Merge pull request #3480 from broadinstitute/add-hail-status-check

Add hail backend - intitial status check

.dockerignore

@@ -5,6 +5,7 @@ static/*
 !static/images/*
 deploy/*
 !deploy/docker/seqr/*
+hail_search/*
 .git
 .vscode
 .idea

.github/workflows/unit-tests.yml

@@ -63,6 +63,21 @@ jobs:
           coverage run --source="./matchmaker","./seqr","./reference_data","./panelapp" --omit="*/migrations/*","*/apps.py" manage.py test -p '*_tests.py' -v 2 reference_data seqr matchmaker panelapp
           coverage report --fail-under=99
 
+  hail_search:
+    runs-on: ubuntu-latest
+    container: hailgenetics/hail:0.2.115
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip wheel
+          pip install -r hail_search/requirements-test.txt
+      - name: Run coverage tests
+        run: |
+          coverage run --source="./hail_search" --omit="./hail_search/__main__.py" -m pytest hail_search/
+          coverage report --fail-under=99
+
   nodejs:
     runs-on: ubuntu-latest
 

hail_search/__main__.py

@@ -0,0 +1,16 @@
+from aiohttp import web
+
+from hail_search.web_app import init_web_app
+
+
+def run():
+    app = init_web_app()
+    web.run_app(
+        app,
+        host='0.0.0.0',  # nosec
+        port=5000,
+        access_log_format='%{From}i "%r" %s %Tfs',
+    )
+
+
+run()

hail_search/requirements-test.in

@@ -0,0 +1,2 @@
+coverage<5.2
+pytest-aiohttp

hail_search/requirements-test.txt

@@ -0,0 +1,48 @@
+#
+# This file is autogenerated by pip-compile with Python 3.9
+# To update, run:
+#
+#    pip-compile hail_search/requirements-test.in
+#
+aiohttp==3.8.4
+    # via pytest-aiohttp
+aiosignal==1.3.1
+    # via aiohttp
+async-timeout==4.0.2
+    # via aiohttp
+attrs==23.1.0
+    # via aiohttp
+charset-normalizer==3.2.0
+    # via aiohttp
+coverage==5.1
+    # via -r hail_search/requirements-test.in
+exceptiongroup==1.1.2
+    # via pytest
+frozenlist==1.3.3
+    # via
+    #   aiohttp
+    #   aiosignal
+idna==3.4
+    # via yarl
+iniconfig==2.0.0
+    # via pytest
+multidict==6.0.4
+    # via
+    #   aiohttp
+    #   yarl
+packaging==23.1
+    # via pytest
+pluggy==1.2.0
+    # via pytest
+pytest==7.4.0
+    # via
+    #   pytest-aiohttp
+    #   pytest-asyncio
+pytest-aiohttp==1.0.4
+    # via -r hail_search/requirements-test.in
+pytest-asyncio==0.21.0
+    # via pytest-aiohttp
+tomli==2.0.1
+    # via pytest
+yarl==1.9.2
+    # via aiohttp

hail_search/test_search.py

@@ -0,0 +1,15 @@
+from aiohttp.test_utils import AioHTTPTestCase
+
+from hail_search.web_app import init_web_app
+
+
+class HailSearchTestCase(AioHTTPTestCase):
+
+    async def get_application(self):
+        return init_web_app()
+
+    async def test_status(self):
+        async with self.client.request('GET', '/status') as resp:
+            self.assertEqual(resp.status, 200)
+            resp_json = await resp.json()
+        self.assertDictEqual(resp_json, {'success': True})

hail_search/web_app.py

@@ -0,0 +1,17 @@
+from aiohttp import web
+import hail as hl
+import logging
+
+
+async def status(request: web.Request) -> web.Response:
+    return web.json_response({'success': True})
+
+
+def init_web_app():
+    logging.basicConfig(level=logging.INFO)
+    hl.init()
+    app = web.Application()
+    app.add_routes([
+        web.get('/status', status),
+    ])
+    return app