From: Diane Trout <diane@caltech.edu>
Date: Thu, 5 Dec 2013 23:06:14 +0000 (-0800)
Subject: Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=86dc57e6227c79cd3f599e3d8bac46a44f961607;hp=-c

Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
---

86dc57e6227c79cd3f599e3d8bac46a44f961607
diff --combined htsworkflow/pipelines/runfolder.py
index 26c592c,da1bbe6..669c5f0
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@@ -129,12 -129,10 +129,12 @@@ class PipelineRun(object)
              return path_fields[-1]
  
      def _get_runfolder_name(self):
 -        if self.gerald is None:
 -            return None
 -        else:
 +        if self.gerald:
              return self.gerald.runfolder_name
 +        elif hasattr(self.image_analysis, 'runfolder_name'):
 +            return self.image_analysis.runfolder_name
 +        else:
 +            return None
      runfolder_name = property(_get_runfolder_name)
  
      def _get_run_dirname(self):
@@@ -363,12 -361,12 +363,12 @@@ def build_hiseq_runs(image_analysis, ru
              p.suffix = suffix
              p.image_analysis = image_analysis
              p.bustard = bustard.bustard(unaligned)
-             assert p.bustard
              if aligned:
                  p.gerald = gerald.gerald(aligned)
              runs.append(p)
-         except IOError, e:
-             LOGGER.error("Ignoring " + str(e))
+         except (IOError, RuntimeError) as e:
+ 	    LOGGER.error("Exception %s", str(e))
+             LOGGER.error("Skipping run in %s", flowcell_id)
      return len(runs) - start
  
  def hiseq_match_aligned_unaligned(aligned, unaligned):