Adding the new Reports component.

diff --git a/gaworkflow/frontend/analys_track/an_urls.py b/gaworkflow/frontend/analys_track/an_urls.py
index 3079cbe4ab516cb6f6044dcaa00f5902cdfc2203..683ae78f5deae109dd6cd2657e2d20aad6796bb1 100644 (file)
--- a/gaworkflow/frontend/analys_track/an_urls.py
+++ b/gaworkflow/frontend/analys_track/an_urls.py
@@ -2,7 +2,7 @@ from django.conf.urls.defaults import *
 
 urlpatterns = patterns('',                                               
     (r'^$', 'gaworkflow.frontend.analys_track.views.index'),
-    (r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.analys_track.views.detail'),
+    #(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'),
 )

diff --git a/gaworkflow/frontend/htsw_reports/LibraryInfo.xml b/gaworkflow/frontend/htsw_reports/LibraryInfo.xml
new file mode 100644 (file)
index 0000000..2a573e3
--- /dev/null
+++ b/gaworkflow/frontend/htsw_reports/LibraryInfo.xml
@@ -0,0 +1,1342 @@
+<?xml version="1.0" ?>
+<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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+<Track Flowcell="FC8880" Lane="34" Filename="070810_FC8880_s34_hct_2_hpa_SL33.align_25.hg18.txt" Count=" 1360438" Complexity="0.277421
+"/>
+</Library>
+<Library Name="SL37">
+<Track Flowcell="FC5399" Lane="2" Filename="070713_FC5399_s2_liver_2_hpa_SL37.align_25.hg18.txt" Count="  374553" Complexity="0.0463636
+"/>
+<Track Flowcell="FC7853" Lane="2" Filename="070709_FC7853_s2_liver_2_hpa_SL37.align_25.hg18.txt" Count=" 1100144" Complexity="0.130257
+"/>
+<Track Flowcell="FC8883" Lane="3" Filename="070720_FC8883_s3_liver_2_hpa_SL37.align_25.hg18.txt" Count=" 1276813" Complexity="0.138016
+"/>
+</Library>
+<Library Name="SL38">
+<Track Flowcell="FC10182" Lane="7" Filename="070925_FC10182_s7_liver_1_msp_SL38.align_25.hg18.txt" Count=" 1039338" Complexity="0.0269867
+"/>
+<Track Flowcell="FC11977" Lane="34" Filename="070928_FC11977_s34_liver_1_msp_SL38.align_25.hg18.txt" Count=" 2094254" Complexity="0.101384
+"/>
+<Track Flowcell="FC7857" Lane="5" Filename="070807_FC7857_s5_liver_1_msp_SL38.align_25.hg18.txt" Count=" 1075706" Complexity="0.0311303
+"/>
+</Library>
+<Library Name="SL39">
+<Track Flowcell="FC5399" Lane="1" Filename="070713_FC5399_s1_liver_1_hpa_SL39.align_25.hg18.txt" Count="  336859" Complexity="0.0247204
+"/>
+<Track Flowcell="FC7853" Lane="1" Filename="070709_FC7853_s1_liver_1_hpa_SL39.align_25.hg18.txt" Count="  973571" Complexity="0.0930633
+"/>
+<Track Flowcell="FC8880" Lane="56" Filename="070810_FC8880_s56_liver_1_hpa_SL39.align_25.hg18.txt" Count="  876351" Complexity="0.184514
+"/>
+<Track Flowcell="FC8883" Lane="4" Filename="070720_FC8883_s4_liver_1_hpa_SL39.align_25.hg18.txt" Count=" 1316822" Complexity="0.107899
+"/>
+</Library>
+<Library Name="SL40">
+<Track Flowcell="FC11862" Lane="7" Filename="070919_FC11862_s7_RNAseq_skeletal_muscle_human_rep1_SL40.align_25.hg18.txt" Count=" 1613090" Complexity="0.000855115
+"/>
+</Library>
+<Library Name="SL41">
+<Track Flowcell="FC11862" Lane="8" Filename="070919_FC11862_s8_RNAseq_skeletal_muscle_human_rep2_SL41.align_25.hg18.txt" Count=" 1036954" Complexity="0.000966241
+"/>
+</Library>
+<Library Name="SL42">
+<Track Flowcell="FC5507" Lane="12" Filename="070703_FC5507_s12_AFP+_1_hpa_SL42.align_25.hg18.txt" Count=" 2297609" Complexity="0.12651
+"/>
+<Track Flowcell="FC7225" Lane="1" Filename="070629_FC7225_s1_AFP+_1_hpa_SL42.align_25.hg18.txt" Count="  921537" Complexity="0.101843
+"/>
+<Track Flowcell="FC7225" Lane="2" Filename="070629_FC7225_s2_AFP+_1_hpa_SL42.align_25.hg18.txt" Count=" 1042305" Complexity="0.107861
+"/>
+</Library>
+<Library Name="SL43">
+<Track Flowcell="FC5507" Lane="3" Filename="070703_FC5507_s3_AFP-_1_hpa_SL43.align_25.hg18.txt" Count=" 1351625" Complexity="0.153815
