Merge in Rami's changes from last friday.

Most of the admin pages work. Though there's a wsgi error with the reports.
I'll try to figure out tomorrow.

the biggest difference between caltech trunk and stanford schemas right now
is caltech is using made_for as a foreign key, and stanford is using it
as a text field.

diff --git a/docs/Conv_StanfordDB_2009Jan20.txt b/docs/Conv_StanfordDB_2009Jan20.txt
new file mode 100644 (file)
index 0000000..aed4bfa
--- /dev/null
+++ b/docs/Conv_StanfordDB_2009Jan20.txt
@@ -0,0 +1,21 @@
+# mostly I just renamed tables
+# 
+
+alter table analys_track_projects rename to analysis_projects;
+alter table analys_track_project rename to analysis_project;
+alter table analys_track_project_tasks rename to analysis_project_tasks;
+alter table analys_track_task rename to analysis_task;
+alter table exp_track_datarun rename to experiments_datarun;
+alter table exp_track_flowcell rename to experiments_flowcell;
+alter table fctracker_affiliation rename to samples_affiliation;
+alter table fctracker_antibody rename to samples_antibody;
+alter table fctracker_cellline rename to samples_cellline;
+alter table fctracker_condition rename to samples_condition;
+alter table fctracker_flowcell rename to samples_flowcell;
+alter table fctracker_library rename to samples_library;
+alter table fctracker_library_affiliations rename to samples_library_affiliations;
+alter table fctracker_library_tags rename to samples_library_tags;
+alter table fctracker_primary rename to samples_primer;
+alter table fctracker_species rename to samples_species;
+alter table fctracker_tag rename to samples_tag;
+alter table htsw_reports_progressreport rename to reports_progressreport;

diff --git a/htsworkflow/frontend/analysis/main.py b/htsworkflow/frontend/analysis/main.py
index 511390b6d8bc9ae5fdc6ebd7a72afb98ce338287..b5217dc3b41a7e6f2b1778ecf53cf61fbff29b52 100644 (file)
--- a/htsworkflow/frontend/analysis/main.py
+++ b/htsworkflow/frontend/analysis/main.py
@@ -66,17 +66,44 @@ def getProjects(request):
           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+'"/>'
+            if t.subject1:
+              outputfile += '\n<Signal Library="'+t.subject1.library_id+'"/>'
+              if t.subject2:
+                outputfile += '\n<Background Library="'+t.subject2.library_id+'"/>'
+              else:
+                outputfile += '\n<Err>Background Library Missing</Err>'
+            else:
+              outputfile += '\n<Err>Signal Library Missing</Err>'
+            outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
             outputfile += '\n</PeakCalling>'
+          
+          if (t.apply_calc == 'Methylseq'):
+            outputfile += '\n<Methylseq TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
+            if t.subject1:
+              outputfile += '\n<Hpa2 Library="'+t.subject1.library_id+'"/>'
+              if t.subject2:
+                outputfile += '\n<Msp1 Library="'+t.subject2.library_id+'"/>'
+              else:
+                outputfile += '\n<Err>Msp1 Library Missing</Err>'
+            else:
+              outputfile += '\n<Err>Hpa2 Library Missing</Err>'
+            outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
+            outputfile += '\n</Methylseq>' 
 
           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+'"/>'
+            if t.subject1:
+              outputfile += '\n<Library Library="'+t.subject1.library_id+'"/>'
+            else:
+              outputfile += '\n<Err>Library Missing</Err>'
+            if t.subject2:
+              outputfile += '\n<Library Library="'+t.subject2.library_id+'"/>'
+            else:
+              outputfile += '\n<Err>Library Missing</Err>'
+            outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
             outputfile += '\n</CompareLibraries>'
 
           #if (t.apply_calc == 'ComparePeakCalls'):                                                                                                                            

diff --git a/htsworkflow/frontend/analysis/models.py b/htsworkflow/frontend/analysis/models.py
index b98cfac652bdcd64f5f23d34938953edeaf1cdbb..e2ddff489b4e5a2f3b71f4bf68671394ad4498a6 100644 (file)
--- a/htsworkflow/frontend/analysis/models.py
+++ b/htsworkflow/frontend/analysis/models.py
@@ -1,12 +1,13 @@
 from django.db import models
 from datetime import datetime
+from htsworkflow.frontend import settings
 from htsworkflow.frontend.samples.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)
+  subject1 = models.ForeignKey(Library,related_name='sbj1_library',verbose_name="Subject1 (Signal/Hpa2)")
+  subject2 = models.ForeignKey(Library,related_name='sbj2_library',verbose_name="Subject2 (Control/Msp1)",blank=True,null=True)
   CALCS = (
       ('QuEST', 'QuEST Peak Calling'),
       ('WingPeaks', 'Wing Peak Calling'),
@@ -14,7 +15,8 @@ class Task(models.Model):
       ('qPCR', 'In Silico qPCR'),
       ('CompareLibs', 'Compare Libaraies'),
       ('ComparePeakCalls','Compare Peak Calls'),
-      ('ProfileReads','Profile Reads')
+      ('ProfileReads','Profile Reads'),
+      ('Methylseq','Methylseq'),
     )
   apply_calc = models.CharField(max_length=50,choices=CALCS,verbose_name='Applied Calculation')
   ## userid = # logged in user
@@ -36,10 +38,9 @@ class Task(models.Model):
         pstr += '%s, ' % (p.project_name) 
       return pstr
 
