'):
             tattr = attr[3].lower() + attr[4:]      # 'getName' -> 'name'
@@ -4085,18 +4085,6 @@ def __bstrap__ (self):
         self.CHILD_WRAPPER_CLASS = 'PlateWrapper'
         self.PARENT_WRAPPER_CLASS = None
 
-    @timeit
-    def getNumberOfFields (self):
-        """
-        Iterates all wells on all plates for this screen and returns highest well sample count
-        """
-        q = self._conn.getQueryService()
-        query = "select p.id, maxindex(p.wells.wellSamples)+1"
-        query += " from ScreenPlateLink spl join spl.parent s join spl.child p"
-        query += " where s.id=%d group by p.id" % self.getId()
-        return dict(unwrap(q.projection(query, None)))
-
-
 ScreenWrapper = _ScreenWrapper
 
 def _letterGridLabel (i):
@@ -4130,6 +4118,52 @@ def __reset__ (self):
         self._childcache = None
         self._gridSize = None
 
+    def _loadPlateAcquisitions(self):
+        p = omero.sys.Parameters()
+        p.map = {}
+        p.map["pid"] = self._obj.id
+        sql = "select pa from PlateAcquisition as pa join fetch pa.plate as p where p.id=:pid"
+        self._obj._plateAcquisitionsSeq = self._conn.getQueryService().findAllByQuery(sql, p)
+        self._obj._plateAcquisitionsLoaded = True
+
+    def countPlateAcquisitions(self):
+        if self._obj.sizeOfPlateAcquisitions() < 0:
+            self._loadPlateAcquisitions()
+        return self._obj.sizeOfPlateAcquisitions()
+
+    def listPlateAcquisitions(self):
+        if not self._obj._plateAcquisitionsLoaded:
+            self._loadPlateAcquisitions()
+        for pa in self._obj.copyPlateAcquisitions():
+            yield PlateAcquisitionWrapper(self._conn, pa)
+
+    @timeit
+    def getNumberOfFields (self, pid=None):
+        """
+        Returns tuple of min and max of indexed collection of well samples 
+        per plate acquisition if exists
+        """
+
+        q = self._conn.getQueryService()
+        sql = "select minIndex(ws), maxIndex(ws) from Well w " \
+            "join w.wellSamples ws where w.plate.id=:oid"
+
+        p = omero.sys.Parameters()
+        p.map = {}
+        p.map["oid"] = self._obj.id
+        if pid is not None:
+            sql += " and ws.plateAcquisition.id=:pid"
+            p.map["pid"] = rlong(pid)
+
+        fields = None
+        try:
+            res = [r for r in unwrap(q.projection(sql, p))[0] if r != None]
+            if len(res) == 2:
+                fields = tuple(res)
+        except:
+            pass
+        return fields
+
     def _listChildren (self, **kwargs):
         """
         Lists Wells in this plate, not sorted. Saves wells to _childcache map, where key is (row, column).
@@ -4218,18 +4252,7 @@ def getRowLabels (self):
         else:
             # this should simply be precalculated!
             return [_letterGridLabel(x) for x in range(self.getGridSize()['rows'])]
-
-    @timeit
-    def getNumberOfFields (self):
-        """
-        Iterates all wells on plate and returns highest well sample count
-        """
-        q = self._conn.getQueryService()
-        query = "select maxindex(p.wells.wellSamples)+1"
-        query += " from Plate p"
-        query += " where p.id=%d group by p.id" % self.getId()
-        return unwrap(q.projection(query, None))[0][0]
-
+
 #        if self._childcache is None:
 #            q = self._conn.getQueryService()
 #            params = omero.sys.Parameters()
@@ -4264,9 +4287,26 @@ def _getQueryString(self):
               "left outer join fetch spl.parent sc"
         return query
 
-
 PlateWrapper = _PlateWrapper
 
+class _PlateAcquisitionWrapper (BlitzObjectWrapper):
+
+    def __bstrap__ (self):
+        self.OMERO_CLASS = 'PlateAcquisition'
+
+    def getName (self):
+        name = super(_PlateAcquisitionWrapper, self).getName()
+        if name is None:
+            if self.startTime is not None and self.endTime is not None:
+                name = "%s - %s" % (datetime.fromtimestamp(self.startTime/1000), datetime.fromtimestamp(self.endTime/1000))
+            else:
+                name = "Plate %i" % self.id
+        return name
+    name = property(getName)
+
+
+PlateAcquisitionWrapper = _PlateAcquisitionWrapper
+
 class _WellWrapper (BlitzObjectWrapper):
     """
     omero_model_WellI class wrapper extends BlitzObjectWrapper.
@@ -7247,6 +7287,7 @@ def refreshWrappers ():
                   "image":ImageWrapper,
                   "screen":ScreenWrapper,
                   "plate":PlateWrapper,
+                  "plateacquisition": PlateAcquisitionWrapper,
                   "well":WellWrapper,
                   "experimenter":ExperimenterWrapper,
                   "experimentergroup":ExperimenterGroupWrapper,

components/tools/OmeroWeb/omeroweb/webclient/views.py

@@ -624,7 +624,7 @@ def load_data(request, o1_type=None, o1_id=None, o2_type=None, o2_id=None, o3_ty
             else:
                 template = "webclient/data/container_subtree.html"
         elif kw.has_key('plate'):
-            fields = manager.plate.getFields(kw.get('acquisition', None))
+            fields = manager.plate.getNumberOfFields(kw.get('acquisition', None))
             if fields is not None:
                 form_well_index = WellIndexForm(initial={'index':index, 'range':fields})
                 if index == 0:
@@ -2906,16 +2906,15 @@ def plateGrid_json (request, pid, field=0, server_id=None, _conn=None, **kwargs)
     """ This view is responsible for showing well data within plate """
 
     conn = None
-    kwargs['viewport_server'] = '/webclient'
     try:
         conn = kwargs["conn"]
     except:
         logger.error(traceback.format_exc())
         return handlerInternalError("Connection is not available. Please contact your administrator.")
-     
+
     if conn is None:
         raise Exception("Connection not available")
-
+    
     return webgateway_views.plateGrid_json(request, pid, field=field, server_id=None, _conn=None, **kwargs)
 
