Replaced 'gaworflow' with 'htsworkflow'; updated settings.py, urls.py etc... Tested...

diff --git a/htswfrontend/htswfrontend/analys_track/an_urls.py b/htswfrontend/htswfrontend/analys_track/an_urls.py
index 683ae78f5deae109dd6cd2657e2d20aad6796bb1..edf0e94b08b398328ff92b5fd9cd008eeadd51fa 100644 (file)
--- a/htswfrontend/htswfrontend/analys_track/an_urls.py
+++ b/htswfrontend/htswfrontend/analys_track/an_urls.py
@@ -1,8 +1,8 @@
 from django.conf.urls.defaults import *
 
 urlpatterns = patterns('',                                               
-    (r'^$', 'gaworkflow.frontend.analys_track.views.index'),
+    (r'^$', 'htswfrontend.analys_track.views.index'),
     #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.analys_track.views.detail'),
-    (r'^updStatus$', 'gaworkflow.frontend.analys_track.main.updStatus'),
-    (r'^getProjects$', 'gaworkflow.frontend.analys_track.main.getProjects'),
+    (r'^updStatus$', 'htswfrontend.analys_track.main.updStatus'),
+    (r'^getProjects$', 'htswfrontend.analys_track.main.getProjects'),
 )

diff --git a/htswfrontend/htswfrontend/analys_track/main.py b/htswfrontend/htswfrontend/analys_track/main.py
index 802ade164691d46efa5d8a608e7d6ccc6634477b..a6251450da855a1e25e0eb89674e2688322edd2c 100644 (file)
--- a/htswfrontend/htswfrontend/analys_track/main.py
+++ b/htswfrontend/htswfrontend/analys_track/main.py
@@ -3,8 +3,8 @@ from django.http import HttpResponse
 from datetime import datetime
 from string import *
 import re
-from gaworkflow.frontend import settings
-from gaworkflow.frontend.analys_track.models import Task, Project
+from htswfrontend import settings
+from htswfrontend.analys_track.models import Task, Project
 from django.core.exceptions import ObjectDoesNotExist
 
 def updStatus(request):

diff --git a/htswfrontend/htswfrontend/analys_track/models.py b/htswfrontend/htswfrontend/analys_track/models.py
index be0bb9c7a1b9606677a5a89762770e5d37933287..10a31143bd659a1f0e610140cba5946e808ade8b 100644 (file)
--- a/htswfrontend/htswfrontend/analys_track/models.py
+++ b/htswfrontend/htswfrontend/analys_track/models.py
@@ -1,6 +1,6 @@
 from django.db import models
 from datetime import datetime
-from gaworkflow.frontend.fctracker.models import Library 
+from htswfrontend.fctracker.models import Library 
 from string import *
 
 class Task(models.Model):

diff --git a/htswfrontend/htswfrontend/exp_track/et_urls.py b/htswfrontend/htswfrontend/exp_track/et_urls.py
index 6acea12b4452902a1b62956e8385873c329fa196..eab87a304ea8e8239dd0357c9cd62c04844f5a49 100755 (executable)
--- a/htswfrontend/htswfrontend/exp_track/et_urls.py
+++ b/htswfrontend/htswfrontend/exp_track/et_urls.py
@@ -2,9 +2,10 @@ from django.conf.urls.defaults import *
 
 urlpatterns = patterns('',
                                                                                                       
-    (r'^$', 'gaworkflow.frontend.exp_track.views.index'),
-    (r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.exp_track.views.detail'),
-    (r'^updStatus$', 'gaworkflow.frontend.exp_track.exptrack.updStatus'),
-    (r'^getConfile$', 'gaworkflow.frontend.exp_track.exptrack.getConfile'),
-    (r'^getLanesNames$', 'gaworkflow.frontend.exp_track.exptrack.getLaneLibs')   
+    (r'^$', 'htswfrontend.exp_track.views.index'),
+    #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.exp_track.views.detail'),
+    (r'^(?P<fcid>.+)/$', 'htswfrontend.exp_track.views.makeFCSheet'),
+    (r'^updStatus$', 'htswfrontend.exp_track.exptrack.updStatus'),
+    (r'^getConfile$', 'htswfrontend.exp_track.exptrack.getConfile'),
+    (r'^getLanesNames$', 'htswfrontend.exp_track.exptrack.getLaneLibs')   
 )

