From 47d648e7e446edcd56c8718b4a112587528fb9be Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sun, 31 Jan 2010 19:09:17 +0100 Subject: Upload facilities added, Ambit disabled --- features/data/hamster_carcinogenicity.csv | 170 +++++++++++++++--------------- features/fminer.feature | 2 +- features/fminer_ambit.feature | 4 +- features/lazar_single_prediction.feature | 5 +- features/step_definitions/fminer_step.rb | 3 +- 5 files changed, 94 insertions(+), 90 deletions(-) diff --git a/features/data/hamster_carcinogenicity.csv b/features/data/hamster_carcinogenicity.csv index 009808f..e9ca269 100644 --- a/features/data/hamster_carcinogenicity.csv +++ b/features/data/hamster_carcinogenicity.csv @@ -1,85 +1,85 @@ -CC=O,true -C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,true -O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,true -C1(N=CNN=1)N,false -Br(=O)(=O)[O-].[K+],true -[Cl-].[Cd+2].[Cl-],false -O=S(=O)([O-])[O-].[Cd+2],false -ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,false -ClCOC,true 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-CN(N)C=O,true -O=C(C(=C)C)OC,false -CNN,true -O=C(C1=CC=CN=C1)CCCN(N=O)C,false -CC1=CC(=O)NC(=S)N1,true -CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,false -O=N[O-].[Na+],false -[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,true -[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,true -O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],false -N(CC(CO)O)(CC(O)C)N=O,true -N(CC(CO)O)(CC(C)=O)N=O,true -N(CC(CO)O)(CCO)N=O,false -O=C(C)CN(N=O)CCO,true -C1C(N(C(CN1N=O)C)C)C,true -N(CC(C)=O)(CC=C)N=O,true -N(CC(CO)O)(C)N=O,true -O=NN1CCOCC1,true -N1C=CC=C(C=1)C2N(N=O)CCC2,true -C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,false -O=NN1CCCCC1,true -O=NN1CCCC1,true -O=C(N(CC(C)=O)N=O)NCCCl,true -N(C(=O)N)(N=O)CC(C)=O,true -C1(CCN=C=S)=CC=CC=C1,false -O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,false -C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,false -O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,false -C1(=CC(=C(O)C=C1)O)C(O)=O,false -O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,false -C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,false -C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,false -OC2=CC1=C(C(O)=C2)C(C(O[C@@H]4O[C@@H]([C@H]([C@H](O)[C@H]4O)O)CO[C@H]3[C@H](O)[C@H](O)[C@H]([C@H](C)O3)O)=C(C5=CC(O)=C(C=C5)O)O1)=O,false -ClC(=CCl)Cl,false -NC(=O)OCC,true -C=CCl,true -N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,false -C1(CN(CC(N1N=O)C)N=O)C,true -N(CCN(C)C)(C)N=O,true -C1(CN(N=O)CC(O1)C)C,true -O1C(N(CC1C)N=O)=O,true -CCOC(=O)N(C)N=O,true -C1N(COC1)N=O,true -O=C(N(CCC1=CC=CC=C1)N=O)N,true -O=NN1CCC1,true -F[B-](F)(F)F.[Na+],false +CC=O,1 +C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,1 +O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,1 +C1(N=CNN=1)N,0 +Br(=O)(=O)[O-].[K+],1 +[Cl-].[Cd+2].[Cl-],0 +O=S(=O)([O-])[O-].[Cd+2],0 +ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,0 +ClCOC,1 +C=C(Cl)C=C,0 +Clc1ccc(cc1)c2ccc(COC(C)(C)C(O)=O)cc2,0 +O=C1OC2=C(C=CC=C2)C=C1,0 +ClC(=C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)Cl,1 +ClC(C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)(Cl)Cl,0 +C=CCN(CC=C)N=O,1 +Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,0 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--git a/features/fminer.feature b/features/fminer.feature index 67dfd39..5e56551 100644 --- a/features/fminer.feature +++ b/features/fminer.feature @@ -11,6 +11,6 @@ Feature: Fminer Examples: |feature |data | |http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12156 |file: hamster_carcinogenicity_ambit.owl| + |http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.owl| # this is too big for sqlite - #|http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.owl| diff --git a/features/fminer_ambit.feature b/features/fminer_ambit.feature index a81c862..a10c1b3 100644 --- a/features/fminer_ambit.feature +++ b/features/fminer_ambit.feature @@ -9,5 +9,7 @@ Feature: Fminer Examples: |feature |dataset_uri | - |http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12100|http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/8| + |http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11847|http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/9| + #|http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12156|http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/9| + #|http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12100|http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/8| diff --git a/features/lazar_single_prediction.feature b/features/lazar_single_prediction.feature index 93e9841..2b18509 100644 --- a/features/lazar_single_prediction.feature +++ b/features/lazar_single_prediction.feature @@ -13,6 +13,7 @@ Feature: Create a model and predict an unknown compound And the model should predict for Examples: - |feature |data |smiles |prediction| - |http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.owl|c1ccccc1NN|true | + |feature |data |smiles |prediction| + |http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12156|file: hamster_carcinogenicity_ambit.owl|c1ccccc1NN|true | + #|http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.owl|c1ccccc1NN|true | diff --git a/features/step_definitions/fminer_step.rb b/features/step_definitions/fminer_step.rb index 5421e33..4adcfa6 100644 --- a/features/step_definitions/fminer_step.rb +++ b/features/step_definitions/fminer_step.rb @@ -1,6 +1,7 @@ When /^I apply fminer for (.*)$/ do |feature_uri| dataset_uri = @uri - @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => dataset_uri, :feature_uri => feature_uri + resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "fminer"), :timeout => 60) + @uri = resource.post :dataset_uri => dataset_uri, :feature_uri => feature_uri @task = OpenTox::Task.find(@uri) @resources << @uri #puts @uri -- cgit v1.2.3