lazar 0.9.3 → 1.0.0

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Files changed (88) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -4
  3. data/README.md +5 -15
  4. data/VERSION +1 -1
  5. data/ext/lazar/extconf.rb +1 -1
  6. data/ext/lazar/rinstall.R +9 -7
  7. data/java/CdkDescriptorInfo.class +0 -0
  8. data/java/CdkDescriptorInfo.java +3 -2
  9. data/java/CdkDescriptors.class +0 -0
  10. data/java/CdkDescriptors.java +28 -28
  11. data/java/Rakefile +3 -3
  12. data/java/{cdk-1.4.19.jar → cdk-2.0-SNAPSHOT.jar} +0 -0
  13. data/lazar.gemspec +6 -7
  14. data/lib/algorithm.rb +2 -11
  15. data/lib/caret.rb +96 -0
  16. data/lib/classification.rb +14 -22
  17. data/lib/compound.rb +21 -87
  18. data/lib/crossvalidation.rb +80 -279
  19. data/lib/dataset.rb +105 -174
  20. data/lib/feature.rb +11 -18
  21. data/lib/feature_selection.rb +42 -0
  22. data/lib/import.rb +122 -0
  23. data/lib/lazar.rb +14 -4
  24. data/lib/leave-one-out-validation.rb +46 -192
  25. data/lib/model.rb +319 -128
  26. data/lib/nanoparticle.rb +98 -0
  27. data/lib/opentox.rb +7 -4
  28. data/lib/overwrite.rb +24 -3
  29. data/lib/physchem.rb +11 -10
  30. data/lib/regression.rb +7 -137
  31. data/lib/rest-client-wrapper.rb +0 -6
  32. data/lib/similarity.rb +65 -0
  33. data/lib/substance.rb +8 -0
  34. data/lib/train-test-validation.rb +69 -0
  35. data/lib/validation-statistics.rb +223 -0
  36. data/lib/validation.rb +17 -100
  37. data/scripts/mg2mmol.rb +17 -0
  38. data/scripts/mirror-enm2test.rb +4 -0
  39. data/scripts/mmol2-log10.rb +32 -0
  40. data/test/compound.rb +4 -94
  41. data/test/data/EPAFHM.medi_log10.csv +92 -0
  42. data/test/data/EPAFHM.mini_log10.csv +16 -0
  43. data/test/data/EPAFHM_log10.csv +581 -0
  44. data/test/data/loael_log10.csv +568 -0
  45. data/test/dataset.rb +195 -133
  46. data/test/descriptor.rb +27 -18
  47. data/test/error.rb +2 -2
  48. data/test/experiment.rb +4 -4
  49. data/test/feature.rb +2 -3
  50. data/test/gridfs.rb +10 -0
  51. data/test/model-classification.rb +106 -0
  52. data/test/model-nanoparticle.rb +128 -0
  53. data/test/model-regression.rb +171 -0
  54. data/test/model-validation.rb +19 -0
  55. data/test/nanomaterial-model-validation.rb +55 -0
  56. data/test/setup.rb +8 -4
  57. data/test/validation-classification.rb +67 -0
  58. data/test/validation-nanoparticle.rb +133 -0
  59. data/test/validation-regression.rb +92 -0
  60. metadata +50 -121
  61. data/test/classification.rb +0 -41
  62. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +0 -13553
  63. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +0 -436
  64. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +0 -568
  65. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +0 -87
  66. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +0 -978
  67. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +0 -1120
  68. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +0 -1113
  69. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +0 -850
  70. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +0 -829
  71. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +0 -1198
  72. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +0 -1505
  73. data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +0 -581
  74. data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +0 -1217
  75. data/test/data/LOAEL_log_mg_corrected_smiles.csv +0 -568
  76. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +0 -568
  77. data/test/data/boiling_points.ext.sdf +0 -11460
  78. data/test/data/cpdb_100.csv +0 -101
  79. data/test/data/hamster_carcinogenicity.ntriples +0 -618
  80. data/test/data/hamster_carcinogenicity.sdf +0 -2805
  81. data/test/data/hamster_carcinogenicity.xls +0 -0
  82. data/test/data/hamster_carcinogenicity.yaml +0 -352
  83. data/test/dataset-long.rb +0 -114
  84. data/test/lazar-long.rb +0 -92
  85. data/test/lazar-physchem-short.rb +0 -31
  86. data/test/prediction_models.rb +0 -20
  87. data/test/regression.rb +0 -43
  88. data/test/validation.rb +0 -108
data/test/data/hamster_carcinogenicity.xls DELETED
