htsworkflow/frontend/analysis/main.py

   1 # some core functions of analysis manager module
   2
   3 from datetime import datetime
   4 from string import *
   5 import re
   6
   7 from django.conf import settings
   8 from django.core.exceptions import ObjectDoesNotExist
   9 from django.http import HttpResponse
  10
  11 from htsworkflow.frontend.analysis.models import Task, Project
  12
  13 def updStatus(request):
  14     ClIP = request.META['REMOTE_ADDR']
  15     #Check client access permission
  16     granted = False
  17     if (ClIP in settings.ALLOWED_ANALYS_IPS):  granted = True
  18     if not granted: return HttpResponse("access denied.")
  19
  20     output=''
  21     taskid=-1;
  22     # Check required param
  23     if 'taskid' in request: taskid = request['taskid']
  24     else:  return HttpResponse('missing param task id')
  25
  26     try:
  27       rec = Task.objects.get(id=taskid)
  28       mytimestamp = datetime.now().__str__()
  29       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  30       if 'msg' in request:
  31         rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
  32       else :
  33         rec.task_status = "Registered ("+mytimestamp+")"
  34       rec.save()
  35       output = "Hello "+settings.ALLOWED_ANALYS_IPS[ClIP]+". Updated status for task "+taskid
  36     except ObjectDoesNotExist:
  37       output = "entry not found: taskid="+taskid
  38
  39     return HttpResponse(output)
  40
  41
  42 def getProjects(request):
  43     ClIP = request.META['REMOTE_ADDR']
  44     #Check client access permission
  45     granted = False
  46     if (ClIP in settings.ALLOWED_ANALYS_IPS):  granted = True
  47     if not granted: return HttpResponse("access denied.")
  48
  49     outputfile = ''
  50
  51     All=False
  52     if ('mode' in request):
  53       if request['mode']=='all':
  54         All=True
  55
  56     try:
  57       if(All):
  58         rec = Project.objects.all().distinct()
  59       else:
  60         rec = Project.objects.filter(tasks__task_status__exact='defined').distinct()
  61
  62       outputfile = '<?xml version="1.0" ?>'
  63       outputfile += '\n<Projects Client="'+settings.ALLOWED_ANALYS_IPS[ClIP]+'">'
  64       for p in rec:
  65         outputfile += '\n'
  66         outputfile += '\n<Project ProjectId="'+p.id.__str__()+'" Name="'+p.project_name+'">'
  67         prj_tasks = p.tasks.all()
  68         for t in prj_tasks:
  69           outputfile += '\n'
  70           if (t.apply_calc == 'QuEST' or t.apply_calc == 'WingPeaks' or t.apply_calc == 'MACS'):
  71             outputfile += '\n<PeakCalling TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Caller="'+t.apply_calc+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  72             if t.subject1:
  73               outputfile += '\n<Signal Library="'+t.subject1.id+'"/>'
  74               if t.subject2:
  75                 outputfile += '\n<Background Library="'+t.subject2.id+'"/>'
  76               else:
  77                 outputfile += '\n<Err>Background Library Missing</Err>'
  78             else:
  79               outputfile += '\n<Err>Signal Library Missing</Err>'
  80             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
  81             outputfile += '\n</PeakCalling>'
  82
  83           if (t.apply_calc == 'Methylseq'):
  84             outputfile += '\n<Methylseq TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  85             if t.subject1:
  86               outputfile += '\n<Hpa2 Library="'+t.subject1.id+'"/>'
  87               if t.subject2:
  88                 outputfile += '\n<Msp1 Library="'+t.subject2.id+'"/>'
  89               else:
  90                 outputfile += '\n<Err>Msp1 Library Missing</Err>'
  91             else:
  92               outputfile += '\n<Err>Hpa2 Library Missing</Err>'
  93             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
  94             outputfile += '\n</Methylseq>'
  95
  96           if (t.apply_calc == 'ProfileReads' or t.apply_calc == 'qPCR'):
  97             outputfile += '\n<'+t.apply_calc+' TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'" Library="'+t.subject1.id+'"/>'
  98
  99           if (t.apply_calc == 'CompareLibs'):
 100             outputfile += '\n<CompareLibraries TaskId="'+t.id.__str__()+'" TF="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
 101             if t.subject1:
 102               outputfile += '\n<Library Library="'+t.subject1.id+'"/>'
 103             else:
 104               outputfile += '\n<Err>Library Missing</Err>'
 105             if t.subject2:
 106               outputfile += '\n<Library Library="'+t.subject2.id+'"/>'
 107             else:
 108               outputfile += '\n<Err>Library Missing</Err>'
 109             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
 110             outputfile += '\n</CompareLibraries>'
 111
 112           #if (t.apply_calc == 'ComparePeakCalls'):
 113           # <ComparePeakCalls Genome="hg18" Caller1="QuEST" Set1="A549 GR Dex ChIP" Caller2="QuEST" Set2="A549 GR EtOH ChIP" />
 114           # 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+'"/>'
 115           # TO DO: Define these new fields in Task: PCaller1 (QuEST,WingPeaks), PCaller2, Set1(FK to self), Set2 (FK..) ALL NULL=TRUE
 116         outputfile += '\n</Project>'
 117       outputfile += '\n</Projects>'
 118     except ObjectDoesNotExist:
 119       outputfile = "<?xml version='1.0' ?><Projects></Projects>"
 120
 121     return HttpResponse(outputfile, mimetype='text/plain')