1 # some core functions of the exp tracker module
2 from django.http import HttpResponse
3 from datetime import datetime
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
12 def updStatus(request):
16 UpdatedStatus = 'unknown'
19 ClIP = request.META['REMOTE_ADDR']
22 if request.has_key('user'):
23 user = request['user']
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.")
30 # ~~~~~~Parameters for the job ~~~~
31 if request.has_key('fcid'):
32 fcid = request['fcid']
34 return HttpResponse('missing fcid')
36 if request.has_key('runf'):
37 runfolder = request['runf']
39 return HttpResponse('missing runf')
42 if request.has_key('updst'):
43 UpdatedStatus = request['updst']
45 return HttpResponse('missing status')
47 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
52 rec = DataRun.objects.get(run_folder=runfolder)
53 rec.run_status = UpdatedStatus
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+")"
61 if UpdatedStatus == '1':
62 rec.run_note = "Started ("+mytimestamp+")"
63 rec.run_start_time = datetime.now()
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
71 #Notify researcher by email
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)
78 def generateConfile(request,fcid):
80 rec = FlowCell.objects.get(flowcell_id=fcid)
81 cnfgfile = 'READ_LENGTH 36\n' # 25
83 cnfgfile += 'ANALYSIS eland_pair\n'
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/
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'
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'
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'
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'
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'
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'
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'
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
115 except ObjectDoesNotExist:
116 cnfgfile = 'Entry not found for fcid = '+fcid
120 def OLD_getConfile(request):
122 ClIP = request.META['REMOTE_ADDR']
123 if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
125 if not granted: return HttpResponse("access denied. IP: "+ClIP)
129 runfolder = 'unknown'
130 if request.has_key('fcid'):
131 fcid = request['fcid']
132 if request.has_key('runf'):
133 runfolder = request['runf']
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
145 cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
147 except ObjectDoesNotExist:
148 cnfgfile = 'Entry not found for RunFolder = '+runfolder
150 return HttpResponse(cnfgfile)
153 def getConfParams(request):
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)
161 if request.has_key('fcid'):
162 fcid = request['fcid']
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'
176 except ObjectDoesNotExist:
177 paramstext = 'Flowcell entry not found for: '+fcid
179 paramstext = 'missing input - flowcell id'
181 return HttpResponse(paramstext)
184 def getLaneLibs(request):
186 ClIP = request.META['REMOTE_ADDR']
187 if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
189 if not granted: return HttpResponse("access denied.")
193 if request.has_key('fcid'):
194 fcid = request['fcid']
196 rec = FlowCell.objects.get(flowcell_id=fcid)
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'
222 return HttpResponse(outputfile)