Binary file
data/test/data/hamster_carcinogenicity.yaml DELETED
@@ -1,352 +0,0 @@
1
- --- !ruby/object:OpenTox::Dataset
2
- compounds:
3
- - http://localhost/compound/InChI=1S/C2H4O/c1-2-3/h2H,1H3
4
- - 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)
5
- - 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)
6
- - http://localhost/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6)
7
- - http://localhost/compound/InChI=1S/BrHO3.K/c2-1(3)4;/h(H,2,3,4);/q;+1/p-1
8
- - http://localhost/compound/InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2
9
- - http://localhost/compound/InChI=1S/Cd.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2
10
- - 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)
11
- - http://localhost/compound/InChI=1S/C2H5ClO/c1-4-2-3/h2H2,1H3
12
- - http://localhost/compound/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2
13
- - 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)
14
- - http://localhost/compound/InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H
15
- - 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
16
- - 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
17
- - http://localhost/compound/InChI=1S/C6H10N2O/c1-3-5-8(7-9)6-4-2/h3-4H,1-2,5-6H2
18
- - 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
19
- - http://localhost/compound/InChI=1S/C3H6ClNO/c1-5(2)3(4)6/h1-2H3
20
- - http://localhost/compound/InChI=1S/C2H8N2/c1-4(2)3/h3H2,1-2H3
21
- - http://localhost/compound/InChI=1S/C2H8N2.2ClH/c1-3-4-2;;/h3-4H,1-2H3;2*1H
22
- - http://localhost/compound/InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
23
- - http://localhost/compound/InChI=1S/C5H11N3O3/c1-2-8(7-11)5(10)6-3-4-9/h9H,2-4H2,1H3,(H,6,10)
24
- - 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)
25
- - http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2
26
- - 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)
27
- - http://localhost/compound/InChI=1S/C5H4O2/c6-4-5-2-1-3-7-5/h1-4H
28
- - http://localhost/compound/InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2
29
- - 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
30
- - http://localhost/compound/InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9
31
- - http://localhost/compound/InChI=1S/H4N2/c1-2/h1-2H2
32
- - http://localhost/compound/InChI=1S/H4N2.H2O4S/c1-2;1-5(2,3)4/h1-2H2;(H2,1,2,3,4)
33
- - 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
34
- - http://localhost/compound/InChI=1S/C2H8N2O/c3-4-1-2-5/h4-5H,1-3H2
35
- - http://localhost/compound/InChI=1S/C6H7N3O/c7-9-6(10)5-1-3-8-4-2-5/h1-4H,7H2,(H,9,10)
36
- - http://localhost/compound/InChI=1S/C6H5NO2/c8-6(9)5-1-3-7-4-2-5/h1-4H,(H,8,9)
37
- - 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)
38
- - 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)
39
- - 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
40
- - 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
41
- - 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
42
- - http://localhost/compound/InChI=1S/C2H6N2O/c1-4(3)2-5/h2H,3H2,1H3
43
- - http://localhost/compound/InChI=1S/C5H8O2/c1-4(2)5(6)7-3/h1H2,2-3H3
44
- - http://localhost/compound/InChI=1S/CH6N2/c1-3-2/h3H,2H2,1H3
45
- - 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
46
- - http://localhost/compound/InChI=1S/C5H6N2OS/c1-3-2-4(8)7-5(9)6-3/h2H,1H3,(H2,6,7,8,9)
47
- - 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)
48
- - http://localhost/compound/InChI=1S/HNO2.Na/c2-1-3;/h(H,2,3);/q;+1/p-1
49
- - 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)
50
- - 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)
51
- - 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
52
- - 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
53
- - http://localhost/compound/InChI=1S/C6H12N2O4/c1-5(10)2-8(7-12)3-6(11)4-9/h6,9,11H,2-4H2,1H3
54
- - http://localhost/compound/InChI=1S/C5H12N2O4/c8-2-1-7(6-11)3-5(10)4-9/h5,8-10H,1-4H2
55
- - http://localhost/compound/InChI=1S/C5H10N2O3/c1-5(9)4-7(6-10)2-3-8/h8H,2-4H2,1H3
56
- - http://localhost/compound/InChI=1S/C7H15N3O/c1-6-4-10(8-11)5-7(2)9(6)3/h6-7H,4-5H2,1-3H3
