However I renamed things to simpler names.
analys_track -> analysis
exp_track -> experiments
fctracker -> samples
htsw_reports -> reports
As a result this check in probably wont work as I haven't finished
updating all the imports
--- /dev/null
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+ (r'^updStatus$', 'htswfrontend.analys_track.main.updStatus'),
+ (r'^getProjects/$', 'htswfrontend.analys_track.main.getProjects'),
+)
--- /dev/null
+# some core functions of analysis manager module
+from django.http import HttpResponse
+from datetime import datetime
+from string import *
+import re
+from htswfrontend import settings
+from htswfrontend.analys_track.models import Task, Project
+from django.core.exceptions import ObjectDoesNotExist
+
+def updStatus(request):
+ ClIP = request.META['REMOTE_ADDR']
+ #Check client access permission
+ granted = False
+ if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)): granted = True
+ if not granted: return HttpResponse("access denied.")
+
+ output=''
+ taskid=-1;
+ # Check required param
+ if request.has_key('taskid'): taskid = request['taskid']
+ else: return HttpResponse('missing param task id')
+
+ try:
+ rec = Task.objects.get(id=taskid)
+ mytimestamp = datetime.now().__str__()
+ mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
+ if request.has_key('msg'):
+ rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
+ else :
+ rec.task_status = "Registered ("+mytimestamp+")"
+ rec.save()
+ output = "Hello "+settings.ALLOWED_ANALYS_IPS[ClIP]+". Updated status for task "+taskid
+ except ObjectDoesNotExist:
+ output = "entry not found: taskid="+taskid
+
+ return HttpResponse(output)
+
+
+def getProjects(request):
+ ClIP = request.META['REMOTE_ADDR']
+ #Check client access permission
+ granted = False
+ if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)): granted = True
+ if not granted: return HttpResponse("access denied.")
+
+ outputfile = ''
+
+ All=False
+ if (request.has_key('mode')):
+ if request['mode']=='all':
+ All=True
+
+ try:
+ if(All):
+ rec = Project.objects.all().distinct()
+ else:
+ rec = Project.objects.filter(tasks__task_status__exact='defined').distinct()
+
+ outputfile = '<?xml version="1.0" ?>'
+ outputfile += '\n<Projects Client="'+settings.ALLOWED_ANALYS_IPS[ClIP]+'">'
+ for p in rec:
+ outputfile += '\n'
+ outputfile += '\n<Project ProjectId="'+p.id.__str__()+'" Name="'+p.project_name+'">'
+ prj_tasks = p.tasks.all()
+ for t in prj_tasks:
+ outputfile += '\n'
+ if (t.apply_calc == 'QuEST' or t.apply_calc == 'WingPeaks' or t.apply_calc == 'MACS'):
+ outputfile += '\n<PeakCalling TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Caller="'+t.apply_calc+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
+ outputfile += '\n<Signal Library="'+t.subject1.library_id+'"/>'
+ outputfile += '\n<Background Library="'+t.subject2.library_id+'"/>'
+ outputfile += '\n</PeakCalling>'
+
+ if (t.apply_calc == 'ProfileReads' or t.apply_calc == 'qPCR'):
+ outputfile += '\n<'+t.apply_calc+' TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'" Library="'+t.subject1.library_id+'"/>'
+
+ if (t.apply_calc == 'CompareLibs'):
+ outputfile += '\n<CompareLibraries TaskId="'+t.id.__str__()+'" TF="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
+ outputfile += '\n<Library Library="'+t.subject1.library_id+'"/>'
+ outputfile += '\n<Library Library="'+t.subject2.library_id+'"/>'
+ outputfile += '\n</CompareLibraries>'
+
+ #if (t.apply_calc == 'ComparePeakCalls'):
+ # <ComparePeakCalls Genome="hg18" Caller1="QuEST" Set1="A549 GR Dex ChIP" Caller2="QuEST" Set2="A549 GR EtOH ChIP" />
+ # outputfile += '\n<ComparePeakCalls TaskId='+t.id.__str__()+' Genome="'+t.subject1.library_species.use_genome_build+'" Caller1="'+t.pcaller1+'" Caller1="'+t.pcaller1+'" Caller2="'+t.pcaller2+'" Set1="'+t.set1+'" Set1="'+t.set2+'"/>'
+ # TO DO: Define these new fields in Task: PCaller1 (QuEST,WingPeaks), PCaller2, Set1(FK to self), Set2 (FK..) ALL NULL=TRUE
+ outputfile += '\n</Project>'
+ outputfile += '\n</Projects>'
+ except ObjectDoesNotExist:
+ outputfile = "<?xml version='1.0' ?><Projects></Projects>"
+
+ return HttpResponse(outputfile, mimetype='text/plain')
--- /dev/null
+from django.db import models
+from datetime import datetime
+from htswfrontend.fctracker.models import Library
+from string import *
+
+class Task(models.Model):
+ task_name = models.CharField(max_length=50,unique=True, db_index=True)
+ subject1 = models.ForeignKey(Library,related_name='sbj1_library',verbose_name="Subject")
+ subject2 = models.ForeignKey(Library,related_name='sbj2_library',verbose_name="Subject 2 / Control",blank=True,null=True)
+ CALCS = (
+ ('QuEST', 'QuEST Peak Calling'),
+ ('WingPeaks', 'Wing Peak Calling'),
+ ('MACS', 'MACS Peak Calling'),
+ ('qPCR', 'In Silico qPCR'),
+ ('CompareLibs', 'Compare Libaraies'),
+ ('ComparePeakCalls','Compare Peak Calls'),
+ ('ProfileReads','Profile Reads')
+ )
+ apply_calc = models.CharField(max_length=50,choices=CALCS,verbose_name='Applied Calculation')
+ ## userid = # logged in user
+ task_status = models.CharField(max_length=500,blank=True,null=True,default='defined')
+ results_location = models.CharField(max_length=2000,blank=True,null=True)
+ submitted_on = models.DateTimeField(core=True,default=datetime.now())
+ run_note = models.CharField(max_length=500,blank=True,null=True)
+
+ def __str__(self):
+ return '"%s" - %s on [%s]/[%s]' % (self.task_name,self.apply_calc,self.subject1,self.subject2)
+
+ def InProjects(self):
+ return '...'
+ ps = self.project_set.all()
+ pstr = 'In '
+ return pstr
+ for p in ps:
+ pstr += '%s, ' % (p.project_name)
+ return pstr
+
+ class Admin:
+ list_display = ('task_name','apply_calc','subject1','subject2','InProjects','submitted_on','task_status')
+ list_filter = ('apply_calc',)
+ search_fields = ['task_name','id','=subject1__library_id','=subject2__library_id']
+ fields = (
+ (None, {
+ 'fields': (('task_name'),('apply_calc'),('subject1'),('subject2'))
+ }),
+ ('system fields', {
+ 'classes': 'collapse',
+ 'fields': (('submitted_on'),('task_status','run_note'))
+ }),
+ )
+
+
+class Project(models.Model):
+ project_name = models.CharField(max_length=50,unique=True, db_index=True)
+ tasks = models.ManyToManyField(Task,related_name='project_tasks',null=True,filter_interface=models.HORIZONTAL)
+ project_notes = models.CharField(max_length=500,blank=True,null=True)
+
+ def __str__(self):
+ return '%s' % (self.project_name)
+
+ def ProjectTasks(self):
+ ptasks = self.tasks.all().order_by('id')
+ surl = 'http://m304-apple-server.stanford.edu/projects/'
+ tstr = '<script>'
+ tstr += 'function togView(eid){'
+ tstr += 'f=document.getElementById(eid);'
+ tstr += 'if(f.height==0){'
+ tstr += 'f.height=600;'
+ tstr += 'f.style.border=\'solid #cccccc 3px\';'
+ tstr += '}else{'
+ tstr += 'f.height=0;'
+ tstr += 'f.style.border=\'none\';'
+ tstr += '}'
+ tstr += '}'
+ tstr += '</script>'
+ Style = ''
+ if len(ptasks) > 8: Style = ' style="height:200px;overflow:auto" '
+ tstr += '<div '+Style+'>'
+ tstr += '<table><tr><th>Tasks</th><th>Job Status</th>'
+ isregistered = False
+ for t in ptasks:
+ tstr += '<tr><td width=250>%s</td><td>%s</td></tr>' % (t.task_name,replace(t.task_status,'Complete','<span style="color:green;font-weight:bolder">Complete</span>'))
+ if t.task_status != 'defined': isregistered = True
+
+ tstr += '</table>'
+ tstr += '</div>'
+ tstr += '<div>'
+ tstr += '<div align=center>'
+ if isregistered:
+ tstr += '<a onClick="togView(\'RFrame'+self.id.__str__()+'\');" href="'+surl+self.id.__str__()+'/" title="View Results Page" target="RFrame'+self.id.__str__()+'">VIEW PROJECT RESULTS</a>'
+ tstr += '<a href="'+surl+self.id.__str__()+'/" title="View Results Page" target="_blank" style="margin-left:10px">(view in new window)</a>'
+ else:
+ tstr += 'REGISTERING ...'
