diff options
| author | Christoph Helma <helma@in-silico.de> | 2009-12-14 09:47:50 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.de> | 2009-12-14 09:47:50 +0100 |
| commit | eaad529266d7208e75784202001d350201ba7da4 (patch) | |
| tree | 5e009395ff93ace3aa342f4bf0fd756e23bf280b | |
| parent | 45802e0a9b7ef6a918c4b7a539261bdba8217d38 (diff) | |
Initial adaptation to RDF/OWL
| -rw-r--r-- | features/data/hamster_carcinogenicity.rdf | 1687 | ||||
| -rw-r--r-- | features/dataset.feature | 2 | ||||
| -rw-r--r-- | features/fminer.feature | 2 | ||||
| -rw-r--r-- | features/lazar.feature | 2 | ||||
| -rw-r--r-- | features/step_definitions/common_steps.rb | 5 | ||||
| -rw-r--r-- | features/step_definitions/fminer_step.rb | 1 | ||||
| -rw-r--r-- | features/step_definitions/lazar_steps.rb | 8 |
7 files changed, 1526 insertions, 181 deletions
diff --git a/features/data/hamster_carcinogenicity.rdf b/features/data/hamster_carcinogenicity.rdf index 1dafcc0..bd4df02 100644 --- a/features/data/hamster_carcinogenicity.rdf +++ b/features/data/hamster_carcinogenicity.rdf @@ -1,258 +1,1605 @@ <?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:about="http://purl.org/dc/elements/1.1/source"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/> </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:about="http://purl.org/dc/elements/1.1/identifier"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/> </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:about="http://purl.org/dc/elements/1.1/title"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/> </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:about="http://www.opentox.org/api/1.1#feature"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> </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:about="http://www.opentox.org/api/1.1#compound"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> </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:about="http://www.opentox.org/api/1.1#values"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> </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:about="http://www.opentox.org/api/1.1#value"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/> </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:about="http://www.opentox.org/api/1.1#Dataset"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/> </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:about="http://www.opentox.org/api/1.1#FeatureValue"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/> </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:about="http://www.opentox.org/api/1.1#Feature"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/> </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:about="http://www.opentox.org/api/1.1#Compound"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/> </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:about="http://www.opentox.org/api/1.1#DataEntry"> + <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/> </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:nodeID="r1260270405r21791r1"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Dataset"/> </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:nodeID="r1260270405r21791r1"> + <ns0:identifier xmlns:ns0="http://purl.org/dc/elements/1.1/">http://localhost:4001/53</ns0:identifier> </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:nodeID="r1260270405r21791r1"> + <ns0:title xmlns:ns0="http://purl.org/dc/elements/1.1/">Hamster Carcinogenicity</ns0:title> </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:nodeID="r1260270405r21791r1"> + <ns0:source xmlns:ns0="http://purl.org/dc/elements/1.1/">http://www.epa.gov/NCCT/dsstox/sdf_cpdbas.html</ns0:source> </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:nodeID="r1260270405r21791r2"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Feature"/> </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:nodeID="r1260270405r21791r2"> + <ns0:identifier xmlns:ns0="http://purl.org/dc/elements/1.1/">http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster</ns0:identifier> </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:nodeID="r1260270405r21791r2"> + <ns0:title xmlns:ns0="http://purl.org/dc/elements/1.1/">Hamster Carcinogenicity</ns0:title> </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:nodeID="r1260270405r21791r2"> + <ns0:source xmlns:ns0="http://purl.org/dc/elements/1.1/">http://www.epa.gov/NCCT/dsstox/sdf_cpdbas.html</ns0:source> </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:nodeID="r1260270405r21791r3"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#FeatureValue"/> </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:nodeID="r1260270405r21791r3"> + <ns0:value xmlns:ns0="http://www.opentox.org/api/1.1#">true</ns0:value> </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:nodeID="r1260270405r21791r4"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#FeatureValue"/> </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:nodeID="r1260270405r21791r4"> + <ns0:value xmlns:ns0="http://www.opentox.org/api/1.1#">false</ns0:value> </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:nodeID="r1260270405r21791r5"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Compound"/> </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:nodeID="r1260270405r21791r5"> + <ns0:identifier xmlns:ns0="http://purl.org/dc/elements/1.1/" rdf:resource="http://localhost:4000/InChI=1S/C5H10N2O/c8-6-7-4-2-1-3-5-7/h1-5H2"/> </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:nodeID="r1260270405r21791r6"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#DataEntry"/> </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:nodeID="r1260270405r21791r6"> + <ns0:compound xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r5"/> </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:nodeID="r1260270405r21791r6"> + <ns0:feature xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r2"/> </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:nodeID="r1260270405r21791r6"> + <ns0:values xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r3"/> </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 xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">true</ns0:ActivityOutcome_CPDBAS_Hamster> + <rdf:Description rdf:nodeID="r1260270405r21791r7"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Compound"/> </rdf:Description> - <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C2H8N2O/c3-4-1-2-5/h4-5H,1-3H2"> - <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + <rdf:Description rdf:nodeID="r1260270405r21791r7"> + <ns0:identifier xmlns:ns0="http://purl.org/dc/elements/1.1/" rdf:resource="http://localhost:4000/InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2"/> </rdf:Description> - <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C6H7N3O/c7-9-6(10)5-1-3-8-4-2-5/h1-4H,7H2,(H,9,10)"> - <ns0:ActivityOutcome_CPDBAS_Hamster xmlns:ns0="http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#">false</ns0:ActivityOutcome_CPDBAS_Hamster> + <rdf:Description rdf:nodeID="r1260270405r21791r8"> + <rdf:type rdf:resource="http://www.opentox.org/api/1.1#DataEntry"/> </rdf:Description> - <rdf:Description rdf:about="http://localhost:4000/InChI=1S/C6H5NO2/c8-6(9)5-1-3-7-4-2-5/h1-4H,(H,8,9)"> - <ns0:ActivityOutcome_CPDBAS_Hamster 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rdf:nodeID="r1260270405r21791r174"> + <ns0:compound xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r173"/> + </rdf:Description> + <rdf:Description rdf:nodeID="r1260270405r21791r174"> + <ns0:feature xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r2"/> + </rdf:Description> + <rdf:Description rdf:nodeID="r1260270405r21791r174"> + <ns0:values xmlns:ns0="http://www.opentox.org/api/1.1#" rdf:nodeID="r1260270405r21791r3"/> </rdf:Description> </rdf:RDF> diff --git a/features/dataset.feature b/features/dataset.feature index d6af70d..7cf130b 100644 --- a/features/dataset.feature +++ b/features/dataset.feature @@ -5,9 +5,7 @@ Feature: 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 response should be <data> Examples: |data| |file: hamster_carcinogenicity.rdf| - |file: kazius.rdf| diff --git a/features/fminer.feature b/features/fminer.feature index e712449..773425a 100644 --- a/features/fminer.feature +++ b/features/fminer.feature @@ -9,6 +9,6 @@ Feature: Fminer Examples: |feature |data | - |http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.rdf| + |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 0e28c51..5534b6f 100644 --- a/features/lazar.feature +++ b/features/lazar.feature @@ -13,5 +13,5 @@ Feature: Create a model and predict an unknown compound Examples: |feature |data |smiles |prediction| - |http://www.epa.gov/ncct/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster|file: hamster_carcinogenicity.rdf|c1ccccc1NN|true | + |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 e2d9f09..51bdc00 100644 --- a/features/step_definitions/common_steps.rb +++ b/features/step_definitions/common_steps.rb @@ -14,8 +14,9 @@ When /^I post (.*) to the (.*) webservice$/ do |data,component| end Then /^I should receive a valid URI$/ do - @response = RestClient.get @uri - #puts @response + #puts @uri + @response = RestClient.get @uri, :accept => '*/*' + puts @response.to_yaml end Then /^the URI should contain (.+)$/ do |result| diff --git a/features/step_definitions/fminer_step.rb b/features/step_definitions/fminer_step.rb index 62696f5..26588de 100644 --- a/features/step_definitions/fminer_step.rb +++ b/features/step_definitions/fminer_step.rb @@ -1,5 +1,6 @@ When /^I apply fminer for (.*)$/ do |feature_uri| dataset_uri = @uri @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => dataset_uri, :feature_uri => feature_uri + #puts @uri @resources << @uri end diff --git a/features/step_definitions/lazar_steps.rb b/features/step_definitions/lazar_steps.rb index 3992bf9..47682cd 100644 --- a/features/step_definitions/lazar_steps.rb +++ b/features/step_definitions/lazar_steps.rb @@ -1,9 +1,6 @@ When /^I create a lazar model for (.*)$/ do |feature_uri| training_uri = @uri - feature_uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "fminer"), :dataset_uri => training_uri, :feature_uri => feature_uri - @resources << feature_uri - #puts File.join(@@config[:services]["opentox-algorithm"], "lazar")+ ":activity_dataset_uri => #{training_uri}, :feature_dataset_uri => #{feature_uri}" - @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :activity_dataset_uri => training_uri, :feature_dataset_uri => feature_uri + @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => training_uri, :feature_uri => feature_uri, :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer") @resources << @uri #puts @uri.to_yaml end @@ -11,7 +8,8 @@ end Then /^the model should predict (.*) for (.*)$/ do |activity,smiles| compound_uri = OpenTox::Compound.new(:smiles => smiles).uri puts @uri - prediction = RestClient.post @uri, :compound_uri => compound_uri + puts compound_uri + prediction = RestClient.post @uri, :compound_uri => compound_uri, :type => "yaml" puts prediction #assert_equal activity.to_s, YAML.load(prediction)[:values]['classification'].to_s end |