57
- - http://localhost/compound/InChI=1S/C6H10N2O2/c1-3-4-8(7-10)5-6(2)9/h3H,1,4-5H2,2H3
58
- - http://localhost/compound/InChI=1S/C4H10N2O3/c1-6(5-9)2-4(8)3-7/h4,7-8H,2-3H2,1H3
59
- - http://localhost/compound/InChI=1S/C4H8N2O2/c7-5-6-1-3-8-4-2-6/h1-4H2
60
- - 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
61
- - 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
62
- - http://localhost/compound/InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2
63
- - http://localhost/compound/InChI=1S/C4H8N2O/c7-5-6-3-1-2-4-6/h1-4H2
64
- - 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)
65
- - http://localhost/compound/InChI=1S/C4H7N3O3/c1-3(8)2-7(6-10)4(5)9/h2H2,1H3,(H2,5,9)
66
- - http://localhost/compound/InChI=1S/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2
67
- - 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)
68
- - 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
69
- - 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
70
- - 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)
71
- - 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
72
- - 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
73
- - 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
74
- - 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
75
- - http://localhost/compound/InChI=1S/C2HCl3/c3-1-2(4)5/h1H
76
- - http://localhost/compound/InChI=1S/C3H7NO2/c1-2-6-3(4)5/h2H2,1H3,(H2,4,5)
77
- - http://localhost/compound/InChI=1S/C2H3Cl/c1-2-3/h2H,1H2
78
- - 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
79
- - 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
80
- - http://localhost/compound/InChI=1S/C5H13N3O/c1-7(2)4-5-8(3)6-9/h4-5H2,1-3H3
81
- - http://localhost/compound/InChI=1S/C6H12N2O2/c1-5-3-8(7-9)4-6(2)10-5/h5-6H,3-4H2,1-2H3
82
- - http://localhost/compound/InChI=1S/C4H6N2O3/c1-3-2-6(5-8)4(7)9-3/h3H,2H2,1H3
83
- - http://localhost/compound/InChI=1S/C4H8N2O3/c1-3-9-4(7)6(2)5-8/h3H2,1-2H3
84
- - http://localhost/compound/InChI=1S/C3H6N2O2/c6-4-5-1-2-7-3-5/h1-3H2
85
- - 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)
86
- - http://localhost/compound/InChI=1S/C3H6N2O/c6-4-5-2-1-3-5/h1-3H2
87
- - http://localhost/compound/InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1
88
- data_entries:
89
- 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:
90
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
91
- - true
92
- http://localhost/compound/InChI=1S/C3H6ClNO/c1-5(2)3(4)6/h1-2H3:
93
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
94
- - true
95
- http://localhost/compound/InChI=1S/C2H8N2O/c3-4-1-2-5/h4-5H,1-3H2:
96
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
97
- - false
98
- http://localhost/compound/InChI=1S/C4H10N2O3/c1-6(5-9)2-4(8)3-7/h4,7-8H,2-3H2,1H3:
99
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
100
- - true
101
- http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2:
102
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
103
- - false
104
- http://localhost/compound/InChI=1S/C5H12N2O4/c8-2-1-7(6-11)3-5(10)4-9/h5,8-10H,1-4H2:
105
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
106
- - false
107
- http://localhost/compound/InChI=1S/C7H15N3O/c1-6-4-10(8-11)5-7(2)9(6)3/h6-7H,4-5H2,1-3H3:
108
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
109
- - true
110
- http://localhost/compound/InChI=1S/C4H8N2O2/c7-5-6-1-3-8-4-2-6/h1-4H2:
111
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
112
- - true
113
- 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:
114
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
115
- - false
116
- http://localhost/compound/InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2:
117
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
118
- - true
119
- http://localhost/compound/InChI=1S/C4H6N2O3/c1-3-2-6(5-8)4(7)9-3/h3H,2H2,1H3:
120
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
121
- - true
122
- http://localhost/compound/InChI=1S/C6H5NO2/c8-6(9)5-1-3-7-4-2-5/h1-4H,(H,8,9):
123
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
124
- - false
125