+
+ tstr += '</div>'
+ tstr += '<iframe width="100%" height="0" frameborder="0" style="background-color:#ffffff" name="RFrame'+self.id.__str__()+'" id="RFrame'+self.id.__str__()+'"/></iframe>'
+ tstr += '</div>'
+ return tstr
+
+ ProjectTasks.allow_tags = True
+
+ def ProjTitle(self):
+ ptasks = self.tasks.all().order_by('id')
+ tasks_counter = '<span style="color:#666666;font-size:85%">('+len(ptasks).__str__() + ' tasks)</span>'
+ htmlstr = '%s<br/>%s' % (self.project_name,tasks_counter)
+ return htmlstr
+
+ ProjTitle.allow_tags = True
+
+ class Admin:
+ list_display = ('ProjTitle','ProjectTasks')
+ list_filter = ()
+ search_fields = ['project_name','=tasks__subject1__library_id','=tasks__subject2__library_id','tasks__subject1__library_name','tasks__subject2__library_name','project_notes']
+ fields = (
+ (None, {
+ 'fields': (('project_name'),('tasks'),('project_notes'))}),
+ )
--- /dev/null
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+
+ (r'^$', 'htswfrontend.exp_track.views.index'),
+ (r'^liblist$', 'htswfrontend.exp_track.views.test_Libs'),
+ #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.exp_track.views.detail'),
+ (r'^(?P<fcid>.+)/$', 'htswfrontend.exp_track.views.makeFCSheet'),
+ (r'^updStatus$', 'htswfrontend.exp_track.exptrack.updStatus'),
+ (r'^getConfile$', 'htswfrontend.exp_track.exptrack.getConfile'),
+ (r'^getLanesNames$', 'htswfrontend.exp_track.exptrack.getLaneLibs')
+)
--- /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 htswfrontend import settings
+from htswfrontend.exp_track.models import FlowCell, DataRun
+from htswfrontend.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(request,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. IP: "+ClIP)
+
+ 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(request,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)
--- /dev/null
+from django.db import models
+from htswfrontend.fctracker.models import *
+
+class FlowCell(models.Model):
+
+ flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
+ run_date = models.DateTimeField(core=True)
+ advanced_run = models.BooleanField(default=False)
+ read_length = models.IntegerField(default=32) #Stanford is currenlty 25
+
+ lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
+ lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
+ lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
+ lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
+ lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
+ lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
+ lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
+ lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
+
+ lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+
+ lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
+
+ # lane_1_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_1_primer")
+ # lane_2_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_2_primer")
+ # lane_3_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_3_primer")
+ # lane_4_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_4_primer")
+ # lane_5_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_5_primer")
+ # lane_6_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_6_primer")
+ # lane_7_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_7_primer")
+ # lane_8_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_8_primer")
+
+ #Machine Names
+ CLUSTER_MAC = (
+ ('M304','Cardinal'),
+ ('R349','R349'),
+ ('Tinkerbell','Tinkerbell'),
+ ('BitBit','BitBit'),
+ )
+
+ SEQ_MAC = (
+ ('EAS149','Stanford'),
+ ('EAS46','EAS46'),
+ ('EAS45','Paris'),
+ ('Britney','Britney'),
+ )
+
+ cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
+ seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
+
+ notes = models.TextField(blank=True)
+
+ def __str__(self):
+ #return '%s (%s)' % (self.flowcell_id, self.run_date)
+ return '%s' % (self.flowcell_id)
+
+ def Create_LOG(self):
+ str = '' #<span style="color:red;font-size:80%;margin-right:3px">New!</span>'
+ str +='<a target=_balnk href="/exp_track/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
+ return str
+ Create_LOG.allow_tags = True
+
+ def Lanes(self):
+ return '<div><span style="margin-right:10px">1)%s</span><span style="margin-right:10px">2)%s</span><span style="margin-right:10px">3)%s</span><span style="margin-right:10px">4)%s</span><span style="margin-right:10px">5)%s</span><span style="margin-right:10px">6)%s</span><span style="margin-right:10px">7)%s</span><span style="margin-right:10px">8)%s</span></div>' % (self.lane_1_library,self.lane_2_library,self.lane_3_library,self.lane_4_library,self.lane_5_library,self.lane_6_library,self.lane_7_library,self.lane_8_library)
+ Lanes.allow_tags = True
+
+ class Meta:
+ ordering = ["-run_date"]
+
+ class Admin:
+ save_on_top = True
+ date_hierarchy = "run_date"
+ save_on_top = True
+ search_fields = ['flowcell_id','seq_mac_id','cluster_mac_id','=lane_1_library__library_id','=lane_2_library__library_id','=lane_3_library__library_id','=lane_4_library__library_id','=lane_5_library__library_id','=lane_6_library__library_id','=lane_7_library__library_id','=lane_8_library__library_id']
+ list_display = ('flowcell_id','seq_mac_id','run_date', 'Create_LOG','Lanes')
+ list_filter = ('seq_mac_id','cluster_mac_id')
+ fields = (
+ (None, {
+ 'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length'),)
+ }),
+ ('Lanes:', {
+ ##'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate', 'lane_1_primer'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate', 'lane_2_primer'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate', 'lane_3_primer'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate', 'lane_4_primer'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate', 'lane_5_primer'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate', 'lane_6_primer'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate', 'lane_7_primer'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate', 'lane_8_primer'),)
+ 'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
+ }),
+ (None, {
+ 'fields' : ('notes',)
+ }),
+ )
+
+
+### -----------------------
+class DataRun(models.Model):
+ ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."
+ run_folder = models.CharField(max_length=50,unique=True, db_index=True)
+ fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
+ config_params = models.TextField(default=ConfTemplate)
+ run_start_time = models.DateTimeField(core=True)
+ RUN_STATUS_CHOICES = (
+ (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
+ (1, 'Data Pipeline Started'),
+ (2, 'Data Pipeline Interrupted'),
+ (3, 'Data Pipeline Finished'),
+ (4, 'CollectReads Started'),
+ (5, 'CollectReads Finished'),
+ (6, 'QC Finished'),
+ (7, 'DONE'),
+ )
+ run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0)
+ run_note = models.TextField(blank=True)
+
+
+ def main_status(self):
+ str = '<div'
+ if self.run_status >= 5:
+ str += ' style="color:green">'
+ str += '<b>'+self.RUN_STATUS_CHOICES[self.run_status][1]+'</b>'
+ str += '<br/><br/>' #<span style="color:red;font-size:80%;">New!</span>'
+ str +='<br/><a target=_balnk href="http://m304-apple-server.stanford.edu/'+self.fcid.flowcell_id+'_QC/'+self.fcid.flowcell_id+'_'+self.run_folder+'_QC_Summary.html" title="View QC Summaries of this run ..." ">View QC Page</a>'
+ else:
+ str += '>'+self.RUN_STATUS_CHOICES[self.run_status][1]
+
+ str += '</div>'
+ return str
+ main_status.allow_tags = True
+
+ main_status.allow_tags = True
+
+ def Flowcell_Info(self):
+ str = '<b>'+self.fcid.__str__()+'</b>'
+ str += ' (c: '+self.fcid.cluster_mac_id+', s: '+self.fcid.seq_mac_id+')'
+ str += '<div style="margin-top:5px;">'
+ str +='<a title="View Lane List here ..." onClick="el = document.getElementById(\'LanesOf'+self.fcid.__str__()+'\');if(el) (el.style.display==\'none\'?el.style.display=\'block\':el.style.display=\'none\')" style="cursor:pointer;color: #5b80b2;">View/hide lanes</a>'
+ str += '<div id="LanesOf'+self.fcid.__str__()+'" style="display:block;border:solid #cccccc 1px;width:350px">'
+ LanesList = '1: '+self.fcid.lane_1_library.__str__()+' ('+self.fcid.lane_1_library.library_species.use_genome_build+')<br/>2: '+self.fcid.lane_2_library.__str__()+' ('+self.fcid.lane_2_library.library_species.use_genome_build+')<br/>3: '+self.fcid.lane_3_library.__str__()+' ('+self.fcid.lane_3_library.library_species.use_genome_build+')<br/>4: '+self.fcid.lane_4_library.__str__()+' ('+self.fcid.lane_4_library.library_species.use_genome_build+')<br/>5: '+self.fcid.lane_5_library.__str__()+' ('+self.fcid.lane_5_library.library_species.use_genome_build+')<br/>6: '+self.fcid.lane_6_library.__str__()+' ('+self.fcid.lane_6_library.library_species.use_genome_build+')<br/>7: '+self.fcid.lane_7_library.__str__()+' ('+self.fcid.lane_7_library.library_species.use_genome_build+')<br/>8: '+self.fcid.lane_8_library.__str__()+' ('+self.fcid.lane_8_library.library_species.use_genome_build+')'
+ str += LanesList ## self.fcid.Lanes()
+ str += '</div>'
+ str += '<div><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a>'
+ #str += '<span style="color:red;font-size:80%;margin-left:15px;margin-right:3px">New!</span>'
+ str +='<a style="margin-left:15px;" target=_balnk href="/exp_track/'+self.fcid.flowcell_id+'" title="View XLS like sheet for this Flowcell LOG ..." ">GA LOG Page</a>'
+ str += '</div>'
+ str += '</div>'
+ return str
+ Flowcell_Info.allow_tags = True
+
+ class Admin:
+ search_fields = ['run_folder','run_note','config_params','=fcid__lane_1_library__library_id','=fcid__lane_2_library__library_id','=fcid__lane_3_library__library_id','=fcid__lane_4_library__library_id','=fcid__lane_5_library__library_id','=fcid__lane_6_library__library_id','=fcid__lane_7_library__library_id','=fcid__lane_8_library__library_id']
+
+ list_display = ('run_folder','Flowcell_Info','run_start_time','main_status','run_note')
+ list_filter = ('run_status','run_start_time')
--- /dev/null
+# Create your views here.
