Merge pull request #280 from gyorilab/flask3

Upgrade to `flask_jwt_extended>3`

.github/workflows/tests.yml

@@ -8,7 +8,7 @@ jobs:
     # Set up postgres
     services:
       postgres:
-        image: postgres:9.6
+        image: postgres:13.13
         env:
           POSTGRES_PASSWORD: password
           POSTGRES_USER: postgres
@@ -26,21 +26,19 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    # Set up Python 3.7
-    - name: Set up Python 3.7
+    # Set up Python 3.9
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: "3.9"
     # Install EMMAA/test dependencies
     - name: Install dependencies
       run: |
         sudo apt-get install libpq-dev
         psql --no-password -h localhost -c 'create database emmaadb_test;' -U postgres
-        wget -nv https://files.pythonhosted.org/packages/91/a1/55b8224cbc9986bbad4b8f0f2dd11892845156b759b3495202d457ca0b73/kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl
-        mv kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
-        unzip kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
         sudo apt-get install graphviz libgraphviz-dev pkg-config
         python -m pip install --upgrade pip
+        pip install kappy==4.1.2
         pip install nose coverage flask pyyaml boto3 openpyxl
         pip install git+https://github.com/sorgerlab/indra.git
         pip uninstall -y enum34
@@ -60,7 +58,7 @@ jobs:
         # cd automates
         # git checkout claytonm/gromet
         # cd ..
-        pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage moto[iam] sqlalchemy_utils termcolor flask-cors
+        pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==4.6.0 gilda tweepy nose coverage 'moto[iam]<5' sqlalchemy_utils termcolor flask-cors==4.0.1
         pip install --no-dependencies .
         pip install -U sqlalchemy==1.3.23
         wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv

emmaa/tests/test_xdd.py

@@ -4,11 +4,11 @@
 
 @attr('nonpublic')
 def test_document_figures_doi():
-    doi = '10.1016/j.apsb.2020.09.003'
+    doi = '10.1136/bmj.n436'
     fig_list = get_document_figures(doi, 'DOI')
     assert fig_list
     # Should be a list of tuples with title and image bytes
-    assert len(fig_list[0]) == 2
+    assert len(fig_list[0]) == 8
 
 
 # This would call database

emmaa_service/api.py

@@ -13,7 +13,7 @@
 from flask_restx import Api, Resource, fields, inputs, abort as restx_abort
 from flask_cors import CORS
 
-from flask_jwt_extended import jwt_optional
+from flask_jwt_extended import jwt_required
 from urllib import parse
 from collections import defaultdict, Counter
 from copy import deepcopy
@@ -1146,14 +1146,14 @@ def session_expiration_check():
 
 
 @app.route('/health')
-@jwt_optional
+@jwt_required(optional=True)
 def health():
     return jsonify({'status': 'pass'})
 
 
 @app.route('/')
 @app.route('/home')
-@jwt_optional
+@jwt_required(optional=True)
 def get_home():
     loaded = request.args.get('loaded')
     loaded = (loaded == 'true')
@@ -1169,7 +1169,7 @@ def get_home():
 
 
 @app.route('/dashboard/<model>')
-@jwt_optional
+@jwt_required(optional=True)
 def get_model_dashboard(model):
     """Render model dashboard page."""
     loaded = request.args.get('loaded')
@@ -1691,7 +1691,7 @@ def get_model_tests_page(model):
 
 
 @app.route('/query')
-@jwt_optional
+@jwt_required(optional=True)
 def get_query_page():
     """Render queries page."""
     loaded = request.args.get('loaded')
@@ -1963,7 +1963,7 @@ def get_all_statements_page(model):
 
 
 @app.route('/demos')
-@jwt_optional
+@jwt_required(optional=True)
 def get_demos_page():
     user, roles = resolve_auth(dict(request.args))
     user_email = user.email if user else ""
@@ -1972,7 +1972,7 @@ def get_demos_page():
 
 
 @app.route('/chat')
-@jwt_optional
+@jwt_required(optional=True)
 def chat_with_the_model():
     model = request.args.get('model', '')
     user, roles = resolve_auth(dict(request.args))
@@ -2057,7 +2057,7 @@ def get_query_tests_page(model):
 
 
 @app.route('/query/submit', methods=['POST'])
-@jwt_optional
+@jwt_required(optional=True)
 def process_query():
     """Get result for a query."""
     # Print inputs.
@@ -2241,7 +2241,7 @@ def email_unsubscribe_post():
 
 
 @app.route('/subscribe/<model>', methods=['POST'])
-@jwt_optional
+@jwt_required(optional=True)
 def model_subscription(model):
     user, roles = resolve_auth(dict(request.args))
     if not roles and not user:
@@ -2323,7 +2323,7 @@ def get_statement_by_paper(model, paper_id, paper_id_type, date, hash_val):
 
 
 @app.route('/curation/submit/<hash_val>', methods=['POST'])
-@jwt_optional
+@jwt_required(optional=True)
 def submit_curation_endpoint(hash_val, **kwargs):
     user, roles = resolve_auth(dict(request.args))
     if not roles and not user:

setup.py

@@ -37,7 +37,7 @@
       install_requires=['indra', 'boto3', 'jsonpickle', 'kappy==4.1.2',
                         'pygraphviz', 'fnvhash', 'sqlalchemy<1.4',
                         'inflection', 'pybel==0.15',
-                        'flask_jwt_extended==3.25.0', 'gilda', 'tweepy'],
-      extras_require={'test': ['nose', 'coverage', 'moto[iam]',
+                        'flask_jwt_extended', 'gilda', 'tweepy'],
+      extras_require={'test': ['nose', 'coverage', 'moto[iam]<5',
                                'sqlalchemy_utils']}
       )