bugfix: more missing buffer flushes

Author: bpblanken

v03_pipeline/lib/reference_datasets/clinvar.py

@@ -113,7 +113,7 @@ def get_submission_summary_ht() -> hl.Table:
         timeout=10,
     ) as r:
         shutil.copyfileobj(r.raw, tmp_file)
-        cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
+    cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
     ht = hl.import_table(
         cloud_tmp_file,
         force=True,

v03_pipeline/lib/reference_datasets/helix_mito.py

@@ -23,7 +23,7 @@ def get_ht(
         delete=False,
     ) as tmp_file, requests.get(url, stream=True, timeout=10) as r:
         shutil.copyfileobj(r.raw, tmp_file)
-        cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
+    cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
     ht = hl.import_table(
         cloud_tmp_file,
         types={

v03_pipeline/lib/reference_datasets/screen.py

@@ -21,7 +21,7 @@ def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table:
         timeout=10,
     ) as r:
         shutil.copyfileobj(r.raw, tmp_file)
-        cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
+    cloud_tmp_file = copy_to_cloud_storage(tmp_file.name)
     ht = hl.import_table(
         cloud_tmp_file,
         no_header=True,