experiments/views.py

   1 from __future__ import absolute_import, print_function, unicode_literals
   2
   3 # Create your views here.
   4 from datetime import datetime
   5 import os
   6
   7 #from django.template import Context, loader
   8 #shortcut to the above modules
   9 from django.contrib.auth.decorators import user_passes_test
  10 from django.conf import settings
  11 from django.core.exceptions import ObjectDoesNotExist
  12 from django.core.mail import EmailMessage, mail_managers
  13 from django.http import HttpResponse
  14 from django.shortcuts import render_to_response, get_object_or_404
  15 from django.template import RequestContext
  16 from django.template.loader import get_template
  17
  18 from .models import DataRun, DataFile, FlowCell, Lane, Sequencer
  19 from .experiments import estimateFlowcellDuration, estimateFlowcellTimeRemaining, roundToDays, \
  20      getUsersForFlowcell, \
  21      makeEmailLaneMap
  22 from samples.changelist import HTSChangeList
  23 from samples.models import HTSUser
  24
  25
  26 def index(request):
  27     all_runs = DataRun.objects.order_by('-run_start_time')
  28     return render_to_response('experiments/index.html',{'data_run_list': all_runs})
  29
  30 def detail(request, run_folder):
  31     html_str = '<h2>Exp Track Details Page</h2>'
  32     html_str += 'Run Folder: '+run_folder
  33     r = get_object_or_404(DataRun,run_folder=run_folder)
  34     return render_to_response('experiments/detail.html',{'run_f': r})
  35
  36 def makeFCSheet(request,fcid):
  37   # get Flowcell by input fcid
  38   # ...
  39   rec = None
  40   try:
  41     rec = FlowCell.objects.get(flowcell_id=fcid)
  42   except ObjectDoesNotExist:
  43     pass
  44   lanes = ['1','2','3','4','5','6','7','8']
  45   return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
  46
  47
  48 @user_passes_test(lambda u: u.is_staff)
  49 def startedEmail(request, pk):
  50     """
  51     Create the we have started processing your samples email
  52     """
  53     fc = get_object_or_404(FlowCell, id=pk)
  54
  55     send = request.REQUEST.get('send',False)
  56     if send in ('1', 'on', 'True', 'true', True):
  57         send = True
  58     else:
  59         send = False
  60
  61     bcc_managers = request.REQUEST.get('bcc', False)
  62     if bcc_managers in ('on', '1', 'True', 'true'):
  63         bcc_managers = True
  64     else:
  65         bcc_managers = False
  66
  67     email_lane = makeEmailLaneMap(fc)
  68     flowcell_users = getUsersForFlowcell(fc)
  69     estimate = estimateFlowcellTimeRemaining(fc)
  70     estimate_low, estimate_high = roundToDays(estimate)
  71     email_verify = get_template('experiments/email_preview.html')
  72     email_template = get_template('experiments/started_email.txt')
  73     sender = settings.NOTIFICATION_SENDER
  74
  75     warnings = []
  76     emails = []
  77
  78     emailless_users = []
  79     for user in flowcell_users:
  80         # provide warning
  81         if user.email is None or len(user.email) == 0:
  82             warnings.append((user.admin_url(), user.username))
  83     user=None
  84
  85     for user_email in email_lane.keys():
  86         sending = ""
  87         # build body
  88         context = RequestContext(request,
  89                                  {u'flowcell': fc,
  90                                   u'lanes': email_lane[user_email],
  91                                   u'runfolder': 'blank',
  92                                   u'finish_low': estimate_low,
  93                                   u'finish_high': estimate_high,
  94                                   u'now': datetime.now(),
  95                                   })
  96
  97         # build view
  98         subject = "Flowcell %s" % ( fc.flowcell_id )
  99         body = email_template.render(context)
 100
 101         if send:
 102             email = EmailMessage(subject, body, sender, to=[user_email])
 103             notified = set()
 104             if bcc_managers:
 105                 for manager in settings.MANAGERS:
 106                     if len(manager) > 0:
 107                         notified.add(manager)
 108             for user in settings.NOTIFICATION_BCC:
 109                 if len(user) > 0:
 110                     notified.add(user)
 111             email.bcc = list(notified)
 112             email.send()
 113
 114         emails.append((user_email, subject, body, sending))
 115
 116     verify_context = RequestContext(
 117         request,
 118         { 'emails': emails,
 119           'flowcell': fc,
 120           'from': sender,
 121           'send': send,
 122           'site_managers': settings.MANAGERS,
 123           'title': fc.flowcell_id,
 124           'warnings': warnings,
 125         })
 126     return HttpResponse(email_verify.render(verify_context))
 127
 128 def finishedEmail(request, pk):
 129     """
 130     """
 131     return HttpResponse("I've got nothing.")
