Update dependencies

.github/workflows/lint.yaml

@@ -37,7 +37,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install Python linting dependencies
         run: pip install black flake8

.github/workflows/test.yaml

@@ -9,10 +9,10 @@ jobs:
       - name: Checkout git commit
         uses: actions/checkout@v1
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.11
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.11
 
       - name: Install test runner
         run: python3 -m pip install tox

Dockerfile

@@ -11,7 +11,7 @@ COPY . .
 RUN npm run build
 
 # -----------------------------------------------------------------------------
-FROM python:3.7 as backend
+FROM python:3.11 as backend
 
 RUN mkdir /opt/cosri-patientsearch
 WORKDIR /opt/cosri-patientsearch

README.md

@@ -9,7 +9,7 @@ All views require Keycloak authentication.  Keycloak roles determine authorizati
 1) `git clone <this repository>`
 2) `cp client_secrets.json.default client_secrets.json`  # Edit to fit
 3) `cp patientsearch.env.default patientsearch.env`  # Edit to fit
-4) `mkvirtualenv patientsearch`  # Python 3.7
+4) `mkvirtualenv patientsearch`  # Python 3.11
 5) `pip install nodeenv`
 6) `nodeenv --python-virtualenv`
 7) `pip install -e .`

patientsearch/api.py

@@ -6,14 +6,14 @@
     make_response,
     redirect,
     request,
-    safe_join,
     session,
     send_from_directory,
 )
-from flask.json import JSONEncoder
+from flask.json.provider import DefaultJSONProvider
 import jwt
 import requests
 from werkzeug.exceptions import Unauthorized, Forbidden
+from werkzeug.utils import safe_join
 from copy import deepcopy
 
 from patientsearch.audit import audit_entry, audit_HAPI_change
@@ -145,11 +145,11 @@ def config_settings(config_key):
     """Non-secret application settings"""
 
     # workaround no JSON representation for datetime.timedelta
-    class CustomJSONEncoder(JSONEncoder):
+    class CustomJSONProvider(DefaultJSONProvider):
         def default(self, obj):
             return str(obj)
 
-    current_app.json_encoder = CustomJSONEncoder
+    current_app.json = CustomJSONProvider
 
     # return selective keys - not all can be be viewed by users, e.g.secret key
     blacklist = ("SECRET", "KEY", "TOKEN", "CREDENTIALS")

patientsearch/config.py

@@ -134,8 +134,7 @@ def load_json_config(potential_json_string):
     )
 
 OIDC_ID_TOKEN_COOKIE_SECURE = False
-OIDC_REQUIRE_VERIFIED_EMAIL = False
-OIDC_SCOPES = ["email", "openid", "roles"]
+OIDC_SCOPES = "email openid roles"
 PROJECT_NAME = os.getenv("PROJECT_NAME", "COSRI")
 REQUIRED_ROLES = json.loads(os.getenv("REQUIRED_ROLES", "[]"))
 UDS_LAB_TYPES = json.loads(os.getenv("UDS_LAB_TYPES", "[]"))

requirements.dev.txt

@@ -1,22 +1,27 @@
+-r requirements.txt
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
-#    pip-compile
+#    pip-compile --extra=dev --output-file=requirements.dev.txt setup.cfg
 #
---requirement requirements.txt
-
-attrs==21.2.0             # via pytest
-importlib-metadata==4.8.1  # via pluggy, pytest
-iniconfig==1.1.1          # via pytest
-packaging==21.0           # via pytest
-pluggy==1.0.0             # via pytest
-py==1.10.0                # via pytest
-pyparsing==2.4.7          # via packaging
-pytest-datadir==1.3.1     # via patientsearch (setup.py)
-pytest-flask==1.2.0       # via patientsearch (setup.py)
-pytest-mock==3.6.1        # via patientsearch (setup.py)
-pytest==6.2.5             # via patientsearch (setup.py), pytest-datadir, pytest-mock
-toml==0.10.2              # via pytest
-typing-extensions==3.10.0.2  # via importlib-metadata
-zipp==3.5.0               # via importlib-metadata
+exceptiongroup==1.2.2
+    # via pytest
+iniconfig==2.0.0
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.2
+    # via
+    #   patientsearch (setup.cfg)
+    #   pytest-datadir
+    #   pytest-flask
+    #   pytest-mock
+pytest-datadir==1.5.0
+    # via patientsearch (setup.cfg)
+pytest-flask==1.3.0
+    # via patientsearch (setup.cfg)
+pytest-mock==3.14.0
+    # via patientsearch (setup.cfg)
+tomli==2.0.1
+    # via pytest