+#from django.template import Context, loader
+#shortcut to the above modules
+from django.shortcuts import render_to_response, get_object_or_404
+#from htswfrontend.fctracker.models import *
+from htswfrontend.exp_track.models import *
+from django.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
+
+def index(request):
+ all_runs = DataRun.objects.all().order_by('-run_start_time')
+ #t = loader.get_template('exptrack/index.html')
+ #c = Context({
+ # 'data_run_list': all_runs,
+ #})
+ #return HttpResponse(t.render(c))
+ # shortcut to the above module usage
+ return render_to_response('exptrack/index.html',{'data_run_list': all_runs})
+
+def detail(request, run_folder):
+ html_str = '<h2>Exp Track Details Page</h2>'
+ html_str += 'Run Folder: '+run_folder
+ r = get_object_or_404(DataRun,run_folder=run_folder)
+ return render_to_response('exptrack/detail.html',{'run_f': r})
+
+def makeFCSheet(request,fcid):
+ # get Flowcell by input fcid
+ # ...
+ rec = None
+ try:
+ rec = FlowCell.objects.get(flowcell_id=fcid)
+ except ObjectDoesNotExist:
+ pass
+ lanes = ['1','2','3','4','5','6','7','8']
+ return render_to_response('exptrack/flowcellSheet.html',{'fc': rec})
+
+def test_Libs(request):
+ str = ''
+ str += '<table border=1><tr><th>Lib ID</th><th>Current Libaray Name (Free Text)</th><th>Auto-composed Libaray Name (antibody + celline + libid + species + [replicate])</th></tr>'
+ allLibs = Library.objects.all()
+ #allLibs = Library.objects.filter(antibody__isnull=False)
+ for L in allLibs:
+ str += '<tr>'
+ str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
+ str += '<td>'
+ str += L.experiment_type+'_'
+ if L.cell_line.cellline_name != 'Unknown':
+ str += L.cell_line.cellline_name+'_'
+
+ try:
+ if L.antibody is not None:
+ str += L.antibody.nickname + '_'
+ except Antibody.DoesNotExist:
+ pass
+
+ str += 'Rep'+L.replicate.__str__()
+ str += '</td></tr>'
+
+ str += '</table>'
+ return HttpResponse(str)
+++ /dev/null
-from django.db import models
-from django.contrib.auth.models import User
-from htsworkflow.frontend import settings
-from htsworkflow.reports.libinfopar import *
-
-# Create your models here.
-
-class Antibody(models.Model):
- antigene = models.CharField(max_length=500, db_index=True)
- # New field Aug/20/08
- # SQL to add column: alter table fctracker_antibody add column "nickname" varchar(20) NULL;
- nickname = models.CharField(max_length=20,blank=True,null=True, db_index=True,verbose_name = 'Short Name')
- catalog = models.CharField(max_length=50, unique=True, db_index=True)
- antibodies = models.CharField(max_length=500, db_index=True)
- source = models.CharField(max_length=500, blank=True, db_index=True)
- biology = models.TextField(blank=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
- class Meta:
- verbose_name_plural = "antibodies"
- ordering = ["antigene"]
- class Admin:
- list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
- list_filter = ('antibodies','source')
- fields = (
- (None, {
- 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
- }),
- )
-
-class Cellline(models.Model):
- cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.cellline_name)
-
- class Meta:
- ordering = ["cellline_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('cellline_name'),('notes'),)
- }),
- )
-
-class Condition(models.Model):
- condition_name = models.CharField(max_length=2000, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.condition_name)
-
- class Meta:
- ordering = ["condition_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('condition_name'),('notes'),)
- }),
- )
-
-class Species(models.Model):
-
- scientific_name = models.CharField(max_length=256, unique=False, db_index=True, core=True)
- common_name = models.CharField(max_length=256, blank=True)
- use_genome_build = models.CharField(max_length=100, blank=False, null=False)
-
- def __str__(self):
- return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build)
-
- class Meta:
- verbose_name_plural = "species"
- ordering = ["scientific_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('scientific_name', 'common_name'), ('use_genome_build'))
- }),
- )
-
-class Affiliation(models.Model):
- name = models.CharField(max_length=256, db_index=True, core=True,verbose_name='Group Name')
- contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')
- email = models.EmailField(null=True,blank=True)
-
- def __str__(self):
- str = self.name
- if self.contact != '':
- str += ' ('+self.contact+')'
- return str
-
- class Meta:
- ordering = ["name","contact"]
- unique_together = (("name", "contact"),)
-
- class Admin:
- list_display = ('name','contact','email')
- fields = (
- (None, {
- 'fields': (('name','contact','email'))
- }),
- )
-
-class Library(models.Model):
-
- library_id = models.CharField(max_length=30, primary_key=True, db_index=True, core=True)
- library_name = models.CharField(max_length=100, unique=True, core=True)
- library_species = models.ForeignKey(Species, core=True)
- cell_line = models.ForeignKey(Cellline,core=True)
- condition = models.ForeignKey(Condition,core=True)
- antibody = models.ForeignKey(Antibody,blank=True,null=True,core=True)
- # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256) NULL;
- affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True,filter_interface=models.HORIZONTAL)
- # New field Aug/19/08
- # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
- REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
- replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,default=1)
-
- EXPERIMENT_TYPES = (
- ('INPUT_RXLCh','INPUT_RXLCh'),
- ('ChIP-seq', 'ChIP-seq'),
- ('Sheared', 'Sheared'),
- ('RNA-seq', 'RNA-seq'),
- ('Methyl-seq', 'Methyl-seq'),
- ('DIP-seq', 'DIP-seq'),
- )
- experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES,
- default='RNA-seq')
-
- creation_date = models.DateField(blank=True, null=True)
- made_for = models.ForeignKey(User)
- made_by = models.CharField(max_length=50, blank=True, default="Lorian")
-
- PROTOCOL_END_POINTS = (
- ('?', 'Unknown'),
- ('Sample', 'Raw sample'),
- ('Progress', 'In progress'),
- ('1A', 'Ligation, then gel'),
- ('PCR', 'Ligation, then PCR'),
- ('1Ab', 'Ligation, PCR, then gel'),
- ('1Aa', 'Ligation, gel, then PCR'),
- ('2A', 'Ligation, PCR, gel, PCR'),
- ('Done', 'Completed'),
- )
- stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
- amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
-
- undiluted_concentration = models.DecimalField("Undiluted concentration (ng/ul)", max_digits=5, decimal_places=2, default=0, blank=True, null=True)
- successful_pM = models.DecimalField(max_digits=5, decimal_places=2, blank=True, null=True)
- ten_nM_dilution = models.BooleanField()
- avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
- notes = models.TextField(blank=True)
-
- def __str__(self):
- return '#%s: %s' % (self.library_id, self.library_name)
-
- class Meta:
- verbose_name_plural = "libraries"
- ordering = ["-creation_date"] #["-library_id"]
-
- def antibody_name(self):
- return self.antibody.nickname
-
- def org(self):
- return self.library_species.common_name
-
- def affiliation(self):
- affs = self.affiliations.all().order_by('name')
- tstr = ''
- ar = []
- for t in affs:
- ar.append(t.__str__())
- return '%s' % (", ".join(ar))
-
-
- def aligned_reads(self):
- res = getLibReads(self.library_id)
- rc = "%1.2f" % (res[1]/1000000.0)
- # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
- if res[0] > 0:
- bgcolor = '#ff3300' # Red
- rc_thr = [10000000,5000000,3000000]
- if self.experiment_type == 'RNA-seq':
- rc_thr = [20000000,10000000,6000000]
-
- if res[1] > rc_thr[0]:
- bgcolor = '#66ff66' # Green
- else:
- if res[1] > rc_thr[1]:
- bgcolor ='#00ccff' # Blue
- else:
- if res[1] > rc_thr[2]:
- bgcolor ='#ffcc33' # Orange
- tstr = '<div style="background-color:'+bgcolor+';color:black">'
- tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
- tstr += '</div>'
- else: tstr = 'not processed yet'
- return tstr
- aligned_reads.allow_tags = True
-
- class Admin:
- date_hierarchy = "creation_date"
- save_as = True
- save_on_top = True
- ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
- search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
- list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
- list_display_links = ('library_id', 'library_name')
-
- list_filter = ('experiment_type','affiliations','library_species','made_for', 'made_by','replicate')
- fields = (
- (None, {
- 'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
- }),
- ('Creation Information:', {
- 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'library_size'), 'notes',)
- }),
- ('Library/Project Affiliation:', {
- 'fields' : (('affiliations'),)
- }),
- )
-
+++ /dev/null
-# Create your views here.
