Merge branch 'api-hotfix-sqlalchemy' into 'master'

Api hotfix sqlalchemy

See merge request !193

code.json

@@ -3,7 +3,7 @@
     "name": "geomag-algorithms",
     "organization": "U.S. Geological Survey",
     "description": "Library for processing Geomagnetic timeseries data.",
-    "version": "1.5.3",
+    "version": "1.5.4",
     "status": "Development",
 
     "permissions": {
@@ -34,7 +34,7 @@
     },
 
     "date": {
-      "metadataLastUpdated": "2022-06-01"
+      "metadataLastUpdated": "2022-10-24"
     }
   }
 ]

docker-entrypoint.sh

@@ -9,10 +9,13 @@ if [ "${WEBSERVICE}" = "false" ]; then
   # run arguments as command, or bash prompt if no arguments
   exec "${@:-/bin/bash}"
 else
+  export LOG_BASIC_CONFIG="${LOG_BASIC_CONFIG:-true}"
+  export LOG_LEVEL="${LOG_LEVEL:-INFO}"
   # run gunicorn server for web service
   exec gunicorn \
       --access-logfile - \
       --bind 0.0.0.0:8000 \
+      --log-level "${LOG_LEVEL}" \
       --threads 2 \
       --workers 2 \
       --worker-class uvicorn.workers.UvicornWorker \

geomagio/api/app.py

@@ -6,13 +6,19 @@ and can be run using uvicorn, or any other ASGI server:
     uvicorn geomagio.api:app
 
 """
+import logging
+import os
+
 from fastapi import FastAPI
 from starlette.responses import RedirectResponse
 
+from . import secure, ws
 from .db import database
-from . import secure
-from . import ws
 
+LOG_BASIC_CONFIG = os.getenv("LOG_BASIC_CONFIG", "false")
+LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO")
+if LOG_BASIC_CONFIG == "true":
+    logging.basicConfig(level=LOG_LEVEL)
 
 app = FastAPI()
 app.mount("/ws/secure", secure.app)

geomagio/api/secure/SessionMiddleware.py

 import json
-from typing import Callable, Dict, Mapping
+import logging
 import uuid
+from typing import Callable, Dict, Mapping
 
 from cryptography.fernet import Fernet
 from starlette.datastructures import MutableHeaders
@@ -73,6 +74,7 @@ class SessionMiddleware:
                 scope["session"] = await self.get_session(session_id)
                 initial_session_was_empty = False
             except Exception:
+                logging.exception(f"Error loading session {session_id}")
                 scope["session"] = {}
         else:
             scope["session"] = {}

pyproject.toml

@@ -17,47 +17,49 @@ packages = [
   {include = "geomagio" }
 ]
 repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.3"
+version = "1.5.4"
 
 
 [tool.poetry.dependencies]
 python = "^3.8,<3.11"
 # core
-numpy = "^1.22.3"
-obspy = "^1.3.0"
-openpyxl = "^3.0.9"
+numpy = "^1.23.4"
+obspy = "^1.3.1"
+openpyxl = "^3.0.10"
 pycurl = {version = "^7.45.1", optional = true}
-pydantic = "^1.9.0"
-requests = "^2.27.1"
-scipy = "^1.8.0"
-typer = "^0.4.0"
+pydantic = "^1.10.2"
+requests = "^2.28.1"
+scipy = "^1.9.3"
+typer = "^0.6.1"
 # webservice
-alembic = "^1.8.0"
-Authlib = "^1.0.0"
-cryptography = "^36.0.2"
-databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
-fastapi = "^0.75.0"
+alembic = "^1.8.1"
+Authlib = "^1.1.0"
+cryptography = "^38.0.1"
+databases = {extras = ["mysql", "sqlite"], version = "^0.6.1"}
+fastapi = "^0.85.1"
 gunicorn = "^20.1.0"
-httpx = "0.22.0"
-SQLAlchemy = "^1.4.32"
+httpx = "0.23.0"
+# 2022-10-24 pin sqlalchemy to 1.4.41 for now
+# 1.4.42 seems to cause issues with databases (https://stackoverflow.com/a/74102692)
+SQLAlchemy = "1.4.41"
 SQLAlchemy-Utc = "^0.14.0"
-uvicorn = {extras = ["standard"], version = "^0.17.6"}
+uvicorn = {extras = ["standard"], version = "^0.19.0"}
 
 
 [tool.poetry.dev-dependencies]
-black = "^22.1.0"
+black = "^22.10.0"
 isort = "^5.10.1"
-mypy = "^0.941"
-poethepoet = "^0.16.0"
-pytest = "^6.2.4"
-pytest-cov = "^2.12.1"
+mypy = "^0.982"
+poethepoet = "^0.16.4"
+pytest = "^7.1.3"
+pytest-cov = "^4.0.0"
 safety = "^1.10.3"
 # type hints
 data-science-types = "^0.2.23"
-openpyxl-stubs = "^0.1.19"
+openpyxl-stubs = "^0.1.24"
 sqlalchemy-stubs = "^0.4"
-types-python-dateutil = "^0.1.6"
-types-requests = "^2.25.6"
+types-python-dateutil = "^2.8.19.2"
+types-requests = "^2.28.11.2"
 
 
 [tool.poetry.extras]
@@ -93,3 +95,6 @@ test = [
   { shell = "coverage html" },
   { shell = "coverage xml" }
 ]
+webservice = [
+  { shell = "uvicorn geomagio.api:app" }
+]