Gemfile.lock update

.gitignore

@@ -1,3 +1,4 @@
+.bundle/
 *.swp
 *.gemtags
 .bundle

Gemfile

@@ -16,6 +16,8 @@ gem 'rest-client'
 gem 'rsolr'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
+gem 'request_store'
+
 
 # Testing
 group :test do
@@ -31,7 +33,6 @@ end
 group :development do
   gem 'rubocop', require: false
 end
-
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ncbo/goo', branch: 'develop'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'

Gemfile.lock

@@ -62,7 +62,9 @@ GEM
     faraday-net_http (3.3.0)
       net-http
     ffi (1.17.0-aarch64-linux-gnu)
+    ffi (1.17.0-arm64-darwin)
     ffi (1.17.0-x86_64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
@@ -190,7 +192,10 @@ GEM
 
 PLATFORMS
   aarch64-linux
-  x86_64-darwin-18
+  arm64-darwin-22
+  x86_64-darwin-21
+  x86_64-darwin-23
+  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 4)
@@ -211,6 +216,7 @@ DEPENDENCIES
   rack
   rack-test (~> 0.6)
   rake (~> 10.0)
+  request_store
   rest-client
   rsolr
   rubocop
@@ -221,4 +227,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.5.19
+   2.4.22

lib/ontologies_linked_data.rb

@@ -1,11 +1,11 @@
-require "goo"
+require 'goo'
 
 # Make sure we're in the load path
-lib_dir = File.dirname(__FILE__)+"/../lib"
+lib_dir = "#{File.dirname(__FILE__)}/../lib"
 $LOAD_PATH.unshift lib_dir unless $LOAD_PATH.include?(lib_dir)
 
 # Setup Goo (repo connection and namespaces)
-require "ontologies_linked_data/config/config"
+require 'ontologies_linked_data/config/config'
 
 # Include other dependent code
 require "ontologies_linked_data/security/authorization"
@@ -31,27 +31,50 @@
 require "ontologies_linked_data/metrics/metrics"
 
 # Require base model
-require "ontologies_linked_data/models/base"
+require 'ontologies_linked_data/models/base'
 
-# Require all models
+# Require all models and services
 project_root = File.dirname(File.absolute_path(__FILE__))
 
+require 'ontologies_linked_data/services/submission_process/submission_process'
+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/services/**/*.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/concerns//**/*.rb").sort
+models.each do |m|
+  require m
+end
+
 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 = Dir.glob("#{project_root}/ontologies_linked_data/models/**/*.rb").sort
 models.each do |m|
   require m
 end
 
+
+
 module LinkedData
   def rootdir
     File.dirname(File.absolute_path(__FILE__))
   end
 
   def bindir
-    File.expand_path(rootdir + '/../bin')
+    File.expand_path("#{rootdir}/../bin")
   end
 end

lib/ontologies_linked_data/config/config.rb

@@ -94,15 +94,13 @@ def config(&block)
     yield @settings, overide_connect_goo if block_given?
 
     # Check to make sure url prefix has trailing slash
-    @settings.rest_url_prefix = @settings.rest_url_prefix + '/' unless @settings.rest_url_prefix[-1].eql?('/')
+    @settings.rest_url_prefix = "#{@settings.rest_url_prefix}/" unless @settings.rest_url_prefix[-1].eql?('/')
 
     puts "(LD) >> Using rdf store #{@settings.goo_host}:#{@settings.goo_port}#{@settings.goo_path_query}"
     puts "(LD) >> Using term search server at #{@settings.search_server_url}"
     puts "(LD) >> Using property search server at #{@settings.property_search_server_url}"
-    puts '(LD) >> Using HTTP Redis instance at '+
-            "#{@settings.http_redis_host}:#{@settings.http_redis_port}"
-    puts '(LD) >> Using Goo Redis instance at '+
-            "#{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
+    puts "(LD) >> Using HTTP Redis instance at #{@settings.http_redis_host}:#{@settings.http_redis_port}"
+    puts "(LD) >> Using Goo Redis instance at #{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
 