diff --git a/htswfrontend/htswfrontend/exp_track/exptrack.py b/htswfrontend/htswfrontend/exp_track/exptrack.py
index 8cd5d6d1b71728366a69df1645d17a4d4d453c3f..bb24da10da927ed1761d3234e591690e54a8b849 100755 (executable)
--- a/htswfrontend/htswfrontend/exp_track/exptrack.py
+++ b/htswfrontend/htswfrontend/exp_track/exptrack.py
@@ -3,9 +3,9 @@ from django.http import HttpResponse
 from datetime import datetime
 from string import *
 import re
-from gaworkflow.frontend import settings
-from gaworkflow.frontend.exp_track.models import FlowCell, DataRun
-from gaworkflow.frontend.fctracker.models import Library
+from htswfrontend import settings
+from htswfrontend.exp_track.models import FlowCell, DataRun
+from htswfrontend.fctracker.models import Library
 from django.core.exceptions import ObjectDoesNotExist
 from django.core.mail import send_mail, mail_admins
 

diff --git a/htswfrontend/htswfrontend/exp_track/models.py b/htswfrontend/htswfrontend/exp_track/models.py
index 209614820029691226d36c6456da46359f7463e9..61c9b3af9a4497669b28e147b8954b6f15aa6a36 100755 (executable)
--- a/htswfrontend/htswfrontend/exp_track/models.py
+++ b/htswfrontend/htswfrontend/exp_track/models.py
@@ -1,5 +1,5 @@
 from django.db import models
-from gaworkflow.frontend.fctracker.models import Library
+from htswfrontend.fctracker.models import Library
 
 class FlowCell(models.Model):
   
@@ -46,14 +46,14 @@ class FlowCell(models.Model):
 
   #Machine Names
   CLUSTER_MAC = (
-      ('M304','M304'),
+      ('M304','Cardinal'),
       ('R349','R349'),
       ('Tinkerbell','Tinkerbell'),
       ('BitBit','BitBit'),
     )
   
   SEQ_MAC = (
-      ('EAS149','EAS149'),
+      ('EAS149','Stanford'),
       ('EAS46','EAS46'),
       ('EAS45','Paris'),
       ('Britney','Britney'),
@@ -68,6 +68,11 @@ class FlowCell(models.Model):
     #return '%s (%s)' % (self.flowcell_id, self.run_date) 
     return '%s' % (self.flowcell_id) 
 
+  def Create_LOG(self):
+    str = '<span style="color:red;font-size:80%;margin-right:3px">New!</span>'
+    str +='<a target=_balnk href="/exp_track/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
+    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)
@@ -81,7 +86,7 @@ class FlowCell(models.Model):
     date_hierarchy = "run_date"
     save_on_top = True
     search_fields = ['flowcell_id','seq_mac_id','cluster_mac_id','=lane_1_library__library_id','=lane_2_library__library_id','=lane_3_library__library_id','=lane_4_library__library_id','=lane_5_library__library_id','=lane_6_library__library_id','=lane_7_library__library_id','=lane_8_library__library_id']
-    list_display = ('flowcell_id','seq_mac_id','run_date', 'Lanes')
+    list_display = ('flowcell_id','seq_mac_id','run_date', 'Create_LOG','Lanes')
     list_filter = ('seq_mac_id','cluster_mac_id')
     fields = (
         (None, {
@@ -132,7 +137,9 @@ class DataRun(models.Model):
     LanesList = '1: '+self.fcid.lane_1_library.__str__()+' ('+self.fcid.lane_1_library.library_species.use_genome_build+')<br/>2: '+self.fcid.lane_2_library.__str__()+' ('+self.fcid.lane_2_library.library_species.use_genome_build+')<br/>3: '+self.fcid.lane_3_library.__str__()+' ('+self.fcid.lane_3_library.library_species.use_genome_build+')<br/>4: '+self.fcid.lane_4_library.__str__()+' ('+self.fcid.lane_4_library.library_species.use_genome_build+')<br/>5: '+self.fcid.lane_5_library.__str__()+' ('+self.fcid.lane_5_library.library_species.use_genome_build+')<br/>6: '+self.fcid.lane_6_library.__str__()+' ('+self.fcid.lane_6_library.library_species.use_genome_build+')<br/>7: '+self.fcid.lane_7_library.__str__()+' ('+self.fcid.lane_7_library.library_species.use_genome_build+')<br/>8: '+self.fcid.lane_8_library.__str__()+' ('+self.fcid.lane_8_library.library_species.use_genome_build+')'
     str += LanesList ## self.fcid.Lanes()
     str += '</div>'
-    str += '<div><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a></div>'
+    str += '<div><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a>'
+    str += '<span style="color:red;font-size:80%;margin-left:15px;margin-right:3px">New!</span>'
+    str +='<a target=_balnk href="/exp_track/'+self.fcid.flowcell_id+'" title="View XLS like sheet for this Flowcell LOG..." ">View LOG Page</a></div>'
     str += '</div>'    
     return str
   Flowcell_Info.allow_tags = True

