update the vocbench connector to create also the ontology if not exis…

…tent

Gemfile.lock

@@ -1,40 +1,3 @@
-GIT
-  remote: https://github.com/lifewatch-eric/ncbo_cron.git
-  revision: 2ff764e536e049220208e3cd6c0ee9f03366df17
-  branch: master
-  specs:
-    ncbo_cron (0.0.1)
-      dante
-      goo
-      google-analytics-data
-      google-apis-analytics_v3
-      mlanett-redis-lock
-      multi_json
-      ncbo_annotator
-      ontologies_linked_data
-      redis
-      rufus-scheduler (~> 2.0.24)
-
-GIT
-  remote: https://github.com/lifewatch-eric/ontologies_linked_data.git
-  revision: 17edfcb470848152dec8939fc6f68f5ed00f83db
-  branch: master
-  specs:
-    ontologies_linked_data (0.0.1)
-      activesupport
-      bcrypt
-      goo
-      json
-      libxml-ruby
-      multi_json
-      oj
-      omni_logger
-      pony
-      rack
-      rack-test
-      rsolr
-      rubyzip
-
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
   revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
@@ -48,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
+  revision: a95245b8c964431505ca6315907440996c59a00d
   branch: development
   specs:
     goo (0.0.2)
@@ -77,7 +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)
@@ -94,7 +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)
@@ -154,7 +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)
@@ -293,7 +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)
@@ -431,7 +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)

controllers/ontologies_controller.rb

@@ -99,13 +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
 
     ##
@@ -185,45 +185,13 @@ def find_latest_submission
       latest
     end
 
-    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)
-      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."
-      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
 

controllers/ontology_submissions_controller.rb

@@ -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
 

helpers/ontology_helper.rb

@@ -7,6 +7,44 @@ module Helpers
     module OntologyHelper
       include Sinatra::Concerns::EcoPortalMetadataExporter
 
+      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)
+        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."
+        end
+
+        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
+        end
+        ont
+      end
+
       ##
       # Create a new OntologySubmission object based on the request data
       def create_submission(ont)

test/controllers/test_ontology_submissions_controller.rb

@@ -271,10 +271,16 @@ def test_upload_eco_portal_metadata
 
     2.times.each do |i|
       header 'Authorization', "apikey token=#{user.apikey}"
-      post "/ontologies/#{@@acronym}/submissions", example_of_input, "CONTENT_TYPE" => "application/json"
+      post "/ontologies/SYPHAX_TEST_VOC/submissions", example_of_input, "CONTENT_TYPE" => "application/json"
       assert_equal 201, last_response.status
 
-      ont = Ontology.find(@@acronym).first
+      ont = Ontology.find('SYPHAX_TEST_VOC').first
+
+      refute_nil ont
+
+      ont.bring_remaining
+
+      assert_equal ont.name, example_of_input["titles"].first["title"]
 
       subs = ont.bring(:submissions).submissions