+"/>
+</Library>
+<Library Name="SL44">
+<Track Flowcell="FC5507" Lane="4" Filename="070703_FC5507_s4_EB_1_hpa_SL44.align_25.hg18.txt" Count=" 1269627" Complexity="0.136441
+"/>
+<Track Flowcell="FC7225" Lane="4" Filename="070629_FC7225_s4_EB_1_hpa_SL44.align_25.hg18.txt" Count=" 1681253" Complexity="0.14852
+"/>
+</Library>
+<Library Name="SL46">
+<Track Flowcell="FC5507" Lane="5" Filename="070703_FC5507_s5_CM_1_hpa_SL46.align_25.hg18.txt" Count=" 1473405" Complexity="0.167396
+"/>
+<Track Flowcell="FC7225" Lane="5" Filename="070629_FC7225_s5_CM_1_hpa_SL46.align_25.hg18.txt" Count=" 1875969" Complexity="0.172404
+"/>
+</Library>
+<Library Name="SL48">
+<Track Flowcell="FC8053" Lane="3" Filename="070724_FC8053_s3_sperm_A_hpa_SL48.align_25.hg18.txt" Count="  364972" Complexity="0.0123675
+"/>
+<Track Flowcell="FC8883" Lane="1" Filename="070720_FC8883_s1_sperm_A_hpa_SL48.align_25.hg18.txt" Count="  642474" Complexity="0.0148881
+"/>
+<Track Flowcell="FC8886" Lane="12" Filename="070802_FC8886_s12_sperm_A_hpa_SL48.align_25.hg18.txt" Count=" 1589274" Complexity="0.0656183
+"/>
+</Library>
+<Library Name="SL49">
+<Track Flowcell="FC8053" Lane="4" Filename="070724_FC8053_s4_sperm_B_hpa_SL49.align_25.hg18.txt" Count="  426192" Complexity="0.022452
+"/>
+<Track Flowcell="FC8883" Lane="2" Filename="070720_FC8883_s2_sperm_B_hpa_SL49.align_25.hg18.txt" Count="  956543" Complexity="0.0549627
+"/>
+<Track Flowcell="FC8886" Lane="34" Filename="070802_FC8886_s34_sperm_B_hpa_SL49.align_25.hg18.txt" Count=" 1697031" Complexity="0.0860284
+"/>
+</Library>
+<Library Name="SL50">
+<Track Flowcell="FC8879" Lane="3" Filename="070717_FC8879_s3_sperm_A_msp_SL50.align_25.hg18.txt" Count="  249065" Complexity="0.00636489
+"/>
+</Library>
+<Library Name="SL53">
+<Track Flowcell="FC10073" Lane="2" Filename="070821_FC10073_s2_d0_ES_C_msp_SL53.align_25.hg18.txt" Count="  459147" Complexity="0.00676683
+"/>
+<Track Flowcell="FC10182" Lane="2" Filename="070925_FC10182_s2_d0_ES_C_msp_SL53.align_25.hg18.txt" Count="  513510" Complexity="0.00721431
+"/>
+<Track Flowcell="FC11862" Lane="345" Filename="070919_FC11862_s345_d0_ES_C_msp_SL53.align_25.hg18.txt" Count=" 1650605" Complexity="0.0675356
+"/>
+</Library>
+<Library Name="SL54">
+<Track Flowcell="FC10073" Lane="456" Filename="070821_FC10073_s456_pancreas_1_hpa_SL54.align_25.hg18.txt" Count=" 4352582" Complexity="0.153353
+"/>
+<Track Flowcell="FC10182" Lane="4" Filename="070925_FC10182_s4_pancreas_1_hpa_SL54.align_25.hg18.txt" Count=" 1136630" Complexity="0.0938974
+"/>
+</Library>
+<Library Name="SL56">
+<Track Flowcell="FC11862" Lane="1" Filename="070919_FC11862_s1_pancreas_2_hpa_SL56.align_25.hg18.txt" Count=" 1359802" Complexity="0.129966
+"/>
+<Track Flowcell="FC11977" Lane="2" Filename="070928_FC11977_s2_pancreas_2_hpa_SL56.align_25.hg18.txt" Count=" 1120271" Complexity="0.12368
+"/>
+</Library>
+<Library Name="SL58">
+<Track Flowcell="FC10073" Lane="78" Filename="070821_FC10073_s78_jurkat_1_hpa_SL58.align_25.hg18.txt" Count="  276664" Complexity="0.0406221
+"/>
+<Track Flowcell="FC10132" Lane="4" Filename="070817_FC10132_s4_jurkat_1_hpa_SL58.align_25.hg18.txt" Count=" 1326942" Complexity="0.161895
+"/>
+<Track Flowcell="FC10182" Lane="6" Filename="070925_FC10182_s6_jurkat_1_hpa_SL58.align_25.hg18.txt" Count=" 1162424" Complexity="0.134029
+"/>
+<Track Flowcell="FC11977" Lane="5" Filename="070928_FC11977_s5_jurkat_1_hpa_SL58.align_25.hg18.txt" Count="  904205" Complexity="0.148663
+"/>
+</Library>
+<Library Name="SL80">
+<Track Flowcell="FC10170" Lane="3" Filename="071010_FC10170_s3_WOL3_cervical_RNA_human_SL80.align_25.hg18.txt" Count="  189349" Complexity="0.0636219
+"/>
+</Library>
+<Library Name="SL81">
