1 from __future__ import absolute_import, print_function, unicode_literals
3 # Create your views here.
4 from datetime import datetime
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, Http404
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
18 from .models import DataRun, DataFile, FlowCell, Lane, Sequencer
19 from rest_framework import viewsets
20 from rest_framework.response import Response
21 from rest_framework.renderers import (TemplateHTMLRenderer,
25 from .admin import LaneOptions
26 from .experiments import estimateFlowcellDuration, estimateFlowcellTimeRemaining, roundToDays, \
27 getUsersForFlowcell, \
29 from .serializers import (
30 ClusterStationSerializer,
34 from samples.changelist import HTSChangeList
35 from samples.models import HTSUser
39 all_runs = DataRun.objects.order_by('-run_start_time')
40 return render_to_response('experiments/index.html',{'data_run_list': all_runs})
42 def detail(request, run_folder):
43 html_str = '<h2>Exp Track Details Page</h2>'
44 html_str += 'Run Folder: '+run_folder
45 r = get_object_or_404(DataRun,run_folder=run_folder)
46 return render_to_response('experiments/detail.html',{'run_f': r})
48 def makeFCSheet(request,fcid):
49 # get Flowcell by input fcid
53 rec = FlowCell.objects.get(flowcell_id=fcid)
54 except ObjectDoesNotExist:
56 lanes = ['1','2','3','4','5','6','7','8']
57 return render_to_response('experiments/flowcellSheet.html',{'fc': rec})
60 @user_passes_test(lambda u: u.is_staff)
61 def startedEmail(request, pk):
63 Create the we have started processing your samples email
65 fc = get_object_or_404(FlowCell, id=pk)
67 send = request.REQUEST.get('send',False)
68 if send in ('1', 'on', 'True', 'true', True):
73 bcc_managers = request.REQUEST.get('bcc', False)
74 if bcc_managers in ('on', '1', 'True', 'true'):
79 email_lane = makeEmailLaneMap(fc)
80 flowcell_users = getUsersForFlowcell(fc)
81 estimate = estimateFlowcellTimeRemaining(fc)
82 estimate_low, estimate_high = roundToDays(estimate)
83 email_verify = get_template('experiments/email_preview.html')
84 email_template = get_template('experiments/started_email.txt')
85 sender = settings.NOTIFICATION_SENDER
91 for user in flowcell_users:
93 if user.email is None or len(user.email) == 0:
94 warnings.append((user.admin_url(), user.username))
97 for user_email in email_lane.keys():
100 context = RequestContext(request,
102 u'lanes': email_lane[user_email],
103 u'runfolder': 'blank',
104 u'finish_low': estimate_low,
105 u'finish_high': estimate_high,
106 u'now': datetime.now(),
110 subject = "Flowcell %s" % ( fc.flowcell_id )
111 body = email_template.render(context)
114 email = EmailMessage(subject, body, sender, to=[user_email])
117 for manager in settings.MANAGERS:
119 notified.add(manager)
120 for user in settings.NOTIFICATION_BCC:
123 email.bcc = list(notified)
126 emails.append((user_email, subject, body, sending))
128 verify_context = RequestContext(
134 'site_managers': settings.MANAGERS,
135 'title': fc.flowcell_id,
136 'warnings': warnings,
138 return HttpResponse(email_verify.render(verify_context))
140 def finishedEmail(request, pk):
143 return HttpResponse("I've got nothing.")
147 class ClusterStationViewSet(viewsets.ReadOnlyModelViewSet):
148 renderer_classes = (TemplateHTMLRenderer,
149 BrowsableAPIRenderer,
151 queryset = ClusterStation.objects.all()
152 serializer_class = ClusterStationSerializer
153 # template_name = 'experiments/cluster_station.html'
155 from pprint import pprint
156 class FlowCellViewSet(viewsets.ReadOnlyModelViewSet):
157 renderer_classes = (TemplateHTMLRenderer,
158 BrowsableAPIRenderer,
160 queryset = FlowCell.objects.all()
161 lookup_field = 'flowcell_id'
162 serializer_class = FlowCellSerializer
163 template_name = 'experiments/flowcell_detail.html'
165 def retrieve(self, request, *args, **kwargs):
166 fc = get_object_or_404(self.queryset, flowcell_id = kwargs['flowcell_id'])
167 context = kwargs.copy()
168 context['request'] = request
169 serializer = FlowCellSerializer(
173 pprint(serializer.data)
174 return Response(serializer.data)
176 #def retrieve(self, request, flowcell_id=None, format=None):
177 # queryset = FlowCell.objects.all()
178 # fc = get_object_or_404(queryset, flowcell_id=flowcell_id)
179 # serializer = FlowCellSerializer(
182 # 'request': request,
190 #def list(self, *args, **kwargs):
191 # template_name = 'experiments/flowcell_index.html'
192 # return super(FlowCellViewSet, self).list(*args, **kwargs)
194 class LaneViewSet(viewsets.ReadOnlyModelViewSet):
195 renderer_classes = (TemplateHTMLRenderer,
196 BrowsableAPIRenderer,
198 queryset = Lane.objects.all()
199 serializer_class = LaneSerializer
200 template_name = 'experiments/flowcell_lane_detail.html'
204 class SequencerViewSet(viewsets.ReadOnlyModelViewSet):
205 renderer_classes = (TemplateHTMLRenderer,
206 BrowsableAPIRenderer,
208 queryset = Sequencer.objects.all()
209 serializer_class = SequencerSerializer
210 template_name = 'experiments/sequencer.html'
212 def flowcell_detail(request, flowcell_id, lane_number=None):
213 fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
214 fc.update_data_runs()
217 if lane_number is not None:
218 lanes = fc.lane_set.filter(lane_number=lane_number)
220 lanes = fc.lane_set.all()
222 context = RequestContext(request,
226 return render_to_response('experiments/flowcell_detail.html',
229 def flowcell_lane_detail(request, lane_pk):
230 lane = get_object_or_404(Lane, id=lane_pk)
231 lane.flowcell.update_data_runs()
234 lane.flowcell.update_data_runs()
235 for run in lane.flowcell.datarun_set.all():
236 files = run.lane_files().get(lane.lane_number, None)
237 dataruns.append((run,
241 context = RequestContext(request,
242 {'lib': lane.library,
244 'flowcell': lane.flowcell,
245 'filtered_dataruns': dataruns})
247 return render_to_response('experiments/flowcell_lane_detail.html',
250 def read_result_file(self, key):
251 """Return the contents of filename if everything is approved
253 data_file = get_object_or_404(DataFile, random_key = key)
255 content_type = 'application/octet-stream'
256 if data_file.file_type.mimetype is not None:
257 content_type = data_file.file_type.mimetype
259 if os.path.exists(data_file.pathname):
260 return HttpResponse(open(data_file.pathname,'rb'),
261 content_type=content_type)
266 def lanes_for(request, username=None):
268 Generate a report of recent activity for a user
271 if username is not None:
273 user = HTSUser.objects.get(username=username)
274 query.update({'library__affiliations__users__id': user.id})
275 except HTSUser.DoesNotExist as e:
276 raise Http404('User not found')
278 fcl = HTSChangeList(request, Lane,
279 list_filter=['library__affiliations',
280 'library__library_species'],
281 search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
283 model_admin=LaneOptions(Lane, None),
287 context = {'lanes': fcl, 'title': 'Lane Index'}
289 return render_to_response(
290 'samples/lanes_for.html',
292 context_instance=RequestContext(request)