htswfrontend/htswfrontend/htsw_reports/q_reports.py

   1 from htswfrontend.exp_track.models import *
   2 from django.http import HttpResponse
   3 from django.core.exceptions import ObjectDoesNotExist
   4 from django.shortcuts import render_to_response, get_object_or_404
   5
   6 arMonth = {"01":"Jan","02":"Feb","03":"Mar","04":"Apr","05":"May","06":"Jun","07":"Jul","08":"Aug","09":"Sep","10":"Oct","11":"Nov","12":"Dec"}
   7 def getBgColor(reads_cnt,exp_type):
   8   # Color Scheme: green is more than 12M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds are ~ double
   9   bgcolor = '#ffcdd0'  # Red is the color for minimum read counts
  10   rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
  11   if exp_type == 'RNA-seq':
  12     rc_thr = [20000000,10000000,6000000]
  13
  14   if reads_cnt > rc_thr[0]:
  15     bgcolor = '#66ff66'  # Green
  16   else:
  17     if reads_cnt > rc_thr[1]:
  18       bgcolor ='#00ccff'  # Blue
  19     else:
  20        if reads_cnt > rc_thr[2]:
  21          bgcolor ='#ffcc33'  # Orange
  22   #tstr = '<div style="background-color:'+bgcolor+';color:black">'
  23   #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
  24   #tstr += '</div>'
  25
  26   return bgcolor
  27
  28 def q_report1(request):
  29   if not request.user.is_authenticated():
  30     str = '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
  31     return render_to_response('htsw_reports/report.html',{'main':str})
  32
  33   EXP = 'ChIP-seq'
  34
  35   if request.has_key('aflid'):
  36     AFL_Id = request['aflid']
  37     try:
  38       AFL = Affiliation.objects.get(id=AFL_Id).name
  39       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
  40     except ObjectDoesNotExist:
  41       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
  42   else:
  43     AFL = 'ENCODE_Tier1'
  44     AFL_CNT = ''
  45     try:
  46       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
  47     except ObjectDoesNotExist:
  48       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
  49
  50   if request.user.username == 'caltech':
  51     if AFL.find('ENCODE') < 0:  return HttpResponse('Record Not Found <div style="margin-right:20px"><a target=_self href="/admin" target=_self>HOME</a></div>')
  52
  53   ### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Q REPORT PART ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  54   start_date = datetime(2009,01,01).date().__str__()
  55   end_date = datetime(2011,01,01)
  56   end_date_text = ''
  57
  58   if request.has_key('start_date'):
  59     start_date = request['start_date']
  60
  61   if request.has_key('end_date'):
  62     end_date = request['end_date']
  63   else: #end_date = today
  64     end_date = end_date.now().date().__str__()
  65     end_date_text = ' (Today)'
  66
  67   DRuns = []
  68   if start_date and end_date:
  69     start_date = datetime(int(start_date.split('-')[0]),int(start_date.split('-')[1]),int(start_date.split('-')[2]),0,0,0)
  70     end_date = datetime(int(end_date.split('-')[0]),int(end_date.split('-')[1]),int(end_date.split('-')[2]),0,0,0)
  71     DRuns = DataRun.objects.filter(run_start_time__range=(start_date, end_date))
  72
  73   QReportText = ''
  74   QReportText += '<div><span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">HOME</a></span><h2>Time Report Generator for ChIP-Seq</h2></div>'
  75   QReportText += '<form action="" method="get" id="qreport_form">'
  76   QReportText += '<p>'
  77   QReportText += EXP+' <select onchange="window.location=\'/htsw_reports/q_report?start_date='+start_date.date().__str__()+'&end_date='+end_date.date().__str__()+'&aflid=\'+this.options[selectedIndex].value; return false;">'
  78
  79   if request.user.username == 'caltech':
