ci: replace Travis CI with GH Actions

.github/workflows/docker-build-publish-drs-filer.yml

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+name: drs-filer
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  publish_to_docker:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/dev'
+
+    name: Build and publish to Docker
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Set up Docker Buildx
+        uses: docker/[email protected]
+
+      - name: Login to Docker Hub
+        uses: docker/[email protected]
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: elixircloud/drs-filer
+
+      - name: Build and push Docker images
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/lint.yml

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+name: Lint workflow
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  linting_and_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    name: Run linting and unit tests
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest coverage coveralls
+
+      - name: Lint with flake8
+        run: flake8
+
+      - name: Run unit tests with coverage
+        run: |
+          coverage run --source drs_filer -m pytest
+          coverage report -m
+          coveralls

.github/workflows/test.yml

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+name: Test Drs-filer API Endpoints
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/[email protected]
+
+    - name: Build and run Docker Compose
+      run: docker-compose up --build -d
+
+    - name: Wait for the services to be ready
+      run: |
+        echo "Waiting for the services to be ready..."
+        for i in {1..10}; do
+          if curl -sSf http://localhost:8080/ga4gh/drs/v1 > /dev/null; then
+            echo "Service is up!"
+            break
+          fi
+          echo "Waiting for the service to be ready..."
+          sleep 3
+        done
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/[email protected]
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest requests
+
+    - name: Test with pytest
+      run: |
+        pytest tests/test.py -v -p no:warnings
+      env:
+        DRS_FILER_URL: http://localhost:8080/ga4gh/drs/v1

