Tests dev

.env-docker.dev

@@ -1,7 +1,7 @@
 FLASK_CONFIGURATION=development
 POSTGRES_USER=postgres
-POSTGRES_PASSWORD=annodb
-POSTGRES_DB=annotation
+POSTGRES_PASSWORD=postgres
+POSTGRES_DB=test_aligned_volume
 
 AUTH_URI=global.daf-apis.com/auth
 STICKY_AUTH_URL=global.daf-apis.com/sticky_auth

.github/workflows/annotationengine.yml

@@ -62,5 +62,8 @@ jobs:
 
       - name: Test with pytest
         shell: bash -l {0}
+        env: 
+          AUTH_DISABLED: true
         run: |
+          python -c "import os; print('AUTH_DISABLED:', os.getenv('AUTH_DISABLED'), type(os.getenv('AUTH_DISABLED')))"
           pytest

annotationengine/api.py

@@ -54,7 +54,7 @@
 def unhandled_exception(e):
     status_code = 500
     user_ip = str(request.remote_addr)
-    tb = traceback.format_exception(etype=type(e), value=e, tb=e.__traceback__)
+    tb = traceback.format_exception(e, value=e, tb=e.__traceback__)
 
     current_app.logger.error(
         {
@@ -317,7 +317,7 @@ def get(self, aligned_volume_name: str, table_name: str, **kwargs):
         db = get_db(aligned_volume_name)
         check_read_permission(db, table_name)
         args = annotation_parser.parse_args()
-
+        
         annotation_ids = args["annotation_ids"]
 
         md = db.database.get_table_metadata(table_name)

docker-compose.yml

@@ -1,7 +1,6 @@
-version: '3'
 services:
     db:
-      image: mdillon/postgis
+      image: postgis/postgis:13-master
       restart: always
       env_file:
         - ./.env-docker.dev 
@@ -21,19 +20,19 @@ services:
         - 8080:8080
       links:
         - db
-    app:
-      image: 'app:tag'
-      build:
-        context: .
-        dockerfile: dev.Dockerfile
-      ports:
-        - 80:80
-      volumes:
-        - .:/app
-      env_file:
-        - ./.env-docker.dev 
-      depends_on:
-        - db
+    # app:
+    #   image: 'app:tag'
+    #   build:
+    #     context: .
+    #     dockerfile: dev.Dockerfile
+    #   ports:
+    #     - 80:80
+    #   volumes:
+    #     - .:/app
+    #   env_file:
+    #     - ./.env-docker.dev 
+    #   depends_on:
+    #     - db
 
 volumes:
   postgres_data:

pytest.ini

@@ -1,7 +1,20 @@
 # pytest.ini
 [pytest]
-addopts = -W error -p no:warnings   
+env =
+    C_FORCE_ROOT=true
+    AUTH_DISABLED=true
+    AUTH_DATABASE_NAME='test_auth'
+    USE_SENTINEL=False
+    USE_LOCAL_TEST_DB=False
+    TEST_MODE='DockerTestingConfig'
+    QUEUE_LENGTH_LIMIT=100
+    QUEUES_TO_THROTTLE="celery"
+    REDIS_HOST="memory://"
+    REDIS_PORT=""
+    REDIS_PASSWORD=""
+addopts = -W error -p no:warnings
 log_cli = true
 log_cli_level = INFO
 log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)
 log_cli_date_format=%Y-%m-%d %H:%M:%S
+testpaths = "test"

