Merge pull request #1007 from jhu-bids/action-updates

GH Action updates: Vocab refresh & Backend tests

.github/workflows/refresh_voc.yml

@@ -3,7 +3,7 @@ name: Refresh vocabulary tables
 on:
   schedule:
 ##    - cron: '0 0 * * 0'  # weekly, sunday 12am
-    - cron: '0 8 * * *'  # every day 6am GMT (3/4am EST/EDT)
+    - cron: '0 8 * * *'  # every day 8am GMT (3/4am EST/EDT)
   workflow_dispatch:
 jobs:
   refresh-vocab-tables:
@@ -50,5 +50,8 @@ jobs:
         run: make refresh-vocab
 
       # Test
+      # todo: This won't actually run, because the Python script will throw an error at the end (only if successful
+      #  refresh happened, which will notify that it completed successfully. So the GitHub action will only get this far
+      #  if there was never any data. However, this test does run daily in a separate action.
       - name: Test
         run: python -m unittest test.test_backend.db.test_refresh_dataset_group_tables.TestCurrentDatasetGroupSetup.test_current_vocab

.github/workflows/test_backend_e2e_and_unit_and_qc.yml

@@ -10,6 +10,8 @@ on:
     branches: [ develop, main ]
   pull_request:
     branches: [ develop, main ]
+  schedule:
+    - cron: '0 14 * * *'  # every day 2pm GMT (9/10am EST/EDT)
 
 jobs:
   test:

backend/db/refresh_dataset_group_tables.py

@@ -31,6 +31,11 @@
 from enclave_wrangler.datasets import download_datasets, get_datetime_dataset_last_updated
 
 
+class NotAnError(Exception):
+    """Used to throw an error that causes a GitHub action notification."""
+    pass
+
+
 def load_dataset_group(dataset_group_name: str, schema: str = SCHEMA, alternate_dataset_dir: Union[Path, str] = None):
     """Load data
 
@@ -109,6 +114,14 @@ def refresh_dataset_group_tables(
             # DB Counts
             print('Updating database counts. This could take a while...')
             counts_update(f'DB refresh: {",".join(dataset_group)}', schema)
+
+        # Vocab refresh only
+        # todo: ideally this notification would happen differently. More comments near bottom of refresh_voc.yml
+        if group_name == 'vocab' and len(dataset_group) == 1:  # Will be the case for GH actions
+            raise NotAnError('Notification: Restart deployment backend.\nThis is not an error. It is only being raised '
+                'as an easy way to trigger a GitHub action notification. Vocabulary refresh has completed '
+                'successfully. Please restart backend to refresh networkx graph.')
+
     print('Done')