  80     Affil_List = Affiliation.objects.filter(name__contains='ENCODE').distinct()
  81   else:
  82     Affil_List = Affiliation.objects.distinct()
  83
  84   for af in Affil_List:
  85     QReportText += '<option value='+af.id.__str__()
  86     if AFL_Id == af.id.__str__():
  87       QReportText += ' selected'
  88     QReportText += '>'+af.name+' '+af.contact+'</option>'
  89   QReportText += '</select>'
  90   QReportText += '&nbsp;&nbsp;&nbsp;&nbsp; Start Date: '
  91   QReportText += '<input type="text" maxlength="10" value="'+start_date.date().__str__()+'" size="10" name="start_date" />'  # class="vDateField" />' # id="id_run_start_time_date"/>'
  92   QReportText += '&nbsp;&nbsp;&nbsp;&nbsp;End Date: <input type="text" maxlength="10" value="'+end_date.date().__str__()+'" size="10" name="end_date" />'
  93   #QReportText += '<span><a href="javascript:DateTimeShortcuts.handleCalendarQuickLink(0, 0);">Today</a> | <a href="javascript:DateTimeShortcuts.openCalendar(0);" id="calendarlink0">'
  94   #QReportText += '<img src="http://myerslab.stanford.edu/media/img/admin/icon_calendar.gif" alt="Calendar"/></a></span>'
  95   #QReportText += 'End Date: <input type="text" maxlength="10" value="" size="10" name="end_date" class="vDateField required" id="end_date"/><span><a href="javascript:DateTimeShortcuts.handleCalendarQuickLink(0, 0);">Today</a> | <a href="javascript:DateTimeShortcuts.openCalendar(0);" id="calendarlink0"><img src="http://myerslab.stanford.edu/media/img/admin/icon_calendar.gif" alt="Calendar"/></a></span>'
  96   QReportText += '<span style="margin-left:10px"><input type="submit" value="Run Report" name="runreport"  /></span></p>'
  97
  98   QReportText +='<div style="border:solid #cccccc 1px;padding:2px;background-color:#FFFFCC;margin-top:5px">'
  99   s_year = start_date.date().__str__().split("-")[0]
 100   s_month = start_date.date().__str__().split("-")[1]
 101   s_day = start_date.date().__str__().split("-")[2]
 102   e_year = end_date.date().__str__().split("-")[0]
 103   e_month = end_date.date().__str__().split("-")[1]
 104   e_day = end_date.date().__str__().split("-")[2]
 105   QReportText += '<h2>For <u>'+AFL+'</u> <u>'+AFL_CNT+'</u>'+' between <u>'+s_year+'-'+arMonth[s_month]+'-'+s_day+'</u> and <u>'+e_year+'-'+arMonth[e_month]+'-'+e_day+end_date_text+'</u></h2>'
 106   QReportText +='<div style="float:left">'
 107   FCText = '<h4>The following Flowcells were sequenced:</h4>'
 108   FCText += '<table border=1><tr><th>Flowcell Id</th><th>Ran On</th></tr>'
 109   libidlist = []
 110   LIB_LANE_COUNT = {}
 111   LIB_FC_SUMMARY = {}
 112   for DR in  DRuns:
 113    libidlist.append(DR.fcid.lane_1_library.library_id)
 114    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_1_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_1_library.library_id] += 1
 115    #else: LIB_LANE_COUNT[DR.fcid.lane_1_library.library_id] = 1
 116    libidlist.append(DR.fcid.lane_2_library.library_id)
 117    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_2_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_2_library.library_id] += 1
 118    #else: LIB_LANE_COUNT[DR.fcid.lane_2_library.library_id] = 1
 119    libidlist.append(DR.fcid.lane_3_library.library_id)
 120    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_3_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_3_library.library_id] += 1
 121    #else: LIB_LANE_COUNT[DR.fcid.lane_3_library.library_id] = 1
 122    libidlist.append(DR.fcid.lane_4_library.library_id)
 123    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_4_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_4_library.library_id] += 1
 124    #else: LIB_LANE_COUNT[DR.fcid.lane_4_library.library_id] = 1
 125    libidlist.append(DR.fcid.lane_5_library.library_id)
