Merge pull request #3531 from broadinstitute/dev

Dev

.dockerignore

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

.github/workflows/unit-tests.yml

@@ -63,6 +63,22 @@ 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: |
+          export DATASETS_DIR=./hail_search/fixtures
+          coverage run --source="./hail_search" --omit="./hail_search/__main__.py","./hail_search/test_utils.py" -m pytest hail_search/
+          coverage report --fail-under=99
+
   nodejs:
     runs-on: ubuntu-latest
 

hail_search/__main__.py

@@ -0,0 +1,20 @@
+from aiohttp import web
+import hail as hl
+import logging
+
+from hail_search.web_app import init_web_app
+
+
+def run():
+    logging.basicConfig(level=logging.INFO)
+    hl.init()
+    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/constants.py

@@ -0,0 +1,13 @@
+GENOME_VERSION_GRCh38_DISPLAY = 'GRCh38'
+
+AFFECTED = 'A'
+UNAFFECTED = 'N'
+AFFECTED_ID = 0
+UNAFFECTED_ID = 1
+
+VARIANT_DATASET = 'VARIANTS'
+
+VARIANT_KEY_FIELD = 'variantId'
+GNOMAD_GENOMES_FIELD = 'gnomad_genomes'
+
+XPOS = 'xpos'

hail_search/fixtures/GRCh38/VARIANTS/annotations.ht/README.txt

@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.109-b71b065e4bb6
+  Created at 2023/07/26 13:13:09

hail_search/fixtures/GRCh38/VARIANTS/families/F000002_2.ht/README.txt

@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.109-b71b065e4bb6
+  Created at 2023/07/26 12:54:13

hail_search/fixtures/GRCh38/VARIANTS/projects/R0001_1kg.ht/README.txt

@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.109-b71b065e4bb6
+  Created at 2023/07/26 16:54:14

hail_search/fixtures/GRCh38/VARIANTS/projects/R0003_test.ht/README.txt

@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.109-b71b065e4bb6
+  Created at 2023/07/26 17:16:57