+<Track Flowcell="FC10170" Lane="4" Filename="071010_FC10170_s4_WOL4_cervical_RNA_human_SL81.align_25.hg18.txt" Count="  208690" Complexity="0.0660763
+"/>
+</Library>
+<Library Name="SL82">
+<Track Flowcell="FC12673" Lane="4" Filename="071023_FC12673_s4_WOL6_cervical_RNA_human_SL82.align_25.hg18.txt" Count="    8190" Complexity="0.0153538
+"/>
+</Library>
+<Library Name="SL83">
+<Track Flowcell="FC10182" Lane="5" Filename="070925_FC10182_s5_NRSF_monoclonal_HTB11_SL83.align_25.hg18.txt" Count="  918491" Complexity="3.05338e-05
+"/>
+<Track Flowcell="FC11977" Lane="1" Filename="070928_FC11977_s1_NRSF_monoclonal_HTB11_SL83.align_25.hg18.txt" Count="  932151" Complexity="0
+"/>
+<Track Flowcell="FC14428" Lane="3" Filename="071102_FC14428_s3_NRSF_monoclonal_HTB11_SL83.align_25.hgt18.txt" Count="  987885" Complexity="0.145496
+"/>
+<Track Flowcell="FC14432" Lane="2" Filename="071026_FC14432_s2_NRSF_monoclonal_HTB11_SL83.align_25.hg18.txt" Count=" 1052331" Complexity="0
+"/>
+<Track Flowcell="FC6420" Lane="678" Filename="080212_FC6420_s678_NRSF_ChIP_HTB-11_SL83.align_25.hg18.txt" Count=" 3489053" Complexity="2.14958e-05
+"/>
+</Library>
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+<Track Flowcell="FC10135" Lane="1" Filename="071005_FC10135_s1_BG02_ES_A_hpa_SL84.align_25.hg18.txt" Count=" 1908138" Complexity="0.0740707
+"/>
+<Track Flowcell="FC12563" Lane="1" Filename="071016_FC12563_s1_BG02_ES_A_hpa_SL84.align_25.hg18.txt" Count=" 1319454" Complexity="0.0576508
+"/>
+</Library>
+<Library Name="SL85">
+<Track Flowcell="FC10135" Lane="2" Filename="071005_FC10135_s2_BG02_ES_B_hpa_SL85.align_25.hg18.txt" Count=" 2046898" Complexity="0.0954383
+"/>
+<Track Flowcell="FC12563" Lane="2" Filename="071016_FC12563_s2_BG02_ES_B_hpa_SL85.align_25.hg18.txt" Count=" 1576213" Complexity="0.0861677
+"/>
+</Library>
+<Library Name="SL86">
+<Track Flowcell="FC10135" Lane="7" Filename="071005_FC10135_s7_H9_hepato_B_hpa_SL86.align_25.hg18.txt" Count=" 1645814" Complexity="0.158642
+"/>
+<Track Flowcell="FC12673" Lane="6" Filename="071023_FC12673_s6_H9_hepato_B_hpa_SL86.align_25.hg18.txt" Count="  581257" Complexity="0.0962566
+"/>
+</Library>
+<Library Name="SL87">
+<Track Flowcell="FC10135" Lane="8" Filename="071005_FC10135_s8_H9_hepato_D_hpa_SL87.align_25.hg18.txt" Count="  894069" Complexity="0.140567
+"/>
+<Track Flowcell="FC12673" Lane="7" Filename="071023_FC12673_s7_H9_hepato_D_hpa_SL87.align_25.hg18.txt" Count="  410824" Complexity="0.069275
+"/>
+</Library>
+<Library Name="SL88">
+<Track Flowcell="FC10135" Lane="3" Filename="071005_FC10135_s3_NRSF_monoclonal_U87_SL88.align_25.hg18.txt" Count=" 1240914" Complexity="4.03932e-06
+"/>
+<Track Flowcell="FC12565" Lane="5" Filename="071019_FC12565_s5_NRSF_monoclonal_U87_SL88.align_25.hg18.txt" Count="  571952" Complexity="0.000164761
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+<Track Flowcell="FC14428" Lane="4" Filename="071102_FC14428_s4_NRSF_monoclonal_U87_SL88.align_25.hg18.txt" Count=" 1114155" Complexity="0.134292
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+<Track Flowcell="FC14432" Lane="4" Filename="071026_FC14432_s4_NRSF_monoclonal_U87_SL88.align_25.hg18.txt" Count="  914576" Complexity="0
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+<Track Flowcell="FC2057R" Lane="6" Filename="071211_FC2057R_s6_U87_monoclonal_NRSF_ChIP_SL88.align_25.hg18.txt" Count="  172579" Complexity="0.0013761
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+<Track Flowcell="FC6192" Lane="345" Filename="080212_FC6192_s345_NRSF_ChIP_UB7_SL88.align_25.hg18.txt" Count=" 3307816" Complexity="9.97637e-05
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+</Library>
+<Library Name="SL89">