- 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:
126
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
127
- - false
128
- 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:
129
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
130
- - false
131
- http://localhost/compound/InChI=1S/C3H6N2O2/c6-4-5-1-2-7-3-5/h1-3H2:
132
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
133
- - true
134
- http://localhost/compound/InChI=1S/C3H7NO2/c1-2-6-3(4)5/h2H2,1H3,(H2,4,5):
135
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
136
- - true
137
- http://localhost/compound/InChI=1S/C5H8O2/c1-4(2)5(6)7-3/h1H2,2-3H3:
138
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
139
- - false
140
- http://localhost/compound/InChI=1S/C2H6N2O/c1-4(3)2-5/h2H,3H2,1H3:
141
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
142
- - true
143
- http://localhost/compound/InChI=1S/C6H12N2O4/c1-5(10)2-8(7-12)3-6(11)4-9/h6,9,11H,2-4H2,1H3:
144
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
145
- - true
146
- http://localhost/compound/InChI=1S/C5H4O2/c6-4-5-2-1-3-7-5/h1-4H:
147
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
148
- - false
149
- http://localhost/compound/InChI=1S/C4H8N2O/c7-5-6-3-1-2-4-6/h1-4H2:
150
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
151
- - true
152
- 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):
153
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
154
- - true
155
- 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):
156
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
157
- - false
158
- http://localhost/compound/InChI=1S/H4N2.H2O4S/c1-2;1-5(2,3)4/h1-2H2;(H2,1,2,3,4):
159
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
160
- - true
161
- http://localhost/compound/InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2:
162
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
163
- - true
164
- 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:
165
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
166
- - false
167
- http://localhost/compound/InChI=1S/C3H6N2O/c6-4-5-2-1-3-5/h1-3H2:
168
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
169
- - true
170
- http://localhost/compound/InChI=1S/C4H8N2O3/c1-3-9-4(7)6(2)5-8/h3H2,1-2H3:
171
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
172
- - true
173
- http://localhost/compound/InChI=1S/C6H10N2O2/c1-3-4-8(7-10)5-6(2)9/h3H,1,4-5H2,2H3:
174
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
175
- - true
176
- 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:
177
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
178
- - false
179
- http://localhost/compound/InChI=1S/BrHO3.K/c2-1(3)4;/h(H,2,3,4);/q;+1/p-1:
180
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
181
- - true
182
- http://localhost/compound/InChI=1S/C2H5ClO/c1-4-2-3/h2H2,1H3:
183
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
184
- - true
185
- 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):
186
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
187
- - false
188
- 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):
189
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
190
- - true
191
- http://localhost/compound/InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2:
192
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
193
- - false
194
- 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:
195
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
196
- - false
197
- http://localhost/compound/InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1:
198
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
199
- - false
200
- 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:
201
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
202
- - false
203
- http://localhost/compound/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6):
204
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
205
- - false
206
- http://localhost/compound/InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H:
207
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
208
- - false
209