-    
 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)
+    tasks = models.ManyToManyField(Task,related_name='project_tasks',null=True) 
     project_notes = models.CharField(max_length=500,blank=True,null=True)
     
     def __str__(self):
@@ -47,7 +48,7 @@ class Project(models.Model):
 
     def ProjectTasks(self):
       ptasks = self.tasks.all().order_by('id')
-      surl = settings.ANALYSIS_SERVER+'/projects/' 
+      surl = settings.TASKS_PROJS_SERVER+'/projects/'
       tstr = '<script>'
       tstr += 'function togView(eid){'
       tstr += 'f=document.getElementById(eid);'
@@ -71,7 +72,6 @@ class Project(models.Model):
           taskdesc += ' and '+t.subject2.library_id
         taskdesc += ' (TaskId:'+t.id.__str__()+')'
         tstr += '<tr><td width=250>%s</td><td>%s</td></tr>'  % (taskdesc,replace(t.task_status,'Complete','<span style="color:green;font-weight:bolder">Complete</span>'))
-
         if t.task_status != 'defined': isregistered = True
 
       tstr += '</table>'

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index a33aa4158d72655c7bf58cfbcb5a82df3c3cdc27..11b019e9ba01f4cbd7bc1ec446985936859ab33b 100644 (file)
--- a/htsworkflow/frontend/experiments/admin.py
+++ b/htsworkflow/frontend/experiments/admin.py
@@ -3,12 +3,32 @@ from django.contrib import admin
 from django.utils.translation import ugettext_lazy as _
 
 class DataRunOptions(admin.ModelAdmin):
-  search_fieldsets = ['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']
+  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')
 
 class FlowCellOptions(admin.ModelAdmin):
     date_hierarchy = "run_date"
     save_on_top = True
-    search_fieldsets = ('flowcell_id',
+    search_fields = ('flowcell_id',
         'seq_mac_id',
         'cluster_mac_id',
         '=lane_1_library__library_id',

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 17a315e2fc68dc0dc50ba7cc81b48331bb4f8e98..350a74691fa76fa278e2d93dac1eaca89794d867 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -1,5 +1,6 @@
 from django.db import models
 from htsworkflow.frontend.samples.models import *
+from django.core.exceptions import ObjectDoesNotExist
 
 class FlowCell(models.Model):
   
@@ -68,16 +69,23 @@ class FlowCell(models.Model):
       return unicode(self.flowcell_id) 
 
   def Create_LOG(self):
-    str = '' #<span style="color:red;font-size:80%;margin-right:3px">New!</span>'
+    str = ''
     str +='<a target=_balnk href="/experiments/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
+    try:
+      t = DataRun.objects.get(fcid=self.id)
+      str +='<br/><a target=_self href="/admin/experiments/datarun/?q='+self.flowcell_id+'" title="Check Data Runs ..." ">DataRun ..</a>'
+    except ObjectDoesNotExist:
+      str += '<br/><span style="color:red">not sequenced</span>'
     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 DataRun(models.Model):
@@ -106,7 +114,7 @@ class DataRun(models.Model):
       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>'
+      str +='<br/><a target=_balnk href="'+settings.TASKS_PROJS_SERVER+'/Flowcells/'+self.fcid.flowcell_id+'/'+self.fcid.flowcell_id+'_QC_Summary.html" title="View QC Summaries of this run ..." ">View QC Page</a>'
     else:
       str += '>'+self.RUN_STATUS_CHOICES[self.run_status][1]
 
@@ -132,4 +140,3 @@ class DataRun(models.Model):
     str += '</div>'    
     return str
   Flowcell_Info.allow_tags = True
-

diff --git a/htsworkflow/frontend/experiments/urls.py b/htsworkflow/frontend/experiments/urls.py
index 62ade81f3d5dbceaa34b31755606d9950c3b2a77..c4df6a889220ce3e60b92530c844e52d4d6b0d1a 100755 (executable)
--- a/htsworkflow/frontend/experiments/urls.py
+++ b/htsworkflow/frontend/experiments/urls.py
@@ -3,7 +3,7 @@ from django.conf.urls.defaults import *
 urlpatterns = patterns('',
                                                                                                       
     (r'^$', 'htsworkflow.frontend.experiments.views.index'),
-    (r'^liblist$', 'htsworkflow.frontend.experiments.views.test_Libs'),
+    #(r'^liblist$', 'htsworkflow.frontend.experiments.views.test_Libs'),
     #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.experiments.views.detail'),
     (r'^(?P<fcid>.+)/$', 'htsworkflow.frontend.experiments.views.makeFCSheet'),
     (r'^updStatus$', 'htsworkflow.frontend.experiments.experiments.updStatus'),

