Don't throw an error if library.cell_line is None.

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

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index b0a61f42117db2c1758b933041e64f0cb2377cb4..dd474a6506b844da3eaaa7d89807769c2975d3e9 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -2,6 +2,8 @@
 import StringIO
 import logging
 import os
+import sys
+
 try:
     import json
 except ImportError, e:
@@ -17,9 +19,11 @@ 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.conversion import unicode_or_none
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
+
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, HttpResponseRedirect, Http404
 from django.shortcuts import render_to_response
@@ -41,11 +45,11 @@ def create_library_context(cl):
     #for lib in library_items.object_list:
     for lib in cl.result_list:
        summary = {}
-       summary['library_id'] = lib.library_id
+       summary['library_id'] = lib.id
        summary['library_name'] = lib.library_name
        summary['species_name' ] = lib.library_species.scientific_name
        if lib.amplified_from_sample is not None:
-           summary['amplified_from'] = lib.amplified_from_sample.library_id
+           summary['amplified_from'] = lib.amplified_from_sample.id
        else:
            summary['amplified_from'] = ''
        lanes_run = 0
@@ -63,7 +67,7 @@ def library(request):
    # build changelist
     fcl = ChangeList(request, Library,
         list_filter=['affiliations', 'library_species'],
-        search_fields=['library_id', 'library_name', 'amplified_from_sample__library_id'],
+        search_fields=['id', 'library_name', 'amplified_from_sample__id'],
         list_per_page=200,
         queryset=Library.objects.filter(hidden__exact=0)
     )
@@ -90,30 +94,26 @@ def library_to_flowcells(request, lib_id):
     """
     
     try:
-      lib = Library.objects.get(library_id=lib_id)
+      lib = Library.objects.get(id=lib_id)
     except:
       return HttpResponse("Library %s does not exist" % (lib_id))
    
     flowcell_list = []
-    interesting_flowcells = {} # aka flowcells we're looking at
-    #for lane in LANE_LIST:
+    flowcell_run_results = {} # aka flowcells we're looking at
     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)
+        if flowcell_id not in flowcell_run_results:
+            flowcell_run_results[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_number in flowcell_list:
         lane_summary, err_list = _summary_stats(fc, lane_number)
 
-        eland_results.extend(_make_eland_results(fc, lane_number, interesting_flowcells))
+        eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
         lane_summary_list.extend(lane_summary)
 
     context = {
@@ -310,9 +310,9 @@ def _summary_stats_old(flowcell_id, lane):
             summary_list.append("Summary report needs to be updated.")
             logging.error("Exception: " + str(e))
        
-        print "----------------------------------"
-        print "-- DOES NOT SUPPORT PAIRED END ---"
-        print "----------------------------------"
+        print >>sys.stderr, "----------------------------------"
+        print >>sys.stderr, "-- DOES NOT SUPPORT PAIRED END ---"
+        print >>sys.stderr, "----------------------------------"
         lane_results = results.gerald.summary[0][lane]
         lrs = lane_results
         
@@ -382,6 +382,7 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
         result_path = cur_fc[cycle]['eland_results'].get(lane, None)
         result_link = make_result_link(fc_id, cycle, lane, result_path)
         results.append({'flowcell_id': fc_id,
+                        'run_date': flowcell.run_date,
                         'cycle': cycle, 
                         'lane': lane, 
                         'summary_url': make_summary_url(flowcell_id, cycle),
@@ -446,7 +447,7 @@ def _files(flowcell_id, lane):
     return '(' + '|'.join(output) + ')'
 
 def library_id_to_admin_url(request, lib_id):
-    lib = Library.objects.get(library_id=lib_id)
+    lib = Library.objects.get(id=lib_id)
     return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
 
 def library_dict(library_id):
@@ -455,10 +456,16 @@ def library_dict(library_id):
     return None if nothing was found
     """
     try:
-        lib = Library.objects.get(library_id = library_id)
+        lib = Library.objects.get(id = library_id)
     except Library.DoesNotExist, e:
         return None
 
+    #lane_info = lane_information(lib.lane_set)
+    lane_info = []
+    for lane in lib.lane_set.all():
+        lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
+                           'lane_number': lane.lane_number} )
+        
     info = {
         # 'affiliations'?
         # 'aligned_reads': lib.aligned_reads,
@@ -467,12 +474,13 @@ def library_dict(library_id):
         #'antibody_name': lib.antibody_name(), # we have no antibodies.
         'antibody_id': lib.antibody_id,
         'avg_lib_size': lib.avg_lib_size,
-        'cell_line': lib.cell_line.cellline_name,
         'cell_line_id': lib.cell_line_id,
+        'cell_line': unicode_or_none(lib.cell_line),
         'experiment_type': lib.experiment_type.name,
         'experiment_type_id': lib.experiment_type_id,
         'id': lib.id,
-        'library_id': lib.library_id,
+        'lane_set': lane_info,
+        'library_id': lib.id,
         'library_name': lib.library_name,
         'library_species': lib.library_species.scientific_name,
         'library_species_id': lib.library_species_id,
@@ -483,8 +491,8 @@ def library_dict(library_id):
         'notes': lib.notes,
         'replicate': lib.replicate,
         'stopping_point': lib.stopping_point,
-        'successful_pM': lib.successful_pM,
-        'undiluted_concentration': unicode(lib.undiluted_concentration)
+        'successful_pM': unicode_or_none(lib.successful_pM),
+        'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
         }
     if lib.library_type_id is None:
         info['library_type'] = None