- http://localhost/compound/InChI=1S/C2HCl3/c3-1-2(4)5/h1H:
210
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
211
- - false
212
- http://localhost/compound/InChI=1S/C2H8N2/c1-4(2)3/h3H2,1-2H3:
213
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
214
- - true
215
- http://localhost/compound/InChI=1S/C6H7N3O/c7-9-6(10)5-1-3-8-4-2-5/h1-4H,7H2,(H,9,10):
216
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
217
- - false
218
- 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:
219
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
220
- - false
221
- http://localhost/compound/InChI=1S/Cd.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2:
222
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
223
- - false
224
- http://localhost/compound/InChI=1S/C5H10N2O3/c1-5(9)4-7(6-10)2-3-8/h8H,2-4H2,1H3:
225
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
226
- - true
227
- 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:
228
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
229
- - false
230
- 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):
231
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
232
- - false
233
- 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):
234
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
235
- - true
236
- 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):
237
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
238
- - true
239
- http://localhost/compound/InChI=1S/CH6N2/c1-3-2/h3H,2H2,1H3:
240
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
241
- - true
242
- 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:
243
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
244
- - false
245
- 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:
246
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
247
- - false
248
- 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):
249
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
250
- - false
251
- http://localhost/compound/InChI=1S/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2:
252
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
253
- - false
254
- 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):
255
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
256
- - false
257
- http://localhost/compound/InChI=1S/C6H12N2O2/c1-5-3-8(7-9)4-6(2)10-5/h5-6H,3-4H2,1-2H3:
258
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
259
- - true
260
- 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):
261
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
262
- - false
263
- 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:
264
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
265
- - true
266
- 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:
267
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
268
- - false
269
- http://localhost/compound/InChI=1S/C5H11N3O3/c1-2-8(7-11)5(10)6-3-4-9/h9H,2-4H2,1H3,(H,6,10):
270
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
271
- - true
272
- 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:
273
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
274
- - false
275
- http://localhost/compound/InChI=1S/H4N2/c1-2/h1-2H2:
276
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
277
- - true
278
- http://localhost/compound/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2:
279
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
280
- - false
281
- 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):
282
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
283
- - false
284
- http://localhost/compound/InChI=1S/C2H8N2.2ClH/c1-3-4-2;;/h3-4H,1-2H3;2*1H:
285
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
286
- - true
287
- 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):
288
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
289
- - true
290
- 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):
291
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
292
- - true
293
- 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):
294
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
295
- - true
296