 126    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_5_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_5_library.library_id] += 1
 127    #else: LIB_LANE_COUNT[DR.fcid.lane_5_library.library_id] = 1
 128    libidlist.append(DR.fcid.lane_6_library.library_id)
 129    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_6_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_6_library.library_id] += 1
 130    #else: LIB_LANE_COUNT[DR.fcid.lane_6_library.library_id] = 1
 131    libidlist.append(DR.fcid.lane_7_library.library_id)
 132    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_7_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_7_library.library_id] += 1
 133    #else: LIB_LANE_COUNT[DR.fcid.lane_7_library.library_id] = 1
 134    libidlist.append(DR.fcid.lane_8_library.library_id)
 135    #if LIB_LANE_COUNT.has_key(DR.fcid.lane_8_library.library_id): LIB_LANE_COUNT[DR.fcid.lane_8_library.library_id] += 1
 136    #else: LIB_LANE_COUNT[DR.fcid.lane_8_library.library_id] = 1
 137    for i in range(1,9):
 138      if LIB_LANE_COUNT.has_key(eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')): LIB_LANE_COUNT[eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')] += 1
 139      else: LIB_LANE_COUNT[eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')] = 1
 140      if LIB_FC_SUMMARY.has_key(eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')): LIB_FC_SUMMARY[eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')] += '<br/>'+DR.fcid.flowcell_id+' (lane '+i.__str__()+')'
 141      else: LIB_FC_SUMMARY[eval('DR.fcid.lane_'+i.__str__()+'_library.library_id')] = DR.fcid.flowcell_id+' (lane '+i.__str__()+')'
 142
 143    FCText += '<tr><td>'+DR.fcid.flowcell_id+'</td><td>'+DR.run_start_time.__str__()+'</td></tr>'
 144
 145   FCText += '</table>'
 146
 147   ## RelevantLibs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,library_id__in=libidlist).order_by('antibody','cell_line')
 148
 149   if EXP == 'ChIP-seq':
 150     RelevantLibs = Library.objects.filter(experiment_type__in=[EXP,'INPUT_RXLCh'],affiliations__name=AFL,affiliations__contact=AFL_CNT,library_id__in=libidlist).order_by('antibody','cell_line')
 151   else:
 152     RelevantLibs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,library_id__in=libidlist).order_by('antibody','cell_line')
 153
 154   rliblist = []
 155
 156   QReportText +='<div style="float:left">'
 157   QReportText += '<h4>'
 158   if RelevantLibs:
 159     QReportText += 'The following <u>'+len(RelevantLibs).__str__()+'</u> '
 160   else:
 161     QReportText += 'No '
 162   QReportText += EXP+' Libraries  were sequenced:</h4>'
 163   QReportText += '<div style="width:200px;background-color:#cccccc;font-size:90%">(bad libraries marked in grey)</div>'
 164   QReportText += '<table border=1><tr><th>Library Id</th><th>Antibody</th><th>Cell line</th><th>Condition</th><th>Replicate</th><th>Lanes ran (during this period)</th></tr>'
 165   for rlib in RelevantLibs:
 166     bgColor = ''
 167     if rlib.libtags().find('Bad library')!=-1: bgColor='#cccccc'
 168     QReportText += '<tr style="background-color:'+bgColor+'"><td><a title="View Library Record" target=_self href=/admin/fctracker/library/?q='+rlib.library_id+'>'+rlib.library_id+'</a></td>'
 169     if rlib.antibody is not None: QReportText += '<td>'+rlib.antibody.nickname+'</td>'
 170     else:
 171       if rlib.experiment_type == 'INPUT_RXLCh':  QReportText += '<td>[INPUT_RXLCh]</td>'
 172       else: QReportText += '<td>none</td>'
 173
 174     QReportText += '<td>'+rlib.cell_line.nickname+'</td>'
 175     QReportText += '<td>'+rlib.condition.nickname+'</td>'
 176     QReportText += '<td>Rep'+rlib.replicate.__str__()+'</td>'
 177     QReportText += '<td><a  title="View Data Runs Record" target=_self href=/admin/exp_track/datarun/?q='+rlib.library_id+'&run_start_time__gte='+start_date.date().__str__()+'&run_start_time__lte='+end_date.date().__str__()+'>'+LIB_LANE_COUNT[rlib.library_id].__str__()+' lanes</a>'