requirements.txt

@@ -1,26 +1,69 @@
-certifi==2021.5.30        # via requests
-charset-normalizer==2.0.6  # via requests
-click==8.0.1              # via flask
-flask-jwt-extended==3.24.1  # via patientsearch (setup.py)
-# pin to last hash of master, to remove requirement of freestanding JSON config file
-git+https://github.com/uwcirg/flask-oidc.git@ed4eb20#egg=flask-oidc
+#
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
+#
+#    pip-compile
+#
+async-timeout==4.0.3
+    # via redis
+blinker==1.8.2
+    # via flask
+cachelib==0.13.0
+    # via flask-session
+certifi==2024.7.4
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via flask
+flask==3.0.3
+    # via
+    #   flask-jwt-extended
+    #   flask-session
+    #   patientsearch (setup.cfg)
+flask-jwt-extended==4.6.0
+    # via patientsearch (setup.cfg)
+flask-session==0.8.0
+    # via patientsearch (setup.cfg)
+flask-oidc==2.2.2
 git+https://github.com/uwcirg/[email protected]
-flask==2.0.1              # via flask-jwt-extended, patientsearch (setup.py)
-flask-session==0.3.2      # via patientsearch (setup.py)
-gunicorn==20.0.4          # via patientsearch (setup.py)
-idna==3.2                 # via requests
-importlib-metadata==4.8.1  # via click
-itsdangerous==2.0.1       # via flask
-jinja2==3.0.1             # via flask
-jmespath==0.10.0          # via patientsearch (setup.py)
-markupsafe==2.0.1         # via jinja2
-python-json-logger==0.1.11
-pyjwt==1.7.1              # via flask-jwt-extended
-redis==3.5.3
-redis-dict==1.5.2         # via patientsearch (setup.py)
-requests==2.26.0          # via patientsearch (setup.py)
-six==1.15.0               # via flask-jwt-extended
-typing-extensions==3.10.0.2  # via importlib-metadata
-urllib3==1.26.7           # via requests
-werkzeug==2.0.1           # via flask, flask-jwt-extended
-zipp==3.5.0               # via importlib-metadata
+gunicorn==23.0.0
+    # via patientsearch (setup.cfg)
+idna==3.7
+    # via requests
+importlib-metadata==8.4.0
+    # via flask
+itsdangerous==2.2.0
+    # via flask
+jinja2==3.1.4
+    # via flask
+jmespath==1.0.1
+    # via patientsearch (setup.cfg)
+markupsafe==2.1.5
+    # via
+    #   jinja2
+    #   werkzeug
+msgspec==0.18.6
+    # via flask-session
+packaging==24.1
+    # via gunicorn
+pyjwt==2.9.0
+    # via flask-jwt-extended
+python-json-logger==2.0.7
+    # via patientsearch (setup.cfg)
+redis==5.0.8
+    # via
+    #   patientsearch (setup.cfg)
+    #   redis-dict
+redis-dict==2.5.0
+    # via patientsearch (setup.cfg)
+requests==2.32.3
+    # via patientsearch (setup.cfg)
+urllib3==2.2.2
+    # via requests
+werkzeug==3.0.3
+    # via
+    #   flask
+    #   flask-jwt-extended
+zipp==3.20.0
+    # via importlib-metadata

tests/conftest.py

@@ -28,7 +28,7 @@ def generate_claims(email, sub, roles):
 def generate_jwt(email="[email protected]", sub="fake-subject", roles=None):
     claims = generate_claims(email, sub, roles)
     encoded = jwt.encode(claims, SECRET, algorithm="HS256")
-    return encoded.decode("utf-8")
+    return encoded
 
 
 @pytest.fixture()