diff --git a/htswfrontend/htswfrontend/exp_track/views.py b/htswfrontend/htswfrontend/exp_track/views.py
index 1d9aa8d05319c0d74d16542f0eb8645906b102b6..37383f29286d77c85678e82cecc329d1ce06d8fe 100755 (executable)
--- a/htswfrontend/htswfrontend/exp_track/views.py
+++ b/htswfrontend/htswfrontend/exp_track/views.py
@@ -2,8 +2,9 @@
 #from django.template import Context, loader
 #shortcut to the above modules
 from django.shortcuts import render_to_response, get_object_or_404
-from gaworkflow.frontend.exp_track.models import DataRun
+from htswfrontend.exp_track.models import *
 from django.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
 
 def index(request):
     all_runs = DataRun.objects.all().order_by('-run_start_time')
@@ -20,3 +21,14 @@ def detail(request, run_folder):
     html_str += 'Run Folder: '+run_folder
     r = get_object_or_404(DataRun,run_folder=run_folder)
     return render_to_response('exptrack/detail.html',{'run_f': r})
+
+def makeFCSheet(request,fcid):
+  # get Flowcell by input fcid
+  # ...
+  rec = None
+  try:
+    rec = FlowCell.objects.get(flowcell_id=fcid)
+  except ObjectDoesNotExist:
+    pass
+  lanes = ['1','2','3','4','5','6','7','8']
+  return render_to_response('exptrack/flowcellSheet.html',{'fc': rec})

diff --git a/htswfrontend/htswfrontend/fctracker/models.py b/htswfrontend/htswfrontend/fctracker/models.py
index d6921ea6285d55715802d3ca8a99433a0a7de4ff..16dd2bf0a0d5e1c550eeb7e6debab9fe7a27e077 100644 (file)
--- a/htswfrontend/htswfrontend/fctracker/models.py
+++ b/htswfrontend/htswfrontend/fctracker/models.py
@@ -1,5 +1,5 @@
 from django.db import models
-from gaworkflow.frontend import settings
+from htswfrontend import settings
 
 class Primer(models.Model):
   primer_name = models.CharField(max_length=100, db_index=True)

