Only allow SOMATIC or GERMLINE values for SV_Status column

cBioPortal · Oct 28, 2024 · c2cbb82 · c2cbb82
1 parent fb81dc6
commit c2cbb82
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/scripts/importer/validateData.py b/scripts/importer/validateData.py
@@ -3217,8 +3217,9 @@ def checkNCBIbuild(ncbi_build):
         def checkSVstatus(sv_status):
             """ Allowed values for SV_Status column are SOMATIC and GERMLINE """
             if sv_status is None:
-                self.logger.warning('No value in SV_Status, assuming the variant is SOMATIC',
-                                  extra={'line_number': self.line_number})
+                self.logger.error('Invalid SV_Status value: possible values are [SOMATIC, GERMLINE]',
+                                  extra={'line_number': self.line_number,
+                                         'cause': sv_status})
             elif sv_status.lower() == 'germline':
                 self.logger.warning('GERMLINE variant identified from the SV_Status value. If this variant is not meant for public release, please remove it.',
                                   extra={'line_number': self.line_number,