add a few more logs (#715)

Author: jklugherz

v03_pipeline/lib/logger.py

@@ -20,7 +20,7 @@
         '': {
             'level': 'INFO',
             'handlers': ['default'],
-            'propagate': True,
+            'propagate': False,
         },
         'py4j': {
             'level': 'CRITICAL',

v03_pipeline/lib/tasks/base/base_hail_table_task.py

@@ -29,6 +29,13 @@ def init_hail(self):
 
 # NB: these are defined over luigi.Task instead of the BaseHailTableTask so that
 # they work on file dependencies.
+
+
+@luigi.Task.event_handler(luigi.Event.DEPENDENCY_DISCOVERED)
+def dependency_discovered(task, dependency):
+    logger.info(f'{task} dependency_discovered {dependency}')
+
+
 @luigi.Task.event_handler(luigi.Event.DEPENDENCY_MISSING)
 def dependency_missing(task):
     logger.info(f'{task} dependency_missing at {task.output()}')

v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset.py

@@ -29,6 +29,9 @@ def reference_dataset_collections(self) -> list[ReferenceDatasetCollection]:
         )
 
     def complete(self) -> bool:
+        logger.info(
+            'Checking if UpdateVariantAnnotationsTableWithUpdatedReferenceDataset is complete',
+        )
         self._datasets_to_update = []
 
         if not super().complete():