diff --git a/htswfrontend/htswfrontend/htsw_reports/LibraryInfo.xml b/htswfrontend/htswfrontend/htsw_reports/LibraryInfo.xml
index 2a573e34f35ff532fb2ffb9796eaaf5203232c40..4e7992a5a1a9778ef696a1b6d652d3c1add58abe 100644 (file)
--- a/htswfrontend/htswfrontend/htsw_reports/LibraryInfo.xml
+++ b/htswfrontend/htswfrontend/htsw_reports/LibraryInfo.xml
@@ -1,1342 +1,1024 @@
-<?xml version="1.0" ?>
+<?xml version="1.0" encoding="UTF-8"?>
 <Libraries>
 <Library Name="SL3">
-<Track Flowcell="FC11862" Lane="2" Filename="070919_FC11862_s2_NRSF_monoclonal_Jurkat_rep2_SL3.align_25.hg18.txt" Count=" 1423565" Complexity="3.52723e-05
-"/>
+<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="070821_FC10073_s3_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2132972" Complexity="7.05745e-06
-"/>
-<Track Flowcell="FC10182" Lane="18" Filename="070925_FC10182_s18_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 4061515" Complexity="1.1612e-05
-"/>
-<Track Flowcell="FC11862" Lane="6" Filename="070919_FC11862_s6_Mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2397558" Complexity="1.71556e-05
-"/>
-<Track Flowcell="FC11977" Lane="8" Filename="070928_FC11977_s8_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 1088135" Complexity="0
-"/>
-<Track Flowcell="FC8053" Lane="78" Filename="070724_FC8053_s78_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 3583766" Complexity="7.16827e-05
-"/>
-<Track Flowcell="FC8883" Lane="78" Filename="070720_FC8883_s78_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 5491316" Complexity="2.00867e-05
-"/>
-<Track Flowcell="FC8886" Lane="7" Filename="070802_FC8886_s7_mock_IP_Jurkat_rep1_SL4.align_25.hg18.txt" Count=" 2417786" Complexity="2.07464e-06
-"/>
+<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="070928_FC11977_s7_hct_1_msp_SL10.align_25.hg18.txt" Count=" 1801596" Complexity="0.295915
-"/>
-<Track Flowcell="FC13593" Lane="678" Filename="071002_FC13593_s678_hct_1_msp_SL10.align_25.hg18.txt" Count=" 7978981" Complexity="0.339224
-"/>
+<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="070000_FCOLD1_s1_SRF_ChIP_Jurkat_Rep1_SL11.align_25.hg18.txt" Count=" 8721730" Complexity="0.00106768
-"/>
+<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="SL14">
-<Track Flowcell="FC10135" Lane="4" Filename="071005_FC10135_s4_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2438679" Complexity="4.51989e-06
-"/>
-<Track Flowcell="FC11977" Lane="6" Filename="070928_FC11977_s6_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2007880" Complexity="0
-"/>
-<Track Flowcell="FC13593" Lane="5" Filename="071002_FC13593_s5_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2533720" Complexity="1.97771e-06
-"/>
+<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="071205_FC201U7_s12345678_mock_IP_PFSK1_SL16.align_25.hg.txt" Count=" 23476737" Complexity="1.1441e-05
-"/>
+<Track Flowcell="FC201U7" Lane="12345678" Filename="Flowcells/FC201U7/071205_FC201U7_s12345678_mock_IP_PFSK1_SL16.align_25.hg.txt" Count=" 23476737" Date="071205"/>
 </Library>
 <Library Name="SL24">
-<Track Flowcell="FC5512" Lane="123" Filename="070609_FC5512_s123_d5_C_hpa_SL24.align_25.hg18.txt" Count=" 1534145" Complexity="0.162748
-"/>
-<Track Flowcell="FC5738" Lane="12" Filename="070605_FC5738_s12_d5_C_hpa_SL24.align_25.hg18.txt" Count="  267543" Complexity="0.0778521
-"/>
-<Track Flowcell="FC6058" Lane="6" Filename="070608_FC6058_s6_d5_C_hpa_SL24.align_25.hg18.txt" Count=" 2174107" Complexity="0.139667
-"/>
+<Track Flowcell="FC5512" Lane="123" Filename="Flowcells/FC5512/070609_FC5512_s123_d5_C_hpa_SL24.align_25.hg18.txt" Count=" 1534145" Date="070609"/>
+<Track Flowcell="FC5738" Lane="12" Filename="Flowcells/FC5738/070605_FC5738_s12_d5_C_hpa_SL24.align_25.hg18.txt" Count="  267543" Date="070605"/>
+<Track Flowcell="FC6058" Lane="6" Filename="Flowcells/FC6058/070608_FC6058_s6_d5_C_hpa_SL24.align_25.hg18.txt" Count=" 2174107" Date="070608"/>
 </Library>
 <Library Name="SL26">
-<Track Flowcell="FC5512" Lane="45" Filename="070609_FC5512_s45_ES_E_hpa_SL26.align_25.hg18.txt" Count="  833887" Complexity="0.177983
-"/>
-<Track Flowcell="FC5738" Lane="4" Filename="070605_FC5738_s4_d0_ES_E_hpa_SL26.align_25.hg18.txt" Count="  324128" Complexity="0.111555
-"/>
-<Track Flowcell="FC6058" Lane="3" Filename="070608_FC6058_s3_ES_E_hpa_SL26.align_25.hg18.txt" Count=" 2385605" Complexity="0.163244
-"/>
-<Track Flowcell="FC8880" Lane="78" Filename="070810_FC8880_s78_d0_ES_E_hpa_SL26.align_25.hg18.txt" Count="   29965" Complexity="0.058805
-"/>
+<Track Flowcell="FC5512" Lane="45" Filename="Flowcells/FC5512/070609_FC5512_s45_ES_E_hpa_SL26.align_25.hg18.txt" Count="  833887" Date="070609"/>
