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 re
   6 from htsworkflow.frontend import settings
   7 from htsworkflow.frontend.experiments.models import FlowCell, DataRun
   8 from htsworkflow.frontend.samples.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
  64       rec.save()
  65       output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
  66     except ObjectDoesNotExist:
  67       output = "entry not found: "+fcid+", "+runfolder
  68
  69
  70     #Notify researcher by email
  71     # Doesn't work
  72     #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
  73     #mail_admins("test subject", "testing , testing", fail_silently=False)
  74     # gives error: (49, "Can't assign requested address")
  75     return HttpResponse(output)
  76
  77 def generateConfile(request,fcid):
  78     #granted = False
  79     #ClIP = request.META['REMOTE_ADDR']
  80     #if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
  81
  82     #if not granted: return HttpResponse("access denied.")
  83
  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(req):
 124     granted = False
 125     ClIP = req.META['REMOTE_ADDR']
 126     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 127
 128     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 129
 130     fcid = 'none'
 131     cnfgfile = 'Nothing found'
 132     runfolder = 'unknown'
 133     request = req.REQUEST
 134     print request, dir(request)
 135     print request['fcid'], request.has_key('fcid')
 136     print request['runf']
 137     if request.has_key('fcid'):
 138       fcid = request['fcid']
 139       if request.has_key('runf'):
 140         runfolder = request['runf']
 141         try:
 142           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 143           cnfgfile = rec.config_params
 144           #match_str = re.compile(r"READ_LENGTH.+$")
 145           match_str = re.compile('^READ_LENGTH.+')
 146           if not match_str.search(cnfgfile):
 147             cnfgfile = generateConfile(request,fcid)
 148             if match_str.search(cnfgfile):
 149               rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 150               rec.config_params = cnfgfile
 151               rec.save()
 152             else:
 153               cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
 154
 155         except ObjectDoesNotExist:
 156           cnfgfile = 'Entry not found for RunFolder = '+runfolder
 157
 158     return HttpResponse(cnfgfile, mimetype='text/plain')
 159
 160 def getLaneLibs(req):
 161     granted = False
 162     ClIP = req.META['REMOTE_ADDR']
 163     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 164
 165     if not granted: return HttpResponse("access denied.")
 166
 167     request = req.REQUEST
 168     fcid = 'none'
 169     outputfile = ''
 170     if request.has_key('fcid'):
 171       fcid = request['fcid']
 172       try:
 173         rec = FlowCell.objects.get(flowcell_id=fcid)
 174         #Ex: 071211
 175         year = datetime.today().year.__str__()
 176         year = replace(year,'20','')
 177         month = datetime.today().month
 178         if month < 10: month = "0"+month.__str__()
 179         else: month = month.__str__()
 180         day = datetime.today().day
 181         if day < 10: day = "0"+day.__str__()
 182         else: day = day.__str__()
 183         mydate = year+month+day
 184         outputfile = '<?xml version="1.0" ?>'
 185         outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
 186         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=""/>'
 187         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=""/>'
 188         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=""/>'
 189         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=""/>'
 190         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=""/>'
 191         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=""/>'
 192         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=""/>'
 193         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=""/>'
 194         outputfile += '\n</SolexaResult>'
 195       except ObjectDoesNotExist:
 196         outputfile = 'Flowcell entry not found for: '+fcid
 197     else: outputfile = 'Missing input: flowcell id'
 198
 199     return HttpResponse(outputfile, mimetype='text/plain')