htswfrontend/htswfrontend/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 htswfrontend import settings
   7 from htswfrontend.exp_track.models import FlowCell, DataRun
   8 from htswfrontend.fctracker.models import Library
   9 from django.core.exceptions import ObjectDoesNotExist
  10 from django.core.mail import send_mail, mail_admins
  11
  12 def updStatus(request):
  13     output=''
  14     user = 'none'
  15     pswd = ''
  16     UpdatedStatus = 'unknown'
  17     fcid = 'none'
  18     runfolder = 'unknown'
  19     ClIP = request.META['REMOTE_ADDR']
  20     granted = False
  21
  22     if request.has_key('user'):
  23       user = request['user']
  24
  25     #Check access permission
  26     if (user == 'rami' and settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
  27     if not granted: return HttpResponse("access denied.")
  28
  29
  30     # ~~~~~~Parameters for the job ~~~~
  31     if request.has_key('fcid'):
  32       fcid = request['fcid']
  33     else:
  34       return HttpResponse('missing fcid')
  35
  36     if request.has_key('runf'):
  37       runfolder = request['runf']
  38     else:
  39       return HttpResponse('missing runf')
  40
  41
  42     if request.has_key('updst'):
  43       UpdatedStatus = request['updst']
  44     else:
  45       return HttpResponse('missing status')
  46
  47     # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  48
  49     # Update Data Run status in DB
  50     # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
  51     try:
  52       rec = DataRun.objects.get(run_folder=runfolder)
  53       rec.run_status = UpdatedStatus
  54
  55       #if there's a message update that too
  56       mytimestamp = datetime.now().__str__()
  57       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  58       if request.has_key('msg'):
  59         rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
  60       else :
  61         if UpdatedStatus == '1':
  62           rec.run_note = "Started ("+mytimestamp+")"
  63           rec.run_start_time = datetime.now()
  64
  65       rec.save()
  66       output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
  67     except ObjectDoesNotExist:
  68       output = "entry not found: "+fcid+", "+runfolder
  69
  70
  71     #Notify researcher by email
  72     # Doesn't work
  73     #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
  74     #mail_admins("test subject", "testing , testing", fail_silently=False)
  75     # gives error: (49, "Can't assign requested address")
  76     return HttpResponse(output)
  77
  78 def generateConfile(request,fcid):
  79     try:
  80       rec = FlowCell.objects.get(flowcell_id=fcid)
  81       cnfgfile = 'READ_LENGTH 36\n'  # 25
  82       if rec.is_paired_end:
  83         cnfgfile += 'ANALYSIS eland_pair\n'
  84       else:
  85         cnfgfile += 'ANALYSIS eland_extended\n'
  86       cnfgfile += 'GENOME_FILE all_chr.fa\n'
  87       cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
  88       genome_dir = 'GENOME_DIR /mnt/encodedisk6/genomes/' # /Volumes/Genomes/
  89       eland_genome = 'ELAND_GENOME /mnt/encodedisk6/genomes/'  # /Volumes/Genomes/
  90
  91       cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n'
  92       cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n'
  93
  94       cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n'
  95       cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n'
  96
  97       cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n'
  98       cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n'
  99
 100       cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n'
 101       cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n'
 102
 103       cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n'
 104       cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n'
 105
 106       cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n'
 107       cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n'
 108
 109       cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n'
 110       cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n'
 111
 112       cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n'
 113       cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build
 114
 115     except ObjectDoesNotExist:
 116       cnfgfile = 'Entry not found for fcid  = '+fcid
 117
 118     return cnfgfile
 119
 120 def OLD_getConfile(request):
 121     granted = False
 122     ClIP = request.META['REMOTE_ADDR']
 123     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 124
 125     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 126
 127     fcid = 'none'
 128     cnfgfile = ''
 129     runfolder = 'unknown'
 130     if request.has_key('fcid'):
 131       fcid = request['fcid']
 132       if request.has_key('runf'):
 133         runfolder = request['runf']
 134         try:
 135           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 136           cnfgfile = rec.config_params
 137           match_str = re.compile('^READ_LENGTH.+')
 138           if not match_str.search(cnfgfile):
 139             cnfgfile = generateConfile(request,fcid)
 140             if match_str.search(cnfgfile):
 141               rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 142               rec.config_params = cnfgfile
 143               rec.save()
 144             else:
 145               cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
 146
 147         except ObjectDoesNotExist:
 148           cnfgfile = 'Entry not found for RunFolder = '+runfolder
 149
 150     return HttpResponse(cnfgfile)
 151
 152
 153 def getConfParams(request):
 154     granted = False
 155     ClIP = request.META['REMOTE_ADDR']
 156     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 157     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 158     fcid = 'none'
 159     paramstext = ''
 160
 161     if request.has_key('fcid'):
 162       fcid = request['fcid']
 163       try:
 164         rec = FlowCell.objects.get(flowcell_id=fcid)
 165         paramstext =  'Lane:'+  rec.lane_1_library.library_id +':'+rec.lane_1_library.library_species.use_genome_build
 166         paramstext += '\nLane:'+rec.lane_2_library.library_id +':'+rec.lane_2_library.library_species.use_genome_build
 167         paramstext += '\nLane:'+rec.lane_3_library.library_id +':'+rec.lane_3_library.library_species.use_genome_build
 168         paramstext += '\nLane:'+rec.lane_4_library.library_id +':'+rec.lane_4_library.library_species.use_genome_build
 169         paramstext += '\nLane:'+rec.lane_5_library.library_id +':'+rec.lane_5_library.library_species.use_genome_build
 170         paramstext += '\nLane:'+rec.lane_6_library.library_id +':'+rec.lane_6_library.library_species.use_genome_build
 171         paramstext += '\nLane:'+rec.lane_7_library.library_id +':'+rec.lane_7_library.library_species.use_genome_build
 172         paramstext += '\nLane:'+rec.lane_8_library.library_id +':'+rec.lane_8_library.library_species.use_genome_build
 173         if rec.is_paired_end: paramstext += '\nIsPairedEnd::1'
 174         else: paramstext += '\nIsPairedEnd::0'
 175
 176       except ObjectDoesNotExist:
 177         paramstext = 'Flowcell entry not found for:  '+fcid
 178     else:
 179       paramstext = 'missing input - flowcell id'
 180
 181     return HttpResponse(paramstext)
 182
 183
 184 def getLaneLibs(request):
 185     granted = False
 186     ClIP = request.META['REMOTE_ADDR']
 187     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 188
 189     if not granted: return HttpResponse("access denied.")
 190
 191     fcid = 'none'
 192     outputfile = ''
 193     if request.has_key('fcid'):
 194       fcid = request['fcid']
 195       try:
 196         rec = FlowCell.objects.get(flowcell_id=fcid)
 197         #Ex: 071211
 198         year = datetime.today().year.__str__()
 199         year = replace(year,'20','')
 200         month = datetime.today().month
 201         if month < 10: month = "0"+month.__str__()
 202         else: month = month.__str__()
 203         day = datetime.today().day
 204         if day < 10: day = "0"+day.__str__()
 205         else: day = day.__str__()
 206         mydate = year+month+day
 207         outputfile = '<?xml version="1.0" ?>'
 208         outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
 209         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=""/>'
 210         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=""/>'
 211         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=""/>'
 212         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=""/>'
 213         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=""/>'
 214         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=""/>'
 215         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=""/>'
 216         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=""/>'
 217         outputfile += '\n</SolexaResult>'
 218       except ObjectDoesNotExist:
 219         outputfile = 'Flowcell entry not found for: '+fcid
 220     else: outputfile = 'Missing input: flowcell id'
 221
 222     return HttpResponse(outputfile)