+<Track Flowcell="FC5738" Lane="4" Filename="Flowcells/FC5738/070605_FC5738_s4_d0_ES_E_hpa_SL26.align_25.hg18.txt" Count="  324128" Date="070605"/>
+<Track Flowcell="FC6058" Lane="3" Filename="Flowcells/FC6058/070608_FC6058_s3_ES_E_hpa_SL26.align_25.hg18.txt" Count=" 2385605" Date="070608"/>
+<Track Flowcell="FC8880" Lane="78" Filename="Flowcells/FC8880/070810_FC8880_s78_d0_ES_E_hpa_SL26.align_25.hg18.txt" Count="   29965" Date="070810"/>
 </Library>
 <Library Name="SL28">
-<Track Flowcell="FC6058" Lane="78" Filename="070608_FC6058_s78_d5_D_hpa_SL28.align_25.hg18.txt" Count=" 4785632" Complexity="0.106048
-"/>
+<Track Flowcell="FC6058" Lane="78" Filename="Flowcells/FC6058/070608_FC6058_s78_d5_D_hpa_SL28.align_25.hg18.txt" Count=" 4785632" Date="070608"/>
 </Library>
 <Library Name="SL30">
-<Track Flowcell="FC6058" Lane="4" Filename="070608_FC6058_s4_ES_F_hpa_SL30.align_25.hg18.txt" Count=" 2383276" Complexity="0.145205
-"/>
+<Track Flowcell="FC6058" Lane="4" Filename="Flowcells/FC6058/070608_FC6058_s4_ES_F_hpa_SL30.align_25.hg18.txt" Count=" 2383276" Date="070608"/>
 </Library>
 <Library Name="SL33">
-<Track Flowcell="FC10182" Lane="3" Filename="070925_FC10182_s3_hct_2_hpa_SL33.align_25.hg18.txt" Count="  740316" Complexity="0.151801
-"/>
-<Track Flowcell="FC5399" Lane="3" Filename="070713_FC5399_s3_hct_2_hpa_SL33.align_25.hg18.txt" Count="  554691" Complexity="0.153255
-"/>
-<Track Flowcell="FC7853" Lane="3" Filename="070709_FC7853_s3_hct_2_hpa_SL33.align_25.hg18.txt" Count="  734854" Complexity="0.178321
-"/>
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 </Library>
 <Library Name="SL332">
-<Track Flowcell="FC20AMC" Lane="7" Filename="080609_FC20AMC_s7_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 2950811" Complexity="0.000165498
-"/>
+<Track Flowcell="303n0aaxx" Lane="3" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1087155" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="4" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s4_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1070083" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="3" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 4289055" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="7" Filename="Flowcells/FC20AMC/080609_FC20AMC_s7_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 2950811" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="3" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s3_RNA-seq_A549_Rep2_Dex_SL332.align_25.hg18.txt" Count=" 1260681" Date="080725"/>
 </Library>
 <Library Name="SL333">
-<Track Flowcell="FC20AMC" Lane="8" Filename="080609_FC20AMC_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 2863677" Complexity="0.000191765
-"/>
+<Track Flowcell="303n0aaxx" Lane="7" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s7_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 1479883" Date="080715"/>
+<Track Flowcell="303n0aaxx" Lane="8" Filename="Flowcells/303n0aaxx/080715_303n0aaxx_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 1429681" Date="080715"/>
+<Track Flowcell="306WKAAXX" Lane="4" Filename="Flowcells/306WKAAXX/080728_306WKAAXX_s4_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 3317843" Date="080728"/>
+<Track Flowcell="FC20AMC" Lane="8" Filename="Flowcells/FC20AMC/080609_FC20AMC_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 2863677" Date="080609"/>
+<Track Flowcell="FC306VCAAXX" Lane="7" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s7_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 3146212" Date="080725"/>
+<Track Flowcell="FC306VCAAXX" Lane="8" Filename="Flowcells/FC306VCAAXX/080725_FC306VCAAXX_s8_RNA-seq_A549_Rep2_EtOH_SL333.align_25.hg18.txt" Count=" 2107413" Date="080725"/>
+</Library>
+<Library Name="SL334">
+<Track Flowcell="303y5aaxx" Lane="5" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s5_Pol2_EtOH_chIP_Rep1_SL334.align_25.hg18.txt" Count=" 4221253" Date="080715"/>
+<Track Flowcell="303y5aaxx" Lane="6" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s6_Pol2_EtOH_chIP_Rep1_SL334.align_25.hg18.txt" Count=" 4389966" Date="080715"/>
+</Library>
+<Library Name="SL335">
+<Track Flowcell="303y5aaxx" Lane="7" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s7_Input_RXLCh_+Dex_SL335.align_25.hg18.txt" Count=" 4320528" Date="080715"/>
+<Track Flowcell="303y5aaxx" Lane="8" Filename="Flowcells/303y5aaxx/080715_303y5aaxx_s8_Input_RXLCh_+Dex_SL335.align_25.hg18.txt" Count=" 3212232" Date="080715"/>
+</Library>
+<Library Name="SL336">
+<Track Flowcell="303PNAXX" Lane="1" Filename="Flowcells/303PNAXX/080718_303PNAXX_s1_Input_Control_RXLCh_Neuro2A_Rep1_SL336.align_25.mm9.txt" Count=" 4919007" Date="080718"/>
