Feature: Add an API endpoint to resolve an ontology URI in diffrent formats

Dockerfile

@@ -7,6 +7,7 @@ RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
   openjdk-11-jre-headless \
   raptor2-utils \
   wait-for-it \
+  libraptor2-dev \
   && rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p /srv/ontoportal/ontologies_api

Gemfile

@@ -15,6 +15,8 @@ gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
 gem 'request_store'
 gem 'parallel'
+gem 'json-ld'
+
 
 # Rack middleware
 gem 'ffi'

Gemfile.lock

@@ -11,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 6c51346b6f150a69391794b7909b30592acbbe0e
+  revision: 3f8b1f0b62c4334306f9ed5cb7b17a1b645e7db3
   branch: development
   specs:
     goo (0.0.2)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: d37aeafbd7bef120917fb4d601f8287a9a859f69
+  revision: 337dce98ec27627d14a440ff2a6ed09483cdac12
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -117,7 +117,7 @@ GEM
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.18.0)
+    capistrano (3.18.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -191,12 +191,12 @@ GEM
       representable (~> 3.0)
       retriable (>= 2.0, < 4.a)
       rexml
-    google-cloud-core (1.6.1)
+    google-cloud-core (1.7.0)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
-    google-cloud-errors (1.3.1)
+    google-cloud-errors (1.4.0)
     google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.5.0)
@@ -230,13 +230,16 @@ GEM
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.7.1)
+    json-ld (3.0.2)
+      multi_json (~> 1.12)
+      rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.7.1)
     jwt (2.8.1)
       base64
     kgio (2.11.4)
-    libxml-ruby (5.0.2)
+    libxml-ruby (5.0.3)
     link_header (0.0.8)
     logger (1.6.0)
     macaddr (1.7.2)
@@ -422,6 +425,7 @@ DEPENDENCIES
   ffi
   goo!
   haml (~> 5.2.2)
+  json-ld
   json-schema (~> 2.0)
   minitest (~> 4.0)
   minitest-stub_any_instance

bin/ontoportal

@@ -76,7 +76,7 @@ build_docker_run_cmd() {
   local goo_path="$3"
   local sparql_client_path="$4"
 
-  local docker_run_cmd="docker compose run --rm -it"
+  local docker_run_cmd="docker compose -p ontoportal_docker run --rm -it --name api-service"
   local bash_cmd=""
 
   # Conditionally add bind mounts only if the paths are not empty
@@ -177,7 +177,7 @@ run_command() {
 dev() {
   echo "Starting OntoPortal API development server..."
 
-  local custom_command="bundle exec shotgun --host 0.0.0.0  --env=development"
+  local custom_command="bundle exec shotgun --host 0.0.0.0  --env=development --port 9393"
   run_command "$custom_command" "$@"
 }
 

controllers/dereference_resource_controller.rb

@@ -0,0 +1,59 @@
+require_relative '../test/test_case'
+
+
+class DereferenceResourceController < ApplicationController
+  namespace "/ontologies" do
+    get "/:acronym/resolve/:uri" do
+      acronym = params[:acronym]
+      uri = params[:uri]
+
+      if acronym.blank? || uri.blank?
+        error 500, "Usage: ontologies/:acronym/resolve/:uri?output_format= OR POST: acronym, uri, output_format parameters"
+      end
+
+      output_format = params[:output_format].presence || 'jsonld'
+      process_request(acronym, uri, output_format)
+    end
+
+    private
+
+    def process_request(acronym_param, uri_param, output_format)
+      acronym = acronym_param
+      uri = URI.decode_www_form_component(uri_param)
+
+      error 500, "INVALID URI" unless valid_url?(uri)
+      sub = LinkedData::Models::Ontology.find(acronym).first&.latest_submission
+
+      error 500, "Ontology not found" unless  sub
+
+      r = Resource.new(sub.id, uri)
+      case output_format
+      when 'jsonld'
+        content_type 'application/json'
+        reply  JSON.parse(r.to_json)
+      when 'json'
+        content_type 'application/json'
+        reply JSON.parse(r.to_json)
+      when 'xml'
+        content_type 'application/xml'
+        reply r.to_xml
+      when 'turtle'
+        content_type 'text/turtle'
+        reply r.to_turtle
+      when 'ntriples'
+        content_type 'application/n-triples'
+        reply r.to_ntriples
+      else
+        error 500, "Invalid output format"
+      end
+
+    end
+
+    def valid_url?(url)
+      uri = URI.parse(url)
+      uri.is_a?(URI::HTTP) || uri.is_a?(URI::HTTPS)
+    rescue URI::InvalidURIError
+      false
+    end
+  end
+end

