refactor actions and styling

.github/workflows/docs.yml

@@ -27,9 +27,9 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/int.yml

@@ -15,9 +15,9 @@ jobs:
     name: Integration Tests
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install requirements

.github/workflows/publish.yml

@@ -8,50 +8,68 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Beacon Docker image to Docker Hub
+    name: Push beacon python Docker image to Docker Hub
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-      - name: Login to DockerHub Registry
-        run: echo '${{ secrets.DOCKER_PASSWORD }}' | docker login -u '${{ secrets.DOCKER_USERNAME }}' --password-stdin
-      - name: Get the version
-        id: vars
-        run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
-      - name: Build the tagged Docker image
-        if:  ${{ steps.vars.outputs.tag != '/master' }}
-        run: docker build . --file Dockerfile --tag cscfi/beacon-python:${{steps.vars.outputs.tag}}
-      - name: Push the tagged Docker image
-        if:  ${{ steps.vars.outputs.tag != '/master' }}
-        run: docker push cscfi/beacon-python:${{steps.vars.outputs.tag}}
-      - name: Build the latest Docker image
-        if:  ${{ steps.vars.outputs.tag == '/master' }}
-        run: docker build . --file Dockerfile --tag cscfi/beacon-python:latest
-      - name: Push the latest Docker image
-        if:  ${{ steps.vars.outputs.tag == '/master' }}
-        run: docker push cscfi/beacon-python:latest
-  push_data_to_registry:
-    name: Push Dataloader Docker image to Docker Hub
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v1
-      - name: Login to DockerHub Registry
-        run: echo '${{ secrets.DOCKER_PASSWORD }}' | docker login -u '${{ secrets.DOCKER_USERNAME }}' --password-stdin
-      - name: Get the version
-        id: vars
-        run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
-      - name: Build the tagged Docker image
-        if:  ${{ steps.vars.outputs.tag != '/master' }}
-        run: |
-          pushd deploy/dataloader
-          docker build . --file Dockerfile --tag cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
-      - name: Push the tagged Docker image
-        if:  ${{ steps.vars.outputs.tag != '/master' }}
-        run: docker push cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
-      - name: Build the latest Docker image
-        if:  ${{ steps.vars.outputs.tag == '/master' }}
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Prepare
+        id: prep
         run: |
-          pushd deploy/dataloader
-          docker build . --file Dockerfile --tag cscfi/beacon-dataloader:latest
-      - name: Push the latest Docker image
-        if:  ${{ steps.vars.outputs.tag == '/master' }}
-        run: docker push cscfi/beacon-dataloader:latest
+          DOCKER_IMAGE=cscfi/beacon-python
+          DOCKER_IMAGE_DATA=cscfi/beacon-python
+          VERSION=edge
+          if [[ $GITHUB_REF == refs/tags/* ]]; then
+            VERSION=${GITHUB_REF#refs/tags/}
+          elif [[ $GITHUB_REF == refs/heads/* ]]; then
+            BRANCH=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
+            if [[ $BRANCH == master ]]; then
+              VERSION=latest
+            fi
+          fi
+          TAGS="${DOCKER_IMAGE}:${VERSION}"
+          TAGS_DATA="${DOCKER_IMAGE_DATA}:${VERSION}"
+          echo ::set-output name=version::${VERSION}
+          echo ::set-output name=tags::${TAGS}
+          echo ::set-output name=tagsData::${TAGS_DATA}
+          echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.prep.outputs.tags }}
+          cache-from: type=registry,ref=cscfi/beacon-python:latest
+          cache-to: type=inline
+          labels: |
+            org.opencontainers.image.source=${{ github.event.repository.clone_url }}
+            org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+            org.opencontainers.image.revision=${{ github.sha }}
+
+      - name: Build and push dataloader
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./deploy/dataloader/Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.prep.outputs.tagsData }}
+          cache-from: type=registry,ref=cscfi/swift-ui:latest
+          cache-to: type=inline
+          labels: |
+            org.opencontainers.image.source=${{ github.event.repository.clone_url }}
+            org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+            org.opencontainers.image.revision=${{ github.sha }}
+

.github/workflows/style.yml

@@ -8,12 +8,12 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.7]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

.github/workflows/unit.yml

@@ -8,12 +8,12 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.6, 3.7.7]
+        python-version: [3.7.7]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

beacon_api/api/exceptions.py

@@ -11,33 +11,32 @@
 from ..conf import CONFIG_INFO
 
 
-def process_exception_data(request: Dict,
-                           host: str,
-                           error_code: int,
-                           error: str) -> Dict:
+def process_exception_data(request: Dict, host: str, error_code: int, error: str) -> Dict:
     """Return request data as dictionary.
 