+</Library>
+<Library Name="SL337">
+<Track Flowcell="303PNAXX" Lane="2" Filename="Flowcells/303PNAXX/080718_303PNAXX_s2_Input_Control_RXLCh_CAD_Rep1_SL337.align_25.mm9.txt" Count=" 5960847" Date="080718"/>
+</Library>
+<Library Name="SL338">
+<Track Flowcell="303PNAXX" Lane="3" Filename="Flowcells/303PNAXX/080718_303PNAXX_s3_Neuro2A_CTCF_Rep1_SL338.align_25.mm9.txt" Count=" 5871158" Date="080718"/>
+</Library>
+<Library Name="SL339">
+<Track Flowcell="303PNAXX" Lane="4" Filename="Flowcells/303PNAXX/080718_303PNAXX_s4_CAD_CTCF_Rep1_SL339.align_25.mm9.txt" Count=" 5226675" Date="080718"/>
+</Library>
+<Library Name="SL340">
+<Track Flowcell="303PNAXX" Lane="5" Filename="Flowcells/303PNAXX/080718_303PNAXX_s5_Neuro2A_USF1_Rep1_SL340.align_25.mm9.txt" Count=" 5113687" Date="080718"/>
+</Library>
+<Library Name="SL341">
+<Track Flowcell="303PNAXX" Lane="6" Filename="Flowcells/303PNAXX/080718_303PNAXX_s6_CAD_USF1_Rep1_SL341.align_25.mm9.txt" Count=" 5580547" Date="080718"/>
+</Library>
+<Library Name="SL342">
+<Track Flowcell="303PNAXX" Lane="7" Filename="Flowcells/303PNAXX/080718_303PNAXX_s7_Neuro2A_USF2_Rep1_SL342.align_25.mm9.txt" Count=" 4845266" Date="080718"/>
+</Library>
+<Library Name="SL343">
+<Track Flowcell="303PNAXX" Lane="8" Filename="Flowcells/303PNAXX/080718_303PNAXX_s8_CAD_USF2_Rep1_SL343.align_25.mm9.txt" Count=" 4722617" Date="080718"/>
 </Library>
 <Library Name="SL344">
-<Track Flowcell="FC20AUL" Lane="5" Filename="080621_FC20AUL_s5_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 1854345" Complexity="2.70366e-06
-"/>
-<Track Flowcell="FC20AUL" Lane="6" Filename="080621_FC20AUL_s6_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 2139393" Complexity="6.09154e-06
-"/>
+<Track Flowcell="FC20AUL" Lane="5" Filename="Flowcells/FC20AUL/080621_FC20AUL_s5_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 1854345" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="6" Filename="Flowcells/FC20AUL/080621_FC20AUL_s6_Input_Control_HMEC_rep1_SL344.align_25.hg18.txt" Count=" 2139393" Date="080621"/>
 </Library>
 <Library Name="SL345">
-<Track Flowcell="FC20AUL" Lane="7" Filename="080621_FC20AUL_s7_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 1981441" Complexity="2.531e-06
-"/>
-<Track Flowcell="FC20AUL" Lane="8" Filename="080621_FC20AUL_s8_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 2279789" Complexity="1.01146e-05
-"/>
+<Track Flowcell="FC20AUL" Lane="7" Filename="Flowcells/FC20AUL/080621_FC20AUL_s7_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 1981441" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="8" Filename="Flowcells/FC20AUL/080621_FC20AUL_s8_Input_Control_HMEC_rep2_SL345.align_25.hg18.txt" Count=" 2279789" Date="080621"/>
 </Library>
 <Library Name="SL350">
-<Track Flowcell="FC20AUL" Lane="1" Filename="080621_FC20AUL_s1_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1211303" Complexity="0
-"/>
-<Track Flowcell="FC20AUL" Lane="2" Filename="080621_FC20AUL_s2_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1646993" Complexity="1.03324e-05
-"/>
+<Track Flowcell="FC20AUL" Lane="1" Filename="Flowcells/FC20AUL/080621_FC20AUL_s1_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1211303" Date="080621"/>
+<Track Flowcell="FC20AUL" Lane="2" Filename="Flowcells/FC20AUL/080621_FC20AUL_s2_ChIPSeq_HMEC_Rep1_RNApol2_SL350.align_25.hg18.txt" Count=" 1646993" Date="080621"/>
 </Library>
 <Library Name="SL351">
-<Track Flowcell="FC20AUL" Lane="3" Filename="080621_FC20AUL_s3_chIPSeq_HMEC_Rep2_RNApol2_SL351.align_25.hg18.txt" Count=" 1810613" Complexity="8.2959e-06
-"/>
-<Track Flowcell="FC20AUL" Lane="4" Filename="080621_FC20AUL_s4_chIPSeq_HMEC_Rep1_RNApol2_SL351.align_25.hg18.txt" Count=" 1866673" Complexity="2.14566e-05
-"/>
+<Track Flowcell="FC20AUL" Lane="3" Filename="Flowcells/FC20AUL/080621_FC20AUL_s3_chIPSeq_HMEC_Rep2_RNApol2_SL351.align_25.hg18.txt" Count=" 1810613" Date="080621"/>
+<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="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"/>
+</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"/>
+</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"/>
+</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"/>
+</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"/>
+</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"/>
+</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>
+<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>
+<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>
-</Libraries>
+</Libraries>
\ No newline at end of file

