Merge pull request #973 from cmu-delphi/v4-schema-revisions-release-prep-flaskalchemy

Build and image with new Flask and SQLAlchemy

Author: melange396

devops/Dockerfile

@@ -3,13 +3,16 @@ WORKDIR /src
 COPY . /src
 RUN npm ci && npm run build
 
-FROM tiangolo/meinheld-gunicorn:python3.7
+FROM tiangolo/meinheld-gunicorn:python3.8
 LABEL org.opencontainers.image.source=https://github.com/cmu-delphi/delphi-epidata
 # use delphi's timezome
 RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime
 
-COPY requirements.txt /app
-RUN pip install --no-cache-dir -r requirements.txt
+COPY requirements.txt /app/requirements_also.txt
+RUN pip install --no-cache-dir -r /tmp/requirements.txt -r requirements_also.txt
+# the file /tmp/requirements.txt is created in the parent docker definition.  (see:
+#   https://github.com/tiangolo/meinheld-gunicorn-docker/blob/master/docker-images/python3.8.dockerfile#L5 )
+# this combined requirements installation ensures all version constrants are accounted for.
 
 # disable python stdout buffering
 ENV PYTHONUNBUFFERED 1

requirements.txt

@@ -1,8 +1,8 @@
 itsdangerous<2.1
 jinja2==3.0.3
-werkzeug<2.1
-Flask==1.1.2
-SQLAlchemy==1.3.22
+werkzeug==2.2.2
+Flask==2.2.2
+SQLAlchemy==1.4.40
 mysqlclient==2.0.2
 python-dotenv==0.15.0
 orjson==3.4.7

src/server/_config.py

@@ -11,7 +11,16 @@
 MAX_COMPATIBILITY_RESULTS = int(3650)
 
 SQLALCHEMY_DATABASE_URI = os.environ.get("SQLALCHEMY_DATABASE_URI", "sqlite:///test.db")
-SQLALCHEMY_ENGINE_OPTIONS = json.loads(os.environ.get("SQLALCHEMY_ENGINE_OPTIONS", "{}"))
+
+# defaults
+SQLALCHEMY_ENGINE_OPTIONS = {
+    "pool_pre_ping": True, # enable ping test for validity of recycled pool connections on connect() calls
+    "pool_recycle": 5      # seconds after which a recycled pool connection is considered invalid
+}
+# update with overrides of defaults or additions from external configs
+SQLALCHEMY_ENGINE_OPTIONS.update(
+    json.loads(os.environ.get("SQLALCHEMY_ENGINE_OPTIONS", "{}")))
+
 SECRET = os.environ.get("FLASK_SECRET", "secret")
 URL_PREFIX = os.environ.get("FLASK_PREFIX", "/")
 

src/server/_query.py

@@ -14,7 +14,7 @@
 )
 
 from sqlalchemy import text
-from sqlalchemy.engine import RowProxy
+from sqlalchemy.engine import Row
 
 from ._common import db, app
 from ._db import metadata
@@ -197,7 +197,7 @@ def filter_pair(pair: TimePair, i) -> str:
 
 
 def parse_row(
-    row: RowProxy,
+    row: Row,
     fields_string: Optional[Sequence[str]] = None,
     fields_int: Optional[Sequence[str]] = None,
     fields_float: Optional[Sequence[str]] = None,
@@ -245,7 +245,7 @@ def run_query(p: APrinter, query_tuple: Tuple[str, Dict[str, Any]]):
     return db.execution_options(stream_results=True).execute(full_query, **params)
 
 
-def _identity_transform(row: Dict[str, Any], _: RowProxy) -> Dict[str, Any]:
+def _identity_transform(row: Dict[str, Any], _: Row) -> Dict[str, Any]:
     """
     identity transform
     """
@@ -257,7 +257,7 @@ def execute_queries(
     fields_string: Sequence[str],
     fields_int: Sequence[str],
     fields_float: Sequence[str],
-    transform: Callable[[Dict[str, Any], RowProxy], Dict[str, Any]] = _identity_transform,
+    transform: Callable[[Dict[str, Any], Row], Dict[str, Any]] = _identity_transform,
 ):
     """
     execute the given queries and return the response to send them
@@ -317,7 +317,7 @@ def execute_query(
     fields_string: Sequence[str],
     fields_int: Sequence[str],
     fields_float: Sequence[str],
-    transform: Callable[[Dict[str, Any], RowProxy], Dict[str, Any]] = _identity_transform,
+    transform: Callable[[Dict[str, Any], Row], Dict[str, Any]] = _identity_transform,
 ):
     """
     execute the given query and return the response to send it