diff options
| author | Christoph Helma <helma@in-silico.de> | 2009-11-24 14:10:02 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.de> | 2009-11-24 14:10:02 +0100 |
| commit | 5dfa70ed7ee259a75bea0f54b83ccfce79e591e0 (patch) | |
| tree | 9809c136ae24487d37e236786216dade93ba903c | |
| parent | 944ca1aa72655b6d8ab306ec344162ac13f0b002 (diff) | |
Tests for RDF and API 1.1
| -rw-r--r-- | features/compound.feature | 19 | ||||
| -rw-r--r-- | features/data/hamster_carcinogenicity.rdf | 258 | ||||
| -rw-r--r-- | features/data/kazius.rdf | 12207 | ||||
| -rw-r--r-- | features/dataset.feature | 40 | ||||
| -rw-r--r-- | features/dataset_large.feature | 15 | ||||
| -rw-r--r-- | features/feature.feature | 13 | ||||
| -rw-r--r-- | features/fminer.feature | 16 | ||||
| -rw-r--r-- | features/lazar.feature | 12 | ||||
| -rw-r--r-- | features/step_definitions/common_steps.rb | 23 | ||||
| -rw-r--r-- | features/step_definitions/dataset_steps.rb | 26 | ||||
| -rw-r--r-- | features/step_definitions/fminer_step.rb | 9 | ||||
| -rw-r--r-- | features/step_definitions/lazar_steps.rb | 21 |
12 files changed, 12524 insertions, 135 deletions
diff --git a/features/compound.feature b/features/compound.feature index 2bc443c..ca2406f 100644 --- a/features/compound.feature +++ b/features/compound.feature @@ -1,17 +1,18 @@ @rest -Feature: Create URI +Feature: Create compound URI Scenario Outline: Create and get URIs - Given <type> is <descriptor> - When I post the parameters to the compound webservice + Given Content-Type is <mime-type> + When I post <descriptor> to the compound webservice Then I should receive a valid URI And the URI should contain <inchi> And the URI response should be <cansmi> Examples: - |descriptor |type |inchi |cansmi | - |CC(=O)CC(C)C#N |smiles|InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3 |CC(CC(=O)C)C#N | - |Benzene |name |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H |c1ccccc1 | - |F[B-](F)(F)F.[Na+] |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 |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|inchi |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H |c1ccccc1 | + |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 | + diff --git a/features/data/hamster_carcinogenicity.rdf b/features/data/hamster_carcinogenicity.rdf new file mode 100644 index 0000000..1dafcc0 --- /dev/null +++ b/features/data/hamster_carcinogenicity.rdf @@ -0,0 +1,258 @@ +<?xml version="1.0" encoding="utf-8"?> +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H4O/c1-2-3/h2H,1H3"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H4N4/c3-2-4-1-5-6-2/h1H,(H3,3,4,5,6)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/BrHO3.K/c2-1(3)4;/h(H,2,3,4);/q;+1/p-1"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/Cd.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H5ClO/c1-4-2-3/h2H2,1H3"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C6H10N2O/c1-3-5-8(7-9)6-4-2/h3-4H,1-2,5-6H2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C3H6ClNO/c1-5(2)3(4)6/h1-2H3"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H8N2/c1-4(2)3/h3H2,1-2H3"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H8N2.2ClH/c1-3-4-2;;/h3-4H,1-2H3;2*1H"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C5H11N3O3/c1-2-8(7-11)5(10)6-3-4-9/h9H,2-4H2,1H3,(H,6,10)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C6H11N3O3/c1-3-9(8-12)6(11)7-4-5(2)10/h3-4H2,1-2H3,(H,7,11)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/CH2O/c1-2/h1H2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C5H4O2/c6-4-5-2-1-3-7-5/h1-4H"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/H4N2/c1-2/h1-2H2"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/InChI=1S/H4N2.H2O4S/c1-2;1-5(2,3)4/h1-2H2;(H2,1,2,3,4)"> + <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + </rdf:Description> + <rdf:Description rdf:about="http://localhost:4000/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"> + <ns0:ActivityOutcome_CPDBAS_Hamster 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</rdf:Description> +</rdf:RDF> diff --git a/features/dataset.feature b/features/dataset.feature index af667ea..d6af70d 100644 --- a/features/dataset.feature +++ b/features/dataset.feature @@ -1,39 +1,13 @@ @rest Feature: Dataset - Scenario Outline: Create dataset - Given name is <name> - When I post the parameters to the dataset webservice + Scenario Outline: Create a dataset + Given Content-Type is application/rdf+xml + When I post <data> to the dataset webservice Then I should receive a valid URI - And the URI should contain <name> + And the URI response should be <data> Examples: - |name| - |Test| - |Rodent Carcinogenicity| - - - Scenario Outline: Add data to a dataset - Given name is <name> - And compound_format is smiles - And a file <filename> - When I post the parameters to the dataset webservice - And I put the file to the dataset URI - Then I should receive a valid URI - And the URI should return a YAML representation - - Examples: - |name|filename| - |Hamster Carcinogenicity|hamster_carcinogenicity.csv| - - Scenario Outline: Add YAML data - Given name is <name> - Given a file <filename> - When I post the parameters to the dataset webservice - And I put YAML data to the dataset URI - Then I should receive a valid URI - And the URI should return a YAML representation - - Examples: - |name|filename| - |Hamster Carcinogenicity BBRC features|hamster_carcinogenicity_bbrc_features.yaml| + |data| + |file: hamster_carcinogenicity.rdf| + |file: kazius.rdf| diff --git a/features/dataset_large.feature b/features/dataset_large.feature deleted file mode 100644 index d847522..0000000 --- a/features/dataset_large.feature +++ /dev/null @@ -1,15 +0,0 @@ -@rest -Feature: Dataset - - Scenario Outline: Add data to a dataset - Given name is <name> - And compound_format is smiles - And a file <filename> - When I post the parameters to the dataset webservice - And I put the file to the dataset URI - Then I should receive a valid URI - And the URI should return a YAML representation - - Examples: - |name|filename| - |Salmonella mutagenicity|kazius.csv| diff --git a/features/feature.feature b/features/feature.feature deleted file mode 100644 index cf8b35e..0000000 --- a/features/feature.feature +++ /dev/null @@ -1,13 +0,0 @@ -@rest -Feature: Create feature URI - - Scenario Outline: Create URIs - Given name is <name> - And <property> is <value> - When I post the parameters to the feature webservice - Then I should receive a valid URI - And the URI should contain <result> - - Examples: - |name |property |value |result| - |Rodent carcinogenicity|classification|active|Rodent carcinogenicity/classification/active| diff --git a/features/fminer.feature b/features/fminer.feature index 0b66b51..e712449 100644 --- a/features/fminer.feature +++ b/features/fminer.feature @@ -1,16 +1,14 @@ @rest Feature: Fminer - Scenario Outline: Add data to a dataset - Given name is <name> - And compound_format is smiles - And a file <filename> - When I apply fminer + Scenario Outline: Create fminer features + Given Content-Type is application/rdf+xml + And I post <data> to the dataset webservice + When I apply fminer for <feature> Then I should receive a valid URI - And the URI should return a YAML representation Examples: - |name |filename | - |Hamster Carcinogenicity|hamster_carcinogenicity.csv| - #|Salmonella mutagenicity|kazius.csv| + |feature |data | + |http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.rdf| + #|http://dx.doi.org/10.1021/jm040835a|file: data/kazius.rdf| diff --git a/features/lazar.feature b/features/lazar.feature index 0a2ff45..0e28c51 100644 --- a/features/lazar.feature +++ b/features/lazar.feature @@ -5,13 +5,13 @@ Feature: Create a model and predict an unknown compound In order to predict the toxicity of a compound Scenario Outline: - Given name is <name> - And compound_format is smiles - And a file <filename> - When I create a lazar model + Given Content-Type is application/rdf+xml + And I post <data> to the dataset webservice + When I create a lazar model for <feature> Then I should receive a valid URI And the model should predict <prediction> for <smiles> Examples: - |name |filename |smiles |prediction| - |Hamster Carcinogenicity|hamster_carcinogenicity.csv|c1ccccc1NN|true | + |feature |data |smiles |prediction| + |http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.rdf|c1ccccc1NN|true | + diff --git a/features/step_definitions/common_steps.rb b/features/step_definitions/common_steps.rb index e0437f5..41985b3 100644 --- a/features/step_definitions/common_steps.rb +++ b/features/step_definitions/common_steps.rb @@ -1,10 +1,15 @@ -Given /^(.*) is (.*)$/ do |name,value| - @params = {} unless @params - @params[name] = value +Given /^Content-Type is (.*)/ do |content_type| + @content_type = content_type end -When /^I post the parameters to the (.