From 0c5ee77a6bfa0b07969a3658333eedcf8f917b7c Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Tue, 13 Feb 2024 11:59:01 +0100 Subject: [PATCH] Add indications_exome_equivalent --- clarity_epp/upload/samples.py | 4 ++++ config.py | 3 +++ 2 files changed, 7 insertions(+) diff --git a/clarity_epp/upload/samples.py b/clarity_epp/upload/samples.py index b858e0c..cba9527 100644 --- a/clarity_epp/upload/samples.py +++ b/clarity_epp/upload/samples.py @@ -166,6 +166,10 @@ def from_helix(lims, email_settings, input_file): if udf_data['Dx Onderzoeksindicatie'] == 'DSD00' and udf_data['Dx Familie status'] == 'Kind': udf_data['Dx Geslacht'] = 'Onbekend' + # Set 'Dx Exoomequivalent' for specific indications + if udf_data['Dx Onderzoeksindicatie'] in config.indications_exome_equivalent: + udf_data['Dx Exoomequivalent'] = config.indications_exome_equivalent[udf_data['Dx Onderzoeksindicatie']] + # Check 'Dx Familienummer' and correct if '/' in udf_data['Dx Familienummer']: udf_data['Dx Import warning'] = ';'.join([ diff --git a/config.py b/config.py index c002932..4b45714 100755 --- a/config.py +++ b/config.py @@ -30,6 +30,9 @@ stoftestcode_mip: '1651', # DEV Dx smMIP v1.2 } +# Update exome equivalent for certain indications +indications_exome_equivalent = {'UBA1': 5, 'PID09': 5} + # Export meetw protocol steps WES meetw_zui_wes_processes = [ 'Dx Sample registratie zuivering v1.1',