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<Libraries>
+<Library Name="SL3">
+<Track Flowcell="FC11862" Lane="2" Filename="Flowcells/FC11862/070919_FC11862_s2_NRSF_monoclonal_Jurkat_rep2_SL3.align_25.hg18.txt" Count=" 1423565" Date="070919"/>
+</Library>
+<Library Name="SL4">
+<Track Flowcell="FC10073" Lane="3" Filename="Flowcells/FC10073/070821_FC10073_s3_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2132972" Date="070821"/>
+<Track Flowcell="FC10182" Lane="18" Filename="Flowcells/FC10182/070925_FC10182_s18_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 4061515" Date="070925"/>
+<Track Flowcell="FC11862" Lane="6" Filename="Flowcells/FC11862/070919_FC11862_s6_Mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2397558" Date="070919"/>
+<Track Flowcell="FC11977" Lane="8" Filename="Flowcells/FC11977/070928_FC11977_s8_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 1088135" Date="070928"/>
+<Track Flowcell="FC8053" Lane="78" Filename="Flowcells/FC8053/070724_FC8053_s78_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 3583766" Date="070724"/>
+<Track Flowcell="FC8883" Lane="78" Filename="Flowcells/FC8883/070720_FC8883_s78_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 5491316" Date="070720"/>
+<Track Flowcell="FC8886" Lane="7" Filename="Flowcells/FC8886/070802_FC8886_s7_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2417786" Date="070802"/>
+</Library>
+<Library Name="SL10">
+<Track Flowcell="FC11977" Lane="7" Filename="Flowcells/FC11977/070928_FC11977_s7_hct_1_msp_SL10.align_25.hg18.txt" Count=" 1801596" Date="070928"/>
+<Track Flowcell="FC13593" Lane="678" Filename="Flowcells/FC13593/071002_FC13593_s678_hct_1_msp_SL10.align_25.hg18.txt" Count=" 7978981" Date="071002"/>
+</Library>
+<Library Name="SL11">
+<Track Flowcell="FCOLD1" Lane="1" Filename="Flowcells/FCOLD1/070000_FCOLD1_s1_SRF_ChIP_Jurkat_Rep1_SL11.align_25.hg18.txt" Count=" 8721730" Date="070000"/>
+</Library>
+<Library Name="SL14">
+<Track Flowcell="FC10135" Lane="4" Filename="Flowcells/FC10135/071005_FC10135_s4_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2438679" Date="071005"/>
+<Track Flowcell="FC11977" Lane="6" Filename="Flowcells/FC11977/070928_FC11977_s6_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2007880" Date="070928"/>
+<Track Flowcell="FC13593" Lane="5" Filename="Flowcells/FC13593/071002_FC13593_s5_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2533720" Date="071002"/>
+</Library>
+<Library Name="SL16">
+<Track Flowcell="FC201U7" Lane="12345678" Filename="Flowcells/FC201U7/071205_FC201U7_s12345678_mock_IP_PFSK1_SL16.align_25.hg.txt" Count=" 23476737" Date="071205"/>
+</Library>
+<Library Name="SL24">
+<Track Flowcell="FC5512" Lane="123" Filename="Flowcells/FC5512/070609_FC5512_s123_d5_C_hpa_SL24.align_25.hg18.txt" Count=" 1534145" Date="070609"/>
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+<Track Flowcell="FC20AUG" Lane="6" Filename="Flowcells/FC20AUG/080612_FC20AUG_s6_A549_Rep2_GR_EtOH_ChIP_SL305.align_25.hg18.txt" Count=" 2182536" Date="080612"/>
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+</Library>
+<Library Name="SL307">
+<Track Flowcell="3072MAAXX" Lane="1" Filename="Flowcells/3072MAAXX/080722_3072MAAXX_s1_A549_EtOH_RX_noIP_SL307.align_25.hg18.txt" Count=" 3727098" Date="080722"/>
+<Track Flowcell="3072MAAXX" Lane="2" Filename="Flowcells/3072MAAXX/080722_3072MAAXX_s2_A549_EtOH_RX_noIP_SL307.align_25.hg18.txt" Count=" 4398655" Date="080722"/>
+<Track Flowcell="FC20AUG" Lane="8" Filename="Flowcells/FC20AUG/080612_FC20AUG_s8_A549_EtOH_RX_noIP_SL307.align_25.hg18.txt" Count=" 3738550" Date="080612"/>
+</Library>
+<Library Name="SL310">
+<Track Flowcell="FC20ATH" Lane="6" Filename="Flowcells/FC20ATH/080602_FC20ATH_s6_RNA-seq_GM12878_Rep2_SL310.align_25.hg18.txt" Count=" 3087245" Date="080602"/>
+</Library>
+<Library Name="SL311">
+<Track Flowcell="FC20AUM" Lane="1" Filename="Flowcells/FC20AUM/080616_FC20AUM_s1_RNASeq_BJ_rep1_SL311.align_25.hg18.txt" Count=" 3688931" Date="080616"/>
+</Library>
+<Library Name="SL312">
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+</Library>
+<Library Name="SL313">
+<Track Flowcell="FC20ATH" Lane="8" Filename="Flowcells/FC20ATH/080602_FC20ATH_s8_RNA-seq_HepG2_Rep2_SL313.align_25.hg18.txt" Count=" 3462781" Date="080602"/>
+</Library>
+<Library Name="SL314">
+<Track Flowcell="FC20AUM" Lane="2" Filename="Flowcells/FC20AUM/080616_FC20AUM_s2_RNA-seq_HMEC_rep1_SL314.align_25.hg18.txt" Count=" 4056466" Date="080616"/>
+</Library>
+<Library Name="SL315">
+<Track Flowcell="FC20AUM" Lane="3" Filename="Flowcells/FC20AUM/080616_FC20AUM_s3_RNA-seq_HMEC_rep2_SL315.align_25.hg18.txt" Count=" 3958633" Date="080616"/>
+</Library>
+<Library Name="SL316">
+<Track Flowcell="306WKAAXX" Lane="5" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s5_RNAseq_Jurkat_rep1_SL316.align_25.hg18.txt" Count=" 2116970" Date="080728"/>
+<Track Flowcell="306WKAAXX" Lane="6" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s6_RNAseq_Jurkat_rep1_SL316.align_25.hg18.txt" Count=" 3213207" Date="080728"/>
+<Track Flowcell="FC20AUM" Lane="4" Filename="Flowcells/FC20AUM/080616_FC20AUM_s4_RNAseq_Jurkat_rep1_SL316.align_25.hg18.txt" Count=" 3926383" Date="080616"/>
+</Library>
+<Library Name="SL317">
+<Track Flowcell="306WKAAXX" Lane="7" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s7_RNAseq_Jurkat_rep2_SL317.align_25.hg18.txt" Count=" 4116201" Date="080728"/>
+<Track Flowcell="306WKAAXX" Lane="8" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s8_RNAseq_Jurkat_rep2_SL317.align_25.hg18.txt" Count=" 3689888" Date="080728"/>
+<Track Flowcell="FC20AUM" Lane="5" Filename="Flowcells/FC20AUM/080616_FC20AUM_s5_RNAseq_Jurkat_rep2_SL317.align_25.hg18.txt" Count=" 4104444" Date="080616"/>
+</Library>
+<Library Name="SL318">
+<Track Flowcell="FC20AMC" Lane="1" Filename="Flowcells/FC20AMC/080609_FC20AMC_s1_ChIP-seq_hESC_K36_repurified_SL318.align_25.hg18.txt" Count=" 971624" Date="080609"/>
+</Library>
+<Library Name="SL319">
+<Track Flowcell="FC20AMC" Lane="2" Filename="Flowcells/FC20AMC/080609_FC20AMC_s2_ChIP-seq_hESC_K27_repurified_SL319.align_25.hg18.txt" Count=" 365209" Date="080609"/>
+</Library>
+<Library Name="SL320">
+<Track Flowcell="FC20AMC" Lane="3" Filename="Flowcells/FC20AMC/080609_FC20AMC_s3_ChIP-seq_hESC_Pol2_repurified_SL320.align_25.hg18.txt" Count=" 643582" Date="080609"/>
+</Library>
+<Library Name="SL321">
+<Track Flowcell="FC20AMC" Lane="4" Filename="Flowcells/FC20AMC/080609_FC20AMC_s4_Input_Control_hESC_Repurified_SL321.align_25.hg18.txt" Count=" 1384822" Date="080609"/>
+</Library>
+<Library Name="SL322">
+<Track Flowcell="FC209TJ" Lane="1" Filename="Flowcells/FC209TJ/080606_FC209TJ_s1_ChIpSeq_hESCday5_K4_SL322.align_25.hg18.txt" Count=" 578452" Date="080606"/>
+</Library>
+<Library Name="SL323">
+<Track Flowcell="FC209TJ" Lane="2" Filename="Flowcells/FC209TJ/080606_FC209TJ_s2_Input_Control_hESCday5_SL323.align_25.hg18.txt" Count=" 1756643" Date="080606"/>
+</Library>
+<Library Name="SL324">
+<Track Flowcell="FC209TJ" Lane="3" Filename="Flowcells/FC209TJ/080606_FC209TJ_s3_ChIpSeq_hESCday5_K27_SL324.align_25.hg18.txt" Count=" 1306396" Date="080606"/>
+</Library>
+<Library Name="SL325">
+<Track Flowcell="FC209TJ" Lane="4" Filename="Flowcells/FC209TJ/080606_FC209TJ_s4_ChIpSeq_hESCday5_K36_SL325.align_25.hg18.txt" Count=" 478866" Date="080606"/>
+</Library>
+<Library Name="SL326">
+<Track Flowcell="FC20AUG" Lane="1" Filename="Flowcells/FC20AUG/080612_FC20AUG_s1_RNA-seq_BJ_Rep2_75_SL326.align_25.hg18.txt" Count=" 3188417" Date="080612"/>
+</Library>
+<Library Name="SL327">
+<Track Flowcell="FC20AUG" Lane="2" Filename="Flowcells/FC20AUG/080612_FC20AUG_s2_RNA-seq_K562_Rep3_75_SL327.align_25.hg18.txt" Count=" 3717306" Date="080612"/>
+</Library>
+<Library Name="SL328">
+<Track Flowcell="FC20AUG" Lane="3" Filename="Flowcells/FC20AUG/080612_FC20AUG_s3_RNA-seq_BJ_Rep2_7_5_SL328.align_25.hg18.txt" Count=" 3864656" Date="080612"/>
+</Library>
+<Library Name="SL329">
+<Track Flowcell="FC20AUG" Lane="4" Filename="Flowcells/FC20AUG/080612_FC20AUG_s4_RNA-seq_K562_Rep3_7_5_SL329.align_25.hg18.txt" Count=" 3915270" Date="080612"/>
+</Library>
+<Library Name="SL330">