diff --git a/htswfrontend/htswfrontend/htsw_reports/libinfopar.py b/htswfrontend/htswfrontend/htsw_reports/libinfopar.py
index b54d7425c0f61eb5e2a2dfecd8b9c2501d05b9c8..923f114bc3591f28f1dd6f31f1c34d614705698c 100644 (file)
--- a/htswfrontend/htswfrontend/htsw_reports/libinfopar.py
+++ b/htswfrontend/htswfrontend/htsw_reports/libinfopar.py
@@ -42,7 +42,7 @@ def getLibReads(libid):
   parser = make_parser()   
   curHandler = LibInfoHandler(searchTerm)
   parser.setContentHandler(curHandler)
-  parser.parse(open('/gaworkflow/gaworkflow/frontend/htsw_reports/LibraryInfo.xml'))
+  parser.parse(open('/htsworkflow/htswfrontend/htswfrontend/htsw_reports/LibraryInfo.xml'))
   arRes = []
   arRes.append(curHandler.LanesCount) 
   arRes.append(curHandler.ReadsCount)

diff --git a/htswfrontend/htswfrontend/htsw_reports/models.py b/htswfrontend/htswfrontend/htsw_reports/models.py
index 782ebed67e51724bb3722bc6b1bd7e946a701e6a..cad61b42852b8015ffda4f0cabe5da8ef700277a 100644 (file)
--- a/htswfrontend/htswfrontend/htsw_reports/models.py
+++ b/htswfrontend/htswfrontend/htsw_reports/models.py
@@ -2,9 +2,9 @@ from django.db import models
 from django.db.models import Q
 from django.core.exceptions import ObjectDoesNotExist
 from datetime import datetime
-from gaworkflow.frontend.fctracker.models import * 
-from gaworkflow.frontend.analys_track.models import *
-from gaworkflow.frontend.exp_track.models import *
+from htswfrontend.fctracker.models import * 
+from htswfrontend.analys_track.models import *
+from htswfrontend.exp_track.models import *
 from string import *
 import re
 ##from p1 import LibInfo