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
index 3b6dbff81de6b19d72bc177055a70bb5238028b7..404103f643b23cb1d6dffaa1c042b22e4ced76e8 100755 (executable)
--- a/htsworkflow/frontend/experiments/views.py
+++ b/htsworkflow/frontend/experiments/views.py
@@ -2,7 +2,6 @@
 #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 htsworkflow.frontend.experiments.models import *
 from django.http import HttpResponse
 from django.core.exceptions import ObjectDoesNotExist
@@ -33,28 +32,3 @@ def makeFCSheet(request,fcid):
     pass
   lanes = ['1','2','3','4','5','6','7','8']
   return render_to_response('experiments/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)  

diff --git a/htsworkflow/frontend/reports/LibraryInfo.xml b/htsworkflow/frontend/reports/LibraryInfo.xml
index 4e7992a5a1a9778ef696a1b6d652d3c1add58abe..ec630b58f1be2702653b83c875111efcc45f3920 100644 (file)
--- a/htsworkflow/frontend/reports/LibraryInfo.xml
+++ b/htsworkflow/frontend/reports/LibraryInfo.xml
@@ -1,1024 +1,1214 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" ?>
 <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"/>
+<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"/>
+<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"/>
+<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"/>
+<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="SL13">
+<Track Flowcell="FC7225" Lane="67" Filename="Flowcells/FCSL13/070629_FC7225_s67_FoxP2_PFSK1_SL13.align_25.hg18.txt" Count=" 3830788" Date="070629" />
+<Track Flowcell="FC5507" Lane="67" Filename="Flowcells/FCSL13/070703_FC5507_s67_FoxP2_PFSK1_SL13.align_25.hg18.txt" Count=" 2694525" Date="070703" />
+<Track Flowcell="FC8053" Lane="56" Filename="Flowcells/FCSL13/070724_FC8053_s56_FoxP2_PFSK1_SL13.align_25.hg18.txt" Count=" 2214065" Date="070724" />
+<Track Flowcell="FC7857" Lane="8" Filename="Flowcells/FCSL13/070807_FC7857_s8_FoxP2_PFSK1_SL13.align_25.hg18.txt" Count=" 1273565" Date="070807" />
 </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"/>
+<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"/>
+<Track Flowcell="FC201U7" Lane="12345678" Filename="Flowcells/FC201U7/071205_FC201U7_s12345678_mock_IP_PFSK1_SL16.align_25.hg.txt" Count=" 23476737" Date="071205" />
 </Library>
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+<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="SL352">
+<Track Flowcell="30CLAAXX" Lane="1" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s1_RNAseq_mouse_skin_gb1_SL352.align_25.mm9.txt" Count=" 3921939" Date="080815" />
+<Track Flowcell="30CLAAXX" Lane="1" Filename="Flowcells/DATA_FROM_HA/080815_30CLAAXX_s1_RNAseq_mouse_skin_gb1_SL352.align_25.mm9.txt" Count=" 1224253" Date="080815" />
+</Library>
+<Library Name="SL353">
+<Track Flowcell="30CLAAXX" Lane="2" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s2_RNAseq_mouse_skin_gb2_SL353.align_25.mm9.txt" Count=" 4617024" Date="080815" />
+</Library>
+<Library Name="SL354">
+<Track Flowcell="30CLAAXX" Lane="3" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s3_RNAseq_mouse_skin_gb3_SL354.align_25.mm9.txt" Count=" 4018744" Date="080815" />
+</Library>
+<Library Name="SL355">
+<Track Flowcell="30CLAAXX" Lane="4" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s4_RNAseq_mouse_skin_gb4_SL355.align_25.mm9.txt" Count=" 3719245" Date="080815" />
+</Library>
+<Library Name="SL356">
+<Track Flowcell="30CLAAXX" Lane="5" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s5_Input_Control_ChIP-seq_protocadherin_tagged_SL356.align_25.hg18.txt" Count=" 6608872" Date="080815" />
+</Library>
+<Library Name="SL357">
+<Track Flowcell="30CLAAXX" Lane="6" Filename="Flowcells/30CLAAXX/080815_30CLAAXX_s6_ChIP-seq_protocadherin_alpha6_tagged_SL357.align_25.hg18.txt" Count=" 6057062" Date="080815" />
 </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"/>
+<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" />
