htsworkflow/frontend/experiments/experiments.py

   1 # some core functions of the exp tracker module
   2 from django.http import HttpResponse
   3 from datetime import datetime
   4 from string import *
   5 import os
   6 import re
   7 from htsworkflow.frontend import settings
   8 from htsworkflow.frontend.experiments.models import FlowCell, DataRun
   9 from htsworkflow.frontend.samples.models import Library
  10 from django.core.exceptions import ObjectDoesNotExist
  11 from django.core.mail import send_mail, mail_admins
  12
  13 def updStatus(request):
  14     output=''
  15     user = 'none'
  16     pswd = ''
  17     UpdatedStatus = 'unknown'
  18     fcid = 'none'
  19     runfolder = 'unknown'
  20     ClIP = request.META['REMOTE_ADDR']
  21
  22     if hasattr(request, 'user'):
  23       user = request.user
  24
  25     #Check access permission
  26     if not (user.is_superuser and settings.ALLOWED_IPS.has_key(ClIP)):
  27         return HttpResponse("%s access denied from %s." % (user, ClIP))
  28
  29     # ~~~~~~Parameters for the job ~~~~
  30     if request.REQUEST.has_key('fcid'):
  31       fcid = request.REQUEST['fcid']
  32     else:
  33       return HttpResponse('missing fcid')
  34
  35     if request.REQUEST.has_key('runf'):
  36       runfolder = request.REQUEST['runf']
  37     else:
  38       return HttpResponse('missing runf')
  39
  40
  41     if request.REQUEST.has_key('updst'):
  42       UpdatedStatus = request.REQUEST['updst']
  43     else:
  44       return HttpResponse('missing status')
  45
  46     # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  47
  48     # Update Data Run status in DB
  49     # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
  50     try:
  51       rec = DataRun.objects.get(run_folder=runfolder)
  52       rec.run_status = UpdatedStatus
  53
  54       #if there's a message update that too
  55       mytimestamp = datetime.now().__str__()
  56       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  57       if request.REQUEST.has_key('msg'):
  58         rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
  59       else :
  60         if UpdatedStatus == '1':
  61           rec.run_note = "Started ("+mytimestamp+")"
  62
  63       rec.save()
  64       output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
  65     except ObjectDoesNotExist:
  66       output = "entry not found: "+fcid+", "+runfolder
  67
  68
  69     #Notify researcher by email
  70     # Doesn't work
  71     #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
  72     #mail_admins("test subject", "testing , testing", fail_silently=False)
  73     # gives error: (49, "Can't assign requested address")
  74     return HttpResponse(output)
  75
  76 def generateConfile(request,fcid):
  77     #granted = False
  78     #ClIP = request.META['REMOTE_ADDR']
  79     #if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
  80
  81     #if not granted: return HttpResponse("access denied.")
  82
  83     config = ['READ_LENGTH 25']
  84     config += ['ANALYSIS eland']
  85     config += ['GENOME_FILE all_chr.fa']
  86     config += ['ELAND_MULTIPLE_INSTANCES 8']
  87     genome_dir = 'GENOME_DIR /Volumes/Genomes/'
  88     eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
  89
  90     try:
  91       fc = FlowCell.objects.get(flowcell_id=fcid)
  92       for lane in fc.lane_set.all():
  93           print dir(lane.library.library_species)
  94           config += [ str(lane.lane_number) +":" + \
  95                       genome_dir + lane.library.library_species.scientific_name ]
  96           config += [ str(lane.lane_number) +":" + \
  97                       eland_genome + lane.library.library_species.scientific_name ]
  98
  99     except ObjectDoesNotExist:
 100       config = 'Entry not found for fcid  = '+fcid
 101
 102     return os.linesep.join(config)
 103
 104 def getConfile(req):
 105     granted = False
 106     ClIP = req.META['REMOTE_ADDR']
 107     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 108
 109     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 110
 111     fcid = 'none'
 112     cnfgfile = 'Nothing found'
 113     runfolder = 'unknown'
 114     request = req.REQUEST
 115     print request, dir(request)
 116     print request['fcid'], request.has_key('fcid')
 117     print request['runf']
 118     if request.has_key('fcid'):
 119       fcid = request['fcid']
 120       if request.has_key('runf'):
 121         runfolder = request['runf']
 122         try:
 123           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 124           cnfgfile = rec.config_params
 125           #match_str = re.compile(r"READ_LENGTH.+$")
 126           match_str = re.compile('^READ_LENGTH.+')
 127           if not match_str.search(cnfgfile):
 128             cnfgfile = generateConfile(request,fcid)
 129             if match_str.search(cnfgfile):
 130               rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 131               rec.config_params = cnfgfile
 132               rec.save()
 133             else:
 134               cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
 135
 136         except ObjectDoesNotExist:
 137           cnfgfile = 'Entry not found for RunFolder = '+runfolder
 138
 139     return HttpResponse(cnfgfile, mimetype='text/plain')
 140
 141 def getLaneLibs(req):
 142     granted = False
 143     ClIP = req.META['REMOTE_ADDR']
 144     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 145
 146     if not granted: return HttpResponse("access denied.")
 147
 148     request = req.REQUEST
 149     fcid = 'none'
 150     outputfile = ''
 151     if request.has_key('fcid'):
 152       fcid = request['fcid']
 153       try:
 154         rec = FlowCell.objects.get(flowcell_id=fcid)
 155         #Ex: 071211
 156         year = datetime.today().year.__str__()
 157         year = replace(year,'20','')
 158         month = datetime.today().month
 159         if month < 10: month = "0"+month.__str__()
 160         else: month = month.__str__()
 161         day = datetime.today().day
 162         if day < 10: day = "0"+day.__str__()
 163         else: day = day.__str__()
 164         mydate = year+month+day
 165         outputfile = '<?xml version="1.0" ?>'
 166         outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
 167         outputfile += '\n<Lane Index="1" Name="'+rec.lane_1_library.library_name+'" Library="'+rec.lane_1_library.library_id+'" Genome="'+rec.lane_1_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 168         outputfile += '\n<Lane Index="2" Name="'+rec.lane_2_library.library_name+'" Library="'+rec.lane_2_library.library_id+'" Genome="'+rec.lane_2_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 169         outputfile += '\n<Lane Index="3" Name="'+rec.lane_3_library.library_name+'" Library="'+rec.lane_3_library.library_id+'" Genome="'+rec.lane_3_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 170         outputfile += '\n<Lane Index="4" Name="'+rec.lane_4_library.library_name+'" Library="'+rec.lane_4_library.library_id+'" Genome="'+rec.lane_4_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 171         outputfile += '\n<Lane Index="5" Name="'+rec.lane_5_library.library_name+'" Library="'+rec.lane_5_library.library_id+'" Genome="'+rec.lane_5_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 172         outputfile += '\n<Lane Index="6" Name="'+rec.lane_6_library.library_name+'" Library="'+rec.lane_6_library.library_id+'" Genome="'+rec.lane_6_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 173         outputfile += '\n<Lane Index="7" Name="'+rec.lane_7_library.library_name+'" Library="'+rec.lane_7_library.library_id+'" Genome="'+rec.lane_7_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 174         outputfile += '\n<Lane Index="8" Name="'+rec.lane_8_library.library_name+'" Library="'+rec.lane_8_library.library_id+'" Genome="'+rec.lane_8_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
 175         outputfile += '\n</SolexaResult>'
 176       except ObjectDoesNotExist:
 177         outputfile = 'Flowcell entry not found for: '+fcid
 178     else: outputfile = 'Missing input: flowcell id'
 179
 180     return HttpResponse(outputfile, mimetype='text/plain')