tests/test.py

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+import os
+import requests
+import time
+import pytest
+
+DRS_FILER_URL = os.getenv('DRS_FILER_URL')
+
+@pytest.fixture(scope="function")
+def get_object_id():
+    object_id = test_create_object()
+    yield object_id
+
+@pytest.fixture(scope="function")
+def get_access_id(get_object_id):
+    access_id = test_get_object(get_object_id).get('access_methods')[0].get('access_id')
+    yield access_id
+
+def handle_error(response):
+    """Helper function to handle common error cases."""
+    if response.status_code == 400:
+        print(f"400 Bad Request: {response.json().get('msg')}")
+    elif response.status_code == 401:
+        print(f"401 Unauthorized: {response.json().get('msg')}")
+    elif response.status_code == 403:
+        print(f"403 Forbidden: {response.json().get('msg')}")
+    elif response.status_code == 404:
+        print(f"404 Not Found: {response.json().get('msg')}")
+    elif response.status_code == 409:
+        print(f"409 Conflict: {response.json()}")
+    elif response.status_code == 500:
+        print(f"500 Internal Server Error: {response.json().get('msg')}")
+    else:
+        print(f"Unexpected status code {response.status_code}: {response.json().get('msg')}")
+
+def test_create_object():
+    data = {
+        "access_methods": [
+            {
+                "access_url": {
+                    "headers": [],
+                    "url": "http://example.com/data"
+                },
+                "region": "us-east-1",
+                "type": "s3"
+            }
+        ],
+        "aliases": [
+            "example_alias"
+        ],
+        "checksums": [
+            {
+                "checksum": "abc123",
+                "type": "sha-256"
+            }
+        ],
+        "contents": [],
+        "created_time": "2024-06-12T12:58:19Z",
+        "description": "An example object",
+        "mime_type": "application/json",
+        "name": "example_object",
+        "size": 1024,
+        "updated_time": "2024-06-12T12:58:19Z",
+        "version": "1.0"
+    }
+
+    response = requests.post(f"{DRS_FILER_URL}/objects", json=data)
+
+    if response.status_code == 200:
+        object_id = response.json()
+        print(f"Created object with ID: {object_id}")
+        return object_id
+    else:
+        handle_error(response)
+        return None
+
+def test_get_objects():
+    response = requests.get(f"{DRS_FILER_URL}/objects")
+    assert response.status_code == 200
+    assert response.json() is not None
+    assert isinstance(response.json(), list)
+    if response.status_code == 200:
+        print("Following are the objects: ")
+        print(response.json())
+    else:
+        handle_error(response)
+
+def test_get_object(get_object_id):
+    object_id = get_object_id
+
+    response = requests.get(f"{DRS_FILER_URL}/objects/{object_id}")
+    assert response.status_code == 200
+    assert response.json()['id'] == object_id
+
+    if response.status_code == 200:
+        print(f"Following is the object retrieved based on {object_id}:")
+        print(response.json())
+        return response.json()
+    elif response.status_code == 202:
+        retry_after = int(response.headers.get("Retry-After", 5))
+        print(f"202 Accepted: Operation is delayed. Retry after {retry_after} seconds.")
+        time.sleep(retry_after)
+        return test_get_object(object_id)  # Retry the request
+    else:
+        handle_error(response)
+        return None
+
+def test_get_object_access(get_object_id, get_access_id):
+    object_id = get_object_id
+    access_id = get_access_id
+    assert object_id is not None, "Object ID should not be None"
+    assert access_id is not None, "Access ID should not be None"
+
+    response = requests.get(f"{DRS_FILER_URL}/objects/{object_id}/access/{access_id}")
+
+    if response.status_code == 200:
+        print(f"Following is the object retrieved based on {object_id} and {access_id}:")
+        print(response.json())
+    elif response.status_code == 202:
+        retry_after = int(response.headers.get("Retry-After", 5))
+        print(f"202 Accepted: Operation is delayed. Retry after {retry_after} seconds.")
+        time.sleep(retry_after)
+        return test_get_object_access(object_id, access_id)  # Retry the request
+    else:
+        handle_error(response)
+
+def test_update_object(get_object_id):
+    object_id = get_object_id
+
+    data = {
+        "access_methods": [
+            {
+                "access_url": {
+                    "headers": ["string"],
+                    "url": "string"
+                },
+                "region": "us-east-1",
+                "type": "s3"
+            },
+            {
+                "access_url": {
+                    "headers": ["string"],
+                    "url": "string"
+                },
+                "region": "us-east-2",
+                "type": "s3"
+            }
+        ],
+        "aliases": ["string"],
+        "checksums": [
+            {
+                "checksum": "string",
+                "type": "sha-256"
+            }
+        ],
+        "contents": [
+            {
+                "contents": [],
+                "drs_uri": [
+                    "drs://drs.example.org/314159",
+                    "drs://drs.example.org/213512"
+                ],
+                "id": "string",
+                "name": "string"
+            }
+        ],
+        "created_time": "2024-07-03T14:16:59.268Z",
+        "description": "string",
+        "mime_type": "application/json",
+        "name": "string",
+        "size": 0,
+        "updated_time": "2024-07-03T14:16:59.268Z",
+        "version": "string"
+    }
+
+    response = requests.put(f"{DRS_FILER_URL}/objects/{object_id}", json=data)
+    assert response.status_code == 200
+
+    if response.status_code == 200:
+        print(f"Updated the object with ID: {object_id}")
+    else:
+        handle_error(response)
+
+def test_delete_object_access(get_object_id, get_access_id):
+    object_id=get_object_id
+    access_id=get_access_id
+
+    response = requests.delete(f"{DRS_FILER_URL}/objects/{object_id}/access/{access_id}")
+
+    if response.status_code == 404:
+        print(f"Object with ID {object_id} or access ID {access_id} not found.")
+    elif response.status_code == 409:
+        print(f"Refusing to delete the last remaining access method for object {object_id}.")
+    elif response.status_code == 200:
+        print(f"Deleted access method with ID {access_id} for object {object_id}.")
+    else:
+        handle_error(response)
+
+def test_delete_object(get_object_id):
+    object_id=get_object_id
+
+    response = requests.delete(f"{DRS_FILER_URL}/objects/{object_id}")
+
+    if response.status_code == 200:
+        print(f"Deleted the object with ID: {object_id}")
+    else:
+        handle_error(response)
+
+def test_post_service_info():
+    data = {
+        "contactUrl": "mailto:[email protected]",
+        "createdAt": "2024-06-12T12:58:19Z",
+        "description": "This service provides...",
+        "documentationUrl": "https://docs.myservice.example.com",
+        "environment": "test",
+        "id": "org.ga4gh.myservice",
+        "name": "My project",
+        "organization": {
+            "name": "My organization",
+            "url": "https://example.com"
+        },
+        "type": {
+            "artifact": "beacon",
+            "group": "org.ga4gh",
+            "version": "1.0.0"
+        },
+        "updatedAt": "2024-06-12T12:58:19Z",
+        "version": "1.0.0"
+    }
+
+    response = requests.post(f"{DRS_FILER_URL}/service-info", json=data)
+    assert response.status_code == 201
+
+    if response.status_code == 201:
+        print("Service info was successfully created.")
+    else:
+        handle_error(response)
+
+def test_get_service_info():
+    response = requests.get(f"{DRS_FILER_URL}/service-info")
+    assert response.status_code == 200
+    service_info = response.json()
+    assert "name" in service_info
+    assert "version" in service_info