+<Track Flowcell="FC10135" Lane="5" Filename="071005_FC10135_s5_FoxP2_polyclonal_pfsk1_SL89.align_25.hg18.txt" Count=" 1992055" Complexity="3.42176e-05
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+<Track Flowcell="FC10170" Lane="56" Filename="071010_FC10170_s56_FoxP2_polyclonal_pfsk1_SL89.align_25.hg18.txt" Count=" 2332472" Complexity="7.95001e-05
+"/>
+<Track Flowcell="FC12673" Lane="5" Filename="071023_FC12673_s5_FoxP2_polyclonal_pfsk1_SL89.align_25.hg18.txt" Count="  754441" Complexity="0.000171359
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+<Track Flowcell="FC14432" Lane="5678" Filename="071026_FC14432_s5678_FoxP2_polyclonal_pfsk1_SL89.align_25.hg18.txt" Count=" 4136620" Complexity="0.000179771
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+</Library>
+<Library Name="SL90">
+<Track Flowcell="FC10135" Lane="6" Filename="071005_FC10135_s6_NlaIII_18_mouse_SL90.align_25.hg18.txt" Count="  925114" Complexity="0.00436595
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+</Library>
+<Library Name="SL91">
+<Track Flowcell="FC10170" Lane="1" Filename="071010_FC10170_s1_BG02_hepato_B_hpa_SL91.align_25.hg18.txt" Count="   53593" Complexity="0.00330628
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+<Track Flowcell="FC12673" Lane="3" Filename="071023_FC12673_s3_BG02_hepato_B_hpa_SL91.align_25.hg18.txt" Count="   34104" Complexity="0.00457018
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+</Library>
+<Library Name="SL92">
+<Track Flowcell="FC10170" Lane="2" Filename="071010_FC10170_s2_BG02_hepato_C_hpa_SL92.align_25.hg18.txt" Count="  101462" Complexity="0.00401172
+"/>
+</Library>
+<Library Name="SL93">
+<Track Flowcell="FC10170" Lane="7" Filename="071010_FC10170_s7_HCT_mCIP_1_SL93.align_25.hg18.txt" Count=" 1110620" Complexity="0.261281
+"/>
+<Track Flowcell="FC12673" Lane="8" Filename="071023_FC12673_s8_HCT_mCIP_1_SL93.align_25.hg18.txt" Count="  348238" Complexity="0.0787244
+"/>
+<Track Flowcell="FC14430" Lane="78" Filename="071030_FC14430_s78_HCT_mCIP_1_SL93.align_25.hg18.txt" Count=" 1271501" Complexity="0.302057
+"/>
+</Library>
+<Library Name="SL94">
+<Track Flowcell="FC10170" Lane="8" Filename="071010_FC10170_s8_HCT_unbound_mCIP_1_SL94.align_25.hg18.txt" Count="  926056" Complexity="0.0682319
+"/>
+</Library>
+<Library Name="SL98">
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+</Library>
+<Library Name="SL299">
+<Track Flowcell="FC209TJ" Lane="8" Filename="080606_FC209TJ_s8_Methylseq_GM12878_R2_msp_2pcr_SL299.align_25.hg18.txt" Count=" 1951342" Complexity="0.32024
+"/>
+</Library>
+<Library Name="SL304">
+<Track Flowcell="FC20AUG" Lane="5" Filename="080612_FC20AUG_s5_A549_Rep2_GR_Dex_ChIP_SL304.align_25.hg18.txt" Count=" 2357287" Complexity="2.52203e-05
+"/>
+</Library>
+<Library Name="SL305">
+<Track Flowcell="FC20AUG" Lane="6" Filename="080612_FC20AUG_s6_A549_Rep2_GR_EtOH_ChIP_SL305.align_25.hg18.txt" Count=" 2182536" Complexity="5.40141e-05
+"/>
+</Library>
+<Library Name="SL306">
+<Track Flowcell="FC20AUG" Lane="7" Filename="080612_FC20AUG_s7_A549_Rep2_Pol2_Dex_ChIP_SL306.align_25.hg18.txt" Count=" 4246636" Complexity="6.60067e-06
+"/>
+</Library>
+<Library Name="SL307">
+<Track Flowcell="FC20AUG" Lane="8" Filename="080612_FC20AUG_s8_A549_EtOH_RX_noIP_SL307.align_25.hg18.txt" Count=" 3738550" Complexity="1.854e-05
+"/>
+</Library>
+<Library Name="SL310">
+<Track Flowcell="FC20ATH" Lane="6" Filename="080602_FC20ATH_s6_RNA-seq_GM12878_Rep2_SL310.align_25.hg18.txt" Count=" 3087245" Complexity="0.000262986
+"/>
+</Library>
+<Library Name="SL311">
+<Track Flowcell="FC20AUM" Lane="1" Filename="080616_FC20AUM_s1_RNASeq_BJ_rep1_SL311.align_25.hg18.txt" Count=" 3688931" Complexity="0.000121181
+"/>
+</Library>
+<Library Name="SL312">