+<Track Flowcell="306WPAAXX" Lane="3" Filename="Flowcells/306WPAAXX/080731_306WPAAXX_s3_ChIP-seq_HepG2_Rep1_TAF250_SL358.align_25.hg18.txt" Count=" 3307317" Date="080731" />
 </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"/>
+<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" />
+<Track Flowcell="306WPAAXX" Lane="4" Filename="Flowcells/306WPAAXX/080731_306WPAAXX_s4_ChIP-seq_HepG2_Rep2_TAF250_SL359.align_25.hg18.txt" Count=" 3232318" Date="080731" />
+<Track Flowcell="30EG4AAXX" Lane="7" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s7_ChIP-seq_HepG2_Rep2_TAF250_SL359.align_25.hg18.txt" Count=" 4307991" Date="080916" />
 </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"/>
+<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"/>
+<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"/>
+<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"/>
+<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="SL368">
+<Track Flowcell="30DRRAAXX" Lane="8" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s8_Input_Control_RXLCh_Neuro2A_Rep2_SL368.align_25.mm9.txt" Count=" 2783931" Date="080919" />
+</Library>
+<Library Name="SL369">
+<Track Flowcell="30DRRAAXX" Lane="7" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s7_Input_Control_RXLCh_CAD_Rep2_SL369.align_25.mm9.txt" Count=" 2520025" Date="080919" />
+</Library>
+<Library Name="SL370">
+<Track Flowcell="30DRRAAXX" Lane="6" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s6_Neuro2A_CTCF_Rep2_SL370.align_25.mm9.txt" Count=" 3046099" Date="080919" />
+</Library>
+<Library Name="SL371">
+<Track Flowcell="30DRRAAXX" Lane="5" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s5_CAD_CTCF_Rep2_SL371.align_25.mm9.txt" Count=" 3466060" Date="080919" />
+</Library>
+<Library Name="SL372">
+<Track Flowcell="30DRRAAXX" Lane="4" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s4_Neuro2A_USF1_Rep2_SL372.align_25.mm9.txt" Count=" 2857481" Date="080919" />
+</Library>
+<Library Name="SL373">
+<Track Flowcell="30DRRAAXX" Lane="3" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s3_CAD_USF1_Rep2_SL373.align_25.mm9.txt" Count=" 3741192" Date="080919" />
+</Library>
+<Library Name="SL374">
+<Track Flowcell="30DRRAAXX" Lane="2" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s2_Neuro2A_USF2_Rep2_SL374.align_25.mm9.txt" Count=" 4160807" Date="080919" />
+</Library>
+<Library Name="SL375">
+<Track Flowcell="30DRRAAXX" Lane="1" Filename="Flowcells/30DRRAAXX/080919_30DRRAAXX_s1_CAD_USF2_Rep2_SL375.align_25.mm9.txt" Count=" 2005344" Date="080919" />
+</Library>
+<Library Name="SL376">
+<Track Flowcell="30CUNAAXX" Lane="1" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s1_A549_P65_Dex_Rep2_SL376.align_25.hg18.txt" Count="  506090" Date="080918" />
+</Library>
+<Library Name="SL377">
+<Track Flowcell="30CUNAAXX" Lane="2" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s2_A549_P65_EtOH_Rep2_SL377.align_25.hg18.txt" Count=" 1618541" Date="080918" />
+</Library>
+<Library Name="SL378">
+<Track Flowcell="30CUNAAXX" Lane="3" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s3_A549_Pol2Ser2_Dex_Rep2_SL378.align_25.hg18.txt" Count=" 2773966" Date="080918" />
+<Track Flowcell="30CUNAAXX" Lane="7" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s7_A549_Pol2Ser2_Dex_Rep2_SL378.align_25.hg18.txt" Count=" 3050258" Date="080918" />
+</Library>
+<Library Name="SL379">
+<Track Flowcell="30CUNAAXX" Lane="4" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s4_A549_Pol2Ser2_EtOH_Rep2_SL379.align_25.hg18.txt" Count=" 1315068" Date="080918" />
+<Track Flowcell="30CUNAAXX" Lane="8" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s8_A549_Pol2Ser2_EtOH_Rep2_SL379.align_25.hg18.txt" Count=" 2957711" Date="080918" />
+</Library>
+<Library Name="SL388">
+<Track Flowcell="30EF9AAXX" Lane="8" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s8_RNAseq_mtN_mtG_7d_SL388.align_25.mm9.txt" Count=" 4555457" Date="080916" />
