add timestamp filter option to get_tables

.github/workflows/annotationengine.yml

@@ -34,10 +34,10 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -48,7 +48,7 @@ jobs:
         with:
           auto-update-conda: true
           auto-activate-base: true
-          python-version: 3.9
+          python-version: "3.10"
       - name: Install dependencies
         shell: bash -l {0}
         run: |

annotationengine/api.py

@@ -16,6 +16,8 @@
 from caveclient.auth import AuthClient
 import werkzeug
 import traceback
+import datetime
+import pytz
 
 from annotationengine.aligned_volume import (
     get_aligned_volumes,
@@ -100,6 +102,14 @@ def handle_invalid_usage(error):
     location="args",
     help="whether to only return valid items",
 )
+query_parser.add_argument(
+    "timestamp",
+    type=str,
+    default=None,
+    location="args",
+    required=False,
+    help="timestamp for filtering results (will default to now if not required)",
+)
 
 
 def check_aligned_volume(aligned_volume):
@@ -243,11 +253,26 @@ def put(self, aligned_volume_name: str) -> FullMetadataSchema:
     @api_bp.expect(query_parser)
     def get(self, aligned_volume_name: str):
         """Get list of annotation tables for a aligned_volume"""
+        args = query_parser.parse_args()
+        timestamp_str = args.get("timestamp", None)
+        if timestamp_str is None:
+            timestamp = datetime.datetime.now(datetime.timezone.utc)
+        else:
+            # fromisoformat accepts common ISO 8601 formats with or without microseconds
+            # (e.g. 2026-02-19T10:30:00 or 2026-02-19T10:30:00.123456)
+            timestamp = datetime.datetime.fromisoformat(
+                timestamp_str.replace("Z", "+00:00")
+            )
+            if timestamp.tzinfo is None:
+                timestamp = pytz.utc.localize(timestamp)
+            else:
+                timestamp = timestamp.astimezone(pytz.utc)
+
         check_aligned_volume(aligned_volume_name)
         db = get_db(aligned_volume_name)
-        args = query_parser.parse_args()
         tables = db.database._get_existing_table_names(
-            filter_valid=args.get("filter_valid", True)
+            filter_valid=args.get("filter_valid", True),
+            filter_timestamp=timestamp
         )
         return tables, 200
 

dev.Dockerfile

@@ -4,8 +4,8 @@ RUN  git config --global http.sslVerify false && \
      mkdir -p /home/nginx/.cloudvolume/secrets && chown -R nginx /home/nginx && usermod -d /home/nginx -s /bin/bash nginx
 
 RUN python -m pip install --upgrade pip
-COPY dev_requirements.txt /app/.
-RUN  pip install -r dev_requirements.txt
+COPY requirements.txt /app/.
+RUN  pip install -r requirements.txt
 COPY timeout.conf /etc/nginx/conf.d/
 COPY . /app
 

dev_requirements.txt

@@ -31,7 +31,7 @@ deprecated==1.2.13
     # via redis
 dynamicannotationdb==5.2.2
     # via -r requirements.in
-emannotationschemas==5.1.1
+emannotationschemas==5.24.12
     # via
     #   -r requirements.in
     #   dynamicannotationdb
@@ -178,7 +178,7 @@ requests==2.27.1
     #   -r requirements.in
     #   caveclient
     #   middle-auth-client
-shapely==1.8.0
+shapely==2.0.3
     # via
     #   dynamicannotationdb
     #   emannotationschemas

requirements.in

@@ -1,6 +1,6 @@
 Flask<2.0
 emannotationschemas>=5.24.13
-dynamicannotationdb>=5.5.1
+dynamicannotationdb>=5.14.1
 caveclient>=4.20.2
 multiwrapper
 jsonschema<4.0

requirements.txt

@@ -27,9 +27,7 @@ click==7.1.2
     # via flask
 decorator==5.1.1
     # via ipython
-deprecated==1.2.13
-    # via redis
-dynamicannotationdb==5.8.1
+dynamicannotationdb==5.14.1
     # via -r requirements.in
 emannotationschemas==5.24.13
     # via
@@ -121,9 +119,7 @@ numpy==1.21.5
 orderedmultidict==1.0.1
     # via furl
 packaging==21.3
-    # via
-    #   geoalchemy2
-    #   redis
+    # via geoalchemy2
 pandas==1.3.5
     # via caveclient
 parso==0.8.3
@@ -153,8 +149,6 @@ pytz==2021.3
     #   dynamicannotationdb
     #   flask-restx
     #   pandas
-redis==4.1.3
-    # via middle-auth-client
 requests==2.27.1
     # via
     #   -r requirements.in
@@ -200,7 +194,5 @@ werkzeug==1.0.1
     #   flask
     #   flask-accepts
     #   flask-restx
-wrapt==1.13.3
-    # via deprecated
 wtforms==3.0.1
     # via flask-admin

test/conftest.py

@@ -58,16 +58,32 @@ def test_aligned_volume():
 
 @pytest.fixture(scope="module")
 def client():
-    flask_app = create_app(config_name="testing")
+    config_name = os.environ.get("FLASK_CONFIGURATION", "testing")
+    flask_app = create_app(config_name=config_name)
     test_logger.info("Starting test flask app...")
 
     # Create a test client using the Flask application configured for testing
     with flask_app.test_client() as testing_client:
         # Establish an application context
         with flask_app.app_context():
             db.create_all()
+            logging.info("yielding testing_client")
             yield testing_client
+            # --- Cleanup Phase ---
+            logging.info("Tearing down testing_client, committing session")
+
+            db.session.commit()
+
+            logging.info("dropping all tables")
+            # 2. Drop the tables
             db.drop_all()
+            logging.info("removing session")
+            # 1. Remove the scoped session to prevent "ResourceBusy" errors
+            db.session.remove()
+            logging.info("disposing engine")
+            # 3. Dispose of the engine to kill the connection pool (The Fix)
+            db.engine.dispose()
+            logging.info("cleanup complete")
 
 
 @pytest.fixture(scope="module")