opentox-client 0.0.2pre → 1.0.0pre1

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Files changed (40) hide show
  1. data/.gitignore +2 -1
  2. data/ChangeLog +2 -0
  3. data/README.markdown +16 -1
  4. data/Rakefile +0 -10
  5. data/VERSION +1 -0
  6. data/bin/opentox-client-install +46 -0
  7. data/lib/authorization.rb +9 -7
  8. data/lib/compound.rb +40 -20
  9. data/lib/dataset.rb +126 -16
  10. data/lib/error.rb +41 -83
  11. data/lib/model.rb +3 -2
  12. data/lib/opentox-client.rb +17 -12
  13. data/lib/opentox.rb +122 -96
  14. data/lib/overwrite.rb +20 -3
  15. data/lib/policy.rb +17 -2
  16. data/lib/rest-client-wrapper.rb +24 -5
  17. data/lib/task.rb +36 -18
  18. data/opentox-client.gemspec +2 -1
  19. metadata +60 -38
  20. data/test/authorization.rb +0 -107
  21. data/test/compound.rb +0 -52
  22. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +0 -13553
  23. data/test/data/EPAFHM.csv +0 -618
  24. data/test/data/EPAFHM.mini.csv +0 -21
  25. data/test/data/ISSCAN-multi.csv +0 -59
  26. data/test/data/cpdb_100.csv +0 -101
  27. data/test/data/hamster_carcinogenicity.csv +0 -86
  28. data/test/data/hamster_carcinogenicity.mini.csv +0 -11
  29. data/test/data/hamster_carcinogenicity.sdf +0 -2805
  30. data/test/data/hamster_carcinogenicity.xls +0 -0
  31. data/test/data/hamster_carcinogenicity.yaml +0 -352
  32. data/test/data/hamster_carcinogenicity_with_errors.csv +0 -88
  33. data/test/data/kazius.csv +0 -4069
  34. data/test/data/multi_cell_call.csv +0 -1067
  35. data/test/data/multicolumn.csv +0 -5
  36. data/test/dataset.rb +0 -99
  37. data/test/error.rb +0 -35
  38. data/test/feature.rb +0 -36
  39. data/test/policy.rb +0 -120
  40. data/test/task.rb +0 -85
data/test/data/EPAFHM.csv DELETED
@@ -1,618 +0,0 @@
1
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- "C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2",7.69E-03
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- "OCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCOC(=O)C2=CC=CC=C2C(=O)OCCCCO",
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- "CCCSCCCCSCCC",1.45E-02
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522