+<Track Flowcell="303n0aaxx" Lane="1" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s1_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 1006720" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="2" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s2_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 1140136" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="1" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s1_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 3860069" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="5" Filename="Flowcells/FC20AMC/080609_FC20AMC_s5_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 2586689" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="1" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s1_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 2607495" Date="080725"/>
+<Track Flowcell="FC306VCAAXX" Lane="2" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s2_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 2538777" Date="080725"/>
+</Library>
+<Library Name="SL331">
+<Track Flowcell="303n0aaxx" Lane="5" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s5_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 2173243" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="6" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s6_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 2197491" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="2" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s2_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 3706943" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="6" Filename="Flowcells/FC20AMC/080609_FC20AMC_s6_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 2877770" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="5" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s5_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 1159780" Date="080725"/>
+<Track Flowcell="FC306VCAAXX" Lane="6" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s6_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 1488352" Date="080725"/>
+</Library>
+<Library Name="SL332">
+<Track Flowcell="303n0aaxx" Lane="3" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1087155" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="4" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s4_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1070083" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="3" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 4289055" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="7" Filename="Flowcells/FC20AMC/080609_FC20AMC_s7_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 2950811" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="3" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1260681" Date="080725"/>
+</Library>
+<Library Name="SL333">
+<Track Flowcell="303n0aaxx" Lane="7" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s7_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 1479883" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="8" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 1429681" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="4" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s4_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 3317843" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="8" Filename="Flowcells/FC20AMC/080609_FC20AMC_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 2863677" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="7" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s7_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 3146212" Date="080725"/>
+<Track Flowcell="FC306VCAAXX" Lane="8" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 2107413" Date="080725"/>
+</Library>
+<Library Name="SL334">
+<Track Flowcell="303y5aaxx" Lane="5" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s5_Pol2_EtOH_chIP_Rep1_SL334.align_25.hg18.txt" Count=" 4221253" Date="080715"/>
+<Track Flowcell="303y5aaxx" Lane="6" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s6_Pol2_EtOH_chIP_Rep1_SL334.align_25.hg18.txt" Count=" 4389966" Date="080715"/>
+</Library>
+<Library Name="SL335">
+<Track Flowcell="303y5aaxx" Lane="7" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s7_Input_RXLCh_+Dex_SL335.align_25.hg18.txt" Count=" 4320528" Date="080715"/>
+<Track Flowcell="303y5aaxx" Lane="8" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s8_Input_RXLCh_+Dex_SL335.align_25.hg18.txt" Count=" 3212232" Date="080715"/>
+</Library>
+<Library Name="SL336">
+<Track Flowcell="303PNAXX" Lane="1" Filename="Flowcells/303PNAXX/080718_303PNAXX_s1_Input_Control_RXLCh_Neuro2A_Rep1_SL336.align_25.mm9.txt" Count=" 4919007" Date="080718"/>
+</Library>
+<Library Name="SL337">
+<Track Flowcell="303PNAXX" Lane="2" Filename="Flowcells/303PNAXX/080718_303PNAXX_s2_Input_Control_RXLCh_CAD_Rep1_SL337.align_25.mm9.txt" Count=" 5960847" Date="080718"/>
+</Library>
+<Library Name="SL338">
+<Track Flowcell="303PNAXX" Lane="3" Filename="Flowcells/303PNAXX/080718_303PNAXX_s3_Neuro2A_CTCF_Rep1_SL338.align_25.mm9.txt" Count=" 5871158" Date="080718"/>
+</Library>
+<Library Name="SL339">
+<Track Flowcell="303PNAXX" Lane="4" Filename="Flowcells/303PNAXX/080718_303PNAXX_s4_CAD_CTCF_Rep1_SL339.align_25.mm9.txt" Count=" 5226675" Date="080718"/>
+</Library>
+<Library Name="SL340">
+<Track Flowcell="303PNAXX" Lane="5" Filename="Flowcells/303PNAXX/080718_303PNAXX_s5_Neuro2A_USF1_Rep1_SL340.align_25.mm9.txt" Count=" 5113687" Date="080718"/>
+</Library>
+<Library Name="SL341">
+<Track Flowcell="303PNAXX" Lane="6" Filename="Flowcells/303PNAXX/080718_303PNAXX_s6_CAD_USF1_Rep1_SL341.align_25.mm9.txt" Count=" 5580547" Date="080718"/>
+</Library>
+<Library Name="SL342">
+<Track Flowcell="303PNAXX" Lane="7" Filename="Flowcells/303PNAXX/080718_303PNAXX_s7_Neuro2A_USF2_Rep1_SL342.align_25.mm9.txt" Count=" 4845266" Date="080718"/>
+</Library>
+<Library Name="SL343">
+<Track Flowcell="303PNAXX" Lane="8" Filename="Flowcells/303PNAXX/080718_303PNAXX_s8_CAD_USF2_Rep1_SL343.align_25.mm9.txt" Count=" 4722617" Date="080718"/>
+</Library>
+<Library Name="SL344">
+<Track Flowcell="FC20AUL" Lane="5" Filename="Flowcells/FC20AUL/080621_FC20AUL_s5_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 1854345" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="6" Filename="Flowcells/FC20AUL/080621_FC20AUL_s6_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 2139393" Date="080621"/>
+</Library>
+<Library Name="SL345">
+<Track Flowcell="FC20AUL" Lane="7" Filename="Flowcells/FC20AUL/080621_FC20AUL_s7_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 1981441" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="8" Filename="Flowcells/FC20AUL/080621_FC20AUL_s8_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 2279789" Date="080621"/>
+</Library>
+<Library Name="SL350">
+<Track Flowcell="FC20AUL" Lane="1" Filename="Flowcells/FC20AUL/080621_FC20AUL_s1_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1211303" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="2" Filename="Flowcells/FC20AUL/080621_FC20AUL_s2_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1646993" Date="080621"/>
+</Library>
+<Library Name="SL351">
+<Track Flowcell="FC20AUL" Lane="3" Filename="Flowcells/FC20AUL/080621_FC20AUL_s3_chIPSeq_HMEC_Rep2_RNApol2_SL351.align_25.hg18.txt" Count=" 1810613" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="4" Filename="Flowcells/FC20AUL/080621_FC20AUL_s4_chIPSeq_HMEC_Rep1_RNApol2_SL351.align_25.hg18.txt" Count=" 1866673" Date="080621"/>
+</Library>
+<Library Name="SL358">
+<Track Flowcell="306WDAAXX" Lane="1" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s1_ChIP-seq_HepG2_Rep1_TAF250_SL358.align_25.hg18.txt" Count=" 3950828" Date="080725"/>
+<Track Flowcell="306WDAAXX" Lane="2" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s2_ChIP-seq_HepG2_Rep1_TAF250_SL358.align_25.hg18.txt" Count=" 4064007" Date="080725"/>
+</Library>
+<Library Name="SL359">
+<Track Flowcell="306WDAAXX" Lane="3" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s3_ChIP-seq_HepG2_Rep2_TAF250_SL359.align_25.hg18.txt" Count=" 2721181" Date="080725"/>
