chore: update python dependencies

Refs: pangaea-data-publisher#380

.github/workflows/ci.yml

@@ -73,7 +73,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.11', '3.8']
+        python-version: ['3.11']
     steps:
     - uses: actions/checkout@v3
     - name: Cache python dependencies
@@ -91,5 +91,10 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install hatch
+
+    # TODO: remove, once dependencies are updated
+    - run: hatch run python -m pip list
+    - run: hatch run python -m pip list --outdated
+
     - name: Run test suite with coverage
       run: hatch run cov

pyproject.toml

@@ -17,33 +17,31 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Information Analysis"
 ]
 dependencies = [
-  "beautifulsoup4~=4.8.2",
-  "configparser~=5.0.2",
-  "connexion[swagger-ui]~=2.9.0",
+  "beautifulsoup4~=4.12",
+  "configparser~=6.0",
+  "connexion[swagger-ui]~=2.10.0",
   "extruct~=0.13.0",
   "feedparser~=6.0.8",
-  "flask~=1.1.4",
-  "flask-cors~=3.0.10",
+  "flask~=2.2.5",  # pin due to flask 2.3.0 json_encoder issue
+  "flask-cors~=4.0",
   "flask-limiter<=2.0.0",
   "hashid~=3.1.4",
-  "idutils~=1.1.5",
-  "jmespath~=0.10.0",
-  "levenshtein~=0.12.0",
-  "lxml~=4.7",
-  "markupsafe~=2.0.1",
+  "idutils~=1.2",
+  "jmespath~=1.0",
+  "levenshtein~=0.21.1",
+  "lxml~=4.9",
   "pandas~=1.3",
   "pyRdfa3~=3.5.3",
   "pyld~=2.0.3",
-  "pyyaml!=6.0.0,!=5.4.0,!=5.4.1",
-  "rapidfuzz~=3.1.2",
+  "pyyaml!=6.0.0,!=5.4.0,!=5.4.1",  # 6.0.1
+  "rapidfuzz~=3.3",
   "rdflib~=6.1.1",
-  "requests~=2.24.0",
+  "requests~=2.31",
   "sparqlwrapper~=1.8.5",
   "tika~=1.24",
   "tldextract~=3.1.2",
   "urlextract~=1.2.0",
-  "waitress~=2.1.1",
-  "werkzeug~=1.0"
+  "waitress~=2.1"
 ]
 description = "FUJI (FAIRsFAIR Data Objects Assessment Service), A service to evaluate FAIR data objects based on FAIRsFAIR Metrics"
 keywords = [

tests/functional/test_evaluation.py

@@ -13,7 +13,8 @@
 HTTP_200_OK = 200
 
 
-@pytest.mark.vcr
+# TODO: Re-enable the vcr canning
+# @pytest.mark.vcr
 def test_evaluation(client: FlaskClient) -> None:
     """Functional test of the /evaluate endpoint.
 

tests/helper/cassettes/test_preprocessor/test_set_mime_types.yaml

@@ -9,7 +9,7 @@ interactions:
       Connection:
       - keep-alive
       User-Agent:
-      - python-requests/2.24.0
+      - python-requests/2.31.0
     method: GET
     uri: https://raw.githubusercontent.com/jshttp/mime-db/master/db.json
   response:
@@ -430,13 +430,13 @@ interactions:
       Cross-Origin-Resource-Policy:
       - cross-origin
       Date:
-      - Thu, 21 Sep 2023 16:02:25 GMT
+      - Mon, 25 Sep 2023 18:07:29 GMT
       ETag:
       - W/"96f0b8a97b963debd2b8196710f6fb55a22c1b719160c77161bc768dee120c17"
       Expires:
-      - Thu, 21 Sep 2023 16:07:25 GMT
+      - Mon, 25 Sep 2023 18:12:29 GMT
       Source-Age:
-      - '262'
+      - '41'
       Strict-Transport-Security:
       - max-age=31536000
       Vary:
@@ -450,15 +450,15 @@ interactions:
       X-Content-Type-Options:
       - nosniff
       X-Fastly-Request-ID:
-      - 7a4c3c5b7178aeafc165bdeb8bf8678e5d474938
+      - b8cdb072c5d83461fe5450e6872cd4f9e3022cf1
       X-Frame-Options:
       - deny
       X-GitHub-Request-Id:
-      - 9A86:1151B:C30A85:CA6A0B:650C605D
+      - DEAC:5405:253AA4D:26E6CD0:651112C5
       X-Served-By:
-      - cache-fra-eddf8230126-FRA
+      - cache-fra-eddf8230078-FRA
       X-Timer:
-      - S1695312145.003301,VS0,VE2
+      - S1695665249.046498,VS0,VE1
       X-XSS-Protection:
       - 1; mode=block
     status: