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