- "C1(Cl)=CC(Cl)=C(Cl)C=C1SSC2=C(Cl)C=C(Cl)C(Cl)=C2",
523
- "C1=C(C)C(C)=CC=C1OP(=O)(OC2=CC(C)=C(C)C=C2)OC3=CC(C)=C(C)C=C3",
524
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525
- "C(O)C#CCCCCCCC",6.94E-03
526
- "N1=C(O)C=CC(Cl)=C1",8.80E+00
527
- "CC(C)SSC(C)C",5.53E-02
528
- "C1(C=O)=C(OC)C=C(OC)C(OC)=C1",2.52E-01
529
- "C=C(C)C(=O)OC(C)C",2.96E-01
530
- "C=CC(O)CCC",3.04E-01
531
- "OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1",1.77E-03
532
- "C1=CN=CC=C1CCC2=CC=NC=C2",8.20E-01
533
- "C1C(=O)N(CC)C(=S)N(CC)C1=O",2.25E+01
534
- "COC(=O)C1=CC=C(C(=O)OC)C=C1[N+]([O-])=O",2.73E-02
535
- "C1=CC(Cl)=CC2N=C(S)SC1=2",1.59E-02
536
- "COC(=O)C1=CC=C(C(=O)OC)C=C1N",4.27E-02
537
- "CCSCCSCC",4.01E-01
538
- "CN(CCCCl)C.[H]Cl",8.41E-01
539
- "C1=C(C(=O)C)C=C([N+]([O-])=O)C(Cl)=C1",2.76E-02
540
- "CC1=CC(Cl)=NC(N)=N1",9.82E-01
541
- "CC1=C(OC)C=CC=C1OC",1.33E-01
542
- "N1=C(N(C)C)C=CC=C1",1.04E+00
543
- "CC(C)(C)CN",5.45E+00
544
- "O=[C@](O)[C@@]3(C)[C@@]1([H])[C@@](CCC3)(C)[C@]2([H])C(C[C@](C=C)(C)CC2)=CC1",2.88E-03
545
- "C1(N)=CC=C(Cl)C=C1C#N",1.87E-01
546
- "ClC(Cl)(C(C)(O)C)Cl.ClC(Cl)(C(C)(O)C)Cl.[H]O[H]",3.62E-01
547
- "CCCCCCCCCCC(=O)C",6.40E-03
548
- "C1=C(/C=C/C=O)C=CC(N(C)C)=C1",3.67E-02
549
- "C(C(=O)O)[N+]1(=CC=CC=C1).[Cl-]",9.33E-01
550
- "ClC1=C([N+]([O-])=O)C(Cl)=C([N+]([O-])=O)C(Cl)=C1",8.18E-04
551
- "ClC1=CC=C([N+](=O)[O-])C=C1C=O",2.09E-02
552
- "N#CC1=C(Cl)C=CC=C1C",9.96E-02
553
- "N1=C(Br)C(O)=CC=C1",2.70E+00
554
- "N1=C(Cl)C(O)=CC=C1",4.80E+00
555
- "C#CCN(CC#C)CC#C",2.26E+00
556
- "CCOC(OCC)CN(C)CC(OCC)OCC",2.41E+00
557
- "NCCCN1CCN(CCCN)CC1",1.55E+01
558
- "OC(CC/C=C(C)/CC/C=C(C)\C)(C)C=C",6.43E-03
559
- "ClCCN1CCCC1.[H]Cl",9.00E-01
560
- "CCCCCCCCCCCN",1.23E-03
561
- "C#CC(O)CCCC",1.57E-02
562
- "C1(C=O)=CC=C(OCC)C=C1",1.87E-01
563
- "O=C(C(C(C1C2)(C)C)(C2)C)C1Br",2.96E-01
564
- "CC(C)=CC1C(C)(C)C1C(=O)OCC2=COC(CC3=CC=CC=C3)=C2",1.82E-05
565
- "CCOP(=S)(OCC)SCSC(C)(C)C",4.61E-05
566
- "BrC(Br)C1=C(C(Br)Br)C=CC=C1",1.04E-03
567
- "C1=C(C(=O)C)C(Cl)=C(Cl)C(Cl)=C1",8.95E-03
568
- "C1(OC)=C(OC)C(OC)=CC=C1C(=O)C",9.47E-01
569
- "CCOC(=O)C(Cl)C(=O)OCC",4.88E-03
570
- "CCNCC1=CC=CC=C1",4.22E-01
571
- "ClC1=CC=CC=[N+]1C.[I-]",7.79E-01
572
