resolve merge with helma

6 files changed, 104 insertions, 95 deletions

diff --git a/features/compound.feature b/features/compound.feature
index ca2406f..7ee2c03 100644
--- a/features/compound.feature
+++ b/features/compound.feature
@@ -10,9 +10,9 @@ Feature: Create compound URI
 
 	Examples:
 		|descriptor                        |mime-type                 |inchi                                                         |cansmi                     |
-		|CC(=O)CC(C)C#N                    |chemical/x-daylight-smiles|InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3                |CC(CC(=O)C)C#N             |
-		|Benzene                           |text/plain                |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
 		|F[B-](F)(F)F.[Na+]                |chemical/x-daylight-smiles|InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1                            |[Na+].F[B-](F)(F)F         |
-		|N#[N+]C1=CC=CC=C1.F[B-](F)(F)F    |chemical/x-daylight-smiles|InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1|N#[N+]c1ccccc1.F[B-](F)(F)F|
-		|InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H|chemical/x-inchi          |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
+	#|CC(=O)CC(C)C#N                    |chemical/x-daylight-smiles|InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3                |CC(CC(=O)C)C#N             |
+		#|Benzene                           |text/plain                |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
+		#|N#[N+]C1=CC=CC=C1.F[B-](F)(F)F    |chemical/x-daylight-smiles|InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1|N#[N+]c1ccccc1.F[B-](F)(F)F|
+		#|InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H|chemical/x-inchi          |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
 
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

-C=C(Cl)C=C,false

-Clc1ccc(cc1)c2ccc(COC(C)(C)C(O)=O)cc2,false

-O=C1OC2=C(C=CC=C2)C=C1,false

-ClC(=C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)Cl,true

-ClC(C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)(Cl)Cl,false

-C=CCN(CC=C)N=O,true

-Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,false

-O=C(N(C)C)Cl,true

-CN(C)N,true

-N(NC)C.[H]Cl.[H]Cl,true

-CCO,false

-O=C(N(CC)N=O)NCCO,true

-O=C(N(CC)N=O)NCC(=O)C,true

-C=O,false

-[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NNC=O,true

-O=CC1=CC=CO1,false

-OCC1CO1,true

-O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,false

-ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,true

-NN,true

-OS(=O)(=O)O.NN,true

-CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,true

-OCCNN,false

-O=C(C1=CC=NC=C1)NN,false

-OC(=O)C1=CC=NC=C1,false

-O=C(NC1=CC=CC(=C1)Cl)OC(C)C,false

-O=C(NC1=CC=CC=C1)OC(C)C,false

-[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],false

-CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,false

-NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,false

-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

+O=C(N(C)C)Cl,1

+CN(C)N,1

+N(NC)C.[H]Cl.[H]Cl,1

+CCO,0

+O=C(N(CC)N=O)NCCO,1

+O=C(N(CC)N=O)NCC(=O)C,1

+C=O,0

+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NNC=O,1

+O=CC1=CC=CO1,0

+OCC1CO1,1

+O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,0

+ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,1

+NN,1

+OS(=O)(=O)O.NN,1

+CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,1

+OCCNN,0

+O=C(C1=CC=NC=C1)NN,0

+OC(=O)C1=CC=NC=C1,0

+O=C(NC1=CC=CC(=C1)Cl)OC(C)C,0

+O=C(NC1=CC=CC=C1)OC(C)C,0

+[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],0

+CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,0

+NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,0

+CN(N)C=O,1

+O=C(C(=C)C)OC,0

+CNN,1

+O=C(C1=CC=CN=C1)CCCN(N=O)C,0

+CC1=CC(=O)NC(=S)N1,1

+CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,0

+O=N[O-].[Na+],0

+[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,1

+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,1

+O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],0

+N(CC(CO)O)(CC(O)C)N=O,1

+N(CC(CO)O)(CC(C)=O)N=O,1

+N(CC(CO)O)(CCO)N=O,0

+O=C(C)CN(N=O)CCO,1

+C1C(N(C(CN1N=O)C)C)C,1

+N(CC(C)=O)(CC=C)N=O,1

+N(CC(CO)O)(C)N=O,1

+O=NN1CCOCC1,1

+N1C=CC=C(C=1)C2N(N=O)CCC2,1

+C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,0

+O=NN1CCCCC1,1

+O=NN1CCCC1,1

+O=C(N(CC(C)=O)N=O)NCCCl,1

+N(C(=O)N)(N=O)CC(C)=O,1

+C1(CCN=C=S)=CC=CC=C1,0

+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,0

+C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,0

+O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,0

+C1(=CC(=C(O)C=C1)O)C(O)=O,0

+O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,0

+C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,0

+C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,0

+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,0

+ClC(=CCl)Cl,0

+NC(=O)OCC,1

+C=CCl,1

+N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,0

+C1(CN(CC(N1N=O)C)N=O)C,1

+N(CCN(C)C)(C)N=O,1

+C1(CN(N=O)CC(O1)C)C,1

+O1C(N(CC1C)N=O)=O,1

+CCOC(=O)N(C)N=O,1

+C1N(COC1)N=O,1

+O=C(N(CCC1=CC=CC=C1)N=O)N,1

+O=NN1CCC1,1

+F[B-](F)(F)F.[Na+],0

diff --git a/features/fminer.feature b/features/fminer.feature
index c1db022..5e56551 100644
--- a/features/fminer.feature
+++ b/features/fminer.feature
@@ -10,6 +10,7 @@ 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|
-	#|http://dx.doi.org/10.1021/jm040835a|file: data/kazius.rdf|
+ # this is too big for sqlite
 
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 <prediction> for <smiles>
 
 	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/common_steps.rb b/features/step_definitions/common_steps.rb
index 35d3d38..e0d31e5 100644
--- a/features/step_definitions/common_steps.rb
+++ b/features/step_definitions/common_steps.rb
@@ -14,6 +14,11 @@ When /^I post (.*) to the (.*) webservice$/ do |data,component|
 	@resources << @uri unless /compound|feature/ =~ component
 end
 
+Given /^The dataset uri is (.*)$/ do |uri|
+	@uri = uri
+	# do not delete this !!
+end
+
 When /^the task is completed$/ do
 	@task.wait_for_completion
 	@uri = @task.resource
@@ -22,7 +27,7 @@ When /^the task is completed$/ do
 end
 
 Then /^I should receive a valid URI$/ do
-	#puts @uri
+	puts @uri
 	@response = RestClient.get @uri, :accept => '*/*'
 	#puts @response.to_yaml
 end
@@ -38,6 +43,8 @@ Then /^the URI response should be (.+)$/ do |data|
 	when /^file:/
 		data = @data
 	end
+	puts data
+	puts @response
 	assert data == @response, true
 end
 
diff --git a/features/step_definitions/fminer_step.rb b/features/step_definitions/fminer_step.rb
index 6254c6d..1cfcead 100644
--- a/features/step_definitions/fminer_step.rb
+++ b/features/step_definitions/fminer_step.rb
@@ -1,7 +1,7 @@
 When /^I apply fminer for (.*)$/ do |feature_uri|
 	dataset_uri = @uri
-  resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "fminer"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-	@uri = resource.post(:dataset_uri => dataset_uri, :feature_uri => feature_uri)
+  resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "fminer"), :timeout => 60, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+	@uri = resource.post :dataset_uri => dataset_uri, :feature_uri => feature_uri
 	@task = OpenTox::Task.find(@uri)
 	@resources << @uri
 	#puts @uri