Merge pull request #612 from sartography/dev

Merge dev into testing

.github/workflows/build-test-image.yml

@@ -0,0 +1,98 @@
+name: build_test_image
+
+on:
+  push:
+    branches: ['testing']
+  workflow_dispatch:
+
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  TESTING: true
+  PB_ENABLED: false
+  SQLALCHEMY_DATABASE_URI: "postgresql://postgres:postgres@localhost:5432/crc_test"
+  PGPASSWORD: postgres
+
+jobs:
+  sonarcloud:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          # Disabling shallow clone is recommended for improving relevancy of reporting
+          fetch-depth: 0
+      - name: SonarCloud Scan
+        uses: sonarsource/sonarcloud-github-action@master
+        with:
+          args: >
+            -Dsonar.organization=sartography
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+  run_tests:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_PASSWORD: postgres
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - uses: browser-actions/setup-chrome@latest
+        with:
+          chrome-version: stable
+      - uses: actions/setup-python@v3
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - run: psql -h localhost -c 'create database crc_test;' -U postgres
+      - run: pip install pipenv
+      - run: pipenv install --dev
+      - run: pipenv run coverage run -m pytest
+      - run: pipenv run coverage xml -i
+
+  build-and-push-image:
+    needs:
+      - run_tests
+      - sonarcloud
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/testing'
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

config/logging.py

@@ -3,7 +3,7 @@
   'disable_existing_loggers': False,
   "loggers": {
     '': {  # root logger
-      'handlers': ['console'],
+      'handlers': ['console', 'file'],
       'level': 'INFO',
       'propagate': True
     },
@@ -36,7 +36,7 @@
   "root": {
     "level": "INFO",
     "handlers": [
-      "console",
+      "console", "file"
     ]
   },
   "handlers": {
@@ -45,6 +45,12 @@
       "class": "logging.StreamHandler",
       "stream": "ext://sys.stdout",
       "level": "INFO"
+    },
+    "file": {
+      "level": "INFO",
+      "formatter": "simple",
+      "class": "logging.FileHandler",
+      "filename": "cr_connect.log"
     }
   }
 }

crc/services/study_service.py

@@ -265,6 +265,7 @@ def update_study_associate(study_id=None, uid=None, role="", send_email=False, a
         if uid is None:
             raise ApiError('uid not specified', "This function requires a uva uid parameter")
 
+        uid = uid.lower()
         if not LdapService.user_exists(uid):
             raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap', "You are trying to grant access to "
                                                                                "%s but they were not found in ldap "

crc/services/workflow_service.py

@@ -139,31 +139,30 @@ def get_workflow_url(workflow):
         return workflow_url
 
     def process_erroring_workflows(self):
-        with app.app_context():    
-            workflows = self.get_erroring_workflows()
-            if len(workflows) > 0:
-                workflow_urls = []
-                if len(workflows) == 1:
-                    workflow = workflows[0]
+        workflows = self.get_erroring_workflows()
+        if len(workflows) > 0:
+            workflow_urls = []
+            if len(workflows) == 1:
+                workflow = workflows[0]
+                workflow_url_link = self.get_workflow_url(workflow)
+                workflow_urls.append(workflow_url_link)
+                message = 'There is one workflow in an error state.'
+                message += f'\n You can restart the workflow at {workflow_url_link}.'
+            else:
+                message = f'There are {len(workflows)} workflows in an error state.'
+                message += '\nYou can restart the workflows at these URLs:'
+                for workflow in workflows:
                     workflow_url_link = self.get_workflow_url(workflow)
                     workflow_urls.append(workflow_url_link)
-                    message = 'There is one workflow in an error state.'
-                    message += f'\n You can restart the workflow at {workflow_url_link}.'
-                else:
-                    message = f'There are {len(workflows)} workflows in an error state.'
-                    message += '\nYou can restart the workflows at these URLs:'
-                    for workflow in workflows:
-                        workflow_url_link = self.get_workflow_url(workflow)
-                        workflow_urls.append(workflow_url_link)
-                        message += f'\n{workflow_url_link}'
-
-                with push_scope() as scope:
-                    scope.user = {"urls": workflow_urls}
-                    scope.set_extra("workflow_urls", workflow_urls)
-                    # this sends a message through sentry
-                    capture_message(message)
-                # We return message so we can use it in a test
-                return message
+                    message += f'\n{workflow_url_link}'
+
+            with push_scope() as scope:
+                scope.user = {"urls": workflow_urls}
+                scope.set_extra("workflow_urls", workflow_urls)
+                # this sends a message through sentry
+                capture_message(message)
+            # We return message so we can use it in a test
+            return message
 
     @staticmethod
     def test_spec(spec_id, validate_study_id=None, test_until=None, required_only=False):

example_data.py

@@ -1,3 +1,5 @@
+# example data for testing
+
 import glob
 import os