- http://localhost/compound/InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3:
297
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
298
- - false
299
- http://localhost/compound/InChI=1S/C5H13N3O/c1-7(2)4-5-8(3)6-9/h4-5H2,1-3H3:
300
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
301
- - true
302
- 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):
303
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
304
- - true
305
- http://localhost/compound/InChI=1S/C5H6N2OS/c1-3-2-4(8)7-5(9)6-3/h2H,1H3,(H2,6,7,8,9):
306
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
307
- - true
308
- 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:
309
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
310
- - true
311
- 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:
312
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
313
- - true
314
- 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:
315
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
316
- - false
317
- http://localhost/compound/InChI=1S/HNO2.Na/c2-1-3;/h(H,2,3);/q;+1/p-1:
318
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
319
- - false
320
- http://localhost/compound/InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9:
321
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
322
- - true
323
- http://localhost/compound/InChI=1S/C2H3Cl/c1-2-3/h2H,1H2:
324
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
325
- - true
326
- http://localhost/compound/InChI=1S/C6H10N2O/c1-3-5-8(7-9)6-4-2/h3-4H,1-2,5-6H2:
327
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
328
- - true
329
- 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:
330
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
331
- - false
332
- 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:
333
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
334
- - true
335
- 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:
336
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
337
- - false
338
- http://localhost/compound/InChI=1S/C4H7N3O3/c1-3(8)2-7(6-10)4(5)9/h2H2,1H3,(H2,5,9):
339
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
340
- - true
341
- http://localhost/compound/InChI=1S/C2H4O/c1-2-3/h2H,1H3:
342
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
343
- - true
344
- features:
345
- http://localhost/dataset/1/feature/hamster_carcinogenicity:
346
- http://www.opentox.org/api/1.1#hasSource: hamster_carcinogenicity.csv
347
- http://purl.org/dc/elements/1.1/title: hamster_carcinogenicity
348
- metadata:
349
- http://www.opentox.org/api/1.1#hasSource: hamster_carcinogenicity.csv
350
- http://purl.org/dc/elements/1.1/title: hamster_carcinogenicity
351
- http://www.w3.org/2001/XMLSchema#anyUri: http://localhost/dataset/1
352
- uri: http://localhost/dataset/1
data/test/dataset-long.rb DELETED
@@ -1,114 +0,0 @@
1
- require_relative "setup.rb"
2
-
3
- class DatasetLongTest < MiniTest::Test
4
-
5
- def test_01_upload_epafhm
6
- f = File.join DATA_DIR, "EPAFHM.csv"
7
- d = OpenTox::Dataset.from_csv_file f
8
- csv = CSV.read f
9
- assert_equal csv.size-1, d.compounds.size
10
- assert_equal csv.first.size-1, d.features.size
11
- assert_equal csv.size-1, d.data_entries.size
12
- d.delete
13
- end
14
-
15
- =begin
16
- # TODO catch OpenBabel segfaults and identify/remove cause
17
- def test_02_upload_multicell
18
- duplicates = [
19
- "http://localhost:8082/compound/InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H",
20
- "http://localhost:8082/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",
21
- "http://localhost:8082/compound/InChI=1S/C2HCl3/c3-1-2(4)5/h1H",
22
- "http://localhost:8082/compound/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2",
23
- "http://localhost:8082/compound/InChI=1S/C4H7Cl/c1-4(2)3-5/h1,3H2,2H3",
24
- "http://localhost:8082/compound/InChI=1S/C8H14O4/c1-5-4-8(11-6(2)9)12-7(3)10-5/h5,7-8H,4H2,1-3H3",
25
- "http://localhost:8082/compound/InChI=1S/C19H30O5/c1-3-5-7-20-8-9-21-10-11-22-14-17-13-19-18(23-15-24-19)12-16(17)6-4-2/h12-13H,3-11,14-15H2,1-2H3",
26
- ]
27
- errors = ['O=P(H)(OC)OC', 'C=CCNN.HCl' ]
28
