Update dependencies to resolve security alerts

.buildkite/pipeline.yml

@@ -57,9 +57,10 @@ steps:
       queue: "scala"
 
   - command:
-      pip3 install --user tox &&
-      cd scripts &&
-      /var/lib/buildkite-agent/.local/bin/tox -e py3
+      - cd scripts
+      - python3 -m venv venv && source venv/bin/activate
+      - pip3 install tox
+      - venv/bin/tox -e py3
     label: "Test Python scripts"
 
   - wait

monitoring/daily_reporter/requirements.txt

@@ -1,27 +1,52 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile
 #
-boto3==1.13.12            # via -r requirements.in
-botocore==1.16.12         # via boto3, s3transfer
-certifi==2020.4.5.1       # via httpx
-chardet==3.0.4            # via httpx
-docutils==0.15.2          # via botocore
-h11==0.9.0                # via httpx
-h2==3.2.0                 # via httpx
-hpack==3.0.0              # via h2
-hstspreload==2020.5.19    # via httpx
-httpx==0.12.1             # via -r requirements.in
-hyperframe==5.2.0         # via h2
-idna==2.9                 # via httpx
-jinja2==2.11.2            # via -r requirements.in
-jmespath==0.10.0          # via boto3, botocore
-markupsafe==1.1.1         # via jinja2
-python-dateutil==2.8.1    # via botocore
-rfc3986==1.4.0            # via httpx
-s3transfer==0.3.3         # via boto3
-six==1.14.0               # via python-dateutil
-sniffio==1.1.0            # via httpx
-urllib3==1.25.9           # via botocore, httpx
+anyio==4.6.0
+    # via httpx
+boto3==1.35.32
+    # via -r requirements.in
+botocore==1.35.32
+    # via
+    #   boto3
+    #   s3transfer
+certifi==2024.8.30
+    # via
+    #   httpcore
+    #   httpx
+exceptiongroup==1.2.2
+    # via anyio
+h11==0.14.0
+    # via httpcore
+httpcore==1.0.6
+    # via httpx
+httpx==0.27.2
+    # via -r requirements.in
+idna==3.10
+    # via
+    #   anyio
+    #   httpx
+jinja2==3.1.4
+    # via -r requirements.in
+jmespath==1.0.1
+    # via
+    #   boto3
+    #   botocore
+markupsafe==2.1.5
+    # via jinja2
+python-dateutil==2.9.0.post0
+    # via botocore
+s3transfer==0.10.2
+    # via boto3
+six==1.16.0
+    # via python-dateutil
+sniffio==1.3.1
+    # via
+    #   anyio
+    #   httpx
+typing-extensions==4.12.2
+    # via anyio
+urllib3==2.2.3
+    # via botocore

monitoring/end_to_end_bag_test/requirements.txt

@@ -1,22 +1,44 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile
 #
-certifi==2020.4.5.1       # via httpx, requests
-chardet==3.0.4            # via httpx, requests
-h11==0.9.0                # via httpx
-h2==3.2.0                 # via httpx
-hpack==3.0.0              # via h2
-hstspreload==2020.5.13    # via httpx
-httpx==0.12.1
-hyperframe==5.2.0         # via h2
-idna==2.9                 # via httpx, requests
-oauthlib==3.1.0           # via requests-oauthlib
-requests-oauthlib==1.3.0  # via wellcome-storage-service
-requests==2.23.0          # via requests-oauthlib
-rfc3986==1.4.0            # via httpx
-sniffio==1.1.0            # via httpx
-urllib3==1.25.9           # via httpx, requests
+anyio==4.6.0
+    # via httpx
+certifi==2024.8.30
+    # via
+    #   httpcore
+    #   httpx
+    #   requests
+charset-normalizer==3.3.2
+    # via requests
+exceptiongroup==1.2.2
+    # via anyio
+h11==0.14.0
+    # via httpcore
+httpcore==1.0.6
+    # via httpx
+httpx==0.27.2
+    # via -r requirements.in
+idna==3.10
+    # via
+    #   anyio
+    #   httpx
+    #   requests
+oauthlib==3.2.2
+    # via requests-oauthlib
+requests==2.32.3
+    # via requests-oauthlib
+requests-oauthlib==1.3.1
+    # via wellcome-storage-service
+sniffio==1.3.1
+    # via
+    #   anyio
+    #   httpx
+typing-extensions==4.12.2
+    # via anyio
+urllib3==2.2.3
+    # via requests
 wellcome-storage-service==1.5.0
+    # via -r requirements.in