 178     QReportText += '<span style="margin-left:40px;cursor:pointer;color:#5B80B2" onClick="el=document.getElementById(\'d_'+rlib.library_id+'\');if(el){el.style.display=(el.style.display==\'none\'?\'block\':\'none\');}">details..</span><div id=d_'+rlib.library_id+'  style="display:none;border:solid 1px #cccccc;padding:3px;width:150px;max-hight:200px;overflow:auto">'+LIB_FC_SUMMARY[rlib.library_id]+'</div>'
 179     QReportText += '</td>'
 180     QReportText += '</tr>'
 181
 182   QReportText += '</table>'
 183   QReportText +='</div>'
 184   QReportText +='<div style="float:left;margin-left:100px">'+FCText+'</div>'
 185
 186   QReportText += '</div>'
 187
 188   return render_to_response('htsw_reports/report.html',{'main': QReportText})
 189   ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ END OF Q REPORT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 190
 191   TFall = Library.objects.values('antibody').order_by('antibody').distinct()
 192   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 193
 194   TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,library_id__in=libidlist)
 195   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 196
 197   # Check Replicate numbers
 198   Reps = 1
 199   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 200   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 201
 202   ########
 203   str = ''
 204   str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">HOME</a></span>'
 205   ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
 206   str += '<span>Select another <b>'+EXP+'</b> Report:</span>  <select onchange="window.location=\'/htsw_reports/report?aflid=\'+this.options[selectedIndex].value; return false;">'
 207   for af in Affiliation.objects.distinct():
 208     str += '<option value='+af.id.__str__()
 209     if AFL_Id == af.id.__str__():
 210       str += ' selected'
 211     str += '>'+af.name+' '+af.contact+'</option>'
 212   str += '</select>'
 213
 214   str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> >  5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 3 M</span></span>'
 215
 216   str += '<span style="margin-left:20px">'
 217   str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 218   str += '  | '
 219   str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 220   str += '<span style="margin-left:20px">(db: '+settings.DB_NAME+')</span>'
 221
 222   str += QReportText
 223
 224   bgc = '#ffffff'
 225   pbgc = '#f7f7f7'
 226   str += '<table border=1 style="margin-top:5px">'
 227   str += '<tr><th style="text-align:right">PROJECT</th><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>'
 228   str += '<tr><th style="text-align:right">CELL LINE</th>'
 229   for H in CLLs:
 230     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 231     tbgc = bgc
 232     bgc = pbgc
 233     pbgc = tbgc
 234   str += '</tr><tr><th style="text-align:left">TF</th>'
 235   bgc = '#ffffff'
 236   pbgc = '#f7f7f7'
 237   for H in CLLs:
 238     for r in range(1,Reps+1):
 239       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 240     tbgc = bgc
 241     bgc = pbgc
 242     pbgc = tbgc
 243   str += '</tr>'
 244   str += '<tr><td align=right><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&experiment_type__exact=INPUT_RXLCh>Total Chromatin</a></td>'
 245   bgc = '#ffffff'
 246   pbgc = '#f7f7f7'
 247   for H in CLLs:
 248     for r in range(1,Reps+1):
 249       repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r,library_id__in=libidlist)
 250
 251       ### TO DO: Replace the above query with: Get DataRuns by StartRunDate BETWEEN FROM_DATE and TO_DATE, Get DataRun.Flowcell.Library records.
