Feature: extract ontology URI automatically in submissions process

lib/ontologies_linked_data.rb

@@ -35,6 +35,10 @@
 # Require all models
 project_root = File.dirname(File.absolute_path(__FILE__))
 
+models = Dir.glob("#{project_root}/ontologies_linked_data/concerns/**/*.rb").sort
+models.each do |m|
+  require m
+end
 # We need to require deterministic - that is why we have the sort.
 models = Dir.glob(project_root + '/ontologies_linked_data/models/**/*.rb').sort
 models.each do |m|

lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb

@@ -0,0 +1,39 @@
+module LinkedData
+  module Concerns
+    module OntologySubmission
+      module MetadataExtractor
+
+        def extract_metadata
+          version_info = extract_version
+          ontology_iri = extract_ontology_iri
+
+          self.version = version_info if version_info
+          self.uri = ontology_iri if ontology_iri
+
+        end
+
+        def extract_version
+
+          query = Goo.sparql_query_client.select(:versionInfo).distinct
+                     .from(self.id)
+                    .where([RDF::URI.new('http://bioportal.bioontology.org/ontologies/versionSubject'),
+                            RDF::URI.new('http://www.w3.org/2002/07/owl#versionInfo'),
+                            :versionInfo])
+
+          sol = query.each_solution.first || {}
+          sol[:versionInfo]&.to_s
+        end
+
+        def extract_ontology_iri
+          query = Goo.sparql_query_client.select(:uri).distinct
+                     .from(self.id)
+                     .where([:uri,
+                             RDF::URI.new('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
+                             RDF::URI.new('http://www.w3.org/2002/07/owl#Ontology')])
+          sol = query.each_solution.first || {}
+          sol[:uri]&.to_s
+        end
+      end
+    end
+  end
+end

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -12,6 +12,8 @@ module Models
 
     class OntologySubmission < LinkedData::Models::Base
 
+      include LinkedData::Concerns::OntologySubmission::MetadataExtractor
+
       FILES_TO_DELETE = ['labels.ttl', 'mappings.ttl', 'obsolete.ttl', 'owlapi.xrdf', 'errors.log']
       FLAT_ROOTS_LIMIT = 1000
 
@@ -473,28 +475,9 @@ def generate_rdf(logger, file_path, reasoning=true)
           logger.flush
         end
         delete_and_append(triples_file_path, logger, mime_type)
-        version_info = extract_version()
-
-        if version_info
-          self.version = version_info
-        end
       end
 
-      def extract_version
 
-        query_version_info = <<eos
-SELECT ?versionInfo
-FROM #{self.id.to_ntriples}
-WHERE {
-<http://bioportal.bioontology.org/ontologies/versionSubject>
- <http://www.w3.org/2002/07/owl#versionInfo> ?versionInfo .
-}
-eos
-        Goo.sparql_query_client.query(query_version_info).each_solution do |sol|
-          return sol[:versionInfo].to_s
-        end
-        return nil
-      end
 
       def process_callbacks(logger, callbacks, action_name, &block)
         callbacks.delete_if do |_, callback|
@@ -971,6 +954,7 @@ def process_submission(logger, options={})
                 zip_dst = unzip_submission(logger)
                 file_path = zip_dst ? zip_dst.to_s : self.uploadFilePath.to_s
                 generate_rdf(logger, file_path, reasoning=reasoning)
+                extract_metadata
                 add_submission_status(status)
                 self.save
               rescue Exception => e

lib/ontologies_linked_data/parser/owlapi.rb

@@ -13,7 +13,7 @@ class RDFFileNotGeneratedException < Parser::ParserException
 
     class OWLAPICommand
       def initialize(input_file, output_repo, opts = {})
-        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.3.8.jar"
+        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.4.1.jar"
         @input_file = input_file
         @output_repo = output_repo
         @master_file = opts[:master_file]