     Generates custom exception messages based on request parameters.
     """
-    data = {'beaconId': '.'.join(reversed(host.split('.'))),
-            "apiVersion": __apiVersion__,
-            'exists': None,
-            'error': {'errorCode': error_code,
-                      'errorMessage': error},
-            'alleleRequest': {'referenceName': request.get("referenceName", None),
-                              'referenceBases': request.get("referenceBases", None),
-                              'includeDatasetResponses': request.get("includeDatasetResponses", "NONE"),
-                              'assemblyId': request.get("assemblyId", None)},
-            # showing empty datasetsAlleRsponse as no datasets found
-            # A null/None would represent no data while empty array represents
-            # none found or error and corresponds with exists null/None
-            'datasetAlleleResponses': []}
+    data = {
+        "beaconId": ".".join(reversed(host.split("."))),
+        "apiVersion": __apiVersion__,
+        "exists": None,
+        "error": {"errorCode": error_code, "errorMessage": error},
+        "alleleRequest": {
+            "referenceName": request.get("referenceName", None),
+            "referenceBases": request.get("referenceBases", None),
+            "includeDatasetResponses": request.get("includeDatasetResponses", "NONE"),
+            "assemblyId": request.get("assemblyId", None),
+        },
+        # showing empty datasetsAlleRsponse as no datasets found
+        # A null/None would represent no data while empty array represents
+        # none found or error and corresponds with exists null/None
+        "datasetAlleleResponses": [],
+    }
     # include datasetIds only if they are specified
     # as per specification if they don't exist all datatsets will be queried
     # Only one of `alternateBases` or `variantType` is required, validated by schema
-    oneof_fields = ["alternateBases", "variantType", "start", "end", "startMin", "startMax",
-                    "endMin", "endMax", "datasetIds"]
-    data['alleleRequest'].update({k: request.get(k) for k in oneof_fields if k in request})
+    oneof_fields = ["alternateBases", "variantType", "start", "end", "startMin", "startMax", "endMin", "endMax", "datasetIds"]
+    data["alleleRequest"].update({k: request.get(k) for k in oneof_fields if k in request})
 
     return data
 
@@ -49,12 +48,11 @@ class BeaconBadRequest(web.HTTPBadRequest):
     Used in conjunction with JSON Schema validator.
     """
 
-    def __init__(self, request: Dict,
-                 host: str, error: str) -> None:
+    def __init__(self, request: Dict, host: str, error: str) -> None:
         """Return custom bad request exception."""
         data = process_exception_data(request, host, 400, error)
         super().__init__(text=json.dumps(data), content_type="application/json")
-        LOG.error(f'401 ERROR MESSAGE: {error}')
+        LOG.error(f"401 ERROR MESSAGE: {error}")
 
 
 class BeaconUnauthorised(web.HTTPUnauthorized):
@@ -64,17 +62,21 @@ class BeaconUnauthorised(web.HTTPUnauthorized):
     Used in conjunction with Token authentication aiohttp middleware.
     """
 
-    def __init__(self, request: Dict,
-                 host: str, error: str, error_message: str) -> None:
+    def __init__(self, request: Dict, host: str, error: str, error_message: str) -> None:
         """Return custom unauthorized exception."""
         data = process_exception_data(request, host, 401, error)
-        headers_401 = {"WWW-Authenticate": f"Bearer realm=\"{CONFIG_INFO.url}\"\n\
-                         error=\"{error}\"\n\
-                         error_description=\"{error_message}\""}
-        super().__init__(content_type="application/json", text=json.dumps(data),
-                         # we use auth scheme Bearer by default
-                         headers=headers_401)
-        LOG.error(f'401 ERROR MESSAGE: {error}')
+        headers_401 = {
+            "WWW-Authenticate": f'Bearer realm="{CONFIG_INFO.url}"\n\
+                         error="{error}"\n\
+                         error_description="{error_message}"'
+        }
+        super().__init__(
+            content_type="application/json",
+            text=json.dumps(data),
+            # we use auth scheme Bearer by default
+            headers=headers_401,
+        )
+        LOG.error(f"401 ERROR MESSAGE: {error}")
 
 
 class BeaconForbidden(web.HTTPForbidden):
@@ -85,12 +87,11 @@ class BeaconForbidden(web.HTTPForbidden):
     but not granted the resource. Used in conjunction with Token authentication aiohttp middleware.
     """
 
-    def __init__(self, request: Dict,
-                 host: str, error: str) -> None:
+    def __init__(self, request: Dict, host: str, error: str) -> None:
         """Return custom forbidden exception."""
         data = process_exception_data(request, host, 403, error)
         super().__init__(content_type="application/json", text=json.dumps(data))
-        LOG.error(f'403 ERROR MESSAGE: {error}')
+        LOG.error(f"403 ERROR MESSAGE: {error}")
 
 
 class BeaconServerError(web.HTTPInternalServerError):
@@ -101,7 +102,6 @@ class BeaconServerError(web.HTTPInternalServerError):
 
     def __init__(self, error: str) -> None:
         """Return custom forbidden exception."""
-        data = {'errorCode': 500,
-                'errorMessage': error}
+        data = {"errorCode": 500, "errorMessage": error}
         super().__init__(content_type="application/json", text=json.dumps(data))
-        LOG.error(f'500 ERROR MESSAGE: {error}')
+        LOG.error(f"500 ERROR MESSAGE: {error}")