Merge pull request #19 from bento-platform/backwards-compatible-moder…

…nize

Update CI action versions, dependencies, and service-info

.github/workflows/build.yml

@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Run Bento build action
-        uses: bento-platform/bento_build_action@v0.6
+        uses: bento-platform/bento_build_action@v0.9.3
         with:
           registry: ghcr.io
           registry-username: ${{ github.actor }}

.github/workflows/lint.yml

@@ -8,7 +8,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
       - name: Install flake8
         run: pip install flake8
       - name: Run linter

.github/workflows/test.yml

@@ -11,8 +11,8 @@ jobs:
       matrix:
         python-version: [ "3.8", "3.10" ]
     steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         name: Set up Python
         with:
           python-version: ${{ matrix.python-version }}

Dockerfile

@@ -2,7 +2,7 @@ FROM ghcr.io/bento-platform/bento_base_image:python-debian-latest
 
 # Use uvicorn (instead of hypercorn) in production since I've found
 # multiple benchmarks showing it to be faster - David L
-RUN pip install --no-cache-dir poetry==1.2.2 "uvicorn[standard]==0.20.0"
+RUN pip install --no-cache-dir poetry==1.3.2 "uvicorn[standard]==0.20.0"
 
 # Backwards-compatible with old BentoV2 container layout
 WORKDIR /drop-box

bento_drop_box_service/app.py

@@ -23,7 +23,7 @@
     BENTO_DEBUG=os.environ.get(
         "CHORD_DEBUG", os.environ.get("BENTO_DEBUG", os.environ.get("QUART_ENV", "production"))
     ).strip().lower() in ("true", "1", "development"),
-    SERVICE_ID=os.environ.get("SERVICE_ID", SERVICE_TYPE),
+    SERVICE_ID=os.environ.get("SERVICE_ID", str(":".join(list(SERVICE_TYPE.values())[:2]))),
     SERVICE_DATA_SOURCE="minio" if MINIO_URL else "local",
     SERVICE_DATA=None if MINIO_URL else SERVICE_DATA,
     MINIO_URL=MINIO_URL,

bento_drop_box_service/constants.py

@@ -1,13 +1,15 @@
 from bento_drop_box_service import __version__
 
 __all__ = [
+    "BENTO_SERVICE_KIND",
     "SERVICE_NAME",
     "SERVICE_TYPE",
 ]
 
+BENTO_SERVICE_KIND = "drop-box"
 SERVICE_NAME = "Bento Drop Box Service"
 SERVICE_TYPE = {
     "group": "ca.c3g.bento",
-    "artifact": "drop-box",
+    "artifact": BENTO_SERVICE_KIND,
     "version": __version__,
 }

bento_drop_box_service/routes.py

@@ -4,9 +4,10 @@
     quart_bad_request_error,
     quart_internal_server_error
 )
+from bento_lib.types import GA4GHServiceInfo
 from bento_drop_box_service import __version__
 from bento_drop_box_service.backend import get_backend
-from bento_drop_box_service.constants import SERVICE_NAME, SERVICE_TYPE
+from bento_drop_box_service.constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE
 
 
 drop_box_service = Blueprint("drop_box_service", __name__)
@@ -48,16 +49,21 @@ async def drop_box_retrieve(path) -> Response:
 @drop_box_service.route("/service-info", methods=["GET"])
 async def service_info() -> Response:
     # Spec: https://github.com/ga4gh-discovery/ga4gh-service-info
-    return jsonify({
+    # Do a little type checking
+    info: GA4GHServiceInfo = {
         "id": current_app.config["SERVICE_ID"],
         "name": SERVICE_NAME,
         "type": SERVICE_TYPE,
         "description": "Drop box service for a Bento platform node.",
         "organization": {
             "name": "C3G",
-            "url": "http://www.computationalgenomics.ca"
+            "url": "https://www.computationalgenomics.ca"
         },
-        "contactUrl": "mailto:[email protected].ca",
+        "contactUrl": "mailto:info@c3g.ca",
         "version": __version__,
-        "env": "dev" if current_app.config["BENTO_DEBUG"] else "prod",
-    })
+        "environment": "dev" if current_app.config["BENTO_DEBUG"] else "prod",
+        "bento": {
+            "serviceKind": BENTO_SERVICE_KIND,
+        },
+    }
+    return jsonify(info)

dev.Dockerfile

@@ -1,6 +1,6 @@
 FROM ghcr.io/bento-platform/bento_base_image:python-debian-latest
 
-RUN pip install --no-cache-dir poetry==1.2.2 "uvicorn[standard]==0.20.0"
+RUN pip install --no-cache-dir poetry==1.3.2 "uvicorn[standard]==0.20.0"
 
 # Backwards-compatible with old BentoV2 container layout
 WORKDIR /drop-box

entrypoint.sh

@@ -2,7 +2,7 @@
 
 if [ -z "${INTERNAL_PORT}" ]; then
   # Set default internal port to 5000
-  INTERNAL_PORT=5000
+  export INTERNAL_PORT=5000
 fi
 
 uvicorn bento_drop_box_service.app:application \

pyproject.toml

@@ -4,12 +4,12 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "bento_drop_box_service"
-version = "0.6.0"
+version = "0.7.0"
 description = "Drop box and basic file management service for the Bento platform."
 authors = ["David Lougheed <[email protected]>", "Simon Chénard <[email protected]>"]
 readme = "README.md"
 packages = [{include = "bento_drop_box_service"}]
-repository = "https://github.com/bento-platform/bento_service_registry"
+repository = "https://github.com/bento-platform/bento_drop_box_service"
 license = "LGPL-3.0-only"
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -21,16 +21,16 @@ classifiers = [
 python = "^3.8"
 boto3 = "^1.26.4"
 quart = "^0.18.3"
-bento-lib = {extras = ["quart"], version = "^4.1.0"}
+bento-lib = {extras = ["quart"], version = "^5.2.0"}
 aiofiles = "^22.1.0"
 
 [tool.poetry.group.dev.dependencies]
-tox = "^3.27.0"
+tox = "^4.2.8"
 codecov = "^2.1.12"
 coverage = "^6.5.0"
 pytest = "^7.2.0"
 pytest-cov = "^4.0.0"
 moto = "^4.0.9"
 flake8 = "^5.0.4"
 pytest-asyncio = "^0.20.1"
-
+debugpy = "^1.6.5"