--- /dev/null
+# some core functions of analysis manager module
+from django.http import HttpResponse
+from datetime import datetime
+from string import *
+import re
+from gaworkflow.frontend import settings
+from gaworkflow.frontend.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)
--- /dev/null
+from django.db import models
+from datetime import datetime
+from gaworkflow.frontend.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',)
+ 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)
+ 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 = ('...',)
+ fields = (
+ (None, {
+ 'fields': (('project_name'),('tasks'),('project_notes'))}),
+ )
projects / htsworkflow.git / commitdiff