Merge branch 'master' of github.com:seung-lab/AnnotationEngine

annotationengine/__init__.py

@@ -67,7 +67,6 @@ def versions():
         app.register_blueprint(views_bp)
         db.init_app(app)
         db.create_all()
-
 
     @app.route("/health")
     def health():

annotationengine/api.py

@@ -9,9 +9,7 @@
 from flask import Response, abort, g, request, current_app
 from flask_accepts import accepts
 from flask_restx import Namespace, Resource, reqparse, inputs
-from middle_auth_client import (
-    auth_requires_permission
-)
+from middle_auth_client import auth_requires_permission
 from marshmallow import ValidationError
 from caveclient.materializationengine import MaterializationClient
 from caveclient.auth import AuthClient
@@ -120,7 +118,6 @@ def get_schema_from_service(annotation_type, endpoint):
 def trigger_supervoxel_lookup(
     aligned_volume_name: str, table_name: str, inserted_ids: list
 ):
-
     # look up datastacks with this
     datastacks = get_datastacks_from_aligned_volumes(aligned_volume_name)
 
@@ -192,7 +189,7 @@ def post(self, aligned_volume_name: str):
                 table_info = db.annotation.create_table(
                     table_name, schema_type, **metadata_dict
                 )
-            except (TableAlreadyExists):
+            except TableAlreadyExists:
                 abort(400, f"Table {table_name} already exists")
             except Exception as e:
                 abort(400, str(e))
@@ -356,12 +353,17 @@ def put(self, aligned_volume_name: str, table_name: str, **kwargs):
         annotations = data.get("annotations")
 
         new_ids = []
-
+        updated_ids_mapping = {}
         for annotation in annotations:
             try:
-                updated_id = db.annotation.update_annotation(table_name, annotation)
-                ((old_id, new_id),) = updated_id.items()
-                new_ids.append(new_id)
+                update_id_map = db.annotation.update_annotation(table_name, annotation)
+                ((old_id, new_id),) = update_id_map.items()
+                new_ids.append(
+                    new_id
+                )  # send a list of new ids to the supervoxel lookup
+                updated_ids_mapping[old_id] = (
+                    new_id  # return a mapping of old to new ids
+                )
             except UpdateAnnotationError as update_error:
                 abort(409, str(update_error))
             except ValidationError as validation_error:
@@ -372,7 +374,7 @@ def put(self, aligned_volume_name: str, table_name: str, **kwargs):
             trigger_supervoxel_lookup(aligned_volume_name, table_name, new_ids)
         except Exception as e:
             logging.error(f"Lookup SVID workflow failed: {e}")
-        return new_ids, 200
+        return updated_ids_mapping, 200
 
     @auth_requires_permission(
         "edit", table_arg="aligned_volume_name", resource_namespace="aligned_volume"

annotationengine/views.py

@@ -20,7 +20,7 @@
 
 
 def wkb_to_numpy(wkb, convert_to_nm=None):
-    """ Fixes single geometry column """
+    """Fixes single geometry column"""
     shp = to_shape(wkb)
     xyz_voxel = np.array([shp.xy[0][0], shp.xy[1][0], shp.z], dtype=np.int)
     if convert_to_nm is not None:
@@ -61,7 +61,6 @@ def index():
     "view", table_arg="aligned_volume_name", resource_namespace="aligned_volume"
 )
 def aligned_volume_view(aligned_volume_name):
-
     db = get_db(aligned_volume_name)
     table_names = db.database._get_existing_table_names()
     query = (
@@ -116,8 +115,8 @@ def table_view(aligned_volume_name, table_name):
     db = get_db(aligned_volume_name)
     check_read_permission(db, table_name)
     md = db.database.get_table_metadata(table_name)
-    if md['reference_table']:
-        RefModel = db.database.cached_table(md['reference_table'])
+    if md["reference_table"]:
+        RefModel = db.database.cached_table(md["reference_table"])
     Model = db.database._get_model_from_table_name(table_name)
     table_size = db.database.get_annotation_table_size(table_name)
     query = db.database.cached_session.query(Model).limit(15)