fix(data-pipeline): update tqdm status bar upon recoverable errors

broadinstitute · Nov 7, 2024 · be906f9 · be906f9
1 parent cf6f7ef
commit be906f9
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/data-pipeline/src/data_pipeline/datasets/clinvar.py b/data-pipeline/src/data_pipeline/datasets/clinvar.py
@@ -113,7 +113,7 @@ def _parse_submission(submission_element, trait_mapping_list_element):
     return submission
 
 
-def _parse_variant(variant_element):
+def _parse_variant(variant_element, tqdm_pbar=None):
     variant = {}
 
     if variant_element.find("./ClassifiedRecord") is None:
@@ -129,9 +129,8 @@ def _parse_variant(variant_element):
             if chromosome == "Un":
                 variant["locations"] = {}
                 allele_element = variant_element.findall("./ClassifiedRecord/SimpleAllele")
-                print(
-                    f' Skipping variant with Allele ID: {allele_element[0].attrib["AlleleID"]} due to anomalous Chromosome value of "Un"'  # noqa
-                )
+                if tqdm_pbar is not None:
+                    tqdm_pbar.set_postfix_str(f'Skipped AlleleID: {allele_element[0].attrib["AlleleID"]} (Chr: Un)')
                 break
 
             variant["locations"][element.attrib["Assembly"]] = {