- f = File.join DATA_DIR, "multi_cell_call.csv"
29
- d = OpenTox::Dataset.from_csv_file f
30
- csv = CSV.read f
31
- assert_equal true, d.features.first.nominal
32
- assert_nil d["index"]
33
- assert_equal csv.size-1-errors.size, d.compounds.size
34
- assert_equal csv.first.size-1, d.features.size
35
- assert_equal csv.size-1-errors.size, d.data_entries.size
36
- p d.warnings
37
- (duplicates+errors).each do |uri|
38
- assert d.warnings.grep %r{#{uri}}
39
- end
40
- d.delete
41
- end
42
- =end
43
-
44
- def test_03_upload_isscan
45
- f = File.join DATA_DIR, "ISSCAN-multi.csv"
46
- d = OpenTox::Dataset.from_csv_file f
47
- csv = CSV.read f
48
- assert_equal csv.size-1, d.compounds.size
49
- assert_equal csv.first.size-1, d.features.size
50
- assert_equal csv.size-1, d.data_entries.size
51
- d.delete
52
- #assert_equal false, URI.accessible?(d.uri)
53
- end
54
-
55
- def test_04_simultanous_upload
56
- threads = []
57
- 3.times do |t|
58
- threads << Thread.new(t) do |up|
59
- d = OpenTox::Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
60
- assert_equal OpenTox::Dataset, d.class
61
- assert_equal 1, d.features.size
62
- assert_equal 85, d.compounds.size
63
- assert_equal 85, d.data_entries.size
64
- csv = CSV.read("#{DATA_DIR}/hamster_carcinogenicity.csv")
65
- csv.shift
66
- assert_equal csv.collect{|r| r[1]}, d.data_entries.flatten
67
- d.delete
68
- end
69
- end
70
- threads.each {|aThread| aThread.join}
71
- end
72
-
73
- def test_05_upload_kazius
74
- f = File.join DATA_DIR, "kazius.csv"
75
- d = OpenTox::Dataset.from_csv_file f
76
- csv = CSV.read f
77
- assert_equal csv.size-1, d.compounds.size
78
- assert_equal csv.first.size-1, d.features.size
79
- assert_equal csv.size-1, d.data_entries.size
80
- assert_empty d.warnings
81
- # 493 COC1=C(C=C(C(=C1)Cl)OC)Cl,1
82
- c = d.compounds[491]
83
- assert_equal c.smiles, "COc1cc(Cl)c(cc1Cl)OC"
84
- assert_equal d.data_entries[491][0], "1"
85
- d.delete
86
- end
87
-
88
- def test_upload_feature_dataset
89
- skip
90
- t = Time.now
91
- f = File.join DATA_DIR, "rat_feature_dataset.csv"
92
- d = Dataset.from_csv_file f
93
- assert_equal 458, d.features.size
94
- d.save
95
- #p "Upload: #{Time.now-t}"
96
- d2 = Dataset.find d.id
97
- t = Time.now
98
- assert_equal d.features.size, d2.features.size
99
- csv = CSV.read f
100
- csv.shift # remove header
101
- assert_empty d2.warnings
102
- assert_equal csv.size, d2.compounds.size
103
- assert_equal csv.first.size-1, d2.features.size
104
- d2.compounds.each_with_index do |compound,i|
105
- row = csv[i]
106
- row.shift # remove compound
107
- assert_equal row, d2.data_entries[i]
108
- end
109
- #p "Dowload: #{Time.now-t}"
110
- d2.delete
111
- assert_nil Dataset.find d.id
112
- end
113
-
114
- end
data/test/lazar-long.rb DELETED
@@ -1,92 +0,0 @@
1
- require_relative "setup.rb"
2
-
3
- class LazarExtendedTest < MiniTest::Test
4
-
5
- def test_lazar_bbrc_ham_minfreq
6
- skip
7
- dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
8
- model = Model::LazarFminerClassification.create(dataset, :min_frequency => 5)
9
- feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
10
- assert_equal dataset.compounds.size, feature_dataset.compounds.size
11
- assert_equal model.feature_calculation_parameters, {"min_frequency"=>5}
12
- #TODO check frequencies, features and confidence
13
- #assert_equal 41, feature_dataset.features.size
14
- #assert_equal 'N-C=N', feature_dataset.features.first.smarts
15
- compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
16
- prediction = model.predict compound
17
- assert_equal "false", prediction[:value]
18
- #assert_equal 0.12380952380952381, prediction[:confidence]
19
- dataset.delete
20
- model.delete
21
- feature_dataset.delete
22
- end
23
-
24
- def test_lazar_bbrc_large_ds
25
- skip
26
- dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
27
- model = Model::LazarFminerClassification.create dataset
28
- feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
29
- model.save
30
- p model.id
31
- assert_equal dataset.compounds.size, feature_dataset.compounds.size
32
- #assert_equal 52, feature_dataset.features.size