 252
 253       str += "<td align=center style='background-color:"+bgc+"'>"
 254       if len(repReads) == 0:
 255         str += 'No Libraries'
 256       else:
 257         cnt = 0
 258         for R1 in repReads:
 259           rres = R1.aligned_m_reads()
 260           # Check data sanlty
 261           if rres[2] != 'OK':
 262             str += '<div style="border:solid red 2px">'+rres[2]
 263           else:
 264             cnt = rres[1]
 265             if cnt > 0:
 266               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
 267               str += "%1.2f" % (cnt/1000000.0)+" M"
 268             else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
 269           str += "<div style='font-size:70%'><a title='View Library Record' target=_self style='font-weight:bold;color:black' href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+" ("+rres[0].__str__()+" lanes)</a>, "+R1.condition.nickname
 270           if R1.libtags().find('Data submitted to DCC') != -1:
 271             str += "<div style='border:solid #666666 1px;'>data submitted</div>"
 272           str += "</div>"
 273           str += "</div>"
 274       str += '</td>'
 275     tbgc = bgc
 276     bgc = pbgc
 277     pbgc = tbgc
 278   str += '</tr>'
 279
 280   for T in TFs:
 281     str += '<tr>'
 282     try:
 283       if T['antibody']:
 284         str += '<td><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&antibody__id__exact='+T['antibody'].__str__()+'>'+Antibody.objects.get(id=T['antibody']).nickname+'</a></td>'
 285     except Antibody.DoesNotExist:
 286       str += '<td>n/a</td>'
 287
 288     bgc = '#ffffff'
 289     pbgc = '#f7f7f7'
 290     for H in CLLs:
 291       for r in range(1,Reps+1):
 292         repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),antibody=T['antibody'].__str__(),replicate=r,library_id__in=libidlist)
 293         str += "<td align=center style='background-color:"+bgc+"'>"
 294         if len(repReads) == 0:
 295           str += 'No Libraries'
 296         else:
 297           cnt = 0
 298           for R1 in repReads:
 299             rres = R1.aligned_m_reads()
 300             # Check data sanity
 301             if rres[2] != 'OK':
 302               str += '<div style="border:solid red 2px">'+rres[2]
 303             else:
 304               cnt = rres[1]
 305               if cnt > 0:
 306                 str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%;margin:2px'>"
 307                 str += "%1.2f" % (cnt/1000000.0)+" M"
 308               else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
 309             str += "<div style='font-size:70%'><a title='View Library Record' target=_self style='font-weight:bold;color:black' href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+" ("+rres[0].__str__()+" lanes)</a>, "+R1.condition.nickname
 310             if R1.libtags().find('Data submitted to DCC') != -1:
 311               str += "<div style='border:solid #666666 1px;'>data submitted</div>"
 312             str += "</div>"
 313             str += "</div>"
 314         str += '</td>'
 315       tbgc = bgc
 316       bgc = pbgc
 317       pbgc = tbgc
 318     str += '</tr>'
 319   str += '</table>'
 320
 321   return render_to_response('htsw_reports/report.html',{'main': str})
 322
 323
 324 def report_RM(request): #for RNA-Seq and Methyl-Seq
 325   if not request.user.is_authenticated():
 326     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 327     return render_to_response('htsw_reports/report.html',{'main':str})
 328
 329   EXP = 'RNA-seq'
 330
 331   if request.has_key('exp'):
 332     EXP = request['exp'] # Methyl-seq
 333
 334   if request.has_key('aflid'):
 335     AFL_Id = request['aflid']
 336     try:
 337       AFL = Affiliation.objects.get(id=AFL_Id).name
 338       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
 339     except ObjectDoesNotExist:
 340       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
 341   else:
 342     AFL = 'ENCODE_Tier1'
 343     AFL_CNT = ''
 344     try:
 345       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
 346     except ObjectDoesNotExist:
 347       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 348
 349   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 350   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 351
 352   ########
 353   # Check Replicate numbers
 354   Reps = 1
 355   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 356   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 357
 358   str = ''
 359   str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self" style="font-size:140%">HOME</a></span>'
 360   str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select onchange="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid=\'+this.options[selectedIndex].value; return false;">'
 361   for af in Affiliation.objects.distinct():
 362     str += '<option value='+af.id.__str__()