requirements.txt

@@ -1,13 +1,11 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile requirements.in
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o requirements.txt
 alembic==1.7.6
     # via dynamicannotationdb
 aniso8601==9.0.1
     # via flask-restx
+appnope==0.1.4
+    # via ipython
 attrs==21.4.0
     # via
     #   caveclient
@@ -51,7 +49,9 @@ flask-accepts==0.18.4
 flask-admin==1.6.0
     # via -r requirements.in
 flask-cors==3.0.10
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   emannotationschemas
 flask-marshmallow==0.14.0
     # via -r requirements.in
 flask-restx==0.5.1
@@ -104,7 +104,7 @@ marshmallow-sqlalchemy==0.27.0
     # via -r requirements.in
 matplotlib-inline==0.1.3
     # via ipython
-middle-auth-client==3.11.1
+middle-auth-client==3.18.1
     # via -r requirements.in
 multiwrapper==0.1.1
     # via -r requirements.in
@@ -160,6 +160,10 @@ requests==2.27.1
     #   -r requirements.in
     #   caveclient
     #   middle-auth-client
+setuptools==75.3.0
+    # via
+    #   ipython
+    #   jsonschema
 shapely==2.0.3
     # via
     #   dynamicannotationdb
@@ -200,6 +204,3 @@ wrapt==1.13.3
     # via deprecated
 wtforms==3.0.1
     # via flask-admin
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools

test/conftest.py

@@ -78,6 +78,7 @@ def app_config(client):
 
 @pytest.fixture()
 def modify_g(client):
+    g.auth_user = {"id": 1}
     g.user = "test"
     g.id = 1
 

test/test_anno_database.py

@@ -5,5 +5,6 @@
 def test_create_db(app_config, mocker):
     with app_config.app_context():
         db = get_db("test_aligned_volume")
-        logging.info(db.__dict__)
-        assert db.__dict__["aligned_volume"] == "test_aligned_volume"
+        logging.info(f"db.__dict__: {db.__dict__}")
+        assert "_aligned_volume" in db.__dict__
+        assert db.__dict__["_aligned_volume"] == "test_aligned_volume"

test/test_api.py

@@ -1,3 +1,4 @@
+from flask import g
 import json
 import logging
 import sys
@@ -7,7 +8,6 @@
 
 aligned_volume_name = "test_aligned_volume"
 
-
 class TestHealthEndpoint:
     def test_health_endpoint(self, client):
         url = "annotation/api/versions"
@@ -44,8 +44,7 @@ def test_post_table(self, client):
                 follow_redirects=True,
             )
             logging.info(response)
-            logging.info(f"RETURN VALUE {response}")
-            assert response.json == {}
+            assert response.json is None
 
     def test_post_table_to_be_deleted(self, client):
         logging.info(client)
@@ -83,10 +82,11 @@ def test_get_tables(self, client):
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
             response = client.get(
-                url, content_type="application/json", follow_redirects=False
+                url, content_type="application/json",
+                follow_redirects=False
             )
             logging.info(response)
-
+            
             assert response.json == ["test_table", "test_table_to_delete"]
 
 
@@ -102,12 +102,13 @@ def test_get_table_metadata(self, client):
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
 
-            response = client.get(url, follow_redirects=False)
+            response = client.get(url,
+                                  follow_redirects=False
+                                  )
             logging.info(response.json)
 
             metadata = {
                 "table_name": "test_table",
-                "created": "2021-11-19T13:19:02.981200",
                 "id": 1,
                 "deleted": None,
                 "description": "Test description",
@@ -116,22 +117,30 @@ def test_get_table_metadata(self, client):
                 "valid": True,
                 "schema_type": "synapse",
                 "user_id": "1",
+                "notice_text": None,
                 "reference_table": None,
                 "voxel_resolution_x": 4.0,
                 "voxel_resolution_z": 40.0,
+                "read_permission": "PUBLIC",
+                "write_permission": "PRIVATE",
             }
-            assert response.json == metadata
+            response_json = response.json
+            del response_json['created']
+            del response_json['last_modified']
+            assert response_json == metadata
 
-    def test_mark_table_to_delete(self, client):
+    def test_mark_table_to_delete(self, client, modify_g):
 
         url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table_to_delete"
-
+        
         with mock.patch(
             "annotationengine.api.check_aligned_volume"
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
 
-            response = client.delete(url, follow_redirects=False)
+            response = client.delete(url,
+                                    follow_redirects=False
+                                    )
             logging.info(response.json)
             assert response.json is True
 