+<Track Flowcell="306WDAAXX" Lane="4" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s4_ChIP-seq_HepG2_Rep2_TAF250_SL359.align_25.hg18.txt" Count=" 3705820" Date="080725"/>
+</Library>
+<Library Name="SL360">
+<Track Flowcell="306WDAAXX" Lane="5" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s5_ChIP-seq_BJ_Fibroblast_Rep1_RNAPol2_SL360.align_25.hg18.txt" Count=" 3104910" Date="080725"/>
+</Library>
+<Library Name="SL361">
+<Track Flowcell="306WDAAXX" Lane="6" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s6_ChIP-seq_BJ_Fibroblast_Rep2_RNAPol2_SL361.align_25.hg18.txt" Count=" 2279682" Date="080725"/>
+</Library>
+<Library Name="SL362">
+<Track Flowcell="306WDAAXX" Lane="7" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s7_Input_Control_BJ_Fibroblast_Rep1_SL362.align_25.hg18.txt" Count=" 1305197" Date="080725"/>
+</Library>
+<Library Name="SL363">
+<Track Flowcell="306WDAAXX" Lane="8" Filename="Flowcells/306WDAAXX/080725_306WDAAXX_s8_Input_Control_BJ_Fibroblast_Rep2_SL363.align_25.hg18.txt" Count=" 1981571" Date="080725"/>
+</Library>
+<Library Name="SL400">
+<Track Flowcell="FCAlyssa" Lane="1" Filename="Flowcells/Alyssa/080731_FCAlyssa_s1_BG_SL400.align_25.mm9.txt" Count=" 3652474" Date="080731"/>
+</Library>
+<Library Name="SL401">
+<Track Flowcell="FCAlyssa" Lane="2" Filename="Flowcells/Alyssa/080731_FCAlyssa_s2_Pol2_SL401.align_25.mm9.txt" Count=" 3895128" Date="080731"/>
+</Library>
+<Library Name="SL402">
+<Track Flowcell="FCAlyssa" Lane="3" Filename="Flowcells/Alyssa/080731_FCAlyssa_s3_CHD1L_SL402.align_25.mm9.txt" Count=" 4498952" Date="080731"/>
+</Library>
+</Libraries>
\ No newline at end of file
--- /dev/null
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+ (r'^updLibInfo$', 'htswfrontend.htsw_reports.libinfopar.refreshLibInfoFile'),
+)
--- /dev/null
+from django.http import HttpResponse
+from datetime import datetime
+from string import *
+import re
+from xml.sax import make_parser
+from xml.sax.handler import ContentHandler
+import urllib
+import urllib2
+import os
+
+'''
+Example library node from LibraryInfo.xml:
+<Library Name="SL14">
+<Track Flowcell="FC10135" Lane="4" Filename="071005_FC10135_s4_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2438679" Complexity="4.51989e-06"/>
+<Track Flowcell="FC11977" Lane="6" Filename="070928_FC11977_s6_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2007880" Complexity="0"/>
+<Track Flowcell="FC13593" Lane="5" Filename="071002_FC13593_s5_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2533720" Complexity="1.97771e-06"/>
+</Library>
+'''
+class LibInfoHandler(ContentHandler):
+
+ def __init__ (self, searchTerm):
+ self.searchTerm= searchTerm
+ self.currlibid = ''
+ self.LanesCount, self.ReadsCount = 0, 0
+ self.Msg = ''
+
+ def startElement(self, name, attrs):
+ if name == 'Library':
+ self.currlibid = attrs.get('Name',"")
+ elif name == 'Track' and self.searchTerm == self.currlibid:
+ self.LanesCount += len(attrs.get('Lane',""))
+ self.ReadsCount += int(attrs.get('Count',""))
+ else:
+ self.Msg += ' | name = '+name+', currlibid = '+ self.currlibid
+ return
+
+ #def characters (self, ch):
+ # return ..
+
+ #def endElement(self, name):
+ # return ..
+
+
+## TO DO: Change this to read the LibraryInfo.xml only ONCE per ReoprtRequest (do it in the models.py). + Read it directly from the analysis_server
+
+def getLibReads(libid):
+ searchTerm= libid
+ parser = make_parser()
+ curHandler = LibInfoHandler(searchTerm)
+ parser.setContentHandler(curHandler)
+ parser.parse(open('/htsworkflow/htswfrontend/htswfrontend/htsw_reports/LibInfo/LibraryInfo.xml'))
+ arRes = []
+ arRes.append(curHandler.LanesCount)
+ arRes.append(curHandler.ReadsCount)
+ return arRes
+
+def getWebPage(url,params):
+ pdata = urllib.urlencode(params)
+ req = urllib2.Request(url,pdata)
+ wpage = urllib2.urlopen(req)
+ restext = wpage.read()
+ wpage.close()
+ return restext
+
+def refreshLibInfoFile(request):
+ varStatus = 'getting conf file from exp trac server'
+ url = 'http://m304-apple-server.stanford.edu/ENCODE/LibraryInfo.xml'
+ params = {}
+ readw = getWebPage(url,params)
+ # make sure file content starts as xml
+ match_str = re.compile('^<\?xml.+')
+ if match_str.search(readw): ##tempstr):
+ # Rename current file with timestamp
+ 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
+ folder = '/htsworkflow/htswfrontend/htswfrontend/htsw_reports/LibInfo/'
+ os.rename(folder+'LibraryInfo.xml',folder+mydate+'_LibraryInfo.xml')
+ # create file in curret folder
+ file_path = os.path.join(folder,'LibraryInfo.xml')
+ f = open(file_path, 'w')
+ f.write(readw)
+ f.close()
+ varStatus = 'OK. LibraryInfo.xml refreshed at Web server.'
+ else:
+ varStatus = 'Failed reading valid LibraryInfo.xml server reply:\n'+readw
+ return HttpResponse(varStatus)
--- /dev/null
+from django.db import models
+from django.db.models import Q
+from django.core.exceptions import ObjectDoesNotExist
+from datetime import datetime
+from htswfrontend.fctracker.models import *
+from htswfrontend.analys_track.models import *
+from htswfrontend.exp_track.models import *
+from string import *
+from htswfrontend.htsw_reports.utils import *
+import re
+##from p1 import LibInfo
+from libinfopar import *
+
+## This is a table based REPORT generator. The goal is to display a Progress Report for all the ENCODE projects, based on Study Name (e.g. NRSF, FOXP2, Methy-Seq on .. etc).
+
+class ProgressReport(models.Model):
+ st_sbj = models.ForeignKey(Project,limit_choices_to = Q(project_name__startswith='ENCODE '),related_name='project',db_index=True,verbose_name="Studied Subject")
+ interactome_complete = models.BooleanField(default=False)
+
+ def Study(self):
+ str = self.st_sbj.__str__()
+ str += '<br/><br/>'
+ str += '<a title="open Project record" href="/admin/analys_track/project/'+self.st_sbj.id.__str__()+'/" target=_self style="font-size:85%">Edit Project</a>'
+ return str
+ Study.allow_tags = True
+
+ def submit_to_DCC(self):
+ varText = ''
+ if self.note_about_DCC:
+ varText += '<br/><u>Note:</u><br/>'+self.note_about_DCC
+ return '%s<br/>%s' % (self.submitted_to_DCC,varText)
+ submit_to_DCC.allow_tags = True
+
+ def submit_to_NCBI(self):
+ varText = ''
+ if self.note_about_NCBI:
+ varText += '<br/><u>Note:</u><br/>'+self.note_about_NCBI
+ return '%s<br/>%s' % (self.submitted_to_NCBI,varText)
+ submit_to_NCBI.allow_tags = True
+
+ ## -- Utility functions <-- This method was transfered to untils.py
+
+ ## --- LIBARAY PREPARATION SECTION
+ def getLibIds(self):
+ ptasks = self.st_sbj.tasks.distinct()
+ arLibs = []
+ for t in ptasks:
+ if t.subject1 is not None:
+ arLibs.append(t.subject1.library_id)
+ if t.subject2 is not None:
+ arLibs.append(t.subject2.library_id)
+ arLibs = unique(arLibs)
+ return arLibs #.sort()
+
+ def getFCInfo(self,libid): ## This is the haviest function
+ arFCLanes = []
+ ##Test return arFCLanes
+ # can't get this to work: FC_L1 = FlowCell.objects.filter(lane_5_library__exact=libid)
+ allFCs = FlowCell.objects.all()
+ for f in allFCs:
+ entry = ''
+ lanes = []
+ #found = False
+# for i in range(1,9):
+# if eval('f.lane_'+i.__str__()+'_library.library_id==libid'):
+# lanes.append(i.__str__())
+# found = True
+
+# maybe a bit faster this way:
+ if f.lane_1_library.library_id==libid:
+ lanes.append('1')
+ #found = True
+ if f.lane_2_library.library_id==libid:
+ lanes.append('2')
+ #found = True
+ if f.lane_3_library.library_id==libid:
+ lanes.append('3')
+ #found = True
+ if f.lane_4_library.library_id==libid:
+ lanes.append('4')
+ #found = True
+ if f.lane_5_library.library_id==libid:
+ lanes.append('5')
+ #found = True
+ if f.lane_6_library.library_id==libid:
+ lanes.append('6')
+ #found = True
+ if f.lane_7_library.library_id==libid:
+ lanes.append('7')
+ #found = True
+ if f.lane_8_library.library_id==libid:
+ lanes.append('8')
+ #found = True
+
+
+ #if found:
+ if len(lanes)>0:
+ rundate = re.sub(pattern="\s.*$",repl="",string=f.run_date.__str__())
+ entry = '<b>'+f.flowcell_id + '</b> Lanes No.: '+','.join(lanes)+' ('+rundate+')'
+ arFCLanes.append(entry)
+ if len(arFCLanes)==0:
+ arFCLanes.append('<font color=red>Flowcell not found.</font>')
+ return arFCLanes
+
+ def ab_batch(self):
+ ## To have the Company's lot number, apearing on the (source) tube, we need to add new Field in Library.
