Merge pull request #380 from CanDIG/hotfix/not-experiment

Miscellaneous indexing fixes

Author: daisieh

htsget_server/database.py

@@ -575,6 +575,13 @@ def create_pos_buckets_for_variantfile(obj):
         session.bulk_insert_mappings(PositionBucketVariantFileAssociation, pbvfs_to_add)
         session.commit()
 
+    with Session() as session:
+        new_variantfile = session.query(VariantFile).filter_by(id=variantfile_id).one_or_none()
+        if new_variantfile is not None:
+            new_variantfile.indexed = 1
+            session.add(new_variantfile)
+            session.commit()
+
     return None
 
 

htsget_server/htsget_operations.py

@@ -352,8 +352,8 @@ def _get_experiment(id_=None):
                     elif drs_obj["type"] == "read":
                         result["reads"].append(drs_obj["name"])
             return result, 200
-    else:
-        return resp.text, resp.status_code
+        return f"{id_} is not an Experiment", 404
+    return resp.text, resp.status_code
 
 
 def _get_htsget_url(id, reference_name, slice_start, slice_end, file_type, data=True):