Merge pull request #30 from bento-platform/rename-refact

refact: remove federation parts + rename to aggregation

.coveragerc

@@ -1,3 +1,3 @@
 [run]
 include =
-    bento_federation_service/*
+    bento_aggregation_service/*

.dockerignore

@@ -0,0 +1,4 @@
+.coverage
+.tox
+
+env

.github/workflows/build.yml

@@ -0,0 +1,32 @@
+name: Build and push bento_aggregation_service
+on:
+  release:
+    types: [ published ]
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Run Bento build action
+        uses: bento-platform/bento_build_action@v0.9.3
+        with:
+          registry: ghcr.io
+          registry-username: ${{ github.actor }}
+          registry-password: ${{ secrets.GITHUB_TOKEN }}
+          image-name: ghcr.io/bento-platform/bento_aggregation_service
+          development-dockerfile: dev.Dockerfile
+          dockerfile: Dockerfile

.github/workflows/lint.yml

@@ -0,0 +1,33 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.10]
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: python -m pip install -r requirements-dev.txt
+
+    - name: Lint
+      run: flake8 ./bento_aggregation_service ./tests

.github/workflows/test.yml

@@ -0,0 +1,36 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.10]
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: python -m pip install -r requirements-dev.txt
+
+    - name: Test
+      run: coverage run -m unittest -v
+
+    - name: Codecov
+      run: codecov

Dockerfile

@@ -0,0 +1,28 @@
+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"
+
+WORKDIR /aggregation
+
+COPY pyproject.toml pyproject.toml
+COPY poetry.toml poetry.toml
+COPY poetry.lock poetry.lock
+
+# Install production dependencies
+# Without --no-root, we get errors related to the code not being copied in yet.
+# But we don't want the code here, otherwise Docker cache doesn't work well.
+RUN poetry install --without dev --no-root
+
+# Manually copy only what's relevant
+# (Don't use .dockerignore, which allows us to have development containers too)
+COPY bento_aggregation_service bento_aggregation_service
+COPY LICENSE LICENSE
+COPY README.md README.md
+COPY run.py run.py
+
+# Install the module itself, locally (similar to `pip install -e .`)
+RUN poetry install --without dev
+
+ENTRYPOINT ["python3", "run.py"]

README.md

@@ -1,39 +1,21 @@
-# Bento Federation Service
+# Bento Aggregation Service
 
-A service for federated search between Bento platform nodes.
+A service for aggregating search results across Bento data services.
 
 ## Environment Variables
 
-`DATABASE`: Defaults to `data/federation.db`
-
-Keeps track of a list of peers to pass federated queries to.
-
 `CHORD_DEBUG`: `true` (insecure) or `false`; default is `false`
 
-`BENTO_FEDERATION_MODE`: `true` or `false`; default is `true`
-
-If set to false, the peer-contacting process will be skipped entirely.
-
 `CHORD_URL`: ex. `http://127.0.0.1:5000/`
 
 By convention, this *should* have a trailing slash; however as of v0.9.1 this 
 is optional.
 
-`CHORD_REGISTRY_URL`: ex. `http://127.0.0.1:5000/`
-
-By convention, this *should* have a trailing slash; however as of v0.9.1 this 
-is optional.
-
-`OIDC_DISCOVERY_URI`:
-ex. `https://keycloak.example.og/auth/realms/master/.well-known/openid-configuration`
-
-By convention *should not* have a trailing slash.
-
 `PORT`: Specified when running via `./run.py`; defaults to `5000`
 
 `SERVICE_URL_BASE_PATH`: Base URL fragment (e.g. `/test/`) for endpoints
 
 Should usually be blank; set to non-blank to locally emulate a proxy prefix
-like `/api/federation`.
+like `/api/aggregation`.
 
 `SOCKET`: Specifies Unix socket location for production deployment

bento_aggregation_service/__init__.py

@@ -0,0 +1,6 @@
+from importlib import metadata
+
+__all__ = ["name", "__version__"]
+
+name = __package__
+__version__ = metadata.version(__package__)

