gaworkflow/frontend/exp_track/main.py

   1 # some core functions of analysis manager module
   2 from django.http import HttpResponse
   3 from datetime import datetime
   4 from string import *
   5 import re
   6 from gaworkflow.frontend import settings
   7 from gaworkflow.frontend.analys_track.models import Task, Project
   8 from django.core.exceptions import ObjectDoesNotExist
   9
  10 def updStatus(request):
  11     ClIP = request.META['REMOTE_ADDR']
  12     #Check client access permission
  13     granted = False
  14     if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)):  granted = True
  15     if not granted: return HttpResponse("access denied.")
  16
  17     output=''
  18     taskid=-1;
  19     # Check required param
  20     if request.has_key('taskid'): taskid = request['taskid']
  21     else:  return HttpResponse('missing param task id')
  22
  23     try:
  24       rec = Task.objects.get(id=taskid)
  25       mytimestamp = datetime.now().__str__()
  26       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  27       if request.has_key('msg'):
  28         rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
  29       else :
  30         rec.task_status = "Registered ("+mytimestamp+")"
  31        rec.save()
  32       output = "Hello "+ALLOWED_ANALYS_IPS[ClIP]+". Updated status for task "+taskid
  33     except ObjectDoesNotExist:
  34       output = "entry not found: taskid="
  35
  36     return HttpResponse(output)
  37
  38
  39 def getProjects(request):
  40     ClIP = request.META['REMOTE_ADDR']
  41     #Check client access permission
  42     granted = False
  43     if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)):  granted = True
  44     if not granted: return HttpResponse("access denied.")
  45
  46     outputfile = ''
  47
  48     All=False
  49     if (request.has_key('mode')):
  50       if request['mode']=='all':
  51         All=True
  52
  53     try:
  54       if(All):
  55         rec = Project.objects.all().distinct()
  56       else:
  57         rec = Project.objects.filter(tasks__task_status__exact='defined').distinct()
  58
  59       outputfile = '<?xml version="1.0" ?>'
  60       outputfile += '\n<Projects Client="'+ALLOWED_ANALYS_IPS[ClIP]+'">'
  61       for p in rec:
  62         outputfile += '\n'
  63         outputfile += '\n<Project ProjectId="'+p.project_id+'" Name="'+p.project_name+'">'
  64         prj_tasks = p.tasks.all()
  65         for t in prj_tasks:
  66           outputfile += '\n'
  67           if (t.apply_calc == 'QuEST' or t.apply_calc == 'WingPeaks'  or t.apply_calc == 'MACS'):
  68             outputfile += '\n<PeakCalling TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Caller="'+t.apply_calc+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  69             outputfile += '\n<Signal Library="'+t.subject1.library_id+'"/>'
  70             outputfile += '\n<Background Library="'+t.subject2.library_id+'"/>'
  71             outputfile += '\n</PeakCalling>'
  72
  73           if (t.apply_calc == 'ProfileReads' or t.apply_calc == 'qPCR'):
  74             outputfile += '\n<'+t.apply_calc+' TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'" Library="'+t.subject1.library_id+'"/>'
  75
  76           if (t.apply_calc == 'CompareLibs'):
  77             outputfile += '\n<CompareLibraries TaskId="'+t.id.__str__()+'" TF="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  78             outputfile += '\n<Library Library="'+t.subject1.library_id+'"/>'
  79             outputfile += '\n<Library Library="'+t.subject2.library_id+'"/>'
  80             outputfile += '\n</CompareLibraries>'
  81
  82           #if (t.apply_calc == 'ComparePeakCalls'):
  83           # <ComparePeakCalls Genome="hg18" Caller1="QuEST" Set1="A549 GR Dex ChIP" Caller2="QuEST" Set2="A549 GR EtOH ChIP" />
  84           # outputfile += '\n<ComparePeakCalls TaskId='+t.id.__str__()+' Genome="'+t.subject1.library_species.use_genome_build+'" Caller1="'+t.pcaller1+'" Caller1="'+t.pcaller1+'" Caller2="'+t.pcaller2+'" Set1="'+t.set1+'" Set1="'+t.set2+'"/>'
  85           # TO DO: Define these new fields in Task: PCaller1 (QuEST,WingPeaks), PCaller2, Set1(FK to self), Set2 (FK..) ALL NULL=TRUE
  86
  87         outputfile += '\n</Project>'
  88       outputfile += '\n</Projects>'
  89     except ObjectDoesNotExist:
  90       outputfile = "<?xml version='1.0' ?><Projects></Projects>"
  91
  92     return HttpResponse(outputfile)