+ arlibs = self.getLibIds()
+ tstr = '<ul>' ##<u><b>Ab</b> from '+len(arlibs).__str__()+' libs</u>: '
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l,antibody__isnull=False)
+ arRows.append('<li>'+rec.antibody.antibodies+' for <b>'+rec.antibody.antigene+'</b> (src:'+rec.antibody.source+', cat:'+rec.antibody.catalog+')</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(unique(arRows))+'</ul>'
+ return tstr
+ ab_batch.allow_tags = True
+
+ def cell_line(self):
+ arlibs = self.getLibIds()
+ tstr = '<ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.cell_line.cellline_name+'</b> ('+rec.condition.condition_name+')</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(unique(arRows))+'</ul>'
+ return tstr
+ cell_line.allow_tags = True
+
+ def cell_harvest_batch(self): # <- data now displayed in "cell_line"
+ ## name + date
+ arlibs = self.getLibIds()
+ tstr = '<ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.condition.condition_name+'</b></li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(unique(arRows))+'</ul>'
+ return tstr
+ cell_harvest_batch.allow_tags = True
+
+ def ChIP_made(self):
+ ## person + date
+ return '...'
+
+ def library(self):
+ ## Lib Id + Date + Person
+ tstr = '<script>'
+ tstr += 'function togit(eid){'
+ tstr += 'f=document.getElementById(eid);'
+ tstr += 'if(f.style.display==\'none\'){'
+ tstr += 'f.style.display=\'block\';'
+ tstr += '}else{'
+ tstr += 'f.style.display=\'none\';'
+ tstr += '}'
+ tstr += '}'
+ tstr += '</script>'
+ arlibs = self.getLibIds() ##.sort()
+ arlibs = arlibs
+ tstr +='<a href=# onClick="togit(\'libInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="libInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
+ arRows = []
+ for l in arlibs:
+ try:
+ rec = Library.objects.get(library_id=l)
+ arRows.append('<li><b>'+rec.library_id+'</b>: '+rec.library_name+'.<br/>Made By: '+rec.made_by+', On: '+ rec.creation_date.__str__()+'</li>')
+ except ObjectDoesNotExist:
+ tstr += ""
+ tstr += "".join(unique(arRows))+'</ul></div>'
+ return tstr
+ library.allow_tags = True
+
+
+ ## -- SEQUENCING SECTION
+ def sequencing(self):
+ ## FCId + Lane + Date
+ arlibs = self.getLibIds()
+ tstr ='<a href=# onClick="togit(\'seqInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="seqInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
+ for l in arlibs:
+ tstr += '<li><b>'+l+'</b>:<br/>'+(' / '.join(self.getFCInfo(l)))+'</li>'
+ tstr += '</ul></div>'
+ return tstr
+ sequencing.allow_tags = True
+
+ def aligned_reads(self):
+ ## Mega reads/lane
+ arlibs = self.getLibIds()
+ tstr = '<a href=# onClick="togit(\'readsInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+ tstr += '<div id="readsInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto">'
+ tstr += '<table><tr><td>Library Id</td><td>Total Lanes</td><td>M Reads</td></tr>'
+ LanesCnt, ReadsCnt = 0, 0
+ for l in arlibs:
+ res = getLibReads(l)
+ LanesCnt += res[0]
+ ReadsCnt += res[1]
+ rc = "%1.2f" % (res[1]/1000000.0)
+ tstr += '<tr><td><b>'+l+'</b></td><td>'+res[0].__str__()+'</td></td><td>'+rc+'</td></tr>'
+ tstr += '</table>'
+ #tstr += '<a target=_blank href="http://m304-apple-server.stanford.edu/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
+ tstr += '</div>'
+ myNum = (ReadsCnt/1000000.0)
+ myNum = "%1.2f" % (myNum)
+ tstr += '<div>Total: <b>'+LanesCnt.__str__()+'</b> lanes and <b>'+myNum+'</b> M Reads</div>'
+ tstr += '<a target=_blank href="http://m304-apple-server.stanford.edu/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
+ return tstr
+ aligned_reads.allow_tags = True
+
+ def peak_calling(self):
+ # date + what etc..
+ return 'coming up ..'
+
+ QPCR = models.CharField(max_length=500,blank=True,null=True)
+ submitted_to_DCC = models.DateTimeField(core=True,blank=True,null=True)
+ submitted_to_NCBI = models.DateTimeField(core=True,blank=True,null=True)
+ note_about_DCC = models.TextField(blank=True)
+ note_about_NCBI = models.TextField(blank=True)
+
+ def __str__(self):
+ return '"%s" - %s' % (self.st_sbj,self.interactome_complete)
+
+ class Meta:
+ #verbose_name_plural = "Reports"
+ ordering = ["id"]
+
+ class Admin:
+ list_display = ('Study','ab_batch','cell_line','library','sequencing','aligned_reads','QPCR','submit_to_DCC','submit_to_NCBI','interactome_complete')
+ ## list_filter = ('interactome_complete')
+
+
+#############################################
--- /dev/null
+def unique(s):
+ """Return a list of the elements in s, but without duplicates.
+ For example, unique([1,2,3,1,2,3]) is some permutation of [1,2,3],
+ unique("abcabc") some permutation of ["a", "b", "c"], and
+ unique(([1, 2], [2, 3], [1, 2])) some permutation of
+ [[2, 3], [1, 2]].
+ For best speed, all sequence elements should be hashable. Then
+ unique() will usually work in linear time.
+ If not possible, the sequence elements should enjoy a total
+ ordering, and if list(s).sort() doesn't raise TypeError it's
+ assumed that they do enjoy a total ordering. Then unique() will
+ usually work in O(N*log2(N)) time.
+ If that's not possible either, the sequence elements must support
+ equality-testing. Then unique() will usually work in quadratic
+ time.
+ """
+
+ n = len(s)
+ if n == 0:
+ return []
+
+ # Try using a dict first, as that's the fastest and will usually
+ # work. If it doesn't work, it will usually fail quickly, so it
+ # usually doesn't cost much to *try* it. It requires that all the
+ # sequence elements be hashable, and support equality comparison.
+ u = {}
+ try:
+ for x in s:
+ u[x] = 1
+ except TypeError:
+ del u # move on to the next method
+ else:
+ return u.keys()
+ # We can't hash all the elements. Second fastest is to sort,
+ # which brings the equal elements together; then duplicates are
+ # easy to weed out in a single pass.
+ # NOTE: Python's list.sort() was designed to be efficient in the
+ # presence of many duplicate elements. This isn't true of all
+ # sort functions in all languages or libraries, so this approach
+ # is more effective in Python than it may be elsewhere.
+ try:
+ t = list(s)
+ t.sort()
+ except TypeError:
+ del t # move on to the next method
+ else:
+ assert n > 0
+ last = t[0]
+ lasti = i = 1
+ while i < n:
+ if t[i] != last:
+ t[lasti] = last = t[i]
+ lasti += 1
+ i += 1
+ return t[:lasti]
+ # Brute force is all that's left.
+ u = []
+ for x in s:
+ if x not in u:
+ u.append(x)
+ return u
--- /dev/null
+from django.db import models
+from django.contrib.auth.models import User
+from htsworkflow.frontend import settings
+from htsworkflow.reports.libinfopar import *
+
+# Create your models here.