monitoring/end_to_end_bag_test/src/end_to_end_bag_test.py

@@ -53,7 +53,7 @@ def main(*args):
     print(ingest_location)
 
     ingest_id = ingest_location.split("/")[-1]
-    return f"https://ingest-inspector.wellcomecollection.org/ingests/{ingest_id}"
+    return f"https://ingest-inspector.wellcomecollection.org/?ingestId={ingest_id}"
 
 
 if __name__ == "__main__":

scripts/test_requirements.in

@@ -1,4 +1,4 @@
-moto<4
+moto
 pytest
 pytest-cov
 coverage

scripts/test_requirements.txt

@@ -1,88 +1,84 @@
 #
-# 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 test_requirements.in
 #
-attrs==22.1.0
-    # via pytest
-boto3==1.24.59
+boto3==1.35.32
     # via moto
-botocore==1.27.59
+botocore==1.35.32
     # via
     #   boto3
     #   moto
     #   s3transfer
-certifi==2022.6.15
+certifi==2024.8.30
     # via requests
-cffi==1.15.1
+cffi==1.17.1
     # via cryptography
-charset-normalizer==2.1.1
+charset-normalizer==3.3.2
     # via requests
-coverage[toml]==6.4.4
+coverage[toml]==7.6.1
     # via
     #   -r test_requirements.in
     #   pytest-cov
-cryptography==37.0.4
+cryptography==43.0.1
     # via moto
-idna==3.3
+exceptiongroup==1.2.2
+    # via pytest
+idna==3.10
     # via requests
-iniconfig==1.1.1
+iniconfig==2.0.0
     # via pytest
-jinja2==3.1.2
+jinja2==3.1.4
     # via moto
 jmespath==1.0.1
     # via
     #   boto3
     #   botocore
-markupsafe==2.1.1
+markupsafe==2.1.5
     # via
     #   jinja2
-    #   moto
-moto==3.1.18
+    #   werkzeug
+moto==5.0.16
     # via -r test_requirements.in
-packaging==21.3
-    # via pytest
-pluggy==1.0.0
+packaging==24.1
     # via pytest
-py==1.11.0
+pluggy==1.5.0
     # via pytest
-pycparser==2.21
+pycparser==2.22
     # via cffi
-pyparsing==3.0.9
-    # via packaging
-pytest-cov==3.0.0
-    # via -r test_requirements.in
-pytest==7.1.2
+pytest==8.3.3
     # via
     #   -r test_requirements.in
     #   pytest-cov
-python-dateutil==2.8.2
+pytest-cov==5.0.0
+    # via -r test_requirements.in
+python-dateutil==2.9.0.post0
     # via
     #   botocore
     #   moto
-pytz==2022.2.1
-    # via moto
-requests==2.28.1
+pyyaml==6.0.2
+    # via responses
+requests==2.32.3
     # via
     #   moto
     #   responses
-responses==0.21.0
+responses==0.25.3
     # via moto
-s3transfer==0.6.0
+s3transfer==0.10.2
     # via boto3
 six==1.16.0
     # via python-dateutil
-tomli==2.0.1
+tomli==2.0.2
     # via
     #   coverage
     #   pytest
-urllib3==1.26.12
+urllib3==1.26.20
     # via
     #   botocore
     #   requests
     #   responses
-werkzeug==2.1.2
+werkzeug==3.0.4
     # via moto
 xmltodict==0.13.0
     # via moto

scripts/tests/test_dynamo.py

@@ -9,7 +9,7 @@
 
 @pytest.fixture
 def client():
-    with moto.mock_dynamodb2():
+    with moto.mock_aws():
         yield boto3.resource("dynamodb", region_name="eu-west-1").meta.client
 
 

scripts/tests/test_s3.py

@@ -7,7 +7,7 @@
 
 @pytest.fixture
 def client():
-    with moto.mock_s3():
+    with moto.mock_aws():
         yield boto3.client("s3", region_name="us-east-1")
 
 

scripts/tests/test_secrets.py

@@ -7,7 +7,7 @@
 
 @pytest.fixture
 def client():
-    with moto.mock_secretsmanager():
+    with moto.mock_aws():
         yield boto3.client("secretsmanager", region_name="eu-west-1")
 
 

scripts/tox.ini

@@ -6,5 +6,5 @@ skipsdist = True
 deps =
     -r{toxinidir}/test_requirements.txt
 commands =
-    coverage run -m py.test tests
+    coverage run -m pytest tests
     coverage report