Update queries for new table distribution model

tmserver/api/feature.py

@@ -287,31 +287,6 @@ def get_feature_values(experiment_id, mapobject_type_id):
         mapobject_type_name = mapobject_type.name
         mapobject_type_ref_type = mapobject_type.ref_type
 
-    if mapobject_type_ref_type in {'Plate', 'Well'}:
-        if well_pos_y is not None:
-            raise MalformedRequestError(
-                'Invalid query parameter "well_pos_y" for mapobjects of type '
-                '"{0}"'.format(mapobject_type_name)
-            )
-        if well_pos_x is not None:
-            raise MalformedRequestError(
-                'Invalid query parameter "well_pos_x" for mapobjects of type '
-                '"{0}"'.format(mapobject_type_name)
-            )
-    if mapobject_type_ref_type == 'Plate':
-        ref_type = 'Plate'
-        if well_name is not None:
-            raise MalformedRequestError(
-                'Invalid query parameter "well_name" for mapobjects of type '
-                '"{0}"'.format(mapobject_type_name)
-            )
-    elif mapobject_type_ref_type == 'Well':
-        ref_type = 'Plate'
-    elif mapobject_type_ref_type == 'Site':
-        ref_type = 'Well'
-    else:
-        ref_type = 'Site'
-
     filename_formatstring = '{experiment}'
     if plate_name is not None:
         filename_formatstring += '_{plate}'
@@ -358,7 +333,7 @@ def generate_feature_matrix(mapobject_type_id, ref_type):
             feature_names = [f.name for f in features]
 
             ref_mapobject_type = session.query(tm.MapobjectType.id).\
-                filter_by(ref_type=ref_type).\
+                filter_by(ref_type=ref_type, id=mapobject_type_id).\
                 one()
 
         w.writerow(tuple(feature_names))
@@ -370,8 +345,7 @@ def generate_feature_matrix(mapobject_type_id, ref_type):
             logger.debug('collect feature values for %s %d', ref_type, ref_id)
             with tm.utils.ExperimentSession(experiment_id) as session:
                 mapobjects = _get_mapobjects_at_ref_position(
-                    session, mapobject_type_id, ref_mapobject_type.id,
-                    ref_id, layer_lut.keys()
+                    session, mapobject_type_id, ref_id, layer_lut.keys()
                 )
                 mapobject_ids = [m.id for m in mapobjects]
 
@@ -422,7 +396,7 @@ def generate_feature_matrix(mapobject_type_id, ref_type):
                 data.truncate(0)
 
     return Response(
-        generate_feature_matrix(mapobject_type_id, ref_type),
+        generate_feature_matrix(mapobject_type_id, mapobject_type_ref_type),
         mimetype='text/csv',
         headers={
             'Content-Disposition': 'attachment; filename={filename}'.format(
@@ -509,19 +483,6 @@ def get_metadata(experiment_id, mapobject_type_id):
                 '"{0}"'.format(mapobject_type_name)
             )
 
-    if mapobject_type_ref_type == 'Plate':
-        ref_type = 'Plate'
-        if well_name is not None:
-            raise MalformedRequestError(
-                'Invalid query parameter "well_name" for mapobjects of type '
-                '"{0}"'.format(mapobject_type_name)
-            )
-    elif mapobject_type_ref_type == 'Well':
-        ref_type = 'Well'
-    elif mapobject_type_ref_type == 'Site':
-        ref_type = 'Site'
-    else:
-        ref_type = 'Site'
 
     def generate_feature_matrix(mapobject_type_id, ref_type):
         data = StringIO()
@@ -579,19 +540,19 @@ def generate_feature_matrix(mapobject_type_id, ref_type):
 
             ref_mapobject_type = session.query(tm.MapobjectType.id).\
                 filter_by(ref_type=ref_type).\
-                one()
+                order_by(tm.MapobjectType.id).\
+                first()
 
         w.writerow(tuple(metadata_names + tool_result_names))
         yield data.getvalue()
         data.seek(0)
         data.truncate(0)
 
         for ref_id in ref_position_lut:
-            logger.debug('collect metadata for %s %d', ref_type, ref_id)
+            logger.info('collect metadata for %s %d', ref_type, ref_id)
             with tm.utils.ExperimentSession(experiment_id) as session:
                 mapobjects = _get_mapobjects_at_ref_position(
-                    session, mapobject_type_id, ref_mapobject_type.id,
-                    ref_id, layer_lut.keys()
+                    session, mapobject_type_id, ref_id, layer_lut.keys()
                 )
                 mapobject_ids = [m.id for m in mapobjects]
 
