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 \
  17      DataRun, \
  18      DataFile, \
  19      FlowCell, \
  20      Lane
  21 from htsworkflow.frontend.experiments.experiments import \
  22      estimateFlowcellDuration, \
  23      estimateFlowcellTimeRemaining, \
  24      roundToDays, \
  25      getUsersForFlowcell, \
  26      makeEmailLaneMap
  27
  28 def index(request):
  29     all_runs = DataRun.objects.order_by('-run_start_time')
  30     #t = loader.get_template('experiments/index.html')
  31     #c = Context({
  32     #    'data_run_list': all_runs,
  33     #})
  34     #return HttpResponse(t.render(c))
  35     # shortcut to the above module usage
  36     return render_to_response('experiments/index.html',{'data_run_list': all_runs})
  37
  38 def detail(request, run_folder):
  39     html_str = '<h2>Exp Track Details Page</h2>'
  40     html_str += 'Run Folder: '+run_folder
  41     r = get_object_or_404(DataRun,run_folder=run_folder)
  42     return render_to_response('experiments/detail.html',{'run_f': r})
  43
  44 def makeFCSheet(request,fcid):
  45   # get Flowcell by input fcid
  46   # ...
  47   rec = None
  48   try:
  49     rec = FlowCell.objects.get(flowcell_id=fcid)
  50   except ObjectDoesNotExist:
  51     pass
  52   lanes = ['1','2','3','4','5','6','7','8']
  53   return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
  54
  55
  56 @user_passes_test(lambda u: u.is_staff)
  57 def startedEmail(request, pk):
  58     """
  59     Create the we have started processing your samples email
  60     """
  61     fc = get_object_or_404(FlowCell, id=pk)
  62
  63     send = request.REQUEST.get('send',False)
  64     if send in ('1', 'on', 'True', 'true', True):
  65         send = True
  66     else:
  67         send = False
  68
  69     bcc_managers = request.REQUEST.get('bcc', False)
  70     if bcc_managers in ('on', '1', 'True', 'true'):
  71         bcc_managers = True
  72     else:
  73         bcc_managers = False
  74
  75     email_lane = makeEmailLaneMap(fc)
  76     flowcell_users = getUsersForFlowcell(fc)
  77     estimate = estimateFlowcellTimeRemaining(fc)
  78     estimate_low, estimate_high = roundToDays(estimate)
  79     email_verify = get_template('experiments/email_preview.html')
  80     email_template = get_template('experiments/started_email.txt')
  81     sender = settings.NOTIFICATION_SENDER
  82
  83     warnings = []
  84     emails = []
  85
  86     emailless_users = []
  87     for user in flowcell_users:
  88         # provide warning
  89         if user.email is None or len(user.email) == 0:
  90             warnings.append((user.admin_url(), user.username))
  91     user=None
  92
  93     for user_email in email_lane.keys():
  94         sending = ""
  95         # build body
  96         context = RequestContext(request,
  97                                  {u'flowcell': fc,
  98                                   u'lanes': email_lane[user_email],
  99                                   u'runfolder': 'blank',
 100                                   u'finish_low': estimate_low,
 101                                   u'finish_high': estimate_high,
 102                                   u'now': datetime.now(),
 103                                   })
 104
 105         # build view
 106         subject = "Flowcell %s" % ( fc.flowcell_id )
 107         body = email_template.render(context)
 108
 109         if send:
 110             email = EmailMessage(subject, body, sender, to=[user_email])
 111             if bcc_managers:
 112                 email.bcc = settings.MANAGERS
 113             email.bcc.append(settings.NOTIFICATION_BCC)
 114             email.send()
 115
 116         emails.append((user_email, subject, body, sending))
 117
 118     verify_context = RequestContext(
 119         request,
 120         { 'emails': emails,
 121           'flowcell': fc,
 122           'from': sender,
 123           'send': send,
 124           'site_managers': settings.MANAGERS,
 125           'title': fc.flowcell_id,
 126           'warnings': warnings,
 127         })
 128     return HttpResponse(email_verify.render(verify_context))
 129
 130 def finishedEmail(request, pk):
 131     """
 132     """
 133     return HttpResponse("I've got nothing.")
 134
 135
 136 def flowcell_detail(request, flowcell_id, lane_number=None):
 137     fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
 138     fc.update_data_runs()
 139
 140
 141     if lane_number is not None:
 142         lanes = fc.lane_set.filter(lane_number=lane_number)
 143     else:
 144         lanes = fc.lane_set.all()
 145
 146     context = RequestContext(request,
 147                              {'flowcell': fc,
 148                               'lanes': lanes})
 149
 150     return render_to_response('experiments/flowcell_detail.html',
 151                               context)
 152
 153 def flowcell_lane_detail(request, lane_pk):
 154     lane = get_object_or_404(Lane, id=lane_pk)
 155     lane.flowcell.update_data_runs()
 156
 157     dataruns = []
 158     for run in lane.flowcell.datarun_set.all():
 159         dataruns.append((run, lane.lane_number, run.lane_files()[lane.lane_number]))
 160
 161     context = RequestContext(request,
 162                              {'lib': lane.library,
 163                               'lane': lane,
 164                               'flowcell': lane.flowcell,
 165                               'filtered_dataruns': dataruns})
 166
 167     return render_to_response('experiments/flowcell_lane_detail.html',
 168                               context)
 169
 170 def read_result_file(self, key):
 171     """Return the contents of filename if everything is approved
 172     """
 173     data_file = get_object_or_404(DataFile, random_key = key)
 174
 175     mimetype = 'application/octet-stream'
 176     if data_file.file_type.mimetype is not None:
 177         mimetype = data_file.file_type.mimetype
 178
 179     if os.path.exists(data_file.pathname):
 180         return HttpResponse(open(data_file.pathname,'r'),
 181                             mimetype=mimetype)
 182
 183     raise Http404
 184
 185