htsworkflow/frontend/analysis/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 htsworkflow.frontend import settings
   7 from htsworkflow.frontend.analysis.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 "+settings.ALLOWED_ANALYS_IPS[ClIP]+". Updated status for task "+taskid
  33     except ObjectDoesNotExist:
  34       output = "entry not found: taskid="+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="'+settings.ALLOWED_ANALYS_IPS[ClIP]+'">'
  61       for p in rec:
  62         outputfile += '\n'
  63         outputfile += '\n<Project ProjectId="'+p.id.__str__()+'" 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             if t.subject1:
  70               outputfile += '\n<Signal Library="'+t.subject1.id+'"/>'
  71               if t.subject2:
  72                 outputfile += '\n<Background Library="'+t.subject2.id+'"/>'
  73               else:
  74                 outputfile += '\n<Err>Background Library Missing</Err>'
  75             else:
  76               outputfile += '\n<Err>Signal Library Missing</Err>'
  77             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
  78             outputfile += '\n</PeakCalling>'
  79
  80           if (t.apply_calc == 'Methylseq'):
  81             outputfile += '\n<Methylseq TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  82             if t.subject1:
  83               outputfile += '\n<Hpa2 Library="'+t.subject1.id+'"/>'
  84               if t.subject2:
  85                 outputfile += '\n<Msp1 Library="'+t.subject2.id+'"/>'
  86               else:
  87                 outputfile += '\n<Err>Msp1 Library Missing</Err>'
  88             else:
  89               outputfile += '\n<Err>Hpa2 Library Missing</Err>'
  90             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
  91             outputfile += '\n</Methylseq>'
  92
  93           if (t.apply_calc == 'ProfileReads' or t.apply_calc == 'qPCR'):
  94             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+'"/>'
  95
  96           if (t.apply_calc == 'CompareLibs'):
  97             outputfile += '\n<CompareLibraries TaskId="'+t.id.__str__()+'" TF="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
  98             if t.subject1:
  99               outputfile += '\n<Library Library="'+t.subject1.id+'"/>'
 100             else:
 101               outputfile += '\n<Err>Library Missing</Err>'
 102             if t.subject2:
 103               outputfile += '\n<Library Library="'+t.subject2.id+'"/>'
 104             else:
 105               outputfile += '\n<Err>Library Missing</Err>'
 106             outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
 107             outputfile += '\n</CompareLibraries>'
 108
 109           #if (t.apply_calc == 'ComparePeakCalls'):
 110           # <ComparePeakCalls Genome="hg18" Caller1="QuEST" Set1="A549 GR Dex ChIP" Caller2="QuEST" Set2="A549 GR EtOH ChIP" />
 111           # 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+'"/>'
 112           # TO DO: Define these new fields in Task: PCaller1 (QuEST,WingPeaks), PCaller2, Set1(FK to self), Set2 (FK..) ALL NULL=TRUE
 113         outputfile += '\n</Project>'
 114       outputfile += '\n</Projects>'
 115     except ObjectDoesNotExist:
 116       outputfile = "<?xml version='1.0' ?><Projects></Projects>"
 117
 118     return HttpResponse(outputfile, mimetype='text/plain')