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raw | patch | inline | side by side (parent: 99734c2)
added grey highlight for bad libraries (by tag text)
authorRami Rauch <rrauch@stanford.edu>
Fri, 20 Feb 2009 22:17:07 +0000 (22:17 +0000)
committerRami Rauch <rrauch@stanford.edu>
Fri, 20 Feb 2009 22:17:07 +0000 (22:17 +0000)
htswfrontend/htswfrontend/htsw_reports/reports.py patch | blob | history

diff --git a/htswfrontend/htswfrontend/htsw_reports/reports.py b/htswfrontend/htswfrontend/htsw_reports/reports.py
index 251bc49f3eed4bc914e1539004625af40c6e8df5..88db4ab7439c264d5831016d52ba70f57ad4ae34 100755 (executable)
--- a/htswfrontend/htswfrontend/htsw_reports/reports.py
+++ b/htswfrontend/htswfrontend/htsw_reports/reports.py
@@ -3,9 +3,11 @@ 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):
+badLibBgColor = '#cccccc'
+def getBgColor(reads_cnt,exp_type,isBadLib):
+  if isBadLib: return badLibBgColor
   # 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                                                                                                                            
+  bgcolor = '#ffcdd0'  # 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]
@@ -25,6 +27,10 @@ def getBgColor(reads_cnt,exp_type):
   return bgcolor
 
 def report1(request):
+  if not request.user.is_authenticated():
+    str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
+    return render_to_response('htsw_reports/report.html',{'main':str})
+
   EXP = 'ChIP-seq'
 
   if request.has_key('aflid'):
@@ -33,7 +39,7 @@ def report1(request):
       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+"'")
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
   else:
     AFL = 'ENCODE_Tier1'
     AFL_CNT = ''
@@ -41,6 +47,9 @@ def report1(request):
       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
     except ObjectDoesNotExist:
       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+  if request.user.username == 'caltech':
+    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>')
   
   TFall = Library.objects.values('antibody').order_by('antibody').distinct()
   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
@@ -55,17 +64,23 @@ def report1(request):
   
   ########
   str = ''
-  str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+  str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">HOME</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 += '<span>Select another <b>'+EXP+'</b> Report:</span>  <select onchange="window.location=\'/htsw_reports/report?aflid=\'+this.options[selectedIndex].value; return false;">'
+
+  if request.user.username == 'caltech':
+    Affil_List = Affiliation.objects.filter(name__contains='ENCODE').distinct()
+  else:
+    Affil_List = Affiliation.objects.distinct()
+    
+  for af in Affil_List:
     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 += '>'+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;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 style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</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>'
@@ -111,10 +126,10 @@ def report1(request):
           else:
             cnt = rres[1]
             if cnt > 0:
-              str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+              str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";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
+            else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
+          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+"</a>, "+R1.condition.nickname
           if R1.libtags().find('Data submitted to DCC') != -1:
             str += "<div style='border:solid #666666 1px;'>data submitted</div>"
           str += "</div>"
@@ -145,16 +160,16 @@ def report1(request):
           cnt = 0
           for R1 in repReads:
             rres = R1.aligned_m_reads()
-            # Check data sanlty
+            # Check data sanity
             if rres[2] != 'OK':
               str += '<div style="border:solid red 2px">'+rres[2]
             else:
               cnt = rres[1]
               if cnt > 0:
-                str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%;margin:2px'>"
+                str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";font-size:140%;margin:2px'>"
                 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
+              else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
+            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+"</a>, "+R1.condition.nickname
             if R1.libtags().find('Data submitted to DCC') != -1:
               str += "<div style='border:solid #666666 1px;'>data submitted</div>"
             str += "</div>"
@@ -170,6 +185,10 @@ def report1(request):
 
 
 def report_RM(request): #for RNA-Seq and Methyl-Seq
+  if not request.user.is_authenticated():
+    str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
+    return render_to_response('htsw_reports/report.html',{'main':str})
+
   EXP = 'RNA-seq'  
 
   if request.has_key('exp'):
@@ -181,7 +200,7 @@ def report_RM(request): #for RNA-Seq and Methyl-Seq
       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+"'")
+      return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
   else:
     AFL = 'ENCODE_Tier1'
     AFL_CNT = ''
@@ -190,6 +209,9 @@ def report_RM(request): #for RNA-Seq and Methyl-Seq
     except ObjectDoesNotExist:
       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 
+  if request.user.username == 'caltech':
+    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>')
+
   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 
@@ -200,23 +222,29 @@ def report_RM(request): #for RNA-Seq and Methyl-Seq
   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 += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self" style="font-size:140%">HOME</a></span>'
+  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;">'
+
+  if request.user.username == 'caltech':
+    Affil_List = Affiliation.objects.filter(name__contains='ENCODE').distinct()
+  else:
+    Affil_List = Affiliation.objects.distinct()
+
+  for af in Affil_List:
     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 += '>'+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;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 style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</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;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 style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</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 += '  | '
@@ -262,10 +290,10 @@ def report_RM(request): #for RNA-Seq and Methyl-Seq
           else:
             cnt = rres[1]
             if cnt > 0:
-              str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
+              str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";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>"
+            else:  str += "<div style='background-color:#ffcdd0;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
+          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+"</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
           str += "<div style='font-size:70%'>\""+R1.library_name+"\""
           if R1.libtags().find('Data submitted to DCC') != -1:
             str += "<div style='width:75%;border:solid #666666 1px;'>data submitted</div>"
@@ -281,6 +309,10 @@ def report_RM(request): #for RNA-Seq and Methyl-Seq
   return render_to_response('htsw_reports/report.html',{'main': str})
 
 def getNotRanFCs(request):
+  if not request.user.is_authenticated():
+    str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
+    return render_to_response('htsw_reports/report.html',{'main':str})
+
   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:
@@ -292,6 +324,10 @@ def getNotRanFCs(request):
   return render_to_response('htsw_reports/report.html',{'main':str})
  
 def test_Libs(request):
+  if not request.user.is_authenticated():
+    str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
+    return render_to_response('htsw_reports/report.html',{'main':str})
+
   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()
htsworkflow sequencing LIMS software