diff --git a/Gemfile.lock b/Gemfile.lock index 8ef8a1ab..d44a5d5c 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -57,7 +57,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 8123ae61988a265daab1664deaed515718827c48 + revision: c4dbcc14a3eb75343e597679ea4532ba53785b8f branch: development specs: ontologies_linked_data (0.0.1) @@ -138,7 +138,7 @@ GEM dante (0.2.0) date (3.3.4) declarative (0.0.20) - docile (1.4.0) + docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) faraday (1.10.3) @@ -211,6 +211,12 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) + grpc (1.65.1) + google-protobuf (>= 3.25, < 5.0) + googleapis-common-protos-types (~> 1.0) + grpc (1.65.1-x86_64-darwin) + google-protobuf (>= 3.25, < 5.0) + googleapis-common-protos-types (~> 1.0) grpc (1.65.1-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) @@ -272,7 +278,7 @@ GEM net-protocol net-ssh (7.2.3) netrc (0.11.0) - newrelic_rpm (9.11.0) + newrelic_rpm (9.12.0) oj (3.16.1) omni_logger (0.1.4) logger diff --git a/controllers/properties_controller.rb b/controllers/properties_controller.rb index f98e9016..45267fe1 100644 --- a/controllers/properties_controller.rb +++ b/controllers/properties_controller.rb @@ -24,7 +24,9 @@ class PropertiesController < ApplicationController get '/:property' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + bring_unmapped = bring_unmapped?(includes_param) + + p = ont.property(prop, submission, display_all_attributes: bring_unmapped) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? reply 200, p end diff --git a/test/controllers/test_properties_controller.rb b/test/controllers/test_properties_controller.rb index 6ef6edeb..2ca7ef88 100644 --- a/test/controllers/test_properties_controller.rb +++ b/test/controllers/test_properties_controller.rb @@ -4,24 +4,24 @@ class TestPropertiesController < TestCase def self.before_suite count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ - process_submission: true, - process_options:{process_rdf: true, extract_metadata: false}, - acronym: "BROSEARCHTEST", - name: "BRO Search Test", - file_path: "./test/data/ontology_files/BRO_v3.2.owl", - ont_count: 1, - submission_count: 1, - ontology_type: "VALUE_SET_COLLECTION" + process_submission: true, + process_options: { process_rdf: true, extract_metadata: false }, + acronym: "BROSEARCHTEST", + name: "BRO Search Test", + file_path: "./test/data/ontology_files/BRO_v3.2.owl", + ont_count: 1, + submission_count: 1, + ontology_type: "VALUE_SET_COLLECTION" }) count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ - process_submission: true, - process_options:{process_rdf: true, extract_metadata: true}, - acronym: "MCCLSEARCHTEST", - name: "MCCL Search Test", - file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl", - ont_count: 1, - submission_count: 1 + process_submission: true, + process_options: { process_rdf: true, extract_metadata: true }, + acronym: "MCCLSEARCHTEST", + name: "MCCL Search Test", + file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl", + ont_count: 1, + submission_count: 1 }) @@ontologies = bro.concat(mccl) @@acronyms = @@ontologies.map { |ont| ont.bring_remaining; ont.acronym } @@ -47,14 +47,33 @@ def test_single_property get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Originator" assert last_response.ok? results = MultiJson.load(last_response.body) + assert results.is_a?(Hash) assert_equal ["Originator"], results["label"] assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Originator", results["@id"] + assert results.key?('range') + assert results.key?('domain') get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23DummyProp" assert_equal 404, last_response.status end + def test_single_property_all_attributes + get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Originator?display=all" + assert last_response.ok? + results = MultiJson.load(last_response.body) + assert_equal ["Originator"], results["label"] + assert results.key?('range') + assert results.key?('domain') + assert_equal results["properties"], { "http://www.w3.org/2000/01/rdf-schema#comment" => ["Originator of a class"], + "http://www.w3.org/2004/02/skos/core#prefLabel" => ["Originator"], + "http://data.bioontology.org/metadata/def/prefLabel" => ["Originator"], + "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" => ["http://www.w3.org/2002/07/owl#DatatypeProperty"], + "http://www.w3.org/2000/01/rdf-schema#domain" => ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Algorithm"], + "http://www.w3.org/2000/01/rdf-schema#label" => ["Originator"], + "http://www.w3.org/2004/02/skos/core#definition" => ["Originator of a class"] } + end + def test_property_roots get "/ontologies/#{@@acronyms.first}/properties/roots" assert last_response.ok? @@ -66,10 +85,10 @@ def test_property_roots assert_includes [18, 13], opr.length # count datatype properties dpr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#DatatypeProperty" } - assert_includes [32,31], dpr.length + assert_includes [32, 31], dpr.length # count annotation properties apr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#AnnotationProperty" } - assert_includes [12,8], apr.length + assert_includes [12, 8], apr.length # check for non-root properties assert_empty pr.select { |p| ["http://www.w3.org/2004/02/skos/core#broaderTransitive", @@ -174,7 +193,7 @@ def test_property_descendants dn = MultiJson.load(last_response.body) assert_equal 2, dn.length assert_equal ["http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#overExpress", - "http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#underExpress"].sort, dn.map { |d| d["@id"] }.sort + "http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#underExpress"].sort, dn.map { |d| d["@id"] }.sort end def test_property_parents @@ -207,7 +226,7 @@ def test_property_children assert_empty ch get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23semanticRelation" - return unless last_response.ok? #depending if owlapi import SKOS + return unless last_response.ok? # depending if owlapi import SKOS get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23semanticRelation/children" assert last_response.ok?