From: Rami Rauch <rrauch@stanford.edu>
Date: Fri, 7 Nov 2008 00:44:40 +0000 (+0000)
Subject: Progress Reports Generator
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=348910598256a535290a99e1a8fb97d92b7138a5

Progress Reports Generator
---

diff --git a/htswfrontend/htswfrontend/htsw_reports/reports.py b/htswfrontend/htswfrontend/htsw_reports/reports.py
new file mode 100755
index 0000000..b6496f0
--- /dev/null
+++ b/htswfrontend/htswfrontend/htsw_reports/reports.py
@@ -0,0 +1,293 @@
+from htswfrontend.exp_track.models import *
+from django.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
+from django.shortcuts import render_to_response, get_object_or_404
+
+def getBgColor(reads_cnt,exp_type):
+  # 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
+  bgcolor = '#ff3300'  # Red is the color for minimum read counts                                                                                                                            
+  rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
+  if exp_type == 'RNA-seq':
+    rc_thr = [20000000,10000000,6000000]
+
+  if reads_cnt > rc_thr[0]:
+    bgcolor = '#66ff66'  # Green                                                                                                                                                                                                                                               
+  else:
+    if reads_cnt > rc_thr[1]:
+      bgcolor ='#00ccff'  # Blue                                                                                                                                                                                                                                               
+    else:
+       if reads_cnt > rc_thr[2]:
+         bgcolor ='#ffcc33'  # Orange                                                                                                                                                                                                                                          
+  #tstr = '<div style="background-color:'+bgcolor+';color:black">'
+  #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+  #tstr += '</div>'
+
+  return bgcolor
+
+def report1(request):
+  EXP = 'ChIP-seq'
+
+  if request.has_key('aflid'):
+    AFL_Id = request['aflid']
+    try:
+      AFL = Affiliation.objects.get(id=AFL_Id).name
+      AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+    except ObjectDoesNotExist:
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+  else:
+    AFL = 'ENCODE_Tier1'
+    AFL_CNT = ''
+    try:
+      AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+    except ObjectDoesNotExist:
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+  
+  TFall = Library.objects.values('antibody').order_by('antibody').distinct()
+  CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+
+  TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+  CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+  # Check Replicate numbers
+  Reps = 1
+  RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+  if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+  
+  ########
+  str = ''
+  str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+  ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
+  str += '<span>Select another <b>'+EXP+'</b> Report:</span>  <select>'
+  for af in Affiliation.objects.distinct():
+    str += '<option value='+af.id.__str__()
+    if AFL_Id == af.id.__str__():
+      str += ' selected'
+    str += ' onclick="window.location=\'/htsw_reports/report?aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'  
+  str += '</select>'
+
+  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:#ff3300"> < 3 M</span></span>' 
+
+  str += '<span style="margin-left:20px">'
+  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>'
+  str += '  | '
+  str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+
+  bgc = '#ffffff' 
+  pbgc = '#f7f7f7'
+  str += '<br/><br/><table border=1 cellspacing="2">'
+  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>'
+  str += '<tr><th style="text-align:right">CELL LINE</th>'
+  for H in CLLs: 
+    str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc 
+  str += '</tr><tr><th style="text-align:left">TF</th>'
+  bgc = '#ffffff'
+  pbgc = '#f7f7f7'
+  for H in CLLs:
+    for r in range(1,Reps+1):
+      str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc
+  str += '</tr>'
+  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>'
+  bgc = '#ffffff'
+  pbgc = '#f7f7f7'
+  for H in CLLs:
+    for r in range(1,Reps+1):
+      repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
+      str += "<td align=center style='background-color:"+bgc+"'>"
+      if len(repReads) == 0:
+        str += 'No Libraries'
+      else:
+        cnt = 0
+        for R1 in repReads:
+          cnt = R1.aligned_m_reads()[1]
+          if cnt > 0:
+            str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+            str += "%1.2f" % (cnt/1000000.0)+" M"
+          else:  str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+          str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+          str += "</div>"
+      str += '</td>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc
+  str += '</tr>' 
+
