new clinvar failure (#5103)

bpblanken · web-flow · commit d21c2b3c1cb2 · 2025-10-28T12:29:20.000-04:00
diff --git a/seqr/management/commands/reload_clinvar_all_variants.py b/seqr/management/commands/reload_clinvar_all_variants.py
@@ -123,6 +123,9 @@ def parse_pathogenicity_and_assertions(classified_record_node: xml.etree.Element
     ).replace(
         ', low penetrance',
         '; low penetrance'
+    ).replace(
+        'Likely pathogenic/Likely pathogenic',
+        'Likely pathogenic'
     )
 
     pathogenicity = pathogenicity_string.split(';')[0].strip()

Original file line number	Diff line number	Diff line change
`@@ -123,6 +123,9 @@ def parse_pathogenicity_and_assertions(classified_record_node: xml.etree.Element`
`123`	`123`	`).replace(`
`124`	`124`	`', low penetrance',`
`125`	`125`	`'; low penetrance'`
	`126`	`+ ).replace(`
	`127`	`+ 'Likely pathogenic/Likely pathogenic',`
	`128`	`+ 'Likely pathogenic'`
`126`	`129`	`)`
`127`	`130`
`128`	`131`	`pathogenicity = pathogenicity_string.split(';')[0].strip()`