email.bcc should be a list, not a nested list.

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

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
old mode 100755 (executable)
new mode 100644 (file)
index 342438d..869ed86
--- 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 +13,12 @@ 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, \
+     Sequencer
 from htsworkflow.frontend.experiments.experiments import \
      estimateFlowcellDuration, \
      estimateFlowcellTimeRemaining, \
@@ -25,10 +32,10 @@ def index(request):
     #c = Context({
     #    'data_run_list': all_runs,
     #})
-    #return HttpResponse(t.render(c)) 
+    #return HttpResponse(t.render(c))
     # shortcut to the above module usage
-    return render_to_response('experiments/index.html',{'data_run_list': all_runs}) 
-    
+    return render_to_response('experiments/index.html',{'data_run_list': all_runs})
+
 def detail(request, run_folder):
     html_str = '<h2>Exp Track Details Page</h2>'
     html_str += 'Run Folder: '+run_folder
@@ -83,7 +90,7 @@ def startedEmail(request, pk):
         if user.email is None or len(user.email) == 0:
             warnings.append((user.admin_url(), user.username))
     user=None
-    
+
     for user_email in email_lane.keys():
         sending = ""
         # build body
@@ -93,7 +100,7 @@ def startedEmail(request, pk):
                                   u'runfolder': 'blank',
                                   u'finish_low': estimate_low,
                                   u'finish_high': estimate_high,
-                                  u'now': datetime.now(),        
+                                  u'now': datetime.now(),
                                   })
 
         # build view
@@ -104,7 +111,7 @@ def startedEmail(request, pk):
             email = EmailMessage(subject, body, sender, to=[user_email])
             if bcc_managers:
                 email.bcc = settings.MANAGERS
-            email.bcc.append(settings.NOTIFICATION_BCC)
+            email.bcc = settings.NOTIFICATION_BCC
             email.send()
 
         emails.append((user_email, subject, body, sending))
@@ -120,30 +127,69 @@ def startedEmail(request, pk):
           'warnings': warnings,
         })
     return HttpResponse(email_verify.render(verify_context))
-    
+
 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 = []
+    lane.flowcell.update_data_runs()
+    for run in lane.flowcell.datarun_set.all():
+        files = run.lane_files().get(lane.lane_number, None)
+        dataruns.append((run,
+                         lane.lane_number,
+                         files))
 
     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
+
+
+def sequencer(request, sequencer_id):
+    sequencer = get_object_or_404(Sequencer, id=sequencer_id)
+    context = RequestContext(request,
+                             {'sequencer': sequencer})
+    return render_to_response('experiments/sequencer.html', context)