Federation search endpoint

config/environments/config.rb.sample

@@ -109,19 +109,38 @@ LinkedData.config do |config|
             }
         ]
         config.federated_portals = {
-              'agroportal' => {
-                api: 'http://data.agroportal.lirmm.fr',
-                ui: 'http://agroportal.lirmm.fr',
-                apikey: '1cfae05f-9e67-486f-820b-b393dec5764b',
-                color: '#1e2251'
-              },
-              'bioportal' => {
-                      api: 'http://data.bioontology.org',
-                      ui: 'http://bioportal.bioontology.org',
-                      apikey: '4a5011ea-75fa-4be6-8e89-f45c8c84844e',
-                      color: '#234979'
-               },
-
+          {
+            name: 'AgroPortal',
+            api: 'https://data.agroportal.lirmm.fr',
+            ui: 'https://agroportal.lirmm.fr/',
+            color: '#3CB371',
+            apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
+            'light-color': '#F1F6FA',
+          },
+          {
+            name: 'BiodivPortal',
+            api: 'https://data.biodivportal.gfbio.org/',
+            ui: 'https://biodivportal.gfbio.org/',
+            apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
+            color: '#349696',
+            'light-color': '#EBF5F5',
+          },
+          {
+            name: 'EcoPortal',
+            ui: 'https://ecoportal.lifewatch.eu/',
+            api: 'https://data.ecoportal.lifewatch.eu/',
+            apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
+            color: '#2076C9',
+            'light-color': '#E9F2FA',
+          },
+          {
+            name: 'EarthPortal',
+            ui: 'https://earthportal.eu/',
+            api: 'https://data.earthportal.eu/',
+            apikey: "c9147279-954f-41bd-b068-da9b0c441288",
+            color: '#404696',
+            'light-color': '#F0F5F6'
+          },
         }
 end
 

