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     granted = False
  22
  23     if request.has_key('user'):
  24       user = request['user']
  25
  26     #Check access permission
  27     if (user == 'rami' and settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
  28     if not granted: return HttpResponse("access denied.")
  29
  30
  31     # ~~~~~~Parameters for the job ~~~~
  32     if request.has_key('fcid'):
  33       fcid = request['fcid']
  34     else:
  35       return HttpResponse('missing fcid')
  36
  37     if request.has_key('runf'):
  38       runfolder = request['runf']
  39     else:
  40       return HttpResponse('missing runf')
  41
  42
  43     if request.has_key('updst'):
  44       UpdatedStatus = request['updst']
  45     else:
  46       return HttpResponse('missing status')
  47
  48     # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  49
  50     # Update Data Run status in DB
  51     # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
  52     try:
  53       rec = DataRun.objects.get(run_folder=runfolder)
  54       rec.run_status = UpdatedStatus
  55
  56       #if there's a message update that too
  57       mytimestamp = datetime.now().__str__()
  58       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
  59       if request.has_key('msg'):
  60         rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
  61       else :
  62         if UpdatedStatus == '1':
  63           rec.run_note = "Started ("+mytimestamp+")"
  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     #granted = False
  80     #ClIP = request.META['REMOTE_ADDR']
  81     #if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
  82
  83     #if not granted: return HttpResponse("access denied.")
  84
  85     config = ['READ_LENGTH 25']
  86     config += ['ANALYSIS eland']
  87     config += ['GENOME_FILE all_chr.fa']
  88     config += ['ELAND_MULTIPLE_INSTANCES 8']
  89     genome_dir = 'GENOME_DIR /Volumes/Genomes/'
  90     eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
  91
  92     try:
  93       fc = FlowCell.objects.get(flowcell_id=fcid)
  94       for lane in fc.lane_set.all():
  95           print dir(lane.library.library_species)
  96           config += [ str(lane.lane_number) +":" + \
  97                       genome_dir + lane.library.library_species.scientific_name ]
  98           config += [ str(lane.lane_number) +":" + \
  99                       eland_genome + lane.library.library_species.scientific_name ]
 100
 101     except ObjectDoesNotExist:
 102       config = 'Entry not found for fcid  = '+fcid
 103
 104     return os.linesep.join(config)
 105
 106 def getConfile(req):
 107     granted = False
 108     ClIP = req.META['REMOTE_ADDR']
 109     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 110
 111     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 112
 113     fcid = 'none'
 114     cnfgfile = 'Nothing found'
 115     runfolder = 'unknown'
 116     request = req.REQUEST
 117     print request, dir(request)
 118     print request['fcid'], request.has_key('fcid')
 119     print request['runf']
 120     if request.has_key('fcid'):
 121       fcid = request['fcid']
 122       if request.has_key('runf'):
 123         runfolder = request['runf']
 124         try:
 125           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 126           cnfgfile = rec.config_params
 127           #match_str = re.compile(r"READ_LENGTH.+$")
 128           match_str = re.compile('^READ_LENGTH.+')
 129           if not match_str.search(cnfgfile):
 130             cnfgfile = generateConfile(request,fcid)
 131             if match_str.search(cnfgfile):
 132               rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
 133               rec.config_params = cnfgfile
 134               rec.save()
 135             else:
 136               cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
 137
 138         except ObjectDoesNotExist:
 139           cnfgfile = 'Entry not found for RunFolder = '+runfolder
 140
 141     return HttpResponse(cnfgfile, mimetype='text/plain')
 142
 143 def getLaneLibs(req):
 144     granted = False
 145     ClIP = req.META['REMOTE_ADDR']
 146     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
 147
 148     if not granted: return HttpResponse("access denied.")
 149
 150     request = req.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+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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+'" PrimerName="" PrimerSeq=""/>'
 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, mimetype='text/plain')