Start supporting multiple libraries per lane, as needed for the HiSeq

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

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
index 342438db356b4140a04c59b3195c2ee3252bb158..08ce6f0e93d0255b72fac17b9ddb39655d081d57 100755 (executable)
--- a/htsworkflow/frontend/experiments/views.py
+++ b/htsworkflow/frontend/experiments/views.py
@@ -1,9 +1,11 @@
 # Create your views here.
 from datetime import datetime
+import os
 
 #from django.template import Context, loader
 #shortcut to the above modules
 from django.contrib.auth.decorators import user_passes_test
+from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
 from django.core.mail import EmailMessage, mail_managers
 from django.http import HttpResponse
@@ -11,7 +13,11 @@ from django.shortcuts import render_to_response, get_object_or_404
 from django.template import RequestContext
 from django.template.loader import get_template
 
-from htsworkflow.frontend.experiments.models import *
+from htsworkflow.frontend.experiments.models import \
+     DataRun, \
+     DataFile, \
+     FlowCell, \
+     Lane
 from htsworkflow.frontend.experiments.experiments import \
      estimateFlowcellDuration, \
      estimateFlowcellTimeRemaining, \
@@ -127,23 +133,53 @@ def finishedEmail(request, pk):
     return HttpResponse("I've got nothing.")
 
 
-def flowcell_detail(request, flowcell_id):
-    fc = get_object_or_404(FlowCell, flowcell_id=flowcell_id)
+def flowcell_detail(request, flowcell_id, lane_number=None):
+    fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
+    fc.update_data_runs()
+
+    
+    if lane_number is not None:
+        lanes = fc.lane_set.filter(lane_number=lane_number)
+    else:
+        lanes = fc.lane_set.all()
 
     context = RequestContext(request,
-                             {'flowcell': fc})
+                             {'flowcell': fc,
+                              'lanes': lanes})
     
     return render_to_response('experiments/flowcell_detail.html',
                               context)
 
-def flowcell_lane_detail(request, flowcell_id, lane_number):
-    fc = get_object_or_404(FlowCell, flowcell_id=flowcell_id)
-    lane = get_object_or_404(fc.lane_set, lane_number=lane_number)
+def flowcell_lane_detail(request, lane_pk):
+    lane = get_object_or_404(Lane, id=lane_pk)
+    lane.flowcell.update_data_runs()
 
+    dataruns = []
+    for run in lane.flowcell.datarun_set.all():
+        dataruns.append((run, lane.lane_number, run.lane_files()[lane.lane_number]))
+        
     context = RequestContext(request,
                              {'lib': lane.library,
                               'lane': lane,
-                              'flowcell': fc})
+                              'flowcell': lane.flowcell,
+                              'filtered_dataruns': dataruns})
     
     return render_to_response('experiments/flowcell_lane_detail.html',
                               context)
+
+def read_result_file(self, key):
+    """Return the contents of filename if everything is approved
+    """
+    data_file = get_object_or_404(DataFile, random_key = key)
+    
+    mimetype = 'application/octet-stream'
+    if data_file.file_type.mimetype is not None:
+        mimetype = data_file.file_type.mimetype
+
+    if os.path.exists(data_file.pathname):
+        return HttpResponse(open(data_file.pathname,'r'),
+                            mimetype=mimetype)
+
+    raise Http404
+      
+