controllers/federation_controller.rb

@@ -0,0 +1,161 @@
+require 'faraday'
+require 'parallel'
+
+class FederationController < ApplicationController
+
+  GATEWAY_URL = "https://terminology.services.base4nfdi.de/api-gateway"
+  GATEWAY_CONNECTION = Faraday.new(url: GATEWAY_URL) do |conn|
+    conn.headers['Accept'] = 'application/json'
+    conn.options.timeout = 30
+    conn.options.open_timeout = 10
+  end
+
+  namespace "/api/federation" do
+
+    get '/search' do
+      query = params[:query] || params[:q]
+
+      if query.nil? || query.strip.empty?
+        error 400, "You must provide a 'query' parameter to execute a search"
+      end
+
+      databases = (params[:database] || "ontoportal,nerc").split(',').map(&:strip)
+
+      # Appels parallèles : un par database pour éviter la limitation du Gateway
+      gateway_results = Parallel.map(databases, in_threads: databases.size) do |db|
+        fetch_gateway(query, db)
+      end
+
+      docs = []
+      errors = []
+
+      gateway_results.each do |result|
+        if result[:error]
+          errors << result[:error]
+        else
+          result[:items].each do |item|
+            if item["backend_type"] == "nerc"
+              docs << map_nvs_item(item)
+            else
+              docs << map_ontoportal_item(item)
+            end
+          end
+        end
+      end
+
+      total_found = docs.size
+
+      page_data = paginate(docs, total_found)
+      page_data[:errors] = errors if errors.any?
+
+      content_type 'application/json'
+      MultiJson.dump(page_data)
+    end
+
+  end
+
+  helpers do
+    def fetch_gateway(query, database)
+      response = GATEWAY_CONNECTION.get("search", { query: query, database: database })
+
+      if response.success?
+        data = MultiJson.load(response.body)
+        items = if data.is_a?(Array)
+                  data
+                elsif data.is_a?(Hash) && data["collection"]
+                  data["collection"]
+                else
+                  []
+                end
+        { items: items }
+      else
+        { error: "Gateway (#{database}) returned HTTP #{response.status}" }
+      end
+    rescue => e
+      { error: "Gateway (#{database}): #{e.message}" }
+    end
+
+    def map_ontoportal_item(item)
+      acronym = item["ontology"]
+      source_api = item["source"]
+      source_name = item["source_name"]
+      ontology_iri = item["ontology_iri"] || "#{source_api}/ontologies/#{acronym}"
+      concept_id = item["@id"] || item["iri"]
+      encoded_id = CGI.escape(concept_id)
+
+      {
+        "prefLabel" => item["label"],
+        "synonym" => Array(item["synonyms"]),
+        "definition" => Array(item["descriptions"]),
+        "obsolete" => item["obsolete"] || false,
+        "matchType" => nil,
+        "ontologyType" => nil,
+        "hasChildren" => item["hasChildren"] || false,
+        "@id" => concept_id,
+        "@type" => item["type"] || "http://www.w3.org/2002/07/owl#Class",
+        "links" => {
+          "self" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}",
+          "ontology" => ontology_iri,
+          "children" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/children",
+          "parents" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/parents",
+          "descendants" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/descendants",
+          "ancestors" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/ancestors",
+          "instances" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/instances",
+          "tree" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/tree",
+          "notes" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/notes",
+          "mappings" => "#{source_api}/ontologies/#{acronym}/classes/#{encoded_id}/mappings",
+          "ui" => item["source_url"] || "#{source_api}/ontologies/#{acronym}?p=classes&conceptid=#{encoded_id}"
+        },
+        "source_portal" => source_name
+      }
+    end
+
+    def map_nvs_item(item)
+      concept_id = item["@id"] || item["iri"]
+
+      {
+        "prefLabel" => item["label"],
+        "synonym" => Array(item["synonyms"]),
+        "definition" => Array(item["descriptions"]),
+        "obsolete" => item["obsolete"] || false,
+        "matchType" => nil,
+        "ontologyType" => nil,
+        "hasChildren" => item["hasChildren"] || false,
+        "@id" => concept_id,
+        "@type" => item["type"] || "http://www.w3.org/2004/02/skos/core#Concept",
+        "links" => {
+          "self" => concept_id,
+          "ontology" => item["ontology_iri"] || item["ontology"],
+          "children" => Array(item["children"]),
+          "parents" => [],
+          "descendants" => [],
+          "ancestors" => [],
+          "instances" => [],
+          "tree" => nil,
+          "notes" => [],
+          "mappings" => [],
+          "ui" => concept_id
+        },
+        "source_portal" => "nvs"
+      }
+    end
+
+    def paginate(docs, total_found)
+      current_page = (params[:page] || 1).to_i
+      pagesize = (params[:pagesize] || 50).to_i
+      page_count = (total_found / pagesize.to_f).ceil
+      start_index = (current_page - 1) * pagesize
+      paged_docs = docs[start_index, pagesize] || []
+
+      {
+        page: current_page,
+        pageCount: page_count,
+        totalCount: total_found,
+        prevPage: current_page > 1 ? current_page - 1 : nil,
+        nextPage: current_page < page_count ? current_page + 1 : nil,
+        collection: paged_docs
+      }
+    end
+  end
+
+end

controllers/federation_portals_controller.rb

@@ -0,0 +1,34 @@
+class FederationPortalsController < ApplicationController
+
+  namespace "/federation_portals" do
+
+    # search?q=water&portals=agroportal,ecoportal,nvs
+    get '/search' do
+      query = params[:query] || params[:q]
+      error 400, "You must provide a 'query' parameter to execute a search" if query.nil? || query.strip.empty?
+
+      portals = selected_portals(params)
+      results = federated_portal_search(portals, query, params)
+
+      current_page = (params[:page] || 1).to_i
+      pagesize = (params[:pagesize] || 50).to_i
+      total_count = results[:totalCount]
+      page_count = (total_count / pagesize.to_f).ceil
+
+      page_data = {
+        page: current_page,
+        pageCount: page_count,
+        totalCount: total_count,
+        prevPage: current_page > 1 ? current_page - 1 : nil,
+        nextPage: current_page < page_count ? current_page + 1 : nil,
+        collection: results[:collection]
+      }
+      page_data[:errors] = results[:errors] if results[:errors].any?
+
+      content_type 'application/json'
+      MultiJson.dump(page_data)
+    end
+
+  end
+
+end