More consistently split the flowcell id and status messages

some flowcells weren't being found because their names were
"flowcell (status)" which meant the code that was trying to find
the run.xml file in the results/flowcells directory was looking
for a directory named "results/flowcell_id (status)" which
wasn't so effective.

We really need a status field

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index 86c15117e8c2440d3ff7d088053a054f2047c8ff..4b6b3775f78c7546866d8121e5ac16224383a2c9 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -9,6 +9,7 @@ from htsworkflow.frontend import settings
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
+from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, HttpResponseRedirect
 from django.shortcuts import render_to_response
 from django.template import RequestContext
@@ -85,11 +86,10 @@ def library_to_flowcells(request, lib_id):
     eland_results = []
     for fc, lane in flowcell_list:
         lane_summary, err_list = _summary_stats(fc, lane)
-        
+
         eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
         lane_summary_list.extend(lane_summary)
 
-
     return render_to_response(
         'samples/library_detail.html',
         {'lib': lib,
@@ -98,11 +98,11 @@ def library_to_flowcells(request, lib_id):
         },
         context_instance = RequestContext(request))
 
-def summaryhtm_fc_cnm(request, fc_id, cnm):
+def summaryhtm_fc_cnm(request, flowcell_id, cnm):
     """
     returns a Summary.htm file if it exists.
     """
-    fc_id, status = parse_flowcell_id(fc_id)
+    fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
     
     if d is None:
@@ -121,11 +121,11 @@ def summaryhtm_fc_cnm(request, fc_id, cnm):
     return HttpResponse(f)
 
 
-def result_fc_cnm_eland_lane(request, fc_id, cnm, lane):
+def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
     """
     returns an eland_file upon calling.
     """
-    fc_id, status = parse_flowcell_id(fc_id)
+    fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
     
     if d is None:
@@ -157,11 +157,11 @@ def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
     return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
 
 
-def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=False):
+def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
     """
     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
     """
-    fc_id, status = parse_flowcell_id(fc_id)
+    fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
     
     if d is None:
@@ -213,30 +213,29 @@ def _summary_stats(flowcell_id, lane_id):
             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
             continue
         
-        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))
     
     return (summary_list, err_list)
 
@@ -315,16 +314,16 @@ def get_eland_result_type(pathname):
         return 'unknown'
 
 def _make_eland_results(flowcell_id, lane, interesting_flowcells):
-
-    cur_fc = interesting_flowcells.get(flowcell_id, None)
+    fc_id, status = parse_flowcell_id(flowcell_id)
+    cur_fc = interesting_flowcells.get(fc_id, None)
     if cur_fc is None:
       return []
 
     results = []
     for cycle in cur_fc.keys():
         result_path = cur_fc[cycle]['eland_results'].get(lane, None)
-        result_link = make_result_link(flowcell_id, cycle, lane, result_path)
-        results.append({'flowcell_id': flowcell_id,
+        result_link = make_result_link(fc_id, cycle, lane, result_path)
+        results.append({'flowcell_id': fc_id,
                         'cycle': cycle, 
                         'lane': lane, 
                         'summary_url': make_summary_url(flowcell_id, cycle),