+<Track Flowcell="FC20ATH" Lane="7" Filename="080602_FC20ATH_s7_RNA-seq_HepG2_Rep1_SL312.align_25.hg18.txt" Count=" 3535250" Complexity="0.00018397
+"/>
+</Library>
+<Library Name="SL313">
+<Track Flowcell="FC20ATH" Lane="8" Filename="080602_FC20ATH_s8_RNA-seq_HepG2_Rep2_SL313.align_25.hg18.txt" Count=" 3462781" Complexity="0.000189175
+"/>
+</Library>
+<Library Name="SL314">
+<Track Flowcell="FC20AUM" Lane="2" Filename="080616_FC20AUM_s2_RNA-seq_HMEC_rep1_SL314.align_25.hg18.txt" Count=" 4056466" Complexity="0.000158949
+"/>
+</Library>
+<Library Name="SL315">
+<Track Flowcell="FC20AUM" Lane="3" Filename="080616_FC20AUM_s3_RNA-seq_HMEC_rep2_SL315.align_25.hg18.txt" Count=" 3958633" Complexity="0.00020159
+"/>
+</Library>
+<Library Name="SL316">
+<Track Flowcell="FC20AUM" Lane="4" Filename="080616_FC20AUM_s4_RNAseq_Jurkat_rep1_SL316.align_25.hg18.txt" Count=" 3926383" Complexity="0.000208663
+"/>
+</Library>
+<Library Name="SL317">
+<Track Flowcell="FC20AUM" Lane="5" Filename="080616_FC20AUM_s5_RNAseq_Jurkat_rep2_SL317.align_25.hg18.txt" Count=" 4104444" Complexity="0.000242854
+"/>
+</Library>
+<Library Name="SL318">
+<Track Flowcell="FC20AMC" Lane="1" Filename="080609_FC20AMC_s1_ChIP-seq_hESC_K36_repurified_SL318.align_25.hg18.txt" Count="  971624" Complexity="0.000149825
+"/>
+</Library>
+<Library Name="SL319">
+<Track Flowcell="FC20AMC" Lane="2" Filename="080609_FC20AMC_s2_ChIP-seq_hESC_K27_repurified_SL319.align_25.hg18.txt" Count="  365209" Complexity="0.000218619
+"/>
+</Library>
+<Library Name="SL320">
+<Track Flowcell="FC20AMC" Lane="3" Filename="080609_FC20AMC_s3_ChIP-seq_hESC_Pol2_repurified_SL320.align_25.hg18.txt" Count="  643582" Complexity="0.000143852
+"/>
+</Library>
+<Library Name="SL321">
+<Track Flowcell="FC20AMC" Lane="4" Filename="080609_FC20AMC_s4_Input_Control_hESC_Repurified_SL321.align_25.hg18.txt" Count=" 1384822" Complexity="8.23403e-05
+"/>
+</Library>
+<Library Name="SL322">
+<Track Flowcell="FC209TJ" Lane="1" Filename="080606_FC209TJ_s1_ChIpSeq_hESCday5_K4_SL322.align_25.hg18.txt" Count="  578452" Complexity="0.000280679
+"/>
+</Library>
+<Library Name="SL323">
+<Track Flowcell="FC209TJ" Lane="2" Filename="080606_FC209TJ_s2_Input_Control_hESCday5_SL323.align_25.hg18.txt" Count=" 1756643" Complexity="5.99904e-05
+"/>
+</Library>
+<Library Name="SL324">
+<Track Flowcell="FC209TJ" Lane="3" Filename="080606_FC209TJ_s3_ChIpSeq_hESCday5_K27_SL324.align_25.hg18.txt" Count=" 1306396" Complexity="0.000126246
+"/>
+</Library>
+<Library Name="SL325">
+<Track Flowcell="FC209TJ" Lane="4" Filename="080606_FC209TJ_s4_ChIpSeq_hESCday5_K36_SL325.align_25.hg18.txt" Count="  478866" Complexity="0.000774083
+"/>
+</Library>
+<Library Name="SL326">
+<Track Flowcell="FC20AUG" Lane="1" Filename="080612_FC20AUG_s1_RNA-seq_BJ_Rep2_75_SL326.align_25.hg18.txt" Count=" 3188417" Complexity="0.000235949
+"/>
+</Library>
+<Library Name="SL327">
+<Track Flowcell="FC20AUG" Lane="2" Filename="080612_FC20AUG_s2_RNA-seq_K562_Rep3_75_SL327.align_25.hg18.txt" Count=" 3717306" Complexity="0.000137965
+"/>
+</Library>
+<Library Name="SL328">
+<Track Flowcell="FC20AUG" Lane="3" Filename="080612_FC20AUG_s3_RNA-seq_BJ_Rep2_7_5_SL328.align_25.hg18.txt" Count=" 3864656" Complexity="0.000191342
+"/>
+</Library>
+<Library Name="SL329">
+<Track Flowcell="FC20AUG" Lane="4" Filename="080612_FC20AUG_s4_RNA-seq_K562_Rep3_7_5_SL329.align_25.hg18.txt" Count=" 3915270" Complexity="0.000134093
+"/>
+</Library>
+<Library Name="SL330">
+<Track Flowcell="FC20AMC" Lane="5" Filename="080609_FC20AMC_s5_RNA-seq_A549_Rep1_Dex_SL330.align_25.hg18.txt" Count=" 2586689" Complexity="0.000176405
+"/>
+</Library>
+<Library Name="SL331">
+<Track Flowcell="FC20AMC" Lane="6" Filename="080609_FC20AMC_s6_RNA-seq_A549_Rep1_EtOH_SL331.align_25.hg18.txt" Count=" 2877770" Complexity="0.00017936