+</Library>
+<Library Name="SL389">
+<Track Flowcell="30EF9AAXX" Lane="7" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s7_RNAseq_mtN_WTG_7d_SL389.align_25.mm9.txt" Count="    2247" Date="080916" />
+</Library>
+<Library Name="SL390">
+<Track Flowcell="30EF9AAXX" Lane="6" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s6_RNAseq_WTN_mtG_7d_SL390.align_25.mm9.txt" Count=" 5472114" Date="080916" />
+</Library>
+<Library Name="SL391">
+<Track Flowcell="30EF9AAXX" Lane="5" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s5_RNAseq_WTN_WTG_7d_SL391.align_25.mm9.txt" Count=" 6010993" Date="080916" />
+</Library>
+<Library Name="SL392">
+<Track Flowcell="30EF9AAXX" Lane="4" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s4_RNAseq_mtG_mtN_7d_SL392.align_25.mm9.txt" Count=" 5573656" Date="080916" />
+</Library>
+<Library Name="SL393">
+<Track Flowcell="30EF9AAXX" Lane="3" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s3_RNAseq_WTG_mtN_7d_SL393.align_25.mm9.txt" Count=" 5993678" Date="080916" />
+</Library>
+<Library Name="SL394">
+<Track Flowcell="30EF9AAXX" Lane="2" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s2_RNAseq_mtG_WTN_7d_SL394.align_25.mm9.txt" Count=" 5988007" Date="080916" />
+</Library>
+<Library Name="SL395">
+<Track Flowcell="30EF9AAXX" Lane="1" Filename="Flowcells/30EF9AAXX/080916_30EF9AAXX_s1_RNAseq_WTG_WTN_7d_SL395.align_25.mm9.txt" Count=" 5716492" Date="080916" />
+</Library>
+<Library Name="SL396">
+<Track Flowcell="30EG4AAXX" Lane="6" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s6_RNAseq_4484-17_occipital_cortex_SL396.align_25.hg18.txt" Count=" 5908254" Date="080916" />
+</Library>
+<Library Name="SL397">
+<Track Flowcell="30EG4AAXX" Lane="5" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s5_RNAseq_4484-6_basal_ganglia_SL397.align_25.hg18.txt" Count=" 5949974" Date="080916" />
+</Library>
+<Library Name="SL398">
+<Track Flowcell="30CUNAAXX" Lane="5" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s5_A549_Pol2Ser2_Dex_Rep3_SL398.align_25.hg18.txt" Count=" 1352310" Date="080918" />
+<Track Flowcell="30EH5AAXX" Lane="1" Filename="Flowcells/30EH5AAXX/080910_30EH5AAXX_s1_A549_Pol2Ser2_Dex_Rep3_SL398.align_25.hg18.txt" Count=" 2249460" Date="080910" />
+</Library>
+<Library Name="SL399">
+<Track Flowcell="30CUNAAXX" Lane="6" Filename="Flowcells/30CUNAAXX/080918_30CUNAAXX_s6_A549_Pol2Ser2_EtOH_Rep3_SL399.align_25.hg18.txt" Count=" 1475564" Date="080918" />
+<Track Flowcell="30EH5AAXX" Lane="2" Filename="Flowcells/30EH5AAXX/080910_30EH5AAXX_s2_A549_Pol2Ser2_EtOH_Rep3_SL399.align_25.hg18.txt" Count=" 2020061" Date="080910" />
+</Library>
+<Library Name="SL415">
+<Track Flowcell="30EH5AAXX" Lane="4" Filename="Flowcells/30EH5AAXX/080910_30EH5AAXX_s4_A549_ChIP_NFkB_Dex_R3_SL415.align_25.hg18.txt" Count=" 1605808" Date="080910" />
+</Library>
+<Library Name="SL419">
+<Track Flowcell="30EG4AAXX" Lane="1" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s1_GM12878_Rep1_NFATc1_SL419.align_25.hg18.txt" Count=" 3203524" Date="080916" />
 </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 Name="SL420">
+<Track Flowcell="30EG4AAXX" Lane="2" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s2_K562_Rep1_NFATc1_SL420.align_25.hg18.txt" Count=" 4198383" Date="080916" />
 </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 Name="SL421">
+<Track Flowcell="30EG4AAXX" Lane="3" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s3_GM12878_Dex_Rep1_GR_ChIP_SL421.align_25.hg18.txt" Count=" 5259681" Date="080916" />
 </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 Name="SL422">
+<Track Flowcell="30EG4AAXX" Lane="4" Filename="Flowcells/30EG4AAXX/080916_30EG4AAXX_s4_GM12878_EtOH_Rep1_GR_ChIP_SL422.align_25.hg18.txt" Count=" 3451771" Date="080916" />
 </Library>
-</Libraries>
\ No newline at end of file
+</Libraries>

