Supprose IVC plot table rows if we don't have data for a lane

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

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
index a2d14bb3823f487bf5719b1be0b05c1b33621af0..a1775d4cb489dd18926e0e1e56e655a3edb88c2a 100755 (executable)
--- a/htsworkflow/frontend/experiments/views.py
+++ b/htsworkflow/frontend/experiments/views.py
@@ -1,10 +1,25 @@
 # Create your views here.
+from datetime import datetime
+import os
+
 #from django.template import Context, loader
 #shortcut to the above modules
-from django.shortcuts import render_to_response, get_object_or_404
-from htsworkflow.frontend.experiments.models import *
-from django.http import HttpResponse
+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
+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 DataRun, DataFile, FlowCell
+from htsworkflow.frontend.experiments.experiments import \
+     estimateFlowcellDuration, \
+     estimateFlowcellTimeRemaining, \
+     roundToDays, \
+     getUsersForFlowcell, \
+     makeEmailLaneMap
 
 def index(request):
     all_runs = DataRun.objects.order_by('-run_start_time')
@@ -32,3 +47,130 @@ def makeFCSheet(request,fcid):
     pass
   lanes = ['1','2','3','4','5','6','7','8']
   return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
+
+
+@user_passes_test(lambda u: u.is_staff)
+def startedEmail(request, pk):
+    """
+    Create the we have started processing your samples email
+    """
+    fc = get_object_or_404(FlowCell, id=pk)
+
+    send = request.REQUEST.get('send',False)
+    if send in ('1', 'on', 'True', 'true', True):
+        send = True
+    else:
+        send = False
+
+    bcc_managers = request.REQUEST.get('bcc', False)
+    if bcc_managers in ('on', '1', 'True', 'true'):
+        bcc_managers = True
+    else:
+        bcc_managers = False
+
+    email_lane = makeEmailLaneMap(fc)
+    flowcell_users = getUsersForFlowcell(fc)
+    estimate = estimateFlowcellTimeRemaining(fc)
+    estimate_low, estimate_high = roundToDays(estimate)
+    email_verify = get_template('experiments/email_preview.html')
+    email_template = get_template('experiments/started_email.txt')
+    sender = settings.NOTIFICATION_SENDER
+
+    warnings = []
+    emails = []
+
+    emailless_users = []
+    for user in flowcell_users:
+        # provide warning
+        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
+        context = RequestContext(request,
+                                 {u'flowcell': fc,
+                                  u'lanes': email_lane[user_email],
+                                  u'runfolder': 'blank',
+                                  u'finish_low': estimate_low,
+                                  u'finish_high': estimate_high,
+                                  u'now': datetime.now(),        
+                                  })
+
+        # build view
+        subject = "Flowcell %s" % ( fc.flowcell_id )
+        body = email_template.render(context)
+
+        if send:
+            email = EmailMessage(subject, body, sender, to=[user_email])
+            if bcc_managers:
+                email.bcc = settings.MANAGERS
+            email.bcc.append(settings.NOTIFICATION_BCC)
+            email.send()
+
+        emails.append((user_email, subject, body, sending))
+
+    verify_context = RequestContext(
+        request,
+        { 'emails': emails,
+          'flowcell': fc,
+          'from': sender,
+          'send': send,
+          'site_managers': settings.MANAGERS,
+          'title': fc.flowcell_id,
+          '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__startswith=flowcell_id)
+    fc.update_data_runs()
+
+    context = RequestContext(request,
+                             {'flowcell': fc})
+    
+    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__startswith=flowcell_id)
+    lane = get_object_or_404(fc.lane_set, lane_number=lane_number)
+    
+    fc.update_data_runs()
+
+    dataruns = []
+    for run in fc.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,
+                              '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
+      
+