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 c72a8335c2677285542c3b894426df49994e1bef..d79d0b83976adc49dff287850e1a71a80796d4d0 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -3,8 +3,10 @@ from htsworkflow.frontend.experiments.models import FlowCell
 from htsworkflow.frontend.samples.changelist import ChangeList
 from htsworkflow.frontend.samples.models import Library
 from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
+from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.eland import ResultLane
 from htsworkflow.frontend import settings
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
@@ -22,7 +24,8 @@ import os
 
 LANE_LIST = [1,2,3,4,5,6,7,8]
 SAMPLES_CONTEXT_DEFAULTS = {
-    'app_name': 'Flowcell/Library Tracker'
+    'app_name': 'Flowcell/Library Tracker',
+    'bcmagic': BarcodeMagicForm()
 }
 
 def create_library_context(cl):
@@ -41,9 +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)
@@ -66,6 +70,7 @@ def library(request):
     
     app_context = {
         'page_name': 'Library Index',
+        'east_region_config_div': 'changelist-filter',
         'body': t.render(c)
     }
     app_context.update(SAMPLES_CONTEXT_DEFAULTS)
@@ -86,30 +91,37 @@ 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 = {
+        'page_name': 'Library Details',
+        'lib': lib,
+        'eland_results': eland_results,
+        'lane_summary_list': lane_summary_list,
+    }
+    context.update(SAMPLES_CONTEXT_DEFAULTS)
+
     return render_to_response(
         'samples/library_detail.html',
-        {'lib': lib,
-         'eland_results': eland_results,
-         'lane_summary_list': lane_summary_list,
-        },
+        context,
         context_instance = RequestContext(request))
 
 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
@@ -230,10 +242,17 @@ def _summary_stats(flowcell_id, lane_id):
         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]
+            end_summary = run.gerald.eland_results.results[end]
+            if end_summary.has_key(lane_id):
+                eland_summary = run.gerald.eland_results.results[end][lane_id]
+            else:
+                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( 
@@ -242,8 +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)
 
@@ -350,7 +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():
@@ -437,4 +457,4 @@ def user_profile(request):
             }
     context.update(SAMPLES_CONTEXT_DEFAULTS)
     return render_to_response('registration/profile.html', context,
-                              context_instance=RequestContext(request))
\ No newline at end of file
+                              context_instance=RequestContext(request))