     connect_goo unless overide_connect_goo
   end
@@ -132,15 +130,14 @@ def connect_goo
                                port: @settings.goo_redis_port)
 
         if @settings.enable_monitoring
-          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:"+
-                    "#{@settings.cube_port}"
+          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:#{@settings.cube_port}"
           conf.enable_cube do |opts|
             opts[:host] = @settings.cube_host
             opts[:port] = @settings.cube_port
           end
         end
       end
-    rescue Exception => e
+    rescue StandardError => e
       abort("EXITING: Cannot connect to triplestore and/or search server:\n  #{e}\n#{e.backtrace.join("\n")}")
     end
   end
@@ -153,23 +150,48 @@ def goo_namespaces
       conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#"))
       conf.add_namespace(:skos, RDF::Vocabulary.new("http://www.w3.org/2004/02/skos/core#"))
       conf.add_namespace(:owl, RDF::Vocabulary.new("http://www.w3.org/2002/07/owl#"))
+      conf.add_namespace(:rdf, RDF::Vocabulary.new("http://www.w3.org/1999/02/22-rdf-syntax-ns#"))
       conf.add_namespace(:rdfs, RDF::Vocabulary.new("http://www.w3.org/2000/01/rdf-schema#"))
-      conf.add_namespace(:metadata,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/"),
-                         default = true)
-      conf.add_namespace(:metadata_def,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
+      conf.add_namespace(:metadata, RDF::Vocabulary.new("http://data.bioontology.org/metadata/"), default = true)
+      conf.add_namespace(:metadata_def, RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
       conf.add_namespace(:dc, RDF::Vocabulary.new("http://purl.org/dc/elements/1.1/"))
       conf.add_namespace(:xsd, RDF::Vocabulary.new("http://www.w3.org/2001/XMLSchema#"))
-      conf.add_namespace(:oboinowl_gen,
-                         RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:oboinowl_gen, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
       conf.add_namespace(:obo_purl, RDF::Vocabulary.new("http://purl.obolibrary.org/obo/"))
-      conf.add_namespace(:umls,
-                         RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
-      conf.id_prefix = "http://data.bioontology.org/"
+      conf.add_namespace(:umls, RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
+      conf.add_namespace(:door, RDF::Vocabulary.new("http://kannel.open.ac.uk/ontology#"))
+      conf.add_namespace(:dct, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+
+      conf.add_namespace(:void, RDF::Vocabulary.new("http://rdfs.org/ns/void#"))
+      conf.add_namespace(:foaf, RDF::Vocabulary.new("http://xmlns.com/foaf/0.1/"))
+      conf.add_namespace(:vann, RDF::Vocabulary.new("http://purl.org/vocab/vann/"))
+      conf.add_namespace(:adms, RDF::Vocabulary.new("http://www.w3.org/ns/adms#"))
+      conf.add_namespace(:voaf, RDF::Vocabulary.new("http://purl.org/vocommons/voaf#"))
+      conf.add_namespace(:dcat, RDF::Vocabulary.new("http://www.w3.org/ns/dcat#"))
+      conf.add_namespace(:mod, RDF::Vocabulary.new("http://www.isibang.ac.in/ns/mod#"))
+      conf.add_namespace(:prov, RDF::Vocabulary.new("http://www.w3.org/ns/prov#"))
+      conf.add_namespace(:cc, RDF::Vocabulary.new("http://creativecommons.org/ns#"))
+      conf.add_namespace(:schema, RDF::Vocabulary.new("http://schema.org/"))
+      conf.add_namespace(:doap, RDF::Vocabulary.new("http://usefulinc.com/ns/doap#"))
+      conf.add_namespace(:bibo, RDF::Vocabulary.new("http://purl.org/ontology/bibo/"))
+      conf.add_namespace(:wdrs, RDF::Vocabulary.new("http://www.w3.org/2007/05/powder-s#"))
+      conf.add_namespace(:cito, RDF::Vocabulary.new("http://purl.org/spar/cito/"))
+      conf.add_namespace(:pav, RDF::Vocabulary.new("http://purl.org/pav/"))
+      conf.add_namespace(:oboInOwl, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:idot, RDF::Vocabulary.new("http://identifiers.org/idot/"))
+      conf.add_namespace(:sd, RDF::Vocabulary.new("http://www.w3.org/ns/sparql-service-description#"))
+      conf.add_namespace(:org, RDF::Vocabulary.new("http://www.w3.org/ns/org#"))
+      conf.add_namespace(:cclicense, RDF::Vocabulary.new("http://creativecommons.org/licenses/"))
+      conf.add_namespace(:nkos, RDF::Vocabulary.new("http://w3id.org/nkos#"))
+      conf.add_namespace(:skosxl, RDF::Vocabulary.new("http://www.w3.org/2008/05/skos-xl#"))
+      conf.add_namespace(:dcterms, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+      conf.add_namespace(:uneskos, RDF::Vocabulary.new("http://purl.org/umu/uneskos#"))
+
+
+      conf.id_prefix = 'http://data.bioontology.org/'
       conf.pluralize_models(true)
     end
   end
-  self.goo_namespaces
+  goo_namespaces
 