 @isUserConnected

components/tools/OmeroWeb/omeroweb/webclient/webclient_gateway.py

@@ -1799,51 +1799,6 @@ def __prepare__ (self, **kwargs):
             self.annotation_counter = kwargs['annotation_counter']
         if kwargs.has_key('link'):
             self.link = kwargs.has_key('link') and kwargs['link'] or None
-
-    def _loadPlateAcquisitions(self):
-        p = omero.sys.Parameters()
-        p.map = {}
-        p.map["pid"] = self._obj.id
-        sql = "select pa from PlateAcquisition as pa join fetch pa.plate as p where p.id=:pid"
-        self._obj._plateAcquisitionsSeq = self._conn.getQueryService().findAllByQuery(sql, p)
-        self._obj._plateAcquisitionsLoaded = True
-
-    def countPlateAcquisitions(self):
-        if self._obj.sizeOfPlateAcquisitions() < 0:
-            self._loadPlateAcquisitions()
-        return self._obj.sizeOfPlateAcquisitions()
-
-    def listPlateAcquisitions(self):
-        if not self._obj._plateAcquisitionsLoaded:
-            self._loadPlateAcquisitions()
-        for pa in self._obj.copyPlateAcquisitions():
-            yield PlateAcquisitionWrapper(self._conn, pa)
-
-    def getFields (self, pid=None):
-        """
-        Returns tuple of min and max of indexed collection of well samples 
-        per plate acquisition if exists
-        """
-
-        q = self._conn.getQueryService()
-        sql = "select minIndex(ws), maxIndex(ws) from Well w " \
-            "join w.wellSamples ws where w.plate.id=:oid"
-
-        p = omero.sys.Parameters()
-        p.map = {}
-        p.map["oid"] = self._obj.id
-        if pid is not None:
-            sql += " and ws.plateAcquisition.id=:pid"
-            p.map["pid"] = rlong(pid)
-
-        fields = None
-        try:
-            res = [r for r in unwrap(q.projection(sql, p))[0] if r != None]
-            if len(res) == 2:
-                fields = tuple(res)
-        except:
-            pass
-        return fields
 
 omero.gateway.PlateWrapper = PlateWrapper
 
@@ -1864,7 +1819,7 @@ def __prepare__ (self, **kwargs):
 
 omero.gateway.WellWrapper = WellWrapper
 
-class PlateAcquisitionWrapper (OmeroWebObjectWrapper, omero.gateway.BlitzObjectWrapper):
+class PlateAcquisitionWrapper (OmeroWebObjectWrapper, omero.gateway.PlateAcquisitionWrapper):
 
     """
     omero_model_PlateI class wrapper overwrite omero.gateway.PlateWrapper
@@ -1873,42 +1828,12 @@ class PlateAcquisitionWrapper (OmeroWebObjectWrapper, omero.gateway.BlitzObjectW
 
     annotation_counter = None
 
-    def __bstrap__ (self):
-        self.OMERO_CLASS = 'PlateAcquisition'
-
     def __prepare__ (self, **kwargs):
         super(PlateAcquisitionWrapper, self).__prepare__(**kwargs)
         if kwargs.has_key('annotation_counter'):
             self.annotation_counter = kwargs['annotation_counter']
 
-    def getName (self):
-        name = super(PlateAcquisitionWrapper, self).getName()
-        if name is None:
-            if self.startTime is not None and self.endTime is not None:
-                name = "%s - %s" % (datetime.fromtimestamp(self.startTime/1000), datetime.fromtimestamp(self.endTime/1000))
-            else:
-                name = "Plate %i" % self.id
-        return name
-    name = property(getName)
-
-    def getFields (self):
-        """
-        Returns max of indexed collection of well samples
-        """
-
-        p = omero.sys.Parameters()
-        p.map = {}
-        p.map["oid"] = self._obj.id
-
-        q = self._conn.getQueryService()
-        sql = "select maxIndex(pa.wellSamples)+1 from PlateAcquisition as pa "\
-            "where pa.id=:oid"
-        try:
-            index = unwrap(q.projection(sql, p))[0][0]
-        except:
-            index = -1
-        return index
-
+omero.gateway.PlateAcquisitionWrapper = PlateAcquisitionWrapper
 
 class ScreenWrapper (OmeroWebObjectWrapper, omero.gateway.ScreenWrapper):
     """
@@ -2031,6 +1956,4 @@ def getOwner(self):
 
         return omero.gateway.ExperimenterWrapper(self, self.owner)
 
-# IMPORTANT to update the map of wrappers 'project', 'dataset', 'image' etc. returned by getObjects()
-omero.gateway.refreshWrappers()
-omero.gateway.KNOWN_WRAPPERS.update({"plateacquisition":PlateAcquisitionWrapper})
+omero.gateway.refreshWrappers()