 132
 133
 134 def flowcell_detail(request, flowcell_id, lane_number=None):
 135     fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
 136     fc.update_data_runs()
 137
 138
 139     if lane_number is not None:
 140         lanes = fc.lane_set.filter(lane_number=lane_number)
 141     else:
 142         lanes = fc.lane_set.all()
 143
 144     context = RequestContext(request,
 145                              {'flowcell': fc,
 146                               'lanes': lanes})
 147
 148     return render_to_response('experiments/flowcell_detail.html',
 149                               context)
 150
 151 def flowcell_lane_detail(request, lane_pk):
 152     lane = get_object_or_404(Lane, id=lane_pk)
 153     lane.flowcell.update_data_runs()
 154
 155     dataruns = []
 156     lane.flowcell.update_data_runs()
 157     for run in lane.flowcell.datarun_set.all():
 158         files = run.lane_files().get(lane.lane_number, None)
 159         dataruns.append((run,
 160                          lane.lane_number,
 161                          files))
 162
 163     context = RequestContext(request,
 164                              {'lib': lane.library,
 165                               'lane': lane,
 166                               'flowcell': lane.flowcell,
 167                               'filtered_dataruns': dataruns})
 168
 169     return render_to_response('experiments/flowcell_lane_detail.html',
 170                               context)
 171
 172 def read_result_file(self, key):
 173     """Return the contents of filename if everything is approved
 174     """
 175     data_file = get_object_or_404(DataFile, random_key = key)
 176
 177     content_type = 'application/octet-stream'
 178     if data_file.file_type.mimetype is not None:
 179         content_type = data_file.file_type.mimetype
 180
 181     if os.path.exists(data_file.pathname):
 182         return HttpResponse(open(data_file.pathname,'rb'),
 183                             content_type=content_type)
 184
 185     raise Http404
 186
 187
 188 def sequencer(request, sequencer_id):
 189     sequencer = get_object_or_404(Sequencer, id=sequencer_id)
 190     context = RequestContext(request,
 191                              {'sequencer': sequencer})
 192     return render_to_response('experiments/sequencer.html', context)
 193
 194
 195 def lanes_for(request, username=None):
 196     """
 197     Generate a report of recent activity for a user
 198     """
 199     query = {}
 200     if username is not None:
 201         try:
 202             user = HTSUser.objects.get(username=username)
 203             query.update({'library__affiliations__users__id': user.id})
 204         except HTSUser.DoesNotExist as e:
 205             raise Http404('User not found')
 206
 207     fcl = HTSChangeList(request, Lane,
 208                         list_filter=['library__affiliations',
 209                                      'library__library_species'],
 210                         search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
 211                         list_per_page=200,
 212                         model_admin=LaneOptions(Lane, None),
 213                         extra_filters=query
 214                         )
 215
 216     context = {'lanes': fcl, 'title': 'Lane Index'}
 217
 218     return render_to_response(
 219         'samples/lanes_for.html',
 220         context,
 221         context_instance=RequestContext(request)
 222     )