*) webservice$/ do |component| - @uri = RestClient.post @@config[:services]["opentox-#{component}"], @params +When /^I post (.*) to the (.*) webservice$/ do |data,component| + #puts @@config[:services]["opentox-#{component}"] + case data + when /^file:/ + data = File.read(File.join(File.dirname(File.expand_path(__FILE__)),"../data",data.sub(/file:\s+/,''))) + @data = data + end + @uri = RestClient.post @@config[:services]["opentox-#{component}"], data, :content_type => @content_type @resources << @uri unless /compound|feature/ =~ component end @@ -18,7 +23,11 @@ Then /^the URI should contain (.+)$/ do |result| assert regexp =~ @uri, true end -Then /^the URI response should be (\S+)$/ do |result| - assert result == @response, true +Then /^the URI response should be (.+)$/ do |data| + case data + when /^file:/ + data = @data + end + assert data == @response, true end diff --git a/features/step_definitions/dataset_steps.rb b/features/step_definitions/dataset_steps.rb index 0ba0f96..e69de29 100644 --- a/features/step_definitions/dataset_steps.rb +++ b/features/step_definitions/dataset_steps.rb @@ -1,26 +0,0 @@ -Given /^a file (.*)$/ do |filename| - @filename = File.join(File.dirname(__FILE__),'..','data', filename) -end - -When /^I put the file to the dataset URI$/ do - call = "curl -X PUT -F 'file=@#{@filename};type=text/csv' -F compound_format=#{@params['compound_format']} #{@uri + '/import'}" - @uri = `#{call}` -end - -Then /^the URI should return a YAML representation$/ do - valid_yaml = false - begin - @yaml_string = RestClient.get(@uri) - yaml = YAML.load(@yaml_string) - valid_yaml = true - rescue - end - assert valid_yaml, true - #puts @yaml_string -end - -When /^I put YAML data to the dataset URI$/ do - yaml = File.read(@filename) - RestClient.put @uri, :features => yaml -end - diff --git a/features/step_definitions/fminer_step.rb b/features/step_definitions/fminer_step.rb index 5c39906..62696f5 100644 --- a/features/step_definitions/fminer_step.rb +++ b/features/step_definitions/fminer_step.rb @@ -1,8 +1,5 @@ -When /^I apply fminer$/ do - @training_uri = RestClient.post @@config[:services]["opentox-dataset"], @params - @resources << @training_uri - call = "curl -X PUT -F 'file=@#{@filename};type=text/csv' -F compound_format=#{@params['compound_format']} #{@training_uri + '/import'}" - `#{call}` - @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => @training_uri +When /^I apply fminer for (.*)$/ do |feature_uri| + dataset_uri = @uri + @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => dataset_uri, :feature_uri => feature_uri @resources << @uri end diff --git a/features/step_definitions/lazar_steps.rb b/features/step_definitions/lazar_steps.rb index 402f8db..bc84159 100644 --- a/features/step_definitions/lazar_steps.rb +++ b/features/step_definitions/lazar_steps.rb @@ -1,18 +1,17 @@ -When /^I create a lazar model$/ do - @training_uri = RestClient.post @@config[:services]["opentox-dataset"], @params - @resources << @training_uri - call = "curl -X PUT -F 'file=@#{@filename};type=text/csv' -F compound_format=#{@params['compound_format']} #{@training_uri + '/import'}" - `#{call}` - @feature_uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => @training_uri - @resources << @feature_uri - @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar_classification"), :activity_dataset_uri => @training_uri, :feature_dataset_uri => @feature_uri +When /^I create a lazar model for (.*)$/ do |feature_uri| + training_uri = @uri + feature_uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => training_uri, :feature_uri => feature_uri + @resources << feature_uri + @uri = RestClient.post File.join(@@config[:services]["opentox-model"], "lazar"), :activity_dataset_uri => training_uri, :feature_dataset_uri => feature_uri @resources << @uri end Then /^the model should predict (.*) for (.*)$/ do |activity,smiles| compound_uri = OpenTox::Compound.new(:smiles => smiles).uri - prediction_uri = RestClient.post @uri, :compound_uri => compound_uri - prediction = RestClient.get prediction_uri - assert_equal activity.to_s, YAML.load(prediction)[:values]['classification'].to_s + puts @uri + prediction = RestClient.post @uri, :compound_uri => compound_uri + puts prediction + #prediction = RestClient.get prediction_uri + #assert_equal activity.to_s, YAML.load(prediction)[:values]['classification'].to_s end |