gaworkflow/frontend/exp_track/exptrack.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 re
   6 from gaworkflow.frontend.exp_track.models import DataRun
   7 from gaworkflow.frontend.fctracker.models import FlowCell, Library
   8 from django.core.exceptions import ObjectDoesNotExist
   9 from django.core.mail import send_mail, mail_admins
  10
  11 def updStatus(request):
  12     output=''
  13     user = 'none'
  14     pswd = ''
  15     UpdatedStatus = 'unknown'
  16     ClIP = 'unknown'
  17     granted = False
  18     fcid = 'none'
  19     runfolder = 'unknown'
  20
  21     if request.has_key('fcid'):
  22       fcid = request['fcid']
  23     else:
  24       return HttpResponse('missing fcid')
  25
  26     if request.has_key('runf'):
  27       runfolder = request['runf']
  28     else:
  29       return HttpResponse('missing runf')
  30
  31     if request.has_key('user'):
  32       user = request['user']
  33     else:
  34       return HttpResponse('access denied')
  35
  36     #TO DO: pswd decode etc..
  37     #if request.has_key('pswd'):
  38     #  pswd = request['pswd']
  39     #else:
  40     #  return HttpResponse('access denied')
  41
  42     ClIP = request.META['REMOTE_ADDR']
  43
  44     #Check permission to update
  45     if (user == 'rami' and (ClIP == '171.65.76.167' or ClIP == '171.65.76.51' or ClIP == '171.65.76.194' or (ClIP == '74.51.115.100' or ClIP == '64.89.97.100'))): ## or ClIP == '127.0.0.1')):
  46       granted = True
  47
  48     if granted:
  49       if request.has_key('updst'):
  50         UpdatedStatus = request['updst']
  51       else:
  52         return HttpResponse('missing status')
  53
  54       # Update Data Run status in DB
  55       # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
  56       try:
  57         rec = DataRun.objects.get(run_folder=runfolder)
  58         rec.run_status = UpdatedStatus
  59
  60         #if there's a message update that too
  61         mytimestamp = datetime.now().__str__()
  62         mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  63         if request.has_key('msg'):
  64           rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
  65         else :
  66           if UpdatedStatus == '1':
  67             rec.run_note = "Started ("+mytimestamp+")"
  68
  69         rec.save()
  70         output = "updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
  71       except ObjectDoesNotExist:
  72         output = "entry not found: "+fcid+", "+runfolder
  73     else:
  74       output ="access denied.. u: "+user+", ClIP: "+ClIP
  75
  76     #Notify researcher by email
  77     # Doesn't work
  78     #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
  79     #mail_admins("test subject", "testing , testing", fail_silently=False)
  80     # gives error: (49, "Can't assign requested address")
  81     return HttpResponse(output)
  82
  83 def generateConfile(fcid):
  84     cnfgfile = 'READ_LENGTH 25\n'
  85     cnfgfile += 'ANALYSIS eland\n'
  86     cnfgfile += 'GENOME_FILE all_chr.fa\n'
  87     cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
  88     genome_dir = 'GENOME_DIR /Volumes/Genomes/'
  89     eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
  90
  91     try:
  92       rec = FlowCell.objects.get(flowcell_id=fcid)
  93
  94       cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n'
  95       cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n'
  96
  97       cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n'
  98       cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n'
  99
 100       cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n'
 101       cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n'
 102
 103       cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n'
 104       cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n'
 105
 106       cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n'
 107       cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n'
 108
 109       cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n'
 110       cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n'
 111
 112       cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n'
 113       cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n'
 114
 115       cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n'
 116       cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build
 117
 118     except ObjectDoesNotExist:
 119       cnfgfile = 'Entry not found for fcid  = '+fcid
 120
 121     return cnfgfile
 122
 123 def getConfile(request):
 124     fcid = 'none'
 125     cnfgfile = ''
 126     runfolder = 'unknown'
 127     if request.has_key('fcid'):
 128       fcid = request['fcid']
 129       if request.has_key('runf'):
 130         runfolder = request['runf']
 131         try:
 132           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 133           cnfgfile = rec.config_params
 134           #match_str = re.compile(r"READ_LENGTH.+$")
 135           match_str = re.compile('^READ_LENGTH.+')
 136           if not match_str.search(cnfgfile):
 137             cnfgfile = generateConfile(fcid)
 138             if match_str.search(cnfgfile):
 139               rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 140               rec.config_params = cnfgfile
 141               rec.save()
 142             else:
 143               cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
 144
 145         except ObjectDoesNotExist:
 146           cnfgfile = 'Entry not found for RunFolder = '+runfolder
 147
 148     return HttpResponse(cnfgfile)
 149
 150 def getLaneLibs(request):
 151     fcid = 'none'
 152     outputfile = ''
 153     if request.has_key('fcid'):
 154       fcid = request['fcid']
 155       try:
 156         rec = FlowCell.objects.get(flowcell_id=fcid)
 157         #Ex: 071211
 158         year = datetime.today().year.__str__()
 159         year = replace(year,'20','')
 160         month = datetime.today().month
 161         if month < 10: month = "0"+month.__str__()
 162         else: month = month.__str__()
 163         day = datetime.today().day
 164         if day < 10: day = "0"+day.__str__()
 165         else: day = day.__str__()
 166         mydate = year+month+day
 167         outputfile = '<?xml version="1.0" ?>'
 168         outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'">'
 169         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+'"/>'
 170         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+'"/>'
 171         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+'"/>'
 172         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+'"/>'
 173         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+'"/>'
 174         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+'"/>'
 175         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+'"/>'
 176         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+'"/>'
 177         outputfile += '\n</SolexaResult>'
 178       except ObjectDoesNotExist:
 179         outputfile = 'Flowcell entry not found for: '+fcid
 180     else: outputfile = 'Missing input: flowcell id'
 181
 182     return HttpResponse(outputfile)