Feature: Add ontology creation Vocbench connector

Gemfile

@@ -19,7 +19,7 @@ gem 'json-ld'
 
 
 # Rack middleware
-gem 'ffi'
+gem 'ffi', '~> 1.15.5'
 gem 'rack-accept', '~> 0.4'
 gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
 gem 'rack-cache', '~> 1.13.0'

Gemfile.lock

@@ -11,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
+  revision: a95245b8c964431505ca6315907440996c59a00d
   branch: development
   specs:
     goo (0.0.2)
@@ -40,7 +40,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: 6bb53a13f514a60513afe25e37c5c69475140452
+  revision: fabd04ef4fa37989d526fc6a7aa1e98830008dae
   branch: master
   specs:
     ncbo_cron (0.0.1)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: a5b56a68e6dc8ecfc9db708d44350342dac38ce6
+  revision: 4cd56da111c2037bf0b606574e6b325bfa74a2f1
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -117,7 +117,7 @@ GEM
     bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
     builder (3.3.0)
-    capistrano (3.19.0)
+    capistrano (3.19.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -165,7 +165,7 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.16.3)
+    ffi (1.15.5)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -256,7 +256,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0604)
+    mime-types-data (3.2024.0702)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -394,7 +394,7 @@ GEM
     strscan (3.1.0)
     systemu (2.6.5)
     temple (0.10.3)
-    tilt (2.3.0)
+    tilt (2.4.0)
     timeout (0.4.1)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
@@ -429,7 +429,7 @@ DEPENDENCIES
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
   faraday (~> 1.9)
-  ffi
+  ffi (~> 1.15.5)
   goo!
   haml (~> 5.2.2)
   json-ld

controllers/ontologies_controller.rb

@@ -47,6 +47,29 @@ class OntologiesController < ApplicationController
       reply(latest || {})
     end
 
+    # Ontology latest submission datacite metadata as Json
+    get "/:acronym/latest_submission/datacite_metadata_json" do
+      params["display"] = 'all'
+      latest = find_latest_submission
+      latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param)) if latest
+      if latest
+        to_data_cite_facet(latest).to_json
+      else
+        reply {}
+      end
+    end
+
+    get "/:acronym/latest_submission/ecoportal_metadata_json" do
+      params["display"] = 'all'
+      latest = find_latest_submission
+      latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param)) if latest
+      if latest
+        to_eco_portal_facet(latest).to_json
+      else
+        reply {}
+      end
+    end
+
     ##
     # Update latest submission of an ontology
     REQUIRES_REPROCESS = ["prefLabelProperty", "definitionProperty", "synonymProperty", "authorProperty", "classType", "hierarchyProperty", "obsoleteProperty", "obsoleteParent"]
@@ -64,7 +87,7 @@ class OntologiesController < ApplicationController
         submission.save
         if (params.keys & REQUIRES_REPROCESS).length > 0 || request_has_file?
           cron = NcboCron::Models::OntologySubmissionParser.new
-          cron.queue_submission(submission, {all: true})
+          cron.queue_submission(submission, { all: true })
         end
       else
         error 422, submission.errors
@@ -76,13 +99,13 @@ class OntologiesController < ApplicationController
     ##
     # Create an ontology
     post do
-      create_ontology
+      create_ontology_with_params
     end
 
     ##
     # Create an ontology with constructed URL
     put '/:acronym' do
-      create_ontology
+      create_ontology_with_params
     end
 
     ##
@@ -123,7 +146,7 @@ class OntologiesController < ApplicationController
       restricted_download = LinkedData::OntologiesAPI.settings.restrict_download.include?(acronym)
       error 403, "License restrictions on download for #{acronym}" if restricted_download && !current_user.admin?
       error 403, "Ontology #{acronym} is not accessible to your user" if ont.restricted? && !ont.accessible?(current_user)
-      latest_submission = ont.latest_submission(status: :rdf)  # Should resolve to latest successfully loaded submission
+      latest_submission = ont.latest_submission(status: :rdf) # Should resolve to latest successfully loaded submission
       error 404, "There is no latest submission loaded for download" if latest_submission.nil?
       latest_submission.bring(:uploadFilePath)
 