helpers/users_helper.rb

@@ -23,9 +23,7 @@ def send_reset_token(email, username)
         error 404, "User not found" unless user
         reset_token = token(36)
         user.resetToken = reset_token
-
-        return user if user.valid?
-
+
         user.save(override_security: true)
         LinkedData::Utils::Notifications.reset_password(user, reset_token)
         user

models/simple_wrappers.rb

@@ -29,3 +29,5 @@
 ProvisionalRelation = LinkedData::Models::ProvisionalRelation
 
 SearchHelper = Sinatra::Helpers::SearchHelper
+
+Resource = LinkedData::Models::Resource

test/controllers/test_dereference_resource_controller.rb

@@ -0,0 +1,191 @@
+require_relative '../test_case'
+require 'rexml/document'
+
+class TestDereferenceResourceController < TestCase
+
+  def self.before_suite
+    LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
+                                                                         process_submission: true,
+                                                                         process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
+                                                                         acronym: 'INRAETHESDEREF',
+                                                                         name: 'INRAETHES',
+                                                                         file_path: './test/data/ontology_files/thesaurusINRAE_nouv_structure.rdf',
+                                                                         ont_count: 1,
+                                                                         ontology_format: 'SKOS',
+                                                                         submission_count: 1
+                                                                       })
+
+    @@graph = "INRAETHESDEREF-0"
+    @@uri = CGI.escape("http://opendata.inrae.fr/thesaurusINRAE/c_6496")
+  end
+
+  def test_dereference_resource_controller_json
+    get "/ontologies/#{@@graph}/resolve/#{@@uri}?output_format=json"
+    assert last_response.ok?
+
+    result = last_response.body
+    expected_result = <<-JSON
+          {
+            "@context": {
+              "ns0": "http://opendata.inrae.fr/thesaurusINRAE/",
+              "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+              "owl": "http://www.w3.org/2002/07/owl#",
+              "skos": "http://www.w3.org/2004/02/skos/core#"
+            },
+            "@graph": [
+              {
+                "@id": "ns0:c_6496",
+                "@type": [
+                  "owl:NamedIndividual",
+                  "skos:Concept"
+                ],
+                "skos:broader": {
+                  "@id": "ns0:c_a9d99f3a"
+                },
+                "skos:topConceptOf": {
+                  "@id": "ns0:mt_65"
+                },
+                "skos:inScheme": [
+                  {
+                    "@id": "ns0:thesaurusINRAE"
+                  },
+                  {
+                    "@id": "ns0:mt_65"
+                  }
+                ],
+                "skos:prefLabel": {
+                  "@value": "altération de l'ADN",
+                  "@language": "fr"
+                }
+              },
+              {
+                "@id": "ns0:mt_65",
+                "skos:hasTopConcept": {
+                  "@id": "ns0:c_6496"
+                }
+              }
+            ]
+          }
+    JSON
+    a = sort_nested_hash(JSON.parse(result))
+    b = sort_nested_hash(JSON.parse(expected_result))
+    assert_equal b, a
+  end
+
+  def test_dereference_resource_controller_xml
+    get "/ontologies/#{@@graph}/resolve/#{@@uri}?output_format=xml"
+    assert last_response.ok?
+
+    result = last_response.body
+
+    expected_result_1 = <<-XML
+          <?xml version="1.0" encoding="UTF-8"?>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:ns0="http://opendata.inrae.fr/thesaurusINRAE/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#">
+            <owl:NamedIndividual rdf:about="http://opendata.inrae.fr/thesaurusINRAE/c_6496">
+              <rdf:type rdf:resource="http://www.w3.org/2004/02/skos/core#Concept"/>
+              <skos:broader rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/c_a9d99f3a"/>
+              <skos:topConceptOf rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/mt_65"/>
+              <skos:inScheme rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/thesaurusINRAE"/>
+              <skos:inScheme rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/mt_65"/>
+              <skos:prefLabel xml:lang="fr">altération de l'ADN</skos:prefLabel>
+            </owl:NamedIndividual>