diff --git a/htsworkflow/frontend/reports/models.py b/htsworkflow/frontend/reports/models.py
index ddcdc535d488a04b05359ee5c43ff5320a7a2d31..b898537ae10b5ac42ee707b90a739370c2d19310 100644 (file)
--- a/htsworkflow/frontend/reports/models.py
+++ b/htsworkflow/frontend/reports/models.py
@@ -204,12 +204,12 @@ class ProgressReport(models.Model):
       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 += '<a target=_blank href="'+settings.TASKS_PROJS_SERVER+'/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>'
+    tstr += '<a target=_blank href="'+settings.TASKS_PROJS_SERVER+'/projects/'+self.st_sbj.id.__str__()+'">Project results page</a>'
     return tstr
   aligned_reads.allow_tags = True
 

diff --git a/htsworkflow/frontend/reports/urls.py b/htsworkflow/frontend/reports/urls.py
index 69a9f12b5656f9eb35ef8d02239be73a7d7f0ffa..5a004f219f3f4eca044f43012c66ffaa0e3e0e24 100644 (file)
--- a/htsworkflow/frontend/reports/urls.py
+++ b/htsworkflow/frontend/reports/urls.py
@@ -1,9 +1,9 @@
 from django.conf.urls.defaults import *
 
 urlpatterns = patterns('',                                               
-    (r'^updLibInfo$', 'htsworkflow.reports.libinfopar.refreshLibInfoFile'),
-    (r'^report$', 'htsworkflow.reports.reports.report1'),
-    (r'^report_RM$', 'htsworkflow.reports.reports.report_RM'),
-    (r'^report_FCs$', 'htsworkflow.reports.reports.getNotRanFCs'),
-    (r'^liblist$', 'htsworkflow.reports.reports.test_Libs')
+    (r'^updLibInfo$', 'htsworkflow.frontend.reports.libinfopar.refreshLibInfoFile'),
+    (r'^report$', 'htsworkflow.frontend.reports.reports.report1'),
+    (r'^report_RM$', 'htsworkflow.frontend.reports.reports.report_RM'),
+    (r'^report_FCs$', 'htsworkflow.frontend.reports.reports.getNotRanFCs'),
+    (r'^liblist$', 'htsworkflow.frontend.reports.reports.test_Libs')
 )