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</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
+"/>
+</Library>
+</Libraries>

diff --git a/gaworkflow/frontend/htsw_reports/__init__.py b/gaworkflow/frontend/htsw_reports/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/gaworkflow/frontend/htsw_reports/libinfopar.py b/gaworkflow/frontend/htsw_reports/libinfopar.py
new file mode 100644 (file)
index 0000000..b54d742
--- /dev/null
+++ b/gaworkflow/frontend/htsw_reports/libinfopar.py
@@ -0,0 +1,50 @@
+from xml.sax import make_parser
+from xml.sax.handler import ContentHandler
+
+
+'''
+Example library node from LibraryInfo.xml:
+<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"/>
+</Library>
+'''
+class LibInfoHandler(ContentHandler):
+
+  def __init__ (self, searchTerm):
+    self.searchTerm= searchTerm
+    self.currlibid = ''
+    self.LanesCount, self.ReadsCount = 0, 0
+    self.Msg = ''
+       
+  def startElement(self, name, attrs):
+    if name == 'Library':     
+      self.currlibid = attrs.get('Name',"")      
+    elif name == 'Track' and self.searchTerm == self.currlibid:
+      self.LanesCount += len(attrs.get('Lane',""))
+      self.ReadsCount += int(attrs.get('Count',""))
+    else:
+      self.Msg += ' | name = '+name+', currlibid = '+ self.currlibid
+    return
+
+  #def characters (self, ch):
+    # return ..
+
+  #def endElement(self, name):
+    # return ..
+
+
+## TO DO: Change this to read the LibraryInfo.xml only ONCE per ReoprtRequest (do it in the models.py). + Read it directly from the analysis_server
+
+def getLibReads(libid):
+  searchTerm= libid
+  parser = make_parser()   
+  curHandler = LibInfoHandler(searchTerm)
+  parser.setContentHandler(curHandler)
+  parser.parse(open('/gaworkflow/gaworkflow/frontend/htsw_reports/LibraryInfo.xml'))
+  arRes = []
+  arRes.append(curHandler.LanesCount) 
+  arRes.append(curHandler.ReadsCount)
+  return arRes
+

diff --git a/gaworkflow/frontend/htsw_reports/models.py b/gaworkflow/frontend/htsw_reports/models.py
new file mode 100644 (file)
index 0000000..782ebed
--- /dev/null
+++ b/gaworkflow/frontend/htsw_reports/models.py
@@ -0,0 +1,302 @@
+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 string import *
+import re
+##from p1 import LibInfo
+from libinfopar import *
+
+## This is a table based REPORT generator. The goal is to display a Progress Report for all the ENCODE projects, based on Study Name (e.g. NRSF, FOXP2, Methy-Seq on .. etc).
+  
+class ProgressReport(models.Model):
+  st_sbj = models.ForeignKey(Project,limit_choices_to = Q(project_name__startswith='ENCODE '),related_name='project',db_index=True,verbose_name="Studied Subject")
+  interactome_complete = models.BooleanField(default=False)
+
+  def Study(self):
+    str = self.st_sbj.__str__()
+    str += '<br/><br/>'
+    str += '<a title="open Project record" href="/admin/analys_track/project/'+self.st_sbj.id.__str__()+'/" target=_self style="font-size:85%">Edit Project</a>'
+    return str  
+  Study.allow_tags = True
+
+  def submit_to_DCC(self):
+    varText = ''
+    if self.note_about_DCC:
+      varText += '<br/><u>Note:</u><br/>'+self.note_about_DCC
+    return '%s<br/>%s' % (self.submitted_to_DCC,varText)
+  submit_to_DCC.allow_tags = True
+
+  def submit_to_NCBI(self):
+    varText = ''
+    if self.note_about_NCBI:
+      varText += '<br/><u>Note:</u><br/>'+self.note_about_NCBI 
+    return '%s<br/>%s' % (self.submitted_to_NCBI,varText)
+  submit_to_NCBI.allow_tags = True
+
+  #REPS = ((1,1),(2,2),(3,3))
+  #replicate = models.PositiveSmallIntegerField(choices=REPS,verbose_name='Replicate Number')   
+  
+  ## -- Utility functions
+  def unique(self,s):
+    """Return a list of the elements in s, but without duplicates.