 end

lib/ontologies_linked_data/diff/bubastis_diff.rb

@@ -10,7 +10,7 @@ class InputFileNotFoundError < Diff::DiffException
     class DiffFileNotGeneratedException < Diff::DiffException
     end
 
-    class BubastisDiffCommand
+    class BubastisDiffCommand < DiffTool
 
       # Bubastis version 1.2
       # 18th December 2014
@@ -37,15 +37,33 @@ class BubastisDiffCommand
       # Loading one file locally and one from the web and outputting results to plain text:
       # java -jar bubastis_1_2.jar -ontology1 "H://disease_ontology_version_1.owl" -ontology2 "http://www.disease.org/diseaseontology_latest.owl" -output "C://my_diff.txt"
 
-      def initialize(input_fileOld, input_fileNew, output_repo)
+      def initialize(old_file_path, new_file_path, output_repo)
         @bubastis_jar_path = LinkedData.bindir + "/bubastis.jar"
-        @input_fileOld = input_fileOld
-        @input_fileNew = input_fileNew
+        @input_fileOld = old_file_path
+        @input_fileNew = new_file_path
         @output_repo = output_repo
         @file_diff_path = nil
         @java_heap_size = LinkedData.settings.java_max_heap_size
       end
 
+
+      def file_diff_path
+        @file_diff_path
+      end
+
+      def diff
+        setup_environment
+        call_bubastis_java_cmd
+        if @file_diff_path.nil?
+          raise DiffFileNotGeneratedException, "Diff file nil"
+        elsif not File.exist?(@file_diff_path)
+          raise DiffFileNotGeneratedException, "Diff file not found in #{@file_diff_path}"
+        end
+        return @file_diff_path
+      end
+
+      private
+
       def setup_environment
         if @input_fileOld.nil? or (not File.exist?(@input_fileOld))
           raise InputFileNotFoundError, "#{@input_fileOld} not found."
@@ -105,21 +123,6 @@ def call_bubastis_java_cmd
         end
         return @file_diff_path
       end
-
-      def file_diff_path
-        @file_diff_path
-      end
-
-      def diff
-        setup_environment
-        call_bubastis_java_cmd
-        if @file_diff_path.nil?
-          raise DiffFileNotGeneratedException, "Diff file nil"
-        elsif not File.exist?(@file_diff_path)
-          raise DiffFileNotGeneratedException, "Diff file not found in #{@file_diff_path}"
-        end
-        return @file_diff_path
-      end
     end
   end
 end

lib/ontologies_linked_data/diff/diff.rb

@@ -1,8 +1,20 @@
 module LinkedData
   module Diff
-    class <<self
+    class << self
       attr_accessor :logger
     end
+
+    class DiffTool
+      def initialize(old_file_path, new_file_path)
+        @old_file_path = old_file_path
+        @new_file_path = new_file_path
+      end
+
+      # @return String  generated path file
+      def diff
+        raise NotImplementedError
+      end
+    end
     class DiffException < Exception
     end
     class MkdirException < DiffException