+++ /dev/null
-# some core functions of the exp tracker module
-from django.http import HttpResponse
-from datetime import datetime
-from string import *
-import re
-from gaworkflow.frontend import settings
-from gaworkflow.frontend.exp_track.models import FlowCell, DataRun
-from gaworkflow.frontend.fctracker.models import Library
-from django.core.exceptions import ObjectDoesNotExist
-from django.core.mail import send_mail, mail_admins
-
-def updStatus(request):
- output=''
- user = 'none'
- pswd = ''
- UpdatedStatus = 'unknown'
- fcid = 'none'
- runfolder = 'unknown'
- ClIP = request.META['REMOTE_ADDR']
- granted = False
-
- if request.has_key('user'):
- user = request['user']
-
- #Check access permission
- if (user == 'rami' and settings.ALLOWED_IPS.has_key(ClIP)): granted = True
- if not granted: return HttpResponse("access denied.")
-
-
- # ~~~~~~Parameters for the job ~~~~
- if request.has_key('fcid'):
- fcid = request['fcid']
- else:
- return HttpResponse('missing fcid')
-
- if request.has_key('runf'):
- runfolder = request['runf']
- else:
- return HttpResponse('missing runf')
-
-
- if request.has_key('updst'):
- UpdatedStatus = request['updst']
- else:
- return HttpResponse('missing status')
-
- # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- # Update Data Run status in DB
- # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
- try:
- rec = DataRun.objects.get(run_folder=runfolder)
- rec.run_status = UpdatedStatus
-
- #if there's a message update that too
- mytimestamp = datetime.now().__str__()
- mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
- if request.has_key('msg'):
- rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
- else :
- if UpdatedStatus == '1':
- rec.run_note = "Started ("+mytimestamp+")"
-
- rec.save()
- output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
- except ObjectDoesNotExist:
- output = "entry not found: "+fcid+", "+runfolder
-
-
- #Notify researcher by email
- # Doesn't work
- #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
- #mail_admins("test subject", "testing , testing", fail_silently=False)
- # gives error: (49, "Can't assign requested address")
- return HttpResponse(output)
-
-def generateConfile(fcid):
- granted = False
- ClIP = request.META['REMOTE_ADDR']
- if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
-
- if not granted: return HttpResponse("access denied.")
-
- cnfgfile = 'READ_LENGTH 25\n'
- cnfgfile += 'ANALYSIS eland\n'
- cnfgfile += 'GENOME_FILE all_chr.fa\n'
- cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
- genome_dir = 'GENOME_DIR /Volumes/Genomes/'
- eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
-
- try:
- rec = FlowCell.objects.get(flowcell_id=fcid)
-
- cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n'
- cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n'
- cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n'
- cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n'
- cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n'
- cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n'
- cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n'
- cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n'
- cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build
-
- except ObjectDoesNotExist:
- cnfgfile = 'Entry not found for fcid = '+fcid
-
- return cnfgfile
-
-def getConfile(request):
- granted = False
- ClIP = request.META['REMOTE_ADDR']
- if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
-
- if not granted: return HttpResponse("access denied.")
-
- fcid = 'none'
- cnfgfile = ''
- runfolder = 'unknown'
- if request.has_key('fcid'):
- fcid = request['fcid']
- if request.has_key('runf'):
- runfolder = request['runf']
- try:
- rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
- cnfgfile = rec.config_params
- #match_str = re.compile(r"READ_LENGTH.+$")
- match_str = re.compile('^READ_LENGTH.+')
- if not match_str.search(cnfgfile):
- cnfgfile = generateConfile(fcid)
- if match_str.search(cnfgfile):
- rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
- rec.config_params = cnfgfile
- rec.save()
- else:
- cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
-
- except ObjectDoesNotExist:
- cnfgfile = 'Entry not found for RunFolder = '+runfolder
-
- return HttpResponse(cnfgfile)
-
-def getLaneLibs(request):
- granted = False
- ClIP = request.META['REMOTE_ADDR']
- if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
-
- if not granted: return HttpResponse("access denied.")
-
- fcid = 'none'
- outputfile = ''
- if request.has_key('fcid'):
- fcid = request['fcid']
- try:
- rec = FlowCell.objects.get(flowcell_id=fcid)
- #Ex: 071211
- year = datetime.today().year.__str__()
- year = replace(year,'20','')
- month = datetime.today().month
- if month < 10: month = "0"+month.__str__()
- else: month = month.__str__()
- day = datetime.today().day
- if day < 10: day = "0"+day.__str__()
- else: day = day.__str__()
- mydate = year+month+day
- outputfile = '<?xml version="1.0" ?>'
- outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- 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=""/>'
- outputfile += '\n</SolexaResult>'
- except ObjectDoesNotExist:
- outputfile = 'Flowcell entry not found for: '+fcid
- else: outputfile = 'Missing input: flowcell id'
-
- return HttpResponse(outputfile)
projects / htsworkflow.git / blobdiff