+    For example, unique([1,2,3,1,2,3]) is some permutation of [1,2,3],
+    unique("abcabc") some permutation of ["a", "b", "c"], and
+    unique(([1, 2], [2, 3], [1, 2])) some permutation of
+    [[2, 3], [1, 2]].
+    For best speed, all sequence elements should be hashable.  Then
+    unique() will usually work in linear time.
+    If not possible, the sequence elements should enjoy a total
+    ordering, and if list(s).sort() doesn't raise TypeError it's
+    assumed that they do enjoy a total ordering.  Then unique() will
+    usually work in O(N*log2(N)) time.
+    If that's not possible either, the sequence elements must support
+    equality-testing.  Then unique() will usually work in quadratic
+    time.
+    """
+
+    n = len(s)
+    if n == 0:
+        return []
+
+    # Try using a dict first, as that's the fastest and will usually
+    # work.  If it doesn't work, it will usually fail quickly, so it
+    # usually doesn't cost much to *try* it.  It requires that all the
+    # sequence elements be hashable, and support equality comparison.
+    u = {}
+    try:
+        for x in s:
+            u[x] = 1
+    except TypeError:
+        del u  # move on to the next method
+    else:
+        return u.keys()
+
+    # We can't hash all the elements.  Second fastest is to sort,
+    # which brings the equal elements together; then duplicates are
+    # easy to weed out in a single pass.
+    # NOTE:  Python's list.sort() was designed to be efficient in the
+    # presence of many duplicate elements.  This isn't true of all
+    # sort functions in all languages or libraries, so this approach
+    # is more effective in Python than it may be elsewhere.
+    try:
+        t = list(s)
+        t.sort()
+    except TypeError:
+        del t  # move on to the next method
+    else:
+        assert n > 0
+        last = t[0]
+        lasti = i = 1
+        while i < n:
+            if t[i] != last:
+                t[lasti] = last = t[i]
+                lasti += 1
+            i += 1
+        return t[:lasti]
+
+    # Brute force is all that's left.
+    u = []
+    for x in s:
+        if x not in u:
+            u.append(x)
+    return u
+
+
+  ## --- LIBARAY PREPARATION SECTION 
+  def getLibIds(self):
+    ptasks = self.st_sbj.tasks.distinct()
+    arLibs = [] 
+    for t in ptasks:
+      if t.subject1 is not None:
+        arLibs.append(t.subject1.library_id)
+      if t.subject2 is not None:
+        arLibs.append(t.subject2.library_id)
+    arLibs = self.unique(arLibs)
+    return arLibs #.sort()
+
+  def getFCInfo(self,libid):   ## This is the haviest function 
+    arFCLanes = []
+    ##Test return arFCLanes
+    # can't get this to work: FC_L1 = FlowCell.objects.filter(lane_5_library__exact=libid)
+    allFCs = FlowCell.objects.all()
+    for f in allFCs:
+      entry = ''
+      lanes = []
+      #found = False
+#      for i in range(1,9):
+#        if eval('f.lane_'+i.__str__()+'_library.library_id==libid'):
+#          lanes.append(i.__str__())
+#          found = True
+
+# maybe a bit faster this way:
+      if f.lane_1_library.library_id==libid:
+          lanes.append('1')
+          #found = True
+      if f.lane_2_library.library_id==libid:
+          lanes.append('2')
+          #found = True
+      if f.lane_3_library.library_id==libid:
+          lanes.append('3')
+          #found = True
+      if f.lane_4_library.library_id==libid:
+          lanes.append('4')
+          #found = True
+      if f.lane_5_library.library_id==libid:
+          lanes.append('5')
+          #found = True
+      if f.lane_6_library.library_id==libid:
+          lanes.append('6')
+          #found = True
+      if f.lane_7_library.library_id==libid:
+          lanes.append('7')
+          #found = True
+      if f.lane_8_library.library_id==libid:
+          lanes.append('8')
+          #found = True
+
+
+      #if found:
+      if len(lanes)>0:
+        rundate = re.sub(pattern="\s.*$",repl="",string=f.run_date.__str__())
+        entry = '<b>'+f.flowcell_id + '</b> Lanes No.: '+','.join(lanes)+' ('+rundate+')' 
+        arFCLanes.append(entry)    
+    if len(arFCLanes)==0:
+      arFCLanes.append('<font color=red>Flowcell not found.</font>')
+    return arFCLanes
+
+  def ab_batch(self):
+    ##  To have the Company's lot number, apearing on the (source) tube, we need to add new Field in Library. 