 363     if AFL_Id == af.id.__str__():
 364       str += ' selected'
 365     str += '>'+af.name+' '+af.contact+'</option>'
 366   str += '</select>'
 367
 368   if EXP == 'RNA-seq':
 369     str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 20 M</span><span style="margin-left:5px;background-color:#00ccff"> >  10 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 6 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 6 M</span></span>'
 370     str += '<span style="margin-left:20px">'
 371     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 372     str += '  | '
 373     str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 374   else:
 375     str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> >  5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 3 M</span></span>'
 376     str += '<span style="margin-left:20px">'
 377     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 378     str += '  | '
 379     str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 380
 381   str += '<br/><br/><table border=1>'
 382   str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
 383   str += '<tr>'
 384   bgc = '#ffffff'
 385   pbgc = '#f7f7f7'
 386   for H in CLLs:
 387     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 388     tbgc = bgc
 389     bgc = pbgc
 390     pbgc = tbgc
 391   str += '</tr><tr>'
 392   bgc = '#ffffff'
 393   pbgc = '#f7f7f7'
 394   for H in CLLs:
 395     for r in range(1,Reps+1):
 396       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 397     tbgc = bgc
 398     bgc = pbgc
 399     pbgc = tbgc
 400   str += '</tr>'
 401
 402   str += '<tr>'
 403   bgc = '#ffffff'
 404   pbgc = '#f7f7f7'
 405   for H in CLLs:
 406     for r in range(1,Reps+1):
 407       repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
 408       str += "<td align=center valign=top style='background-color:"+bgc+"'>"
 409       if len(repReads) == 0:
 410         str += 'No Libraries'
 411       else:
 412         cnt = 0
 413         for R1 in repReads:
 414           rres = R1.aligned_m_reads()
 415           # Check data sanlty
 416           if rres[2] != 'OK':
 417             str += '<div style="border:solid red 2px">'+rres[2]
 418           else:
 419             cnt = rres[1]
 420             if cnt > 0:
 421               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
 422               str += "%1.2f" % (cnt/1000000.0)+" M"
 423             else:  str += "<div style='background-color:#ffcdd0;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
 424           str += "<div style='font-size:80%'><a title='View Record' style='color:black' target=_self href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+" ("+rres[0].__str__()+" lanes)</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
 425           str += "<div style='font-size:70%'>\""+R1.library_name+"\""
 426           if R1.libtags().find('Data submitted to DCC') != -1:
 427             str += "<div style='width:75%;border:solid #666666 1px;'>data submitted</div>"
 428           str += "</div>"
 429           str += "</div>"
 430       str += '</td>'
 431     tbgc = bgc
 432     bgc = pbgc
 433     pbgc = tbgc
 434   str += '</tr>'
 435   str += '</table>'
 436
 437   return render_to_response('htsw_reports/report.html',{'main': str})
 438
 439 def getNotRanFCs(request):
 440   if not request.user.is_authenticated():
 441     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 442     return render_to_response('htsw_reports/report.html',{'main':str})
 443
 444   FCall = FlowCell.objects.order_by('-run_date').distinct()
 445   str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
 446   for f in FCall:
 447     try:
 448       t = DataRun.objects.get(fcid=f.id)
 449     except ObjectDoesNotExist:
 450       str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
 451   str += "</table>"
 452   return render_to_response('htsw_reports/report.html',{'main':str})
 453
 454 def test_Libs(request):
 455   if not request.user.is_authenticated():
 456     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 457     return render_to_response('htsw_reports/report.html',{'main':str})
 458
 459   str = ''
 460   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>'
 461   allLibs = Library.objects.all()
 462   #allLibs = Library.objects.filter(antibody__isnull=False)
 463   for L in allLibs:
 464     str += '<tr>'
 465     str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
 466     str += '<td>'
 467     str += L.experiment_type+'_'
 468     if L.cell_line.cellline_name != 'Unknown':
 469       str += L.cell_line.cellline_name+'_'
 470
 471     try:
 472       if L.antibody is not None:
 473         str += L.antibody.nickname + '_'
 474     except Antibody.DoesNotExist:
 475       pass
 476
 477     str += 'Rep'+L.replicate.__str__()
 478     str += '</td></tr>'
 479
 480   str += '</table>'
 481   return HttpResponse(str)