+            <rdf:Description rdf:about="http://opendata.inrae.fr/thesaurusINRAE/mt_65">
+              <skos:hasTopConcept rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/c_6496"/>
+            </rdf:Description>
+          </rdf:RDF>
+    XML
+
+    expected_result_2 = <<-XML
+        <?xml version="1.0" encoding="UTF-8"?>
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:ns0="http://opendata.inrae.fr/thesaurusINRAE/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:owl="http://www.w3.org/2002/07/owl#">
+          <skos:Concept rdf:about="http://opendata.inrae.fr/thesaurusINRAE/c_6496">
+            <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+            <skos:inScheme rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/thesaurusINRAE"/>
+            <skos:inScheme rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/mt_65"/>
+            <skos:prefLabel xml:lang="fr">altération de l'ADN</skos:prefLabel>
+            <skos:topConceptOf rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/mt_65"/>
+            <skos:broader rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/c_a9d99f3a"/>
+          </skos:Concept>
+          <rdf:Description rdf:about="http://opendata.inrae.fr/thesaurusINRAE/mt_65">
+            <skos:hasTopConcept rdf:resource="http://opendata.inrae.fr/thesaurusINRAE/c_6496"/>
+          </rdf:Description>
+        </rdf:RDF>
+      XML
+
+
+    clean_xml = -> (x) { x.strip.gsub('/>', '').gsub('</', '').gsub('<', '').gsub('>', '').split(' ').reject(&:empty?)}
+
+
+    a = result.gsub('\\"', '"')[1..-2].split("\\n").map{|x| clean_xml.call(x)}.flatten
+    b_1 = expected_result_1.split("\n").map{|x| clean_xml.call(x)}.flatten
+    b_2 = expected_result_2.split("\n").map{|x| clean_xml.call(x)}.flatten
+
+    assert_includes [b_1.sort, b_2.sort], a.sort
+  end
+
+  def test_dereference_resource_controller_ntriples
+    get "/ontologies/#{@@graph}/resolve/#{@@uri}?output_format=ntriples"
+    assert last_response.ok?
+
+    result = last_response.body
+    expected_result = <<-NTRIPLES
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#NamedIndividual> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2004/02/skos/core#Concept> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/2004/02/skos/core#broader> <http://opendata.inrae.fr/thesaurusINRAE/c_a9d99f3a> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/2004/02/skos/core#topConceptOf> <http://opendata.inrae.fr/thesaurusINRAE/mt_65> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/2004/02/skos/core#inScheme> <http://opendata.inrae.fr/thesaurusINRAE/thesaurusINRAE> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/2004/02/skos/core#inScheme> <http://opendata.inrae.fr/thesaurusINRAE/mt_65> .
+          <http://opendata.inrae.fr/thesaurusINRAE/c_6496> <http://www.w3.org/2004/02/skos/core#prefLabel> "alt\\\\u00E9rationdel'ADN"@fr .
+          <http://opendata.inrae.fr/thesaurusINRAE/mt_65> <http://www.w3.org/2004/02/skos/core#hasTopConcept> <http://opendata.inrae.fr/thesaurusINRAE/c_6496> .
+    NTRIPLES
+    a = result.gsub('\\"', '"').gsub(' ', '')[1..-2].split("\\n").reject(&:empty?)
+    b = expected_result.gsub(' ', '').split("\n").reject(&:empty?)
+    assert_equal b.sort, a.sort
+  end
+
+  def test_dereference_resource_controller_turtle
+    get "/ontologies/#{@@graph}/resolve/#{@@uri}?output_format=turtle"
+    assert last_response.ok?
+
+    result = last_response.body
+    expected_result = <<-TURTLE
+          @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+          @prefix ns0: <http://opendata.inrae.fr/thesaurusINRAE/> .
+          @prefix owl: <http://www.w3.org/2002/07/owl#> .
+          @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+
+          ns0:c_6496
+              a owl:NamedIndividual, skos:Concept ;
+              skos:broader ns0:c_a9d99f3a ;
+              skos:inScheme ns0:mt_65, ns0:thesaurusINRAE ;
+              skos:prefLabel "altération de l'ADN"@fr ;
+              skos:topConceptOf ns0:mt_65 .
+
+          ns0:mt_65
+              skos:hasTopConcept ns0:c_6496 .
+    TURTLE
+    a = result.gsub('\\"', '"').gsub(' ', '')[1..-2].split("\\n").reject(&:empty?)
+    b = expected_result.gsub(' ', '').split("\n").reject(&:empty?)
+
+    assert_equal b.sort, a.sort
+  end
+
+  private
+
+  def sort_nested_hash(hash)
+    sorted_hash = {}
+
+    hash.each do |key, value|
+      if value.is_a?(Hash)
+        sorted_hash[key] = sort_nested_hash(value)
+      elsif value.is_a?(Array)
+        sorted_hash[key] = value.map { |item| item.is_a?(Hash) ? sort_nested_hash(item) : item }.sort_by { |item| item.to_s }
+      else
+        sorted_hash[key] = value
+      end
+    end
+
+    sorted_hash.sort.to_h
+  end
+
+end