@@ -148,46 +171,27 @@ class OntologiesController < ApplicationController
     end
 
     private
-
-    def create_ontology
-      params ||= @params
-
-      # acronym must be well formed
-      params['acronym'] = params['acronym'].upcase # coerce new ontologies to upper case
-
-      # ontology acronym must be unique
-      ont = Ontology.find(params['acronym']).first
-      if ont.nil?
-        ont = instance_from_params(Ontology, params)
+    def find_latest_submission
+      ont = Ontology.find(params["acronym"]).first
+      error 404, "You must provide a valid `acronym` to retrieve an ontology" if ont.nil?
+      include_status = params["include_status"]
+      ont.bring(:acronym, :submissions)
+      if include_status
+        latest = ont.latest_submission(status: include_status.to_sym)
       else
-        error_msg = <<-ERR
-        Ontology already exists, see #{ont.id}
-        To add a new submission, POST to: /ontologies/#{params['acronym']}/submission.
-        To modify the resource, use PATCH.
-        ERR
-        error 409, error_msg
-      end
-
-      # ontology name must be unique
-      ont_names = Ontology.where.include(:name).to_a.map {|o| o.name }
-      if ont_names.include?(ont.name)
-        error 409, "Ontology name is already in use by another ontology."
+        latest = ont.latest_submission(status: :any)
       end
+      check_last_modified(latest) if latest
+      latest
+    end
 
+    def create_ontology_with_params
+      ont = create_ontology
       if ont.valid?
-        ont.save
-        # Send an email to the administrator to warn him about the newly created ontology
-        begin
-          if !LinkedData.settings.admin_emails.nil? && !LinkedData.settings.admin_emails.empty?
-            LinkedData::Utils::Notifications.new_ontology(ont)
-          end
-        rescue Exception => e
-        end
+        reply 201, ont
       else
         error 422, ont.errors
       end
-
-      reply 201, ont
     end
   end
 
@@ -204,7 +208,7 @@ def create_ontology
       else
         onts = Ontology.where.filter(Goo::Filter.new(:viewOf).unbound).include(Ontology.goo_attrs_to_load(includes_param)).to_a
       end
-      options = {also_include_views: allow_views, status: (params["include_status"] || "ANY")}
+      options = { also_include_views: allow_views, status: (params["include_status"] || "ANY") }
       subs = retrieve_latest_submissions(options)
       metrics_include = LinkedData::Models::Metric.goo_attrs_to_load(includes_param)
       LinkedData::Models::OntologySubmission.where.models(subs.values).include(metrics: metrics_include).all
@@ -220,7 +224,7 @@ def create_ontology
           metrics = nil
         end
 
-        resp << {ontology: ont, latest_submission: subs[ont.acronym], metrics: metrics}
+        resp << { ontology: ont, latest_submission: subs[ont.acronym], metrics: metrics }
       end
 
       reply resp

controllers/ontology_submissions_controller.rb

@@ -2,8 +2,8 @@ class OntologySubmissionsController < ApplicationController
   get "/submissions" do
     check_last_modified_collection(LinkedData::Models::OntologySubmission)
     options = {
-               also_include_views: params["also_include_views"],
-               status: (params["include_status"] || "ANY")
+      also_include_views: params["also_include_views"],
+      status: (params["include_status"] || "ANY")
     }
     subs = retrieve_latest_submissions(options)
     subs = subs.values unless page?
@@ -43,7 +43,16 @@ class OntologySubmissionsController < ApplicationController
     # Create a new submission for an existing ontology
     post do
       ont = Ontology.find(params["acronym"]).include(Ontology.attributes).first
-      error 422, "You must provide a valid `acronym` to create a new submission" if ont.nil?
+      params["name"] ||= params["titles"]&.first&.dig('title')
+
+      if params["name"] && params["acronym"] && ont.nil?
+        params["hasOntologyLanguage"] = "SKOS"
+        params["administeredBy"] = [ current_user.username ]
+        ont = create_ontology
+      elsif ont.nil?
+        error 422, "You must provide a valid `acronym` to create a new submission"
+      end
+
       reply 201, create_submission(ont)
     end
 
