diff options
-rw-r--r-- | data/hamster_carcinogenicity.yaml | 172 | ||||
-rw-r--r-- | example.rb | 3 | ||||
-rw-r--r-- | lib/ot_predictions.rb | 2 | ||||
-rw-r--r-- | nightly/nightly.rb | 17 | ||||
-rw-r--r-- | validation/validation_test.rb | 4 |
5 files changed, 101 insertions, 97 deletions
diff --git a/data/hamster_carcinogenicity.yaml b/data/hamster_carcinogenicity.yaml index 14ef015..395ec47 100644 --- a/data/hamster_carcinogenicity.yaml +++ b/data/hamster_carcinogenicity.yaml @@ -87,175 +87,175 @@ compounds: - http://localhost/compound/InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1 data: http://localhost/compound/InChI=1S/C14H8Cl4/c15-11-5-1-9(2-6-11)13(14(17)18)10-3-7-12(16)8-4-10/h1-8H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C3H6ClNO/c1-5(2)3(4)6/h1-2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C2H8N2O/c3-4-1-2-5/h4-5H,1-3H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C4H10N2O3/c1-6(5-9)2-4(8)3-7/h4,7-8H,2-3H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C5H12N2O4/c8-2-1-7(6-11)3-5(10)4-9/h5,8-10H,1-4H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C7H15N3O/c1-6-4-10(8-11)5-7(2)9(6)3/h6-7H,4-5H2,1-3H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C4H8N2O2/c7-5-6-1-3-8-4-2-6/h1-4H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C16H13N/c1-2-8-15(9-3-1)17-16-11-10-13-6-4-5-7-14(13)12-16/h1-12,17H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C4H6N2O3/c1-3-2-6(5-8)4(7)9-3/h3H,2H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H5NO2/c8-6(9)5-1-3-7-4-2-5/h1-4H,(H,8,9): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/2C2H4O2.4H2O.3Pb/c2*1-2(3)4;;;;;;;/h2*1H3,(H,3,4);4*1H2;;;/q;;;;;;3*+2/p-6: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C17H17ClO6/c1-8-5-9(19)6-12(23-4)17(8)16(20)13-10(21-2)7-11(22-3)14(18)15(13)24-17/h6-8H,5H2,1-4H3/t8-,17?/m1/s1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C3H6N2O2/c6-4-5-1-2-7-3-5/h1-3H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C3H7NO2/c1-2-6-3(4)5/h2H2,1H3,(H2,4,5): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C5H8O2/c1-4(2)5(6)7-3/h1H2,2-3H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C2H6N2O/c1-4(3)2-5/h2H,3H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H12N2O4/c1-5(10)2-8(7-12)3-6(11)4-9/h6,9,11H,2-4H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C5H4O2/c6-4-5-2-1-3-7-5/h1-4H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C4H8N2O/c7-5-6-3-1-2-4-6/h1-4H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C9H11N3O2/c10-9(13)12(11-14)7-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H2,10,13): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C14H14ClN3O2S/c1-8-4-3-5-10(9(8)2)16-12-6-11(15)17-14(18-12)21-7-13(19)20/h3-6H,7H2,1-2H3,(H,19,20)(H,16,17,18): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/H4N2.H2O4S/c1-2;1-5(2,3)4/h1-2H2;(H2,1,2,3,4): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C10H13N3O2/c1-13(12-15)7-3-5-10(14)9-4-2-6-11-8-9/h2,4,6,8H,3,5,7H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C3H6N2O/c6-4-5-2-1-3-5/h1-3H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C4H8N2O3/c1-3-9-4(7)6(2)5-8/h3H2,1-2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H10N2O2/c1-3-4-8(7-10)5-6(2)9/h3H,1,4-5H2,2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C14H9Cl5/c15-11-5-1-9(2-6-11)13(14(17,18)19)10-3-7-12(16)8-4-10/h1-8,13H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/BrHO3.K/c2-1(3)4;/h(H,2,3,4);/q;+1/p-1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C2H5ClO/c1-4-2-3/h2H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C10H12ClNO2/c1-7(2)14-10(13)12-9-5-3-4-8(11)6-9/h3-7H,1-2H3,(H,12,13): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C8H5N3O4S/c12-4-9-8-10-5(3-16-8)6-1-2-7(15-6)11(13)14/h1-4H,(H,9,10,12): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C20H19N3.ClH/c1-13-12-16(6-11-19(13)23)20(14-2-7-17(21)8-3-14)15-4-9-18(22)10-5-15;/h2-12,21H,22-23H2,1H3;1H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C2HCl3/c3-1-2(4)5/h1H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C2H8N2/c1-4(2)3/h3H2,1-2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H7N3O/c7-9-6(10)5-1-3-8-4-2-5/h1-4H,7H2,(H,9,10): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C12H8Cl6O/c13-8-9(14)11(16)5-3-1-2(6-7(3)19-6)4(5)10(8,15)12(11,17)18/h2-7H,1H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/Cd.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C5H10N2O3/c1-5(9)4-7(6-10)2-3-8/h8H,2-4H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C27H30O16/c1-8-17(32)20(35)22(37)26(40-8)39-7-15-18(33)21(36)23(38)27(42-15)43-25-19(34)16-13(31)5-10(28)6-14(16)41-24(25)9-2-3-11(29)12(30)4-9/h2-6,8,15,17-18,20-23,26-33,35-38H,7H2,1H3/t8-,15+,17-,18+,20+,21-,22+,23+,26+,27?