33
- #assert_equal '[#17&A]-[#6&A]', feature_dataset.features.first.name
34
- compound = OpenTox::Compound.from_inchi("InChI=1S/C10H9NO2S/c1-8-2-4-9(5-3-8)13-6-10(12)11-7-14/h2-5H,6H2,1H3")
35
- prediction = model.predict compound
36
- assert_equal "1", prediction[:value]
37
- #p prediction
38
- #prediction = prediction_dataset.data_entries.first
39
- #assert_in_delta 0.025, prediction[:confidence], 0.001
40
- #assert_equal 0.025885845574483608, prediction[:confidence]
41
- # with compound change in training_dataset see:
42
- # https://github.com/opentox/opentox-test/commit/0e78c9c59d087adbd4cc58bab60fb29cbe0c1da0
43
- #assert_equal 0.02422364949075546, prediction[:confidence]
44
- dataset.delete
45
- model.delete
46
- feature_dataset.delete
47
- end
48
-
49
- def test_lazar_fminer_kazius
50
- skip
51
- t = Time.now
52
- dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
53
- p "Dataset upload: #{Time.now-t}"
54
- t = Time.now
55
- model = Model::LazarFminerClassification.create(dataset, :min_frequency => 100)
56
- p "Feature mining: #{Time.now-t}"
57
- t = Time.now
58
- feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
59
- assert_equal feature_dataset.compounds.size, dataset.compounds.size
60
- #model = Model::Lazar.find('55bcf5bf7a7838381200017e')
61
- #p model.id
62
- #prediction_times = []
63
- 2.times do
64
- compound = Compound.from_smiles("Clc1ccccc1NN")
65
- prediction = model.predict compound
66
- p prediction
67
- #assert_equal "1", prediction[:value]
68
- #assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
69
- end
70
- #dataset.delete
71
- #feature_dataset.delete
72
- end
73
-
74
- def test_lazar_kazius
75
- t = Time.now
76
- dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
77
- p "Dataset upload: #{Time.now-t}"
78
- t = Time.now
79
- model = Model::LazarClassification.create(dataset)
80
- p "Feature mining: #{Time.now-t}"
81
- t = Time.now
82
- 2.times do
83
- compound = Compound.from_smiles("Clc1ccccc1NN")
84
- prediction = model.predict compound
85
- #p prediction
86
- assert_equal "1", prediction[:value]
87
- #assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
88
- end
89
- dataset.delete
90
- end
91
-
92
- end
data/test/lazar-physchem-short.rb DELETED
@@ -1,31 +0,0 @@
1
- require_relative "setup.rb"
2
-
3
- class LazarPhyschemDescriptorTest < MiniTest::Test
4
- def test_epafhm
5
-
6
- skip
7
- @descriptors = OpenTox::Algorithm::Descriptor::OBDESCRIPTORS.keys
8
- refute_empty @descriptors
9
-
10
- # UPLOAD DATA
11
- training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
12
- feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors
13
- scaled_feature_dataset = feature_dataset.scale
14
- model = Model::LazarRegression.create training_dataset
15
- model.neighbor_algorithm = "physchem_neighbors"
16
- model.neighbor_algorithm_parameters = {
17
- :feature_calculation_algorithm => "OpenTox::Algorithm::Descriptor.physchem",
18
- :descriptors => @descriptors,
19
- :feature_dataset_id => scaled_feature_dataset.id,
20
- :min_sim => 0.3
21
- }
22
- model.save
23
- compound = Compound.from_smiles "CC(C)(C)CN"
24
- prediction = model.predict compound
25
- refute_nil prediction[:value]
26
- refute_nil prediction[:confidence]
27
- prediction[:neighbors].each do |line|
28
- assert_operator line[1], :>, 0.3
29
- end
30
- end
31
- end
data/test/prediction_models.rb DELETED
@@ -1,20 +0,0 @@
1
- require_relative "setup.rb"
2
-
3
- class PredictionModelTest < MiniTest::Test
4
-
5
- def test_prediction_model
6
- pm = Model::Prediction.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
7
- [:endpoint,:species,:source].each do |p|
8
- refute_empty pm[p]
9
- end
10
- assert pm.classification?
11
- refute pm.regression?
12
- pm.crossvalidations.each do |cv|
13
- p cv
14
- assert cv.accuracy > 0.74, "Crossvalidation accuracy (#{cv.accuracy}) should be larger than 0.75. This may happen due to an unfavorable training/test set split."
15
- end
16
- prediction = pm.predict Compound.from_smiles("CCCC(NN)C")
17
- assert_equal "true", prediction[:value]
18
- pm.delete
19
- end
20
- end