+    arlibs = self.getLibIds()
+    tstr = '<ul>' ##<u><b>Ab</b> from '+len(arlibs).__str__()+' libs</u>: '
+    arRows = []
+    for l in arlibs:
+      try:
+        rec = Library.objects.get(library_id=l,antibody__isnull=False)
+        arRows.append('<li>'+rec.antibody.antibodies+' for <b>'+rec.antibody.antigene+'</b> (src:'+rec.antibody.source+', cat:'+rec.antibody.catalog+')</li>')
+      except ObjectDoesNotExist:
+        tstr += ""
+    tstr += "".join(self.unique(arRows))+'</ul>'
+    return tstr
+  ab_batch.allow_tags = True
+
+  def cell_line(self):                                                                                           
+    arlibs = self.getLibIds()
+    tstr = '<ul>'
+    arRows = []                                                                                                                                     
+    for l in arlibs:
+      try:
+        rec = Library.objects.get(library_id=l)
+        arRows.append('<li><b>'+rec.cell_line.cellline_name+'</b> ('+rec.condition.condition_name+')</li>')
+      except ObjectDoesNotExist:
+        tstr += ""                                                                                                                               
+    tstr += "".join(self.unique(arRows))+'</ul>'
+    return tstr
+  cell_line.allow_tags = True
+
+  def cell_harvest_batch(self): # <- data now displayed in "cell_line"
+    ## name + date  
+    arlibs = self.getLibIds()
+    tstr = '<ul>'
+    arRows = []
+    for l in arlibs:
+      try:
+        rec = Library.objects.get(library_id=l)
+        arRows.append('<li><b>'+rec.condition.condition_name+'</b></li>')
+      except ObjectDoesNotExist:
+        tstr += ""
+    tstr += "".join(self.unique(arRows))+'</ul>'
+    return tstr
+  cell_harvest_batch.allow_tags = True
+
+  def ChIP_made(self):
+    ## person + date                                                                                                                                                                                                             
+    return '...'
+
+  def library(self):
+    ## Lib Id + Date + Person
+    tstr = '<script>'
+    tstr += 'function togit(eid){'
+    tstr += 'f=document.getElementById(eid);'
+    tstr += 'if(f.style.display==\'none\'){'
+    tstr += 'f.style.display=\'block\';'
+    tstr += '}else{'
+    tstr += 'f.style.display=\'none\';'
+    tstr += '}'
+    tstr += '}'
+    tstr += '</script>'
+    arlibs = self.getLibIds() ##.sort()
+    arlibs = arlibs
+    tstr +='<a href=# onClick="togit(\'libInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+    tstr += '<div id="libInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'
+    arRows = []
+    for l in arlibs:
+      try:
+        rec = Library.objects.get(library_id=l)
+        arRows.append('<li><b>'+rec.library_id+'</b>: '+rec.library_name+'.<br/>Made By: '+rec.made_by+', On: '+ rec.creation_date.__str__()+'</li>')
+      except ObjectDoesNotExist:
+        tstr += ""
+    tstr += "".join(self.unique(arRows))+'</ul></div>'
+    return tstr
+  library.allow_tags = True
+
+
+  ## -- SEQUENCING SECTION 
+  def sequencing(self):
+    ## FCId + Lane + Date
+    arlibs = self.getLibIds()
+    tstr ='<a href=# onClick="togit(\'seqInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+    tstr += '<div id="seqInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto"><ul>'    
+    for l in arlibs:
+      tstr += '<li><b>'+l+'</b>:<br/>'+(' / '.join(self.getFCInfo(l)))+'</li>'
+    tstr += '</ul></div>'
+    return tstr
+  sequencing.allow_tags = True
+  
+  def aligned_reads(self):
+    ## Mega reads/lane                                              
+    arlibs = self.getLibIds()
+    tstr = '<a href=# onClick="togit(\'readsInfo'+self.st_sbj.project_name+'\')">view /hide</a>'
+    tstr += '<div id="readsInfo'+self.st_sbj.project_name+'" style="display:block;border:solid #cccccc 1px;width:200px;height:300px;overflow:auto">'
+    tstr += '<table><tr><td>Library Id</td><td>Total Lanes</td><td>M Reads</td></tr>'
+    LanesCnt, ReadsCnt = 0, 0
+    for l in arlibs:      
+      res = getLibReads(l)
+      LanesCnt += res[0]
+      ReadsCnt += res[1]
+      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 += '</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>'
+    return tstr
+  aligned_reads.allow_tags = True
+
+  def peak_calling(self):
+    # date + what etc..
+    return 'coming up ..'
+
+  QPCR = models.CharField(max_length=500,blank=True,null=True)    
+  submitted_to_DCC = models.DateTimeField(core=True,blank=True,null=True)
+  submitted_to_NCBI = models.DateTimeField(core=True,blank=True,null=True)
+  note_about_DCC =  models.TextField(blank=True)
+  note_about_NCBI = models.TextField(blank=True)
+  
+  def __str__(self):
+      return '"%s" - %s' % (self.st_sbj,self.interactome_complete)
+
+  class Meta:
+    #verbose_name_plural = "Reports"
+    ordering = ["id"]
+
+  class Admin:
+    list_display = ('Study','ab_batch','cell_line','library','sequencing','aligned_reads','QPCR','submit_to_DCC','submit_to_NCBI','interactome_complete')
+    ## list_filter = ('interactome_complete')
+    

diff --git a/gaworkflow/frontend/settings.py b/gaworkflow/frontend/settings.py
index 938ed4e25ea4c170f557f94c25d5b399a1e3d081..79ca3d766dd706d71192d30fe553888df5420d74 100644 (file)
--- a/gaworkflow/frontend/settings.py
+++ b/gaworkflow/frontend/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('/gaworkflow/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.