/m0/s1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C12H12N2O3/c1-2-12(8-6-4-3-5-7-8)9(15)13-11(17)14-10(12)16/h3-7H,2H2,1H3,(H2,13,14,15,16,17): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C8H6N4O4S/c13-4-9-11-8-10-5(3-17-8)6-1-2-7(16-6)12(14)15/h1-4H,(H,9,13)(H,10,11): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C9H7N3O4S/c1-5(13)10-9-11-6(4-17-9)7-2-3-8(16-7)12(14)15/h2-4H,1H3,(H,10,11,13): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/CH6N2/c1-3-2/h3H,2H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C12H9NO2/c14-13(15)11-7-6-9-5-4-8-2-1-3-10(11)12(8)9/h1-3,6-7H,4-5H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C15H10O7.2H2O/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6;;/h1-5,16-19,21H;2*1H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C7H6O4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H,(H,10,11): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C20H22O3/c1-20(2,19(21)22)23-16-12-10-15(11-13-16)18-9-5-7-14-6-3-4-8-17(14)18/h3-4,6,8,10-13,18H,5,7,9H2,1-2H3,(H,21,22): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C6H12N2O2/c1-5-3-8(7-9)4-6(2)10-5/h5-6H,3-4H2,1-2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C10H13NO2/c1-8(2)13-10(12)11-9-6-4-3-5-7-9/h3-8H,1-2H3,(H,11,12): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C6H14N2O4/c1-5(10)2-8(7-12)3-6(11)4-9/h5-6,9-11H,2-4H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C19H24N2O2/c22-18-13-20(19(23)15-7-2-1-3-8-15)12-17-16-9-5-4-6-14(16)10-11-21(17)18/h4-6,9,15,17H,1-3,7-8,10-13H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C5H11N3O3/c1-2-8(7-11)5(10)6-3-4-9/h9H,2-4H2,1H3,(H,6,10): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C14H19N3S.ClH/c1-16(2)9-10-17(12-13-6-5-11-18-13)14-7-3-4-8-15-14;/h3-8,11H,9-10,12H2,1-2H3;1H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/H4N2/c1-2/h1-2H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C17H17ClO3/c1-17(2,16(19)20)21-11-12-3-5-13(6-4-12)14-7-9-15(18)10-8-14/h3-10H,11H2,1-2H3,(H,19,20): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C2H8N2.2ClH/c1-3-4-2;;/h3-4H,1-2H3;2*1H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H10ClN3O3/c1-5(11)4-10(9-13)6(12)8-3-2-7/h2-4H2,1H3,(H,8,12): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H11N3O3/c1-3-9(8-12)6(11)7-4-5(2)10/h3-4H2,1-2H3,(H,7,11): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C11H8N2O5/c12-11(14)8(9-2-1-5-17-9)6-7-3-4-10(18-7)13(15)16/h1-6H,(H2,12,14): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C5H13N3O/c1-7(2)4-5-8(3)6-9/h4-5H2,1-3H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C15H13NO/c1-10(17)16-13-6-7-15-12(9-13)8-11-4-2-3-5-14(11)15/h2-7,9H,8H2,1H3,(H,16,17): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C5H6N2OS/c1-3-2-4(8)7-5(9)6-3/h2H,1H3,(H2,6,7,8,9): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C9H11N3O/c13-11-12-6-2-4-9(12)8-3-1-5-10-7-8/h1,3,5,7,9H,2,4,6H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H12N4O2/c1-5-3-9(7-11)4-6(2)10(5)8-12/h5-6H,3-4H2,1-2H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C19H17N3.ClH/c20-16-7-1-13(2-8-16)19(14-3-9-17(21)10-4-14)15-5-11-18(22)12-6-15;/h1-12,20H,21-22H2;1H: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/HNO2.Na/c2-1-3;/h(H,2,3);/q;+1/p-1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C2H3Cl/c1-2-3/h2H,1H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C6H10N2O/c1-3-5-8(7-9)6-4-2/h3-4H,1-2,5-6H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C9H11N3O2/c13-10-12-6-2-4-9(12)8-3-1-5-11(14)7-8/h1,3,5,7,9H,2,4,6H2: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C15H13NO2/c1-10(17)16(18)13-6-7-15-12(9-13)8-11-4-2-3-5-14(11)15/h2-7,9,18H,8H2,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): false + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): false http://localhost/compound/InChI=1S/C4H7N3O3/c1-3(8)2-7(6-10)4(5)9/h2H2,1H3,(H2,5,9): - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true http://localhost/compound/InChI=1S/C2H4O/c1-2-3/h2H,1H3: - - http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB): true + - http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB): true features: -- http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB) +- http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB) title: Hamster Carcinogenicity (DSSTOX/CPDB) @@ -6,8 +6,7 @@ class Example @@file=File.new("data/hamster_carcinogenicity.yaml","r") @@file_type="text/x-yaml" @@model=File.join @@config[:services]["opentox-model"],"1" - #@@feature="http://localhost/toxmodel/feature%23Hamster%20Carcinogenicity%20(DSSTOX/CPDB)" - @@feature= "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)" + @@feature= URI.encode("http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)") @@alg = File.join @@config[:services]["opentox-algorithm"],"lazar" @@alg_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer") @@data=File.join @@config[:services]["opentox-dataset"],"1" diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb index 6d02466..2e3e927 100644 --- a/lib/ot_predictions.rb +++ b/lib/ot_predictions.rb @@ -82,7 +82,7 @@ module Lib prediction_dataset = OpenTox::Dataset.find prediction_dataset_uri raise "prediction dataset not found: '"+prediction_dataset_uri.to_s+"'" unless prediction_dataset - raise "prediction dataset feature not found: '"+predicted_variable+"', available features: "+prediction_dataset.features.inspect if prediction_dataset.features.index(predicted_variable)==nil + raise "prediction-feature not found: '"+predicted_variable+"' in prediction-dataset: "+prediction_dataset_uri.to_s+", available features: "+prediction_dataset.features.inspect if prediction_dataset.features.index(predicted_variable)==nil raise "more predicted than test compounds test:"+@compounds.size.to_s+" < prediction:"+ prediction_dataset.compounds.size.to_s if @compounds.size < prediction_dataset.compounds.size diff --git a/nightly/nightly.rb b/nightly/nightly.rb index 710c842..e97480a 100644 --- a/nightly/nightly.rb +++ b/nightly/nightly.rb @@ -31,6 +31,8 @@ class Nightly Thread.new do begin b.build + rescue => ex + LOGGER.error "uncaught nightly build error: "+ex.message ensure running.delete(b.class.to_s.gsub(/Nightly::/, "")+b.object_id.to_s) end @@ -42,6 +44,7 @@ class Nightly wait += 1 sleep 1 end + LOGGER.debug "Nighlty report, all benchmarks done "+running.inspect section_about = report.add_section(report.get_root_element, "About this report") report.add_paragraph(section_about, @@ -196,7 +199,7 @@ class Nightly begin LOGGER.debug "Validate: "+@algs[i].to_s @validations[i] = Util.validate_alg(@train_data, @test_data, @test_class_data, - @algs[i], URI.decode(@pred_feature), @alg_params[i]).to_s + @algs[i], @pred_feature, @alg_params[i]).to_s to_compare << @validations[i] if OpenTox::Utils.is_uri?(@validations[i]) begin @@ -245,11 +248,12 @@ class Nightly end def build() - @algs = [ "http://opentox.ntua.gr:3003/algorithm/mlr", + @algs = [ + "http://opentox.ntua.gr:3003/algorithm/mlr", "http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNregression", File.join(@@config[:services]["opentox-majority"],["/regr/algorithm"]) ] - @alg_params = [nil, "dataset_service=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset", nil] + @alg_params = [ nil, "dataset_service=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset", nil] @train_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/342" @test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/342" @pred_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/103141" @@ -303,13 +307,14 @@ class Nightly def build() @algs = [File.join(@@lazar_server,"lazar"), File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]) ] @alg_params = ["feature_generation_uri="+File.join(@@lazar_server,"fminer"),nil] - @pred_feature = "http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB)" + @pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)" - LOGGER.debug "pepare hamster datasets" + LOGGER.debug "prepare hamster datasets" @test_class_data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n") - split = Util.split_dataset(@test_class_data, URI.decode(@pred_feature), 0.9, 1) + split = Util.split_dataset(@test_class_data, @pred_feature, 0.9, 1) @train_data = split[0].to_s @test_data = split[1].to_s + raise "could not split "+@train_data.to_s+" "+@test_data.to_s unless OpenTox::Utils.is_uri?(@train_data) and OpenTox::Utils.is_uri?(@test_data) super end end diff --git a/validation/validation_test.rb b/validation/validation_test.rb index d5529fe..50e93bb 100644 --- a/validation/validation_test.rb +++ b/validation/validation_test.rb @@ -88,8 +88,8 @@ class ValidationTest < Test::Unit::TestCase upload_uri = upload_data(dataset, File.new("data/hamster_carcinogenicity.yaml","r")) ex.orig_data = upload_uri end - ex.act_feat = "http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB)" - #ex.act_feat = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)" + #ex.act_feat = "http://localhost/toxmodel/feature#Hamster Carcinogenicity (DSSTOX/CPDB)" + ex.act_feat = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)" ex.train_data = File.join(dataset,"2") ex.test_data = File.join(dataset,"3") |