+  for T in TFs:
+    str += '<tr>'
+    try:
+      if T['antibody']:
+        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>'
+    except Antibody.DoesNotExist:
+      str += '<td>n/a</td>'
+
+    bgc = '#ffffff'
+    pbgc = '#f7f7f7'
+    for H in CLLs:
+      for r in range(1,Reps+1):
+        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)
+        str += "<td align=center style='background-color:"+bgc+"'>"
+        if len(repReads) == 0: 
+          str += 'No Libraries'
+        else:
+          cnt = 0
+          for R1 in repReads:
+            cnt = R1.aligned_m_reads()[1]
+            if cnt > 0:
+              str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+              str += "%1.2f" % (cnt/1000000.0)+" M"
+            else:  str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+            str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+            str += "</div>"
+        str += '</td>'
+      tbgc = bgc
+      bgc = pbgc
+      pbgc = tbgc
+    str += '</tr>'
+  str += '</table>'
+
+  return render_to_response('htsw_reports/report.html',{'main': str})
+
+
+def report_RM(request): #for RNA-Seq and Methyl-Seq
+  EXP = 'RNA-seq'  
+
+  if request.has_key('exp'):
+    EXP = request['exp'] # Methyl-seq
+
+  if request.has_key('aflid'):
+    AFL_Id = request['aflid']
+    try:
+      AFL = Affiliation.objects.get(id=AFL_Id).name
+      AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+    except ObjectDoesNotExist:
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+  else:
+    AFL = 'ENCODE_Tier1'
+    AFL_CNT = ''
+    try:
+      AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+    except ObjectDoesNotExist:
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+  CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+  CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+  ########
+  # Check Replicate numbers
+  Reps = 1
+  RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+  if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+                                                                                                                                                                              
+  str = ''
+  str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self">Main Page</a></span>'
+  str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
+  for af in Affiliation.objects.distinct():
+    str += '<option value='+af.id.__str__()
+    if AFL_Id == af.id.__str__():
+      str += ' selected'
+    str += ' onclick="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
+  str += '</select>'
+
+  if EXP == 'RNA-seq':
+    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:#ff3300"> < 6 M</span></span>'
+    str += '<span style="margin-left:20px">'
+    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>'
+    str += '  | '
+    str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+  else:
+    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:#ff3300"> < 3 M</span></span>'
+    str += '<span style="margin-left:20px">'
+    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>'
+    str += '  | '
+    str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
+
+  str += '<br/><br/><table border=1 cellspacing="2">'
+  str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
+  str += '<tr>'
+  bgc = '#ffffff'
+  pbgc = '#f7f7f7'
+  for H in CLLs:
+    str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc
+  str += '</tr><tr>'
+  bgc = '#ffffff'
+  pbgc = '#f7f7f7'
+  for H in CLLs:
+    for r in range(1,Reps+1):
+      str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc
+  str += '</tr>'
+
+  str += '<tr>' 
+  bgc = '#ffffff'
+  pbgc = '#f7f7f7'
+  for H in CLLs:
+    for r in range(1,Reps+1):
+      repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)                                                                                                                    
+      str += "<td align=center valign=top style='background-color:"+bgc+"'>"
+      if len(repReads) == 0:
+        str += 'No Libraries'
+      else:
+        cnt = 0
+        for R1 in repReads:
+          cnt = R1.aligned_m_reads()[1]
+          if cnt > 0:
+            str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
+            str += "%1.2f" % (cnt/1000000.0)+" M"
+          else:  str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
+          str += "<div style='font-size:80%'><a title='View Record' target=_self href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
+          str += "<div style='font-size:70%'>\""+R1.library_name+"\"</div"
+          str += "</div>"
+      str += '</td>'
+    tbgc = bgc
+    bgc = pbgc
+    pbgc = tbgc
+  str += '</tr>'
+  str += '</table>'
+
+  return render_to_response('htsw_reports/report.html',{'main': str})
+
+def getNotRanFCs(request):
+  FCall = FlowCell.objects.order_by('-run_date').distinct()
+  str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
+  for f in FCall:
+    try:
+      t = DataRun.objects.get(fcid=f.id)
+    except ObjectDoesNotExist:
+      str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
+  str += "</table>"
+  return render_to_response('htsw_reports/report.html',{'main':str})
+ 
+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)