diff --git a/scripts/importer/validateData.py b/scripts/importer/validateData.py index cceb2222..4c926653 100755 --- 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,