🔧 Add deletion of indexd gfs on delete study resource

dataservice/api/study/resources.py

@@ -133,23 +133,36 @@ def delete(self, kf_id):
         if st is None:
             abort(404, 'could not find {} `{}`'.format('study', kf_id))
 
-        db.session.delete(st)
+        # -- Delete genomic_files from indexd --
+        from dataservice.api.participant.models import Participant
+        from dataservice.api.biospecimen.models import Biospecimen
+        from dataservice.api.genomic_file.models import GenomicFile
+        from dataservice.api.common.model import delete_indexd
+        # GenomicFiles for this study
+        gfs = (GenomicFile.query.join(GenomicFile.biospecimen)
+               .join(Biospecimen.participant)
+               .filter(Participant.study_id == kf_id)).all()
+        # Delete from indexd
+        [delete_indexd(None, None, gf) for gf in gfs]
+
+        # Delete study - will execute db cascade delete
+        Study.query.filter_by(kf_id=kf_id).delete()
         db.session.commit()
 
-        # Delete orphans
+        # -- Delete orphans ---
         # Families
         from dataservice.api.family.models import Family
-        q = (db.session.query(Family)
-             .filter(~Family.participants.any()))
-        q.delete(synchronize_session=False)
+        (db.session.query(Family)
+         .filter(~Family.participants.any())).delete(
+            synchronize_session=False)
 
         # Sequencing experiments
         from dataservice.api.sequencing_experiment.models import (
             SequencingExperiment
         )
-        q = (db.session.query(SequencingExperiment)
-             .filter(~SequencingExperiment.genomic_files.any()))
-        q.delete(synchronize_session=False)
+        (db.session.query(SequencingExperiment)
+         .filter(~SequencingExperiment.genomic_files.any())).delete(
+            synchronize_session=False)
 
         db.session.commit()