diff --git a/htswfrontend/htswfrontend/settings.py b/htswfrontend/htswfrontend/settings.py
index 79ca3d766dd706d71192d30fe553888df5420d74..2e6cc4bcf0e738348a4798baf647f0941abaf7ae 100644 (file)
--- a/htswfrontend/htswfrontend/settings.py
+++ b/htswfrontend/htswfrontend/settings.py
@@ -15,7 +15,7 @@ EMAIL_HOST = 'myerslab.stanford.edu'
 EMAIL_PORT = 25
 
 DATABASE_ENGINE = 'sqlite3'           # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
-DATABASE_NAME = os.path.abspath('/gaworkflow/dev_fctracker.db') # Or path to database file if using sqlite3.
+DATABASE_NAME = os.path.abspath('/htsworkflow/htswfrontend/dev_fctracker.db') # Or path to database file if using sqlite3.
 DATABASE_USER = ''             # Not used with sqlite3.
 DATABASE_PASSWORD = ''         # Not used with sqlite3.
 DATABASE_HOST = ''             # Set to empty string for localhost. Not used with sqlite3.
@@ -69,7 +69,7 @@ MIDDLEWARE_CLASSES = (
     'django.middleware.doc.XViewMiddleware',
 )
 
-ROOT_URLCONF = 'gaworkflow.frontend.urls'
+ROOT_URLCONF = 'htswfrontend.urls'
 
 TEMPLATE_DIRS = (
     # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
@@ -84,10 +84,10 @@ INSTALLED_APPS = (
     'django.contrib.contenttypes',
     'django.contrib.sessions',
     'django.contrib.sites',
-    'gaworkflow.frontend.fctracker',
-    'gaworkflow.frontend.exp_track',
-    'gaworkflow.frontend.analys_track', 
-    'gaworkflow.frontend.htsw_reports',
+    'htswfrontend.fctracker',
+    'htswfrontend.exp_track',
+    'htswfrontend.analys_track', 
+    'htswfrontend.htsw_reports',
     'django.contrib.databrowse',
 )
 

diff --git a/htswfrontend/htswfrontend/urls.py b/htswfrontend/htswfrontend/urls.py
index 43475324224a33eff8e32b45ceaaca3a365f596c..3455cded5b4b00eeebf42a4f7e20c752e56fc6dd 100644 (file)
--- a/htswfrontend/htswfrontend/urls.py
+++ b/htswfrontend/htswfrontend/urls.py
@@ -10,9 +10,9 @@ urlpatterns = patterns('',
     # Admin:
      (r'^admin/', include('django.contrib.admin.urls')),
     # ExpTrack:
-     (r'^exp_track/', include('gaworkflow.frontend.exp_track.et_urls')),
+     (r'^exp_track/', include('htswfrontend.exp_track.et_urls')),
     # AnalysTrack:                                                                                                                                                           
-     (r'^analys_track/', include('gaworkflow.frontend.analys_track.an_urls')),
+     (r'^analys_track/', include('htswfrontend.analys_track.an_urls')),
     # Report Views:
     # (r'^reports/', include('gaworkflow.frontend....urls')),
 )