run.image_version = run_xml_data.image_analysis.version
run.basecall_software = run_xml_data.bustard.software
run.basecall_version = run_xml_data.bustard.version
- run.alignment_software = run_xml_data.gerald.software
- run.alignment_version = run_xml_data.gerald.version
+ # we're frequently not running alignments
+ if run_xml_data.gerald:
+ run.alignment_software = run_xml_data.gerald.software
+ run.alignment_version = run_xml_data.gerald.version
run.last_update_time = datetime.datetime.now()
run.save()
continue
run = load_pipeline_run_xml(xmlpath)
+ # skip if we don't have available metadata.
+ if run.gerald is None or run.gerald.summary is None:
+ continue
+
gerald_summary = run.gerald.summary.lane_results
key = SampleKey(lane=lane_id, sample='s')
eland_results = list(run.gerald.eland_results.find_keys(key))