@@ -143,13 +152,15 @@ def test_get_row_count(self, client):
             "annotationengine.api.check_aligned_volume"
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
-            response = client.get(url, follow_redirects=False)
+            response = client.get(url,
+                                  follow_redirects=False
+                                  )
             logging.info(response.json)
             assert response.json == 0
 
 
 class TestAnnotationsEndpoints:
-    def test_post_annotations(self, client):
+    def test_post_annotations(self, client, modify_g):
 
         url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
         data = {
@@ -158,6 +169,7 @@ def test_post_annotations(self, client):
                     "pre_pt": {"position": [31, 31, 0]},
                     "ctr_pt": {"position": [32, 32, 0]},
                     "post_pt": {"position": [33, 33, 0]},
+                    "size": 1,
                 },
             ]
         }
@@ -166,29 +178,43 @@ def test_post_annotations(self, client):
         auth_user.id = 1
 
         with mock.patch(
-            "annotationengine.api.check_aligned_volume"
+            "annotationengine.api.check_aligned_volume",
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
-
-            response = client.post(
-                url,
-                data=json.dumps(data),
-                content_type="application/json",
-                follow_redirects=False,
-            )
-            logging.info(response)
-            assert response.json == [1]
+            with mock.patch(
+                "annotationengine.api.trigger_supervoxel_lookup",
+            ) as mock_trigger_supervoxel_lookup:
+                mock_trigger_supervoxel_lookup.return_value = None
+
+                response = client.post(
+                    url,
+                    data=json.dumps(data),
+                    content_type="application/json",
+                    follow_redirects=False,
+                )
+                logging.info(response)
+                assert response.json == [1]
 
     def test_get_annotations(self, client):
         url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
-        data = {"annotation_ids": [1]}
+        data = {"annotation_ids": "1"}
         with mock.patch(
             "annotationengine.api.check_aligned_volume"
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
-            response = client.get(url, data=json.dumps(data), follow_redirects=False)
+            response = client.get(url, query_string=data,
+                                  follow_redirects=False
+                                  )
             logging.info(response)
-            assert response.json == [1]
+            logging.info(response.json)
+            logging.info(response.json[0])
+            assert response.json[0]["id"] == 1
+            assert response.json[0]["pre_pt_position"] == [31, 31, 0]
+            assert response.json[0]["ctr_pt_position"] == [32, 32, 0]
+            assert response.json[0]["post_pt_position"] == [33, 33, 0]
+            assert response.json[0]["valid"] == True
+            assert response.json[0]["superceded_id"] == None
+            assert response.json[0]["deleted"] == 'None'
 
     def test_update_annotations(self, client):
         url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
@@ -199,16 +225,23 @@ def test_update_annotations(self, client):
                     "pre_pt": {"position": [22, 22, 0]},
                     "ctr_pt": {"position": [32, 32, 0]},
                     "post_pt": {"position": [33, 33, 0]},
+                    "size": 1,
                 },
             ]
         }
         with mock.patch(
             "annotationengine.api.check_aligned_volume"
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
-            response = client.post(url, data=json.dumps(data), follow_redirects=False)
-            logging.info(response)
-            assert response.json == {1: 2}
+            with mock.patch(
+                "annotationengine.api.trigger_supervoxel_lookup",
+            ) as mock_trigger_supervoxel_lookup:
+                mock_trigger_supervoxel_lookup.return_value = None
+                response = client.put(url, data=json.dumps(data),
+                                   follow_redirects=False
+                                   )
+                logging.info(response)
+                assert response.json == {'1': 2}
 
     def test_delete_annotations(self, client):
         url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
@@ -218,6 +251,8 @@ def test_delete_annotations(self, client):
             "annotationengine.api.check_aligned_volume"
         ) as mock_aligned_volumes:
             mock_aligned_volumes.return_value = aligned_volume_name
-            response = client.delete(url, data=json.dumps(data), follow_redirects=False)
+            response = client.delete(url, data=json.dumps(data),
+                                     follow_redirects=False
+                                     )
             logging.info(response)
             assert response.json == [2]