From 4a2529df5d2bdaa83d1661730c3791560d58df37 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 5 Dec 2013 16:28:12 -0800 Subject: [PATCH] Attempt to be robust to not having an alignment in our RunXml file --- htsworkflow/frontend/experiments/models.py | 6 ++++-- htsworkflow/frontend/samples/views.py | 4 ++++ 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py index 7a41d3d..5152c40 100644 --- a/htsworkflow/frontend/experiments/models.py +++ b/htsworkflow/frontend/experiments/models.py @@ -248,8 +248,10 @@ class FlowCell(models.Model): 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() diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py index 7150d08..e50b5b3 100644 --- a/htsworkflow/frontend/samples/views.py +++ b/htsworkflow/frontend/samples/views.py @@ -296,6 +296,10 @@ def _summary_stats(flowcell_id, lane_id, library_id): 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)) -- 2.30.2