merged #143 - Refactor: ontology_submission.rb file to isolate the pr…

…ocessing steps

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 +31,47 @@
 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 base services
+require 'ontologies_linked_data/services/submission_process/submission_process'
+
+# 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/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)
         @bubastis_jar_path = LinkedData.bindir + "/bubastis.jar"
-        @input_fileOld = input_fileOld
-        @input_fileNew = input_fileNew
-        @output_repo = output_repo
+        @input_fileOld = old_file_path
+        @input_fileNew = new_file_path
+        @output_repo = File.expand_path(@input_fileNew).gsub(File.basename(@input_fileNew),'')
         @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