@@ -59,6 +68,18 @@ class OntologySubmissionsController < ApplicationController
       reply ont_submission
     end
 
+    # Ontology a submission datacite metadata as Json
+    get "/:ontology_submission_id/datacite_metadata_json" do
+      params["display"] = 'all'
+      ont = Ontology.find(params["acronym"]).include(:acronym).first
+      check_last_modified_segment(LinkedData::Models::OntologySubmission, [ont.acronym])
+      ont_submission = ont.submission(params["ontology_submission_id"])
+      error 404, "`submissionId` not found" if ont_submission.nil?
+      # ont_submission.bring(*OntologySubmission.goo_attrs_to_load(includes_param))
+      ont_submission.bring(*OntologySubmission.goo_attrs_to_load(includes_param))
+      to_data_cite_facet(ont_submission)
+    end
+
     ##
     # Update an existing submission of an ontology
     REQUIRES_REPROCESS = ["prefLabelProperty", "definitionProperty", "synonymProperty", "authorProperty", "classType", "hierarchyProperty", "obsoleteProperty", "obsoleteParent"]
@@ -170,5 +191,4 @@ def delete_submissions(startId, endId)
 
   end
 
-
 end

helpers/concerns/data_cite_metadata_exporter.rb

@@ -0,0 +1,82 @@
+module Sinatra
+  module Concerns
+    module DataCiteMetadataExporter
+
+      def to_date_cite(sub)
+        hash  = {
+          url: sub.publication.first ? sub.publication.first&.to_s : sub.URI&.to_s,
+          version: sub.version,
+          description: sub.description,
+          publicationYear: sub.released&.year,
+          publisher: sub.publisher.map{|p| p.name}.join(', '),
+          creators: to_data_cite_creators(sub.hasCreator),
+          identifier: search_doi(sub.identifier) || sub.identifier.first&.to_s,
+          identifierType: identifier_type(sub),
+          titles: [{title: sub.ontology.name, titleType: ''}] + sub.alternative.map { |x| { title: x, titleType: 'AlternativeTitle' } },
+          resourceTypeGeneral: 'Dataset',
+          resourceType: sub.isOfType.to_s.split('/').last
+        }
+
+        identifier = hash.delete(:identifier)
+        identifier_type = hash.delete(:identifierType)
+        hash[:doi] = identifier if identifier_type.eql?('DOI')
+
+        hash[:types] = {
+          resourceTypeGeneral: hash.delete(:resourceTypeGeneral),
+          resourceType: hash.delete(:resourceType),
+        }
+        hash
+      end
+
+      private
+
+      def identifier_type(sub)
+        identifiers = sub.identifier
+
+        return 'None' if identifiers.nil? || identifiers.empty?
+
+        search_doi(identifiers).nil? ? 'Other' : 'DOI'
+      end
+
+      def to_data_cite_creators(creators)
+        creators.map do |creator|
+          {
+            nameType: creator.agentType.eql?('person') ? 'Personal' : 'Organizational',
+            givenName: creator.name.split(' ').first,
+            familyName: creator.name.split(' ').drop(1).join(' '),
+            creatorName: creator.name,
+            affiliations: to_data_cite_affiliations(creator.affiliations),
+            nameIdentifiers: to_data_cite_identifiers(creator.identifiers)
+          }
+        end
+      end
+
+      def to_data_cite_identifiers(identifiers)
+        identifiers.map do |identifier|
+          {
+            nameIdentifierScheme: identifier.schemaAgency,
+            schemeURI: identifier.schemeURI,
+            nameIdentifier: identifier.notation
+          }
+        end
+
+      end
+
+      def to_data_cite_affiliations(affiliations)
+        affiliations.map do |affiliation|
+          identifier = affiliation.identifiers.first
+          {
+            affiliationIdentifierScheme: identifier&.schemaAgency,
+            affiliationIdentifier: "#{identifier&.schemeURI}#{identifier&.notation}",
+            affiliation: affiliation.name
+          }
+        end
+      end
+
+      def search_doi(identifiers)
+        identifiers.select { |i| i.start_with?('http://doi.org') || i.start_with?('https://doi.org') }.first&.to_s
+      end
+
+    end
+  end
+end