Provide a dummy eland result lane class if there's nothing appropriate in the xml

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

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index e64ce6748660c8034b4e8589399fed138a1a6d8b..3fbfe792fd9224a5c68f78d4abaf7f1ac91b999f 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
@@ -14,12 +16,17 @@ from django.http import HttpResponse, HttpResponseRedirect
 from django.shortcuts import render_to_response
 from django.template import RequestContext
 from django.template.loader import get_template
+from django.contrib.auth.decorators import login_required
 
 import StringIO
 import logging
 import os
 
 LANE_LIST = [1,2,3,4,5,6,7,8]
+SAMPLES_CONTEXT_DEFAULTS = {
+    'app_name': 'Flowcell/Library Tracker',
+    'bcmagic': BarcodeMagicForm()
+}
 
 def create_library_context(cl):
     """
@@ -59,7 +66,17 @@ def library(request):
     context.update(create_library_context(fcl))
     t = get_template('samples/library_index.html')
     c = RequestContext(request, context)
-    return HttpResponse( t.render(c) )
+    
+    app_context = {
+        'page_name': 'Library Index',
+        'east_region_config_div': 'changelist-filter',
+        'body': t.render(c)
+    }
+    app_context.update(SAMPLES_CONTEXT_DEFAULTS)
+    
+    app_t = get_template('flowcell_libraries_app.html')
+    app_c = RequestContext(request, app_context)
+    return HttpResponse( app_t.render(app_c) )
 
 def library_to_flowcells(request, lib_id):
     """
@@ -91,12 +108,17 @@ def library_to_flowcells(request, lib_id):
         eland_results.extend(_make_eland_results(fc, lane, 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):
@@ -217,7 +239,11 @@ 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
@@ -320,17 +346,19 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
     if cur_fc is None:
       return []
 
+    flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
     # Loop throw storage devices if a result has been archived
     storage_id_list = []
-    for lts in cur_fc.longtermstorage_set.all():
-        for sd in lts.storage_devices.all():
-            # Use barcode_id if it exists
-            if sd.barcode_id is not None and sd.barcode_id != '':
-                storage_id_list.append(sd.barcode_id)
-            # Otherwise use UUID
-            else:
-                storage_id_list.append(sd.uuid)
-    
+    if cur_fc is not None:
+        for lts in flowcell.longtermstorage_set.all():
+            for sd in lts.storage_devices.all():
+                # Use barcode_id if it exists
+                if sd.barcode_id is not None and sd.barcode_id != '':
+                    storage_id_list.append(sd.barcode_id)
+                # Otherwise use UUID
+                else:
+                    storage_id_list.append(sd.uuid)
+        
     # Formatting for template use
     if len(storage_id_list) == 0:
         storage_ids = None
@@ -409,3 +437,17 @@ def library_id_to_admin_url(request, lib_id):
     lib = Library.objects.get(library_id=lib_id)
     return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
 
+@login_required
+def user_profile(request):
+    """
+    Information about the user
+    """
+    context = {
+                'page_name': 'User Profile',
+                'media': '',
+                #'bcmagic': BarcodeMagicForm(),
+                #'select': 'settings',
+            }
+    context.update(SAMPLES_CONTEXT_DEFAULTS)
+    return render_to_response('registration/profile.html', context,
+                              context_instance=RequestContext(request))