- try:
- run = load_pipeline_run_xml(xmlpath)
- gerald_summary = run.gerald.summary.lane_results
- for end in range(len(gerald_summary)):
- eland_summary = run.gerald.eland_results.results[end][lane_id]
- # add information to lane_summary
- eland_summary.flowcell_id = flowcell_id
- eland_summary.clusters = gerald_summary[end][lane_id].cluster
- eland_summary.cycle_width = cycle_width
- if hasattr(eland_summary, 'genome_map'):
- eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
- eland_summary.genome_map,
- eland_summary.mapped_reads)
-
- # grab some more information out of the flowcell db
- flowcell = FlowCell.objects.get(flowcell_id=fc_id)
- pm_field = 'lane_%d_pM' % (lane_id)
- eland_summary.successful_pm = getattr(flowcell, pm_field)
-
- summary_list.append(eland_summary)
-
- except Exception, e:
- summary_list.append("Summary report needs to be updated.")
- logging.error("Exception: " + str(e))
+ run = load_pipeline_run_xml(xmlpath)
+ gerald_summary = run.gerald.summary.lane_results
+ for end in range(len(gerald_summary)):
+ eland_summary = run.gerald.eland_results.results[end][lane_id]
+ # add information to lane_summary
+ eland_summary.flowcell_id = flowcell_id
+ eland_summary.clusters = gerald_summary[end][lane_id].cluster
+ eland_summary.cycle_width = cycle_width
+ if hasattr(eland_summary, 'genome_map'):
+ eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
+ eland_summary.genome_map,
+ eland_summary.mapped_reads)
+
+ # grab some more information out of the flowcell db
+ flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
+ pm_field = 'lane_%d_pM' % (lane_id)
+ eland_summary.successful_pm = getattr(flowcell, pm_field)
+
+ summary_list.append(eland_summary)
+
+ #except Exception, e:
+ # summary_list.append("Summary report needs to be updated.")
+ # logging.error("Exception: " + str(e))