Merge pull request #68 from ScilifelabDataCentre/feature/shinyproxy

Feature/shinyproxy

.github/workflows/serve-shinyproxy.yml

@@ -0,0 +1,78 @@
+name: Serve-Shinyproxy workflow
+
+on:
+  push:
+    paths:
+      - "serve-shinyproxy/**"
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: 'Checkout GitHub Action'
+        uses: actions/checkout@main
+
+      - name: 'Build test image'
+        run: |
+            docker build -t ghcr.io/scilifelabdatacentre/serve-shinyproxy:latest ./serve-shinyproxy
+
+      - name: Run Trivy vulnerability scanner
+        uses: aquasecurity/[email protected]
+        with:
+          image-ref: 'ghcr.io/scilifelabdatacentre/serve-shinyproxy:latest'
+          format: 'table'
+          severity: 'CRITICAL,HIGH'
+          timeout: '30m0s'
+          exit-code: '0'
+
+      - name: 'Run tests'
+        env:
+          IMAGE_NAME: ghcr.io/scilifelabdatacentre/serve-shinyproxy:latest
+        run: | 
+          pip install -r ./serve-shinyproxy/tests/requirements.txt
+          python3 -m pytest ./serve-shinyproxy
+
+  push: 
+    if: | 
+      github.ref == 'refs/heads/main' &&
+      github.repository == 'scilifelabdatacentre/serve-images'
+    needs: build_and_test
+    runs-on: ubuntu-latest
+    concurrency:
+      group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+      cancel-in-progress: true
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: 'Checkout github action'
+        uses: actions/checkout@main
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/scilifelabdatacentre/serve-shinyproxy
+          tags: |
+            type=raw,value={{date 'YYMMDD-HHmm' tz='Europe/Stockholm'}}
+
+      - name: 'Login to GHCR'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+
+      - name: Publish image to GHCR
+        uses: docker/build-push-action@v3
+        with:
+          file: ./serve-shinyproxy/Dockerfile
+          context: ./serve-shinyproxy
+          push: true
+          build-args: version=${{ github.ref_name }}
+          tags: |
+            ${{ steps.meta.outputs.tags }}
+            ghcr.io/scilifelabdatacentre/serve-shinyproxy:latest
+          labels: ${{ steps.meta.outputs.labels }}

dev_scripts/run_shinyproxy.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+set -o errexit
+
+docker build -t shinyproxy-dev-img ../serve-shinyproxy
+python3 -m venv venv
+source ./venv/bin/activate
+python3 -m pip install --upgrade pip
+pip install -r ../serve-shinyproxy/tests/requirements.txt
+export IMAGE_NAME=shinyproxy-dev-img
+python3 -m pytest ../serve-shinyproxy/

serve-shinyproxy/Dockerfile

@@ -0,0 +1,9 @@
+FROM openanalytics/shinyproxy:3.0.2
+
+ENV SHINY_USER shinyproxy
+RUN chown $SHINY_USER:$SHINY_USER /opt/shinyproxy/
+
+WORKDIR /opt/shinyproxy
+USER $SHINY_USER
+
+CMD ["java", "-noverify",  "-jar", "/opt/shinyproxy/shinyproxy.jar", "--spring.jmx.enabled=false", "--spring.config.location=/opt/shinyproxy/application.yml"]

serve-shinyproxy/tests/requirements.txt

@@ -0,0 +1,2 @@
+docker
+pytest

serve-shinyproxy/tests/test_api.py

@@ -0,0 +1,61 @@
+import os
+import requests
+import docker
+import time
+
+PORT = 8080  # Shinyproxy port
+TIMEOUT_CALL = 5  # the timeout in seconds of the client request call
+
+client = docker.from_env()
+container = client.containers.run(
+    image=os.environ["IMAGE_NAME"],
+    ports={f"{PORT}/tcp": PORT},
+    detach=True,
+)
+time.sleep(10)  # Update this somehow.
+container.reload()
+
+
+def test_container_status():
+    """Test that the Shinyproxy container is running."""
+    assert container.status == "running"
+
+
+def test_container_ports():
+    """Test of the expected container port."""
+    assert len(container.ports) == 1, "There should be 1 port"
+    assert container.ports[f"{PORT}/tcp"][0]["HostPort"] == str(PORT)
+
+
+def test_login():
+    url = _get_url(container) + "/login"
+    max_attempts = 50
+
+    for attempt in range(1, max_attempts + 1):
+        try:
+            print("URL is: ", url)
+            response = requests.get(url, timeout=TIMEOUT_CALL)
+            if response.status_code == 200:
+                print("Shinyproxy is up and running!")
+                assert True
+                break
+        except:
+            pass
+
+        if attempt == max_attempts:
+            RuntimeError(
+                f"Shinyproxy did not become ready after {max_attempts} attempts"
+            )
+            assert False
+
+        print(
+            f"Attempt {attempt} failed, waiting for 10 seconds before trying again..."
+        )
+        time.sleep(10)
+
+
+def _get_url(container):
+    """Gets the URL of the container."""
+    ip = container.attrs["NetworkSettings"]["Networks"]["bridge"]["IPAddress"]
+    url = "http://{}:{}".format(ip, PORT)
+    return url