# 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 htswfrontend.fctracker.models import *
-from htswfrontend.exp_track.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, \
+ Lane, \
+ Sequencer
+from htsworkflow.frontend.experiments.experiments import \
+ estimateFlowcellDuration, \
+ estimateFlowcellTimeRemaining, \
+ roundToDays, \
+ getUsersForFlowcell, \
+ makeEmailLaneMap
def index(request):
- all_runs = DataRun.objects.all().order_by('-run_start_time')
- #t = loader.get_template('exptrack/index.html')
- #c = Context({
- # 'data_run_list': all_runs,
- #})
- #return HttpResponse(t.render(c))
- # shortcut to the above module usage
- return render_to_response('exptrack/index.html',{'data_run_list': all_runs})
-
+ all_runs = DataRun.objects.order_by('-run_start_time')
+ return render_to_response('experiments/index.html',{'data_run_list': all_runs})
+
def detail(request, run_folder):
html_str = '<h2>Exp Track Details Page</h2>'
html_str += 'Run Folder: '+run_folder
r = get_object_or_404(DataRun,run_folder=run_folder)
- return render_to_response('exptrack/detail.html',{'run_f': r})
+ return render_to_response('experiments/detail.html',{'run_f': r})
def makeFCSheet(request,fcid):
# get Flowcell by input fcid
except ObjectDoesNotExist:
pass
lanes = ['1','2','3','4','5','6','7','8']
- return render_to_response('exptrack/flowcellSheet.html',{'fc': rec})
-
-def test_Libs(request):
- str = ''
- str += '<table border=1><tr><th>Lib ID</th><th>Current Libaray Name (Free Text)</th><th>Auto-composed Libaray Name (antibody + celline + libid + species + [replicate])</th></tr>'
- allLibs = Library.objects.all()
- #allLibs = Library.objects.filter(antibody__isnull=False)
- for L in allLibs:
- str += '<tr>'
- str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
- str += '<td>'
- str += L.experiment_type+'_'
- if L.cell_line.cellline_name != 'Unknown':
- str += L.cell_line.cellline_name+'_'
-
- try:
- if L.antibody is not None:
- str += L.antibody.nickname + '_'
- except Antibody.DoesNotExist:
- pass
-
- str += 'Rep'+L.replicate.__str__()
- str += '</td></tr>'
-
- str += '</table>'
- return HttpResponse(str)
+ 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])
+ notified = set()
+ if bcc_managers:
+ for manager in settings.MANAGERS:
+ if len(manager) > 0:
+ notified.add(manager)
+ for user in settings.NOTIFICATION_BCC:
+ if len(user) > 0:
+ notified.add(user)
+ email.bcc = list(notified)
+ 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, lane_number=None):
+ fc = get_object_or_404(FlowCell, flowcell_id__startswith=flowcell_id)
+ fc.update_data_runs()
+
+
+ if lane_number is not None:
+ lanes = fc.lane_set.filter(lane_number=lane_number)
+ else:
+ lanes = fc.lane_set.all()
+
+ context = RequestContext(request,
+ {'flowcell': fc,
+ 'lanes': lanes})
+
+ return render_to_response('experiments/flowcell_detail.html',
+ context)
+
+def flowcell_lane_detail(request, lane_pk):
+ lane = get_object_or_404(Lane, id=lane_pk)
+ lane.flowcell.update_data_runs()
+
+ dataruns = []
+ lane.flowcell.update_data_runs()
+ for run in lane.flowcell.datarun_set.all():
+ files = run.lane_files().get(lane.lane_number, None)
+ dataruns.append((run,
+ lane.lane_number,
+ files))
+
+ context = RequestContext(request,
+ {'lib': lane.library,
+ 'lane': lane,
+ 'flowcell': lane.flowcell,
+ '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
+
+
+def sequencer(request, sequencer_id):
+ sequencer = get_object_or_404(Sequencer, id=sequencer_id)
+ context = RequestContext(request,
+ {'sequencer': sequencer})
+ return render_to_response('experiments/sequencer.html', context)
projects / htsworkflow.git / blobdiff