bento_aggregation_service/app.py

@@ -0,0 +1,70 @@
+from __future__ import annotations
+
+import bento_aggregation_service
+import tornado.gen
+import tornado.ioloop
+import tornado.web
+
+from datetime import datetime
+from tornado.web import RequestHandler, url
+
+from .constants import (
+    SERVICE_ID,
+    SERVICE_TYPE,
+    SERVICE_NAME,
+    PORT,
+    BASE_PATH,
+    CHORD_DEBUG,
+    CHORD_URL_SET,
+    DEBUGGER_PORT,
+)
+from .search.handlers.datasets import DatasetsSearchHandler
+from .search.handlers.private_dataset import PrivateDatasetSearchHandler
+
+
+# noinspection PyAbstractClass,PyAttributeOutsideInit
+class ServiceInfoHandler(RequestHandler):
+    async def get(self):
+        # Spec: https://github.com/ga4gh-discovery/ga4gh-service-info
+        self.write({
+            "id": SERVICE_ID,
+            "name": SERVICE_NAME,  # TODO: Should be globally unique?
+            "type": SERVICE_TYPE,
+            "description": "Aggregation service for a Bento platform node.",
+            "organization": {
+                "name": "C3G",
+                "url": "https://www.computationalgenomics.ca"
+            },
+            "contactUrl": "mailto:david.lougheed@mail.mcgill.ca",
+            "version": bento_aggregation_service.__version__
+        })
+
+
+class Application(tornado.web.Application):
+    def __init__(self, base_path: str):
+        super().__init__([
+            url(f"{base_path}/service-info", ServiceInfoHandler),
+            url(f"{base_path}/dataset-search", DatasetsSearchHandler),
+            url(f"{base_path}/private/dataset-search/([a-zA-Z0-9\\-_]+)", PrivateDatasetSearchHandler),
+        ])
+
+
+application = Application(BASE_PATH)
+
+
+def run():  # pragma: no cover
+    if not CHORD_URL_SET:
+        print(f"[{SERVICE_NAME} {datetime.utcnow()}] CHORD_URL is not set, terminating...")
+        exit(1)
+
+    if CHORD_DEBUG:
+        try:
+            # noinspection PyPackageRequirements,PyUnresolvedReferences
+            import debugpy
+            debugpy.listen(("0.0.0.0", DEBUGGER_PORT))
+            print("debugger attached")
+        except ImportError:
+            print("debugpy not found")
+
+    application.listen(PORT)
+    tornado.ioloop.IOLoop.current().start()

bento_federation_service/constants.py → bento_aggregation_service/constants.py

@@ -7,10 +7,8 @@
 __all__ = [
     "BASE_PATH",
     "CHORD_DEBUG",
-    "BENTO_FEDERATION_MODE",
     "CHORD_URL",
     "CHORD_HOST",
-    "CHORD_REGISTRY_URL",
 
     "OIDC_DISCOVERY_URI",
 
@@ -24,11 +22,12 @@
     "SERVICE_ID",
     "SERVICE_NAME",
 
-    "SERVICE_SOCKET",
+    "PORT",
+    "DEBUGGER_PORT",
 
-    "INITIALIZE_IMMEDIATELY",
+    "CHORD_URL_SET",
 
-    "CHORD_URLS_SET",
+    "USE_GOHAN",
 
     "TIMEOUT",
     "WORKERS",
@@ -55,12 +54,10 @@ def _env_url_trailing_slash(var: str) -> str:
 BASE_PATH = os.environ.get("SERVICE_URL_BASE_PATH", "")
 
 CHORD_DEBUG = _env_to_bool("CHORD_DEBUG")
-BENTO_FEDERATION_MODE = _env_to_bool("BENTO_FEDERATION_MODE", default=True)
 
 # Set CHORD_URL and CHORD_REGISTRY_URL to environment values, or blank if not
 # available.
 CHORD_URL = _env_url_trailing_slash("CHORD_URL")
-CHORD_REGISTRY_URL = _env_url_trailing_slash("CHORD_REGISTRY_URL")
 
 CHORD_HOST = urllib.parse.urlparse(CHORD_URL or "").netloc or ""
 OIDC_DISCOVERY_URI = os.environ.get("OIDC_DISCOVERY_URI")
@@ -69,16 +66,18 @@ def _env_url_trailing_slash(var: str) -> str:
 
 SERVICE_ORGANIZATION = "ca.c3g.bento"
 SERVICE_ARTIFACT = "federation"
-SERVICE_TYPE_NO_VERSION = f"{SERVICE_ORGANIZATION}:{SERVICE_ARTIFACT}"
-SERVICE_TYPE = f"{SERVICE_TYPE_NO_VERSION}:{__version__}"
-SERVICE_ID = os.environ.get("SERVICE_ID", SERVICE_TYPE_NO_VERSION)
-SERVICE_NAME = "Bento Federation Service"
-
-SERVICE_SOCKET = os.environ.get("SERVICE_SOCKET", "/tmp/federation.sock")
-
-INITIALIZE_IMMEDIATELY = _env_to_bool("INITIALIZE_IMMEDIATELY", default=True)
-
-CHORD_URLS_SET = CHORD_URL != "" and CHORD_REGISTRY_URL != ""
+SERVICE_TYPE = {
+    "group": "ca.c3g.bento",
+    "artifact": SERVICE_ARTIFACT,
+    "version": __version__,
+}
+SERVICE_ID = os.environ.get("SERVICE_ID", ":".join(list(SERVICE_TYPE.values())[:2]))
+SERVICE_NAME = "Bento Aggregation Service"
+
+PORT = int(os.environ.get("PORT", "5000"))
+DEBUGGER_PORT = int(os.environ.get("DEBUGGER_PORT", "5879"))
+
+CHORD_URL_SET = CHORD_URL != ""
 
 USE_GOHAN = _env_to_bool("USE_GOHAN")
 

bento_aggregation_service/search/constants.py

@@ -0,0 +1,7 @@
+from __future__ import annotations
+
+from bento_aggregation_service.constants import CHORD_HOST
+
+__all__ = ["DATASET_SEARCH_HEADERS"]
+
+DATASET_SEARCH_HEADERS = {"Host": CHORD_HOST}