Merge pull request #36 from CanDIG/daisieh-patch-1

All sorts of fixes to get tests back up

.github/workflows/test.yml

@@ -0,0 +1,46 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - develop
+      - master
+  pull_request:
+    branches:
+      - develop
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+    services:
+      postgres:
+        image: postgres:12
+        env:
+          POSTGRES_DB: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_USER: postgres
+        ports:
+          - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    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.txt
+    - name: Test
+      run: |
+        export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="postgres" && export POSTGRES_PORT=5432
+        coverage run ./manage.py test
+    - name: Codecov
+      run: codecov

.travis.yml

@@ -1,8 +1,7 @@
 dist: focal
 language: python
 python:
-  - "3.6"
-  - "3.8"
+  - "3.7"
 addons:
   postgresql: "12"
   apt:
@@ -13,10 +12,7 @@ before_install:
   - sudo -u postgres psql -U postgres -p 5433 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
 install:
   - pip install -r requirements.txt
-  - pip install .
 script:
   - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5433
-  - python3 -m tox
+  - python3 -m coverage run ./manage.py test
   - codecov
-  - rm -rf chord_metadata_service
-  - python3 -m coverage run ./manage.py test chord_metadata_service

chord_metadata_service/chord/ingest.py

@@ -226,7 +226,7 @@
                     "id": "readset_files",
                     "type": "file[]",
                     "required": True,
-                    "extensions": [".cram", ".bam", ".bigWig", ".bigBed"]
+                    "extensions": [".cram", ".bam", ".bigWig", ".bigBed", ".bw", ".bb"]
                 }
             ],
             "outputs": [

chord_metadata_service/mcode/api_views.py

@@ -55,12 +55,20 @@ def get_queryset(self):
             queryset = m.CancerGeneticVariant.objects.all()
         return queryset
 
-
 class GenomicRegionStudiedViewSet(McodeModelViewSet):
     serializer_class = s.GenomicRegionStudiedSerializer
     filter_backends = [DjangoFilterBackend]
     filter_class = f.GenomicRegionStudiedFilter
 
+    def get_queryset(self):
+        if hasattr(self.request, "allowed_datasets"):
+            allowed_datasets = self.request.allowed_datasets
+            queryset = m.GenomicRegionStudied.objects\
+                .filter(genomicsreport__mcodepacket__table__ownership_record__dataset__title__in=allowed_datasets)
+        else:
+            queryset = m.GenomicRegionStudied.objects.all()
+        return queryset
+
 
 GENOMIC_REPORT_PREFETCH = (
     "genetic_specimen",
@@ -71,15 +79,6 @@ class GenomicRegionStudiedViewSet(McodeModelViewSet):
     "genetic_variant",
 )
 
-    def get_queryset(self):
-        if hasattr(self.request, "allowed_datasets"):
-            allowed_datasets = self.request.allowed_datasets
-            queryset = m.GenomicRegionStudied.objects\
-                .filter(genomicsreport__mcodepacket__table__ownership_record__dataset__title__in=allowed_datasets)
-        else:
-            queryset = m.GenomicRegionStudied.objects.all()
-        return queryset
-
 
 class GenomicsReportViewSet(McodeModelViewSet):
     serializer_class = s.GenomicsReportSerializer
@@ -101,11 +100,6 @@ class LabsVitalViewSet(McodeModelViewSet):
     filter_backends = [DjangoFilterBackend]
     filter_class = f.LabsVitalFilter
 
-
-CANCER_CONDITION_PREFETCH = (
-    "tnmstaging_set",
-)
-
     def get_queryset(self):
         if hasattr(self.request, "allowed_datasets"):
             allowed_datasets = self.request.allowed_datasets
@@ -116,6 +110,11 @@ def get_queryset(self):
         return queryset
 
 
+CANCER_CONDITION_PREFETCH = (
+    "tnmstaging_set",
+)
+
+
 class CancerConditionViewSet(McodeModelViewSet):
     serializer_class = s.CancerConditionSerializer
     renderer_classes = tuple(McodeModelViewSet.renderer_classes) + (ARGORenderer,)
@@ -137,11 +136,6 @@ class TNMStagingViewSet(McodeModelViewSet):
     filter_backends = [DjangoFilterBackend]
     filter_class = f.TNMStagingFilter
 
-
-CANCER_RELATED_PROCEDURE = (
-    "reason_reference",
-)
-
     def get_queryset(self):
         if hasattr(self.request, "allowed_datasets"):
             allowed_datasets = self.request.allowed_datasets
@@ -152,6 +146,11 @@ def get_queryset(self):
         return queryset
 
 
+CANCER_RELATED_PROCEDURE = (
+    "reason_reference",
+)
+
+
 class CancerRelatedProcedureViewSet(McodeModelViewSet):
     serializer_class = s.CancerRelatedProcedureSerializer
     renderer_classes = tuple(McodeModelViewSet.renderer_classes) + (ARGORenderer,)
@@ -174,6 +173,15 @@ class MedicationStatementViewSet(McodeModelViewSet):
     filter_backends = [DjangoFilterBackend]
     filter_class = f.MedicationStatementFilter
 
+    def get_queryset(self):
+        if hasattr(self.request, "allowed_datasets"):
+            allowed_datasets = self.request.allowed_datasets
+            queryset = m.MedicationStatement.objects\
+                .filter(mcodepacket__table__ownership_record__dataset__title__in=allowed_datasets)
+        else:
+            queryset = m.MedicationStatement.objects.all()
+        return queryset
+
 
 MCODEPACKET_PREFETCH = (
     "cancer_condition",
@@ -186,15 +194,6 @@ class MedicationStatementViewSet(McodeModelViewSet):
     "genomics_report",
 )
 
-    def get_queryset(self):
-        if hasattr(self.request, "allowed_datasets"):
-            allowed_datasets = self.request.allowed_datasets
-            queryset = m.MedicationStatement.objects\
-                .filter(mcodepacket__table__ownership_record__dataset__title__in=allowed_datasets)
-        else:
-            queryset = m.MedicationStatement.objects.all()
-        return queryset
-
 
 class MCodePacketViewSet(McodeModelViewSet):
     serializer_class = s.MCodePacketSerializer

chord_metadata_service/package.cfg

@@ -1,4 +1,4 @@
 [package]
 name = katsu
-version = 2.6.0
+version = 2.7.0
 authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire

chord_metadata_service/phenopackets/api_views.py

@@ -4,6 +4,8 @@
 from rest_framework.decorators import api_view, permission_classes
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
+from django.utils.decorators import method_decorator
+from django.views.decorators.cache import cache_page
 from django_filters.rest_framework import DjangoFilterBackend
 
 from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, FHIRRenderer

chord_metadata_service/restapi/api_views.py

@@ -1,4 +1,7 @@
 from collections import Counter
+
+from django.views.decorators.cache import cache_page
+
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
 from rest_framework.decorators import api_view, permission_classes