Dependabot: urllib3 and boto3 updates

.github/workflows/build.yaml

@@ -13,10 +13,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Create k3s Cluster
-        uses: debianmaster/actions-k3s@v1.0.5
+      - name: Setup microk8s
+        uses: fenio/setup-microk8s@v5.0.1
         with:
-          version: 'latest'
+          version: 'latest/stable'
+          addons: 'dns,ingress'
+          wait-for-ready: true
 
       - name: Create namespace
         run: kubectl create ns tesk
@@ -44,7 +46,7 @@ jobs:
         run: helm list -n tesk && kubectl get all -n tesk
 
       - name: curl URL
-        run: curl localhost -vL
+        run: curl localhost/ga4gh/tes/v1/service-info
 
       - name: Configure Git
         run: |
@@ -57,4 +59,4 @@ jobs:
           skip_existing: true
         env:
           CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
-
+

source/tesk-core/containers/filer.Dockerfile

@@ -1,10 +1,10 @@
 # Builder: produce wheels
 
-FROM alpine:3.10 as builder
+FROM alpine:3.19 as builder
 
-RUN apk add --no-cache python3
+RUN apk add --no-cache python3 py3-pip
 RUN apk add --no-cache git
-RUN python3 -m pip install --upgrade setuptools pip wheel
+RUN python3 -m pip install --upgrade setuptools pip wheel --break-system-packages
 
 WORKDIR /app/
 COPY . .
@@ -13,12 +13,12 @@ RUN python3 setup.py bdist_wheel
 
 # Install: copy tesk-core*.whl and install it with dependencies
 
-FROM alpine:3.10
+FROM alpine:3.19
 
-RUN apk add --no-cache python3
+RUN apk add --no-cache python3 py3-pip
 
 COPY --from=builder /app/dist/tesk*.whl /root/
-RUN python3 -m pip install --disable-pip-version-check --no-cache-dir /root/tesk*.whl
+RUN python3 -m pip install --disable-pip-version-check --no-cache-dir /root/tesk*.whl --break-system-packages
 
 USER 100
 

source/tesk-core/containers/taskmaster.Dockerfile

@@ -1,10 +1,10 @@
 # Builder: produce wheels
 
-FROM alpine:3.10 as builder
+FROM alpine:3.19 as builder
 
-RUN apk add --no-cache python3
+RUN apk add --no-cache python3 py3-pip
 RUN apk add --no-cache git
-RUN python3 -m pip install --upgrade setuptools pip wheel
+RUN python3 -m pip install --upgrade setuptools pip wheel --break-system-packages
 
 WORKDIR /app/
 COPY . .
@@ -13,12 +13,12 @@ RUN python3 setup.py bdist_wheel
 
 # Install: copy tesk-core*.whl and install it with dependencies
 
-FROM alpine:3.10
+FROM alpine:3.19
 
-RUN apk add --no-cache python3
+RUN apk add --no-cache python3 py3-pip
 
 COPY --from=builder /app/dist/tesk*.whl /root/
-RUN python3 -m pip install --disable-pip-version-check --no-cache-dir /root/tesk*.whl
+RUN python3 -m pip install --disable-pip-version-check --no-cache-dir /root/tesk*.whl --break-system-packages
 
 RUN adduser --uid 100 -S taskmaster
 USER 100

source/tesk-core/setup.py

@@ -10,14 +10,20 @@
 
 INSTALL_DEPS = ['kubernetes==9.0.0',
                 'requests>=2.20.0',
-                'urllib3==1.26.19',
-                'boto3==1.16.18',
+
+                # urllib3 constraint
+                'urllib3>=1.26,<2.0 ; python_version < "3.10"',
+                'urllib3>=2.0,<3.0 ; python_version >= "3.10"',
+
+                # boto3 constraint
+                'boto3<=1.28 ; python_version == "3.8"',
+                'boto3>=1.28,<2.0 ; python_version >= "3.9"',
                 ]
 TEST_DEPS = [ 'pytest',
             'pyfakefs',
             'pytest-mock'
             , 'fs',
-            'moto',
+            'moto<5',
             'pytest-localftpserver'
             ]
 

source/tesk-core/src/tesk_core/filer_class.py

@@ -81,6 +81,8 @@ def add_s3_mount(self):
 
         env = self.getEnv()
         env.append({"name": "AWS_CONFIG_FILE", "value": "/aws/config"})
+        env.append({"name": "AWS_REQUEST_CHECKSUM_CALCULATION", "value": "WHEN_REQUIRED"})
+        env.append({"name": "AWS_RESPONSE_CHECKSUM_VALIDATION", "value": "WHEN_REQUIRED"})
         env.append(
             {
                 "name": "AWS_SHARED_CREDENTIALS_FILE",