diff --git a/htsworkflow/frontend/samples/admin.py b/htsworkflow/frontend/samples/admin.py
index f8d45d0789695b35df9c93deca0f460e4dcf220f..62e43fb2329d093d4c277ec19c62394a09622871 100644 (file)
--- a/htsworkflow/frontend/samples/admin.py
+++ b/htsworkflow/frontend/samples/admin.py
@@ -6,6 +6,8 @@ class Library_Inline(admin.TabularInline):
   model = Library
 
 class CelllineOptions(admin.ModelAdmin):
+    list_display = ('cellline_name', 'nickname', 'notes')
+    search_fields = ('cellline_name', 'nickname', 'notes')
     fieldsets = (
       (None, {
           'fields': (('cellline_name'),('notes'),)
@@ -16,7 +18,7 @@ class LibraryOptions(admin.ModelAdmin):
     date_hierarchy = "creation_date"
     save_as = True
     save_on_top = True
-    search_fieldsets = (
+    search_fields = (
         'library_id',
         'library_name',
         'cell_line__cellline_name',
@@ -78,6 +80,7 @@ class AffiliationOptions(admin.ModelAdmin):
 #   inlines = [Library_Inline]
 
 class AntibodyOptions(admin.ModelAdmin):
+    search_fields = ('antigene','nickname','catalog','antibodies','source','biology','notes')
     list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
     list_filter = ('antibodies','source')
     fieldsets = (

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 9cc0b926f8af1d0cd617735e6e2d0686ef0f7f7b..34cf26077bf08310d4164cb079c09d485669815e 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -135,7 +135,9 @@ class Library(models.Model):
                                      default='RNA-seq')
   
   creation_date = models.DateField(blank=True, null=True)
-  made_for = models.ForeignKey(User)
+  # made_for = models.ForeignKey(User)
+  made_for = models.CharField(max_length=50, blank=True, 
+      verbose_name='ChIP/DNA/RNA Made By')
   made_by = models.CharField(max_length=50, blank=True, default="Lorian")
   
   PROTOCOL_END_POINTS = (

diff --git a/htsworkflow/frontend/templates/admin/index.html b/htsworkflow/frontend/templates/admin/index.html
new file mode 100644 (file)
index 0000000..e712275
--- /dev/null
+++ b/htsworkflow/frontend/templates/admin/index.html
@@ -0,0 +1,135 @@
+{% extends "admin/base_site.html" %}
+{% load i18n %}
+
+{% block stylesheet %}{% load adminmedia %}{% admin_media_prefix %}css/dashboard.css{% endblock %}
+
+{% block coltype %}colMS{% endblock %}
+
+{% block bodyclass %}dashboard{% endblock %}
+
+{% block breadcrumbs %}{% endblock %}
+
+{% block content %}
+<div id="content-main">
+
+{% if app_list %}
+    {% for app in app_list %}
+        <div class="module">
+        <table summary="{% blocktrans with app.name as name %}Models available in the {{ name }} application.{% endblocktrans %}">
+        <caption><a href="{{ app.app_url }}" class="section">{% blocktrans with app.name as name %}{{ name }}{% endblocktrans %}</a></caption>
+        {% for model in app.models %}
+            <tr>
+            {% if model.perms.change %}
+                <th scope="row"><a href="{{ model.admin_url }}">{{ model.name }}</a></th>
+            {% else %}
+                <th scope="row">{{ model.name }}</th>
+            {% endif %}
+
+            {% if model.perms.add %}
+                <td><a href="{{ model.admin_url }}add/" class="addlink">{% trans 'Add' %}</a></td>
+            {% else %}
+                <td>&nbsp;</td>
+            {% endif %}
+
+            {% if model.perms.change %}
+                <td><a href="{{ model.admin_url }}" class="changelink">{% trans 'Change' %}</a></td>
+            {% else %}
+                <td>&nbsp;</td>
+            {% endif %}
+            </tr>
+        {% endfor %}
+        </table>
+        </div>
+    {% endfor %}
+{% else %}
+    <p>{% trans "You don't have permission to edit anything." %}</p>
+{% endif %}
+</div>
+
+      <div class="module">
+        <table>
+          <caption><span style="color:red">New!</span> Reports <span style="color:black;font-size:80%">(Note: Some features currently work only on Firefox)</span></caption>
+            <tr>
+             <th scope="row"><a href="/reports/report" target=_self>ChIP-Seq Reports</a></th>
+             <th scope="row"></th><td></td><td>&nbsp;</td><td></td><td>&nbsp;</td>
+            </tr>
+            <tr>
+             <th scope="row"><a href="/reports/report_RM" target=_self>RNA-Seq Reports</a></th>
+             <th scope="row"></th><td></td><td>&nbsp;</td><td></td><td>&nbsp;</td>
+            </tr>
+            <tr>
+             <th scope="row"><a href="/reports/report_RM?exp=Methyl-seq" target=_self>Methyl-Seq Reports</a></th>
+             <th scope="row"></th><td></td><td>&nbsp;</td><td></td><td>&nbsp;</td>
+            </tr>
+       </table>
+       </div>
+       <div class="module">
+        <table>
+          <caption>Docs & Tools</caption>
+            <tr>
+             <th scope="row"><a href="http://illumina-mac.stanford.edu/SequencingSummaries/SequencingSummary.html" target=_blank>Sequencing Summary Page</a></th>
+             <th scope="row"></th>
+             <td></td>
+             <td>&nbsp;</td>
+             <td></td>
+             <td>&nbsp;</td>
+            </tr>
+            <tr>
+             <th scope="row"><a href="http://m304-apple-server.stanford.edu/PrimerDesign" target=_blank>ChIP QC Primer Design</a>&nbsp;&nbsp;
+             <a href="http://m304-apple-server.stanford.edu/ValidationDesign/" target=_blank>ChIP Validation Design</a>
+             </th>
+             <th scope="row"></th>
+             <td></td>
+             <td>&nbsp;</td>
+             <td></td>
+             <td>&nbsp;</td>
+            </tr>
+            <tr>
+             <th scope="row"><a href="http://myers.hudsonalpha.org/content/protocols.html" target=_blank>Protocols - Myers Lab</a></th>
+             <th scope="row"></th>
+             <td></td>
+             <td>&nbsp;</td>
+             <td></td>
+             <td>&nbsp;</td>
+            </tr>
+            <tr>
+             <th scope="row"><a href="https://woldlab.caltech.edu/html/protocols" target=_blank>Protocols - Wold Lab</a></th>             
+             <th scope="row"></th>
+             <td></td>
+             <td>&nbsp;</td>
+            <td></td>
+             <td>&nbsp;</td>
+            </tr>
+           <tr>
+             <th scope="row"><a href="http://www.ncbi.nlm.nih.gov/pubmed/18711362" target=_blank>QuEST</a></th>
+             <th scope="row"></th>
+             <td></td>
+             <td>&nbsp;</td>
+           <td></td>
+            <td>&nbsp;</td>
+            </tr>
+        </table>
+        </div>
+</div>
+{% endblock %}
+
+
+{% block sidebar %}
+<div id="content-related">
+    <div class="module" id="recent-actions-module">
+        <h2>{% trans 'Recent Actions' %}</h2>
+        <h3>{% trans 'My Actions' %}</h3>
+            {% load log %}
+            {% get_admin_log 10 as admin_log for_user user %}
+            {% if not admin_log %}
+            <p>{% trans 'None available' %}</p>
+            {% else %}
+            <ul class="actionlist">
+            {% for entry in admin_log %}
+            <li class="{% if entry.is_addition %}addlink{% endif %}{% if entry.is_change %}changelink{% endif %}{% if entry.is_deletion %}deletelink{% endif %}">{% if not entry.is_deletion %}<a href="{{ entry.get_admin_url }}">{% endif %}{{ entry.object_repr }}{% if not entry.is_deletion %}</a>{% endif %}<br /><span class="mini quiet">{% filter capfirst %}{% trans entry.content_type.name %}{% endfilter %}</span></li>
+            {% endfor %}
+            </ul>
+            {% endif %}
+    </div>
+</div>
+{% endblock %}

