htsworkflow/frontend/experiments/views.py

   1 # Create your views here.
   2 from datetime import datetime
   3 import os
   4
   5 #from django.template import Context, loader
   6 #shortcut to the above modules
   7 from django.contrib.auth.decorators import user_passes_test
   8 from django.conf import settings
   9 from django.core.exceptions import ObjectDoesNotExist
  10 from django.core.mail import EmailMessage, mail_managers
  11 from django.http import HttpResponse
  12 from django.shortcuts import render_to_response, get_object_or_404
  13 from django.template import RequestContext
  14 from django.template.loader import get_template
  15
  16 from htsworkflow.frontend.experiments.models import DataRun, DataFile, FlowCell
  17 from htsworkflow.frontend.experiments.experiments import \
  18      estimateFlowcellDuration, \
  19      estimateFlowcellTimeRemaining, \
  20      roundToDays, \
  21      getUsersForFlowcell, \
  22      makeEmailLaneMap
  23
  24 def index(request):
  25     all_runs = DataRun.objects.order_by('-run_start_time')
  26     #t = loader.get_template('experiments/index.html')
  27     #c = Context({
  28     #    'data_run_list': all_runs,
  29     #})
  30     #return HttpResponse(t.render(c))
  31     # shortcut to the above module usage
  32     return render_to_response('experiments/index.html',{'data_run_list': all_runs})
  33
  34 def detail(request, run_folder):
  35     html_str = '<h2>Exp Track Details Page</h2>'
  36     html_str += 'Run Folder: '+run_folder
  37     r = get_object_or_404(DataRun,run_folder=run_folder)
  38     return render_to_response('experiments/detail.html',{'run_f': r})
  39
  40 def makeFCSheet(request,fcid):
  41   # get Flowcell by input fcid
  42   # ...
  43   rec = None
  44   try:
  45     rec = FlowCell.objects.get(flowcell_id=fcid)
  46   except ObjectDoesNotExist:
  47     pass
  48   lanes = ['1','2','3','4','5','6','7','8']
  49   return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
  50
  51
  52 @user_passes_test(lambda u: u.is_staff)
  53 def startedEmail(request, pk):
  54     """
  55     Create the we have started processing your samples email
  56     """
  57     fc = get_object_or_404(FlowCell, id=pk)
  58
  59     send = request.REQUEST.get('send',False)
  60     if send in ('1', 'on', 'True', 'true', True):
  61         send = True
  62     else:
  63         send = False
  64
  65     bcc_managers = request.REQUEST.get('bcc', False)
  66     if bcc_managers in ('on', '1', 'True', 'true'):
  67         bcc_managers = True
  68     else:
  69         bcc_managers = False
  70
  71     email_lane = makeEmailLaneMap(fc)
  72     flowcell_users = getUsersForFlowcell(fc)
  73     estimate = estimateFlowcellTimeRemaining(fc)
  74     estimate_low, estimate_high = roundToDays(estimate)
  75     email_verify = get_template('experiments/email_preview.html')
  76     email_template = get_template('experiments/started_email.txt')
  77     sender = settings.NOTIFICATION_SENDER
  78
  79     warnings = []
  80     emails = []
  81
  82     emailless_users = []
  83     for user in flowcell_users:
  84         # provide warning
  85         if user.email is None or len(user.email) == 0:
  86             warnings.append((user.admin_url(), user.username))
  87     user=None
  88
  89     for user_email in email_lane.keys():
  90         sending = ""
  91         # build body
  92         context = RequestContext(request,
  93                                  {u'flowcell': fc,
  94                                   u'lanes': email_lane[user_email],
  95                                   u'runfolder': 'blank',
  96                                   u'finish_low': estimate_low,
  97                                   u'finish_high': estimate_high,
  98                                   u'now': datetime.now(),
  99                                   })
 100
 101         # build view
 102         subject = "Flowcell %s" % ( fc.flowcell_id )
 103         body = email_template.render(context)
 104
 105         if send:
 106             email = EmailMessage(subject, body, sender, to=[user_email])
 107             if bcc_managers:
 108                 email.bcc = settings.MANAGERS
 109             email.bcc.append(settings.NOTIFICATION_BCC)
 110             email.send()
 111
 112         emails.append((user_email, subject, body, sending))
 113
 114     verify_context = RequestContext(
 115         request,
 116         { 'emails': emails,
 117           'flowcell': fc,
 118           'from': sender,
 119           'send': send,
 120           'site_managers': settings.MANAGERS,
 121           'title': fc.flowcell_id,
 122           'warnings': warnings,
 123         })
 124     return HttpResponse(email_verify.render(verify_context))
 125
 126 def finishedEmail(request, pk):
 127     """
 128     """
 129     return HttpResponse("I've got nothing.")
 130
 131
 132 def flowcell_detail(request, flowcell_id):
 133     fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
 134     fc.update_data_runs()
 135
 136     context = RequestContext(request,
 137                              {'flowcell': fc})
 138
 139     return render_to_response('experiments/flowcell_detail.html',
 140                               context)
 141
 142 def flowcell_lane_detail(request, flowcell_id, lane_number):
 143     fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
 144     lane = get_object_or_404(fc.lane_set, lane_number=lane_number)
 145
 146     fc.update_data_runs()
 147
 148     context = RequestContext(request,
 149                              {'lib': lane.library,
 150                               'lane': lane,
 151                               'flowcell': fc})
 152
 153     return render_to_response('experiments/flowcell_lane_detail.html',
 154                               context)
 155
 156 def read_result_file(self, key):
 157     """Return the contents of filename if everything is approved
 158     """
 159     data_file = get_object_or_404(DataFile, random_key = key)
 160
 161     mimetype = 'application/octet-stream'
 162     if data_file.file_type.mimetype is not None:
 163         mimetype = data_file.file_type.mimetype
 164
 165     if os.path.exists(data_file.pathname):
 166         return HttpResponse(open(data_file.pathname,'r'),
 167                             mimetype=mimetype)
 168
 169     raise Http404
 170
 171