+
+class Antibody(models.Model):
+ antigene = models.CharField(max_length=500, db_index=True)
+ # New field Aug/20/08
+ # SQL to add column: alter table fctracker_antibody add column "nickname" varchar(20) NULL;
+ nickname = models.CharField(max_length=20,blank=True,null=True, db_index=True,verbose_name = 'Short Name')
+ catalog = models.CharField(max_length=50, unique=True, db_index=True)
+ antibodies = models.CharField(max_length=500, db_index=True)
+ source = models.CharField(max_length=500, blank=True, db_index=True)
+ biology = models.TextField(blank=True)
+ notes = models.TextField(blank=True)
+ def __str__(self):
+ return '%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
+ class Meta:
+ verbose_name_plural = "antibodies"
+ ordering = ["antigene"]
+ class Admin:
+ list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
+ list_filter = ('antibodies','source')
+ fields = (
+ (None, {
+ 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
+ }),
+ )
+
+class Cellline(models.Model):
+ cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
+ notes = models.TextField(blank=True)
+ def __str__(self):
+ return '%s' % (self.cellline_name)
+
+ class Meta:
+ ordering = ["cellline_name"]
+
+ class Admin:
+ fields = (
+ (None, {
+ 'fields': (('cellline_name'),('notes'),)
+ }),
+ )
+
+class Condition(models.Model):
+ condition_name = models.CharField(max_length=2000, unique=True, db_index=True)
+ notes = models.TextField(blank=True)
+ def __str__(self):
+ return '%s' % (self.condition_name)
+
+ class Meta:
+ ordering = ["condition_name"]
+
+ class Admin:
+ fields = (
+ (None, {
+ 'fields': (('condition_name'),('notes'),)
+ }),
+ )
+
+class Species(models.Model):
+
+ scientific_name = models.CharField(max_length=256, unique=False, db_index=True, core=True)
+ common_name = models.CharField(max_length=256, blank=True)
+ use_genome_build = models.CharField(max_length=100, blank=False, null=False)
+
+ def __str__(self):
+ return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build)
+
+ class Meta:
+ verbose_name_plural = "species"
+ ordering = ["scientific_name"]
+
+ class Admin:
+ fields = (
+ (None, {
+ 'fields': (('scientific_name', 'common_name'), ('use_genome_build'))
+ }),
+ )
+
+class Affiliation(models.Model):
+ name = models.CharField(max_length=256, db_index=True, core=True,verbose_name='Group Name')
+ contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')
+ email = models.EmailField(null=True,blank=True)
+
+ def __str__(self):
+ str = self.name
+ if self.contact != '':
+ str += ' ('+self.contact+')'
+ return str
+
+ class Meta:
+ ordering = ["name","contact"]
+ unique_together = (("name", "contact"),)
+
+ class Admin:
+ list_display = ('name','contact','email')
+ fields = (
+ (None, {
+ 'fields': (('name','contact','email'))
+ }),
+ )
+
+class Library(models.Model):
+
+ library_id = models.CharField(max_length=30, primary_key=True, db_index=True, core=True)
+ library_name = models.CharField(max_length=100, unique=True, core=True)
+ library_species = models.ForeignKey(Species, core=True)
+ cell_line = models.ForeignKey(Cellline,core=True)
+ condition = models.ForeignKey(Condition,core=True)
+ antibody = models.ForeignKey(Antibody,blank=True,null=True,core=True)
+ # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256) NULL;
+ affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True,filter_interface=models.HORIZONTAL)
+ # New field Aug/19/08
+ # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
+ REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
+ replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,default=1)
+
+ EXPERIMENT_TYPES = (
+ ('INPUT_RXLCh','INPUT_RXLCh'),
+ ('ChIP-seq', 'ChIP-seq'),
+ ('Sheared', 'Sheared'),
+ ('RNA-seq', 'RNA-seq'),
+ ('Methyl-seq', 'Methyl-seq'),
+ ('DIP-seq', 'DIP-seq'),
+ )
+ experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES,
+ default='RNA-seq')
+
+ creation_date = models.DateField(blank=True, null=True)
+ made_for = models.ForeignKey(User)
+ made_by = models.CharField(max_length=50, blank=True, default="Lorian")
+
+ PROTOCOL_END_POINTS = (
+ ('?', 'Unknown'),
+ ('Sample', 'Raw sample'),
+ ('Progress', 'In progress'),
+ ('1A', 'Ligation, then gel'),
+ ('PCR', 'Ligation, then PCR'),
+ ('1Ab', 'Ligation, PCR, then gel'),
+ ('1Aa', 'Ligation, gel, then PCR'),
+ ('2A', 'Ligation, PCR, gel, PCR'),
+ ('Done', 'Completed'),
+ )
+ stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
+ amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
+
+ undiluted_concentration = models.DecimalField("Undiluted concentration (ng/ul)", max_digits=5, decimal_places=2, default=0, blank=True, null=True)
+ successful_pM = models.DecimalField(max_digits=5, decimal_places=2, blank=True, null=True)
+ ten_nM_dilution = models.BooleanField()
+ avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
+ notes = models.TextField(blank=True)
+
+ def __str__(self):
+ return '#%s: %s' % (self.library_id, self.library_name)
+
+ class Meta:
+ verbose_name_plural = "libraries"
+ ordering = ["-creation_date"] #["-library_id"]
+
+ def antibody_name(self):
+ return self.antibody.nickname
+
+ def org(self):
+ return self.library_species.common_name
+
+ def affiliation(self):
+ affs = self.affiliations.all().order_by('name')
+ tstr = ''
+ ar = []
+ for t in affs:
+ ar.append(t.__str__())
+ return '%s' % (", ".join(ar))
+
+
+ def aligned_reads(self):
+ res = getLibReads(self.library_id)
+ rc = "%1.2f" % (res[1]/1000000.0)
+ # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
+ if res[0] > 0:
+ bgcolor = '#ff3300' # Red
+ rc_thr = [10000000,5000000,3000000]
+ if self.experiment_type == 'RNA-seq':
+ rc_thr = [20000000,10000000,6000000]
+
+ if res[1] > rc_thr[0]:
+ bgcolor = '#66ff66' # Green
+ else:
+ if res[1] > rc_thr[1]:
+ bgcolor ='#00ccff' # Blue
+ else:
+ if res[1] > rc_thr[2]:
+ bgcolor ='#ffcc33' # Orange
+ tstr = '<div style="background-color:'+bgcolor+';color:black">'
+ tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+ tstr += '</div>'
+ else: tstr = 'not processed yet'
+ return tstr
+ aligned_reads.allow_tags = True
+
+ class Admin:
+ date_hierarchy = "creation_date"
+ save_as = True
+ save_on_top = True
+ ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
+ search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
+ list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
+ list_display_links = ('library_id', 'library_name')
+
+ list_filter = ('experiment_type','affiliations','library_species','made_for', 'made_by','replicate')
+ fields = (
+ (None, {
+ 'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
+ }),
+ ('Creation Information:', {
+ 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'library_size'), 'notes',)
+ }),
+ ('Library/Project Affiliation:', {
+ 'fields' : (('affiliations'),)
+ }),
+ )
+
--- /dev/null
+# Create your views here.
\ No newline at end of file
+"""
+Generate settings for the Django Application.
+
+To make it easier to customize the application the settings can be
+defined in a configuration file read by ConfigParser.
+
+The options understood by this module are (with their defaults):
+
+ [frontend]
+ email_host=localhost
+ email_port=25
+ database_engine=sqlite3
+ database_name=/path/to/db
+
+ [admins]
+ #name1=email1
+
+ [allowed_hosts]
+ #name1=ip
+ localhost=127.0.0.1
+
+ [allowed_analysis_hosts]
+ #name1=ip
+ localhost=127.0.0.1
+
+"""
+import ConfigParser
import os
+def options_to_list(dest, section_name):
+ """
+ Load a options from section_name and store in a dictionary
+ """
+ if options.has_section(section_name):
+ for name in options.options(section_name):
+ dest.append( options.get(section_name, name) )
+
+def options_to_dict(dest, section_name):
+ """
+ Load a options from section_name and store in a dictionary
+ """
+ if options.has_section(section_name):
+ for name in options.options(section_name):
+ dest[name] = options.get(section_name, name)
+
+# define your defaults here
+options = ConfigParser.SafeConfigParser(
+ { 'email_host': 'localhost',
+ 'email_port': '25',
+ 'database_engine': 'sqlite3',
+ 'database_name':
+ os.path.abspath('/htsworkflow/htswfrontend/dev_fctracker.db'),
+ 'time_zone': 'America/Los_Angeles',
+ })
+
+options.read([os.path.expanduser("~/.htsworkflow.ini"),
+ '/etc/htsworkflow.ini',])
+
# Django settings for elandifier project.
DEBUG = True
TEMPLATE_DEBUG = DEBUG
-ADMINS = (
- # ('Your Name', 'your_email@domain.com'),
-)
+ADMINS = []
+options_to_list(ADMINS, 'admins')
MANAGERS = ADMINS
-DATABASE_ENGINE = 'sqlite3' # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
-DATABASE_NAME = os.path.abspath('../../fctracker.db') # Or path to database file if using sqlite3.
+EMAIL_HOST = options.get('frontend', 'email_host')
+EMAIL_PORT = int(options.get('frontend', 'email_port'))
+
+# 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
+DATABASE_ENGINE = options.get('frontend', 'database_engine')
+
+# Or path to database file if using sqlite3.
+DATABASE_NAME = options.get('frontend', 'database_name' )
DATABASE_USER = '' # Not used with sqlite3.
DATABASE_PASSWORD = '' # Not used with sqlite3.
DATABASE_HOST = '' # Set to empty string for localhost. Not used with sqlite3.
# although not all variations may be possible on all operating systems.
# If running in a Windows environment this must be set to the same as your
# system time zone.
-TIME_ZONE = 'America/Los_Angeles'
+TIME_ZONE = options.get('frontend', 'time_zone')
# Language code for this installation. All choices can be found here:
# http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
# Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
# Always use forward slashes, even on Windows.
# Don't forget to use absolute paths, not relative paths.
- os.path.abspath("../../templates"),
+ os.path.abspath("../templates"),
)
INSTALLED_APPS = (
'django.contrib.sites',
'htsworkflow.frontend.eland_config',
'htsworkflow.frontend.fctracker',
+ # modules from htsworkflow branch
+ #'htswfrontend.exp_track',
+ #'htswfrontend.analys_track',
+ #'htswfrontend.htsw_reports',
'django.contrib.databrowse',
)
# Project specific settings
-UPLOADTO_HOME = os.path.abspath('../../uploads')
-UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
-UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
-UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
+ALLOWED_IPS={'localhost': '127.0.0.1'}
+options_to_dict(ALLOWED_IPS, 'allowed_hosts')
+
+ALLOWED_ANALYS_IPS = {'localhost': '127.0.0.1'}
+options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
+#UPLOADTO_HOME = os.path.abspath('../../uploads')
+#UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
+#UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
+#UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
(r'^eland_config/', include('htsworkflow.frontend.eland_config.urls')),
# Admin:
(r'^admin/', include('django.contrib.admin.urls')),
- # Databrowser:
- (r'^databrowse/(.*)', databrowse.site.root),
+ # ExpTrack:
+ (r'^experiments/', include('htswfrontend.experiments.et_urls')),
+ # AnalysTrack:
+ (r'^analysis/', include('htswfrontend.analysis.an_urls')),
+ # Report Views:
+ # (r'^reports/', include('gaworkflow.frontend....urls')),
)
projects / htsworkflow.git / commitdiff