Don't crash if there are no lane result summary entries when rendering

[htsworkflow.git] / htsworkflow / frontend / samples / views.py

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index 3fbfe792fd9224a5c68f78d4abaf7f1ac91b999f..d79d0b83976adc49dff287850e1a71a80796d4d0 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -44,9 +44,10 @@ def create_library_context(cl):
        else:
            summary['amplified_from'] = ''
        lanes_run = 0
-       for lane_id in LANE_LIST:
-           lane = getattr(lib, 'lane_%d_library' % (lane_id,))
-           lanes_run += len( lane.all() )
+       #for lane_id in LANE_LIST:
+       #    lane = getattr(lib, 'lane_%d_library' % (lane_id,))
+       #    lanes_run += len( lane.all() )
+       lanes_run = lib.lane_set.count()
        summary['lanes_run'] = lanes_run
        summary['is_archived'] = lib.is_archived()
        records.append(summary)
@@ -90,22 +91,24 @@ def library_to_flowcells(request, lib_id):
    
     flowcell_list = []
     interesting_flowcells = {} # aka flowcells we're looking at
-    for lane in LANE_LIST:
-        lane_library = getattr(lib, 'lane_%d_library' % (lane,))
-        for fc in lane_library.all():
-            flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
-            if flowcell_id not in interesting_flowcells:
-                interesting_flowcells[flowcell_id] = get_flowcell_result_dict(flowcell_id)
-            flowcell_list.append((fc.flowcell_id, lane))
+    #for lane in LANE_LIST:
+    for lane in lib.lane_set.all():
+        #lane_library = getattr(lib, 'lane_%d_library' % (lane,))
+        #for fc in lane_library.all():
+        fc = lane.flowcell
+        flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
+        if flowcell_id not in interesting_flowcells:
+            interesting_flowcells[flowcell_id] = get_flowcell_result_dict(flowcell_id)
+        flowcell_list.append((fc.flowcell_id, lane.lane_number))
 
     flowcell_list.sort()
     
     lane_summary_list = []
     eland_results = []
-    for fc, lane in flowcell_list:
-        lane_summary, err_list = _summary_stats(fc, lane)
+    for fc, lane_number in flowcell_list:
+        lane_summary, err_list = _summary_stats(fc, lane_number)
 
-        eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
+        eland_results.extend(_make_eland_results(fc, lane_number, interesting_flowcells))
         lane_summary_list.extend(lane_summary)
 
     context = {
@@ -246,7 +249,10 @@ def _summary_stats(flowcell_id, lane_id):
                 eland_summary = ResultLane(lane_id=lane_id, end=end)
             # add information to lane_summary
             eland_summary.flowcell_id = flowcell_id
-            eland_summary.clusters = gerald_summary[end][lane_id].cluster
+            if len(gerald_summary) > end and gerald_summary[end].has_key(lane_id):
+                eland_summary.clusters = gerald_summary[end][lane_id].cluster
+            else:
+                eland_summary.clusters = 'n/a'
             eland_summary.cycle_width = cycle_width
             if hasattr(eland_summary, 'genome_map'):
                 eland_summary.summarized_reads = runfolder.summarize_mapped_reads( 
@@ -255,8 +261,9 @@ def _summary_stats(flowcell_id, lane_id):
 
             # 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)
+            #pm_field = 'lane_%d_pM' % (lane_id)
+            lane_obj = flowcell.lane_set.get(lane_number=lane_id)
+            eland_summary.successful_pm = lane_obj.pM
 
             summary_list.append(eland_summary)
 
@@ -363,7 +370,7 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
     if len(storage_id_list) == 0:
         storage_ids = None
     else:
-        storage_ids = ', '.join(storage_id_list)
+        storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
 
     results = []
     for cycle in cur_fc.keys():