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Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
runfolder.py
diff --git
a/htsworkflow/pipelines/runfolder.py
b/htsworkflow/pipelines/runfolder.py
index 7c06e217de63d5733e524ae551f06eea40528e11..669c5f03363dfc8c647730133af71678319d0336 100644
(file)
--- a/
htsworkflow/pipelines/runfolder.py
+++ b/
htsworkflow/pipelines/runfolder.py
@@
-129,10
+129,12
@@
class PipelineRun(object):
return path_fields[-1]
def _get_runfolder_name(self):
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
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):
runfolder_name = property(_get_runfolder_name)
def _get_run_dirname(self):
@@
-361,12
+363,12
@@
def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
p.suffix = suffix
p.image_analysis = image_analysis
p.bustard = bustard.bustard(unaligned)
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)
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):
return len(runs) - start
def hiseq_match_aligned_unaligned(aligned, unaligned):