@@ -668,7 +629,7 @@ def generate_feature_matrix(mapobject_type_id, ref_type):
                 data.truncate(0)
 
     return Response(
-        generate_feature_matrix(mapobject_type_id, ref_type),
+        generate_feature_matrix(mapobject_type_id, mapobject_type_ref_type),
         mimetype='text/csv',
         headers={
             'Content-Disposition': 'attachment; filename={filename}'.format(

tmserver/api/mapobject.py

@@ -146,16 +146,7 @@ def _get_matching_layers(session, tpoint):
 
 
 def _get_mapobjects_at_ref_position(session, mapobject_type_id,
-        ref_mapobject_type_id, ref_id, segmentation_layer_ids):
-    ref_segmentation = session.query(
-            tm.MapobjectSegmentation.geom_polygon
-        ).\
-        join(tm.Mapobject).\
-        filter(
-            tm.Mapobject.ref_id == ref_id,
-            tm.Mapobject.mapobject_type_id == ref_mapobject_type_id
-        ).\
-        one()
+        ref_id, segmentation_layer_ids):
 
     return session.query(
             tm.Mapobject.id, tm.MapobjectSegmentation.label,
@@ -164,9 +155,7 @@ def _get_mapobjects_at_ref_position(session, mapobject_type_id,
         join(tm.MapobjectSegmentation).\
         filter(
             tm.Mapobject.mapobject_type_id == mapobject_type_id,
-            tm.MapobjectSegmentation.geom_centroid.ST_Intersects(
-                ref_segmentation.geom_polygon
-            ),
+            tm.Mapobject.partition_key == ref_id,
             tm.MapobjectSegmentation.segmentation_layer_id.in_(
                 segmentation_layer_ids
             )
@@ -176,14 +165,14 @@ def _get_mapobjects_at_ref_position(session, mapobject_type_id,
 
 
 def _get_border_mapobjects_at_ref_position(session, mapobject_ids,
-        ref_mapobject_type_id, ref_id):
+        ref_type_id, ref_id):
     ref_segmentation = session.query(
             tm.MapobjectSegmentation.geom_polygon
         ).\
         join(tm.Mapobject).\
         filter(
-            tm.Mapobject.ref_id == ref_id,
-            tm.Mapobject.mapobject_type_id == ref_mapobject_type_id
+            tm.Mapobject.partition_key == ref_id,
+            tm.Mapobject.mapobject_type_id == ref_type_id
         ).\
         one()
 
@@ -305,7 +294,7 @@ def update_mapobject_type(experiment_id, mapobject_type_id):
 )
 @jwt_required()
 @decode_query_ids('write')
-def delete_mapobject_typed(experiment_id, mapobject_type_id):
+def delete_mapobject_type(experiment_id, mapobject_type_id):
     """
     .. http:delete:: /api/experiments/(string:experiment_id)/mapobject_types/(string:mapobject_type_id)
 
@@ -451,18 +440,21 @@ def add_segmentations(experiment_id, mapobject_type_id):
             ).\
             one()
         y_offset, y_offset = site.offset
+        site_id = site.id
 
         metadata = SegmentationImageMetadata(
-            mapobject_type_id, site.id, tpoint, zplane
+            mapobject_type_id, site_id, tpoint, zplane
         )
         image = SegmentationImage(array, metadata)
 
     # We need to use a raw connection, since we insert into a distributed table.
     with tm.utils.ExperimentConnection(experiment_id) as connection:
         for label, polygon in image.extract_polygons(y_offset, x_offset):
-            mapobject_id = tm.Mapobject.add(connection, mapobject_type_id)
+            mapobject_id = tm.Mapobject.add(
+                connection, site_id, mapobject_type_id
+            )
             tm.MapobjectSegmentation.add(
-                connection, mapobject_id, segmentation_layer_id,
+                connection, site_id, mapobject_id, segmentation_layer_id,
                 polygon=polygon, label=label
             )