- "C1=CC(Br)=CC=C1C(=O)C2=CC=CN=C2",7.78E-02
573
- "C1=CC=CC=C1C(=O)C2=CC=NC=C2",5.62E-01
574
- "CC1(C)CCC(C)(C)O1",1.31E+00
575
- "N1=C([N+]([O-])=O)C(O)=CC=C1",1.19E+00
576
- "C1(CC)=CC=CC(CC)=C1N(COC)C(=O)CCl",1.85E-02
577
- "NC1=CC=C(CCCCCCCC)C=C1",5.84E-04
578
- "CSC(C)=NOC(=O)NC",1.30E-02
579
- "N1=C(O)C=CC=C1Cl",1.65E+00
580
- "NC1=NN=C(C)C(C)=N1",7.67E+00
581
- "C1=CC([N+]([O-])=O)=CC([N+](=O)[O-])=C1OC2=CC=C(Br)C=C2",
582
- "O=CC1=CC=C(N(CC)CC)C=C1O",2.77E-02
583
- "N1=C(C)C=CC=C1Cl",1.82E+00
584
- "C#CC(CCC(C)C)(C)O",3.49E-01
585
- "CC1=C(C)OC(C)=N1",4.04E+00
586
- "CC(=O)C(C)CN(C)C",6.58E-02
587
- "C1=CC([N+](=O)[O-])=CC=C1OC2=CC(C)=C(Cl)C=C2",
588
- "C1=CC=C(Br)C=C1C(=O)N",4.63E-01
589
- "O=C(C(=NOC(=O)NC)SC)N(C)C",3.09E-02
590
- "NC1=C(C(C)C)C=CC=C1C(C)C",8.63E-02
591
- "[Na+].[N-]=[N+]=[N-]",8.40E-02
592
- "C[N+](C1=CC=CC=C1)(C)C.[O-]S(=O)(=O)OC",1.00E+00
593
- "ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)C(=C(Cl)Cl)Cl",
594
- "CC(C)(O)C(F)(C(F)F)F",3.64E+00
595
- "CCC(N)C",3.76E+00
596
- "COCCCNCC1=CC(OC)=C(OC)C(OC)=C1",5.05E-01
597
- "BrCC1OCCCC1",1.15E+00
598
- "NC1=CC=C(CCCCCCCCCC)C=C1",2.66E-04
599
- "NC1=CC=C(OCCCCCC)C=C1",1.56E-02
600
- "C1([N+](=O)[O-])=CC(Cl)=CC=C1C(=O)OC",1.28E-01
601
- "C1(C=O)=C([N+](=O)[O-])C=CC(O)=C1",2.51E-01
602
- "O=C(C(C1=CC=C(C=C1)Cl)C(C)C)OC(C2=CC=CC(=C2)OC3=CC=CC=C3)C#N",1.21E-05
603
- "C1=CC=C(OC2=CC=CC=C2)C=C1COC(=O)C3C(C)(C)C3C=C(Cl)Cl",4.09E-05
604
- "CCSCCCCSCC",3.40E-02
605
- "CCCCCCCCOC1=CC=CC=C1NC(=O)C",1.71E-03
606
- "C1=CC(C(C)(C)C)=CC=C1C(=O)N",1.80E-01
607
- "CSCCCCCCSC",5.66E-02
608
- "CC(O)C#C",1.67E-01
609
- "C1(C)=C(C)C=CC=C1OP(=O)(OC2=C(C)C(C)=CC=C2)OC3=C(C)C(C)=CC=C3",
610
- "C1C(=CC=C[N+]=1CC2C=CC=CC=2)S(=O)(=O)[O-]",9.67E+00
611
- "C1=CC(C(C)(C)C)=CC=C1OC2=CC=CC(C=O)=C2",1.45E-03
612
- "O=C(OC(C2=CC=CC(OC3=CC=CC=C3)=C2)C#N)[C@H](C1=CC=C(OC(F)F)C=C1)[C@H](C)C",4.21E-07
613
- "ClC1=CC=CC(Cl)=C1OP(=O)(OC2=C(Cl)C=CC=C2Cl)OC3=C(Cl)C=CC=C3Cl",
614
- "C1=C(C=O)C=CC=C1OC2=CC(Cl)=C(Cl)C=C2",1.12E-03
615
- "[Na+].O.O.[O-]C1=C([N+]([O-])=O)C=C([N+]([O-])=O)C2=CC=CC=C12",1.45E-02
616
- "CC(C)(C)C1=CC=C(C=C)C=C1",3.06E-03
617
- "O=P(OCC)(SCCSCC)OCC",6.19E-02
618
- "ClCC1=CC(C=C)=CC=C1",2.03E-03