diff --git a/htsworkflow/frontend/templates/experiments/flowcellSheet.html b/htsworkflow/frontend/templates/experiments/flowcellSheet.html
index 189ed10e7c4fd63a7d25dd657e0846fd554c48d0..66b7b4d19a863ef13346bd24f3174f06c0cb282e 100644 (file)
--- a/htsworkflow/frontend/templates/experiments/flowcellSheet.html
+++ b/htsworkflow/frontend/templates/experiments/flowcellSheet.html
@@ -1,199 +1,117 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG</title>
-
+<html><head><title>{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG</title>
 <style type="text/css">
-  table, td 
-  {
-    border-color: #600;
-    border-style: solid;
-  }
-  table
-  {
-    border-width: 0 0 1px 1px;
-    border-spacing: 0;
-    border-collapse: collapse;
-  }
-  td
+<!--
+TD
   {
-    margin:0 ;
-    padding: 4px;
-    border-width: 1px 1px 0 0;
+  color:black;
+  font-size:9pt;
+  font-face:Arial;
   }
+-->
 </style>
-</head>
-<body>
-  <p>{% if fc %}</p>
-<table>
-<thead>
-  <td colspan="3"><b>GA SEQUENCING (SOLEXA) LOG</b></td>
-</thead>
-<tbody>
-<tr>
-<td>Date Run Started</td>
-<td colspan="2">{{ fc.run_date }}</td>
-</tr>
-<tr>
-<td>Cluster station used</td>
-<td colspan="2" nowrap>{{ fc.cluster_mac_id }}</td>
-</tr>
-<tr>
-<td>GA used</td>
-<td colspan="2" nowrap>{{ fc.seq_mac_id }}</td>
-</tr>
-<tr>
-<td>Flowcell number</td>
-<td colspan="2" nowrap>{{ fc.flowcell_id }}</td>
-</tr>
-<tr>
-<td>Number of Tiles per Lane</td>
-<td>100</td>
-</tr>
-<tr>
-<td>Number of Cycles</td>
-<td>{{ fc.read_length }}</td>
-</tr>
-</tbody>
-</table>
-<br/>
-<table>
-<thead>
-  <td>
-    <font point-size="9" face="Arial">
-      <b>SAMPLE INFORMATION</b>
-  </font>
-</thead>
-<tbody>
-<tr>
-<td>&nbsp;</td>
-<td>FC#</td>
-<td>&nbsp;</td>
-<td>&nbsp;</td>
-<td>&nbsp;</td>
-<td>&nbsp;</td>
-<td>&nbsp;</td>
-<td colspan="2" nowrap>FC bar code</td>
-</tr>
-<tr>
-<td valign="middle" nowrap>Lane</td>
-<td>1</td>
-<td>2</td>
-<td>3</td>
-<td>4</td>
-<td>5</td>
-<td>6</td>
-<td>7</td>
-<td>8</td>
-</tr>
-<tr>
-<td valign="middle" nowrap>Solexa Library Number</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_library.library_id }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_library.library_id }}</td>
-</tr>
-<tr>
-<td valign="middle" nowrap>Sample Name</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_library.library_name }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_library.library_name }}</td>
-</tr>
-<tr>
-<td valign="middle" nowrap>Organism</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_1_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_2_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_3_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_4_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_5_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_6_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_7_library.library_species.common_name }}</td>
-<td bgcolor="#CCFFCC">{{
-fc.lane_8_library.library_species.common_name }}</td>
-</tr>
-<tr>
-<td valign="middle" nowrap>Submitter</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_library.made_by }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_library.made_by }}</td>
+</head><body>
+{% if fc %}
+<table border="1" cellspacing="1">
+<tr><td colspan=2 nowrap><b>GA SEQUENCING (SOLEXA) LOG</b></td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>Date Run Started</td><td colspan=2>{{ fc.run_date }}</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>Cluster station used</td><td colspan=2 nowrap>{{ fc.cluster_mac_id }}</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>GA used</td><td colspan=2 nowrap>{{ fc.seq_mac_id }}</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+
+<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>Flowcell number</td><td colspan=2 nowrap>{{ fc.flowcell_id }}</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>Number of Tiles per Lane</td><td>100</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>Number of Cycles</td><td>{{ fc.read_length  }}</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td><font point-size="9" face="Arial"><b>SAMPLE INFORMATION</b><font></td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr><td>&nbsp;</td><td>FC#</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td colspan=2 nowrap>FC bar code</td></tr>
+
+<tr><td valign=middle nowrap>Lane</td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>7</td><td>8</td></tr>
+<tr><td valign=middle nowrap>Solexa Library Number</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.library_id }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.library_id }}</td></tr>
+
+<tr><td valign=middle nowrap>Sample Name</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.library_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.library_name }}</td>
 </tr>
-<tr>
-<td valign="middle" nowrap>First time run?</td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
-<td bgcolor="#CCFFCC"></td>
+
+<tr><td valign=middle nowrap>Organism</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.library_species.common_name }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.library_species.common_name }}</td>
 </tr>
-<tr>
-<td valign="middle" nowrap>Average Library Size (bp)</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_library.avg_lib_size }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_library.avg_lib_size }}</td>
+
+<tr><td valign=middle nowrap>Submitter</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.made_by }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.made_by }}</td>
 </tr>
-<tr>
-<td valign="middle" nowrap>Template Concentration (ng/ul)</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_library.undiluted_concentration
-}}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_library.undiluted_concentration
-}}</td>
+
+
+<tr><td valign=middle nowrap>First time run?</td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td></tr>
+
+<tr><td valign=middle nowrap>Average Library Size (bp)</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.avg_lib_size }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.avg_lib_size }}</td>
+</tr>  
+
+<tr><td valign=middle nowrap>Template Concentration (ng/ul)</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_library.undiluted_concentration }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_library.undiluted_concentration }}</td>
 </tr>
-<tr>
-<td valign="middle" nowrap>Run Concentration (pM)</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_1_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_2_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_3_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_4_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_5_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_6_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_7_pM }}</td>
-<td bgcolor="#CCFFCC">{{ fc.lane_8_pM }}</td>
+
+<tr><td valign=middle nowrap>Run Concentration (pM)</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_1_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_2_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_3_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_4_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_5_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_6_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_7_pM }}</td>
+<td bgcolor=#CCFFCC>{{ fc.lane_8_pM }}</td>
 </tr>
-</tbody>
+
 </table>
+
 {% else %}
-<p>Flowcell object missing. Can't create sheet.</p>
+    <p>Flowcell object missing. Can't create sheet.</p>
 {% endif %}
-</body>
-</html>
+
+</body></html

diff --git a/htsworkflow/frontend/urls.py b/htsworkflow/frontend/urls.py
index 95552bd65f86d20d635d8102dac1a4ecf4d42077..b8b9e5ec348e2a19e5466db8366028dca89847e1 100644 (file)
--- a/htsworkflow/frontend/urls.py
+++ b/htsworkflow/frontend/urls.py
@@ -18,7 +18,7 @@ urlpatterns = patterns('',
     # AnalysTrack:
     #(r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
     # Report Views:
-    # (r'^reports/', include('gaworkflow.frontend....urls')),
+    (r'^reports/', include('htsworkflow.frontend.reports.urls')),
     
     # databrowser
     #(r'^databrowse/(.*)', databrowse.site.root)