From: Diane Trout <diane@caltech.edu>
Date: Fri, 6 Dec 2013 00:28:12 +0000 (-0800)
Subject: Attempt to be robust to not having an alignment in our RunXml file
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=4a2529df5d2bdaa83d1661730c3791560d58df37

Attempt to be robust to not having an alignment in our RunXml file
---

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))