Use save_file for external repositories

app/models/repository/git.rb

@@ -54,16 +54,6 @@ def save_file(tmp_file, filepath, message, user, do_parse: true)
     version
   end
 
-  def save_file_only(tmp_file, filepath, message, user)
-    commit = nil
-    git.add_file(user_info(user), tmp_file, filepath, message) do |commit_oid|
-      commit = commit_oid
-    end
-    commit_for!(commit, user)
-    touch
-    commit
-  end
-
   def commit_for!(commit_oid, pusher)
     instance = Commit.where(repository_id: self,
                             commit_oid: commit_oid).

features/step_definitions/ontology_versions_steps.rb

@@ -8,7 +8,7 @@
   repository = @ontology.repository
   user = repository.permissions.first.subject
   Tempfile.create('testfile') do |f|
-    repository.save_file_only(f.path, @ontology.path, 'add ontology file', user)
+    repository.save_file(f.path, @ontology.path, 'add ontology file', user, do_parse: false)
   end
 end
 

lib/external_repository.rb

@@ -22,8 +22,8 @@ def repository
 
     def add_to_repository(iri, message, user, location: iri)
       tmp_path = download_iri(location)
-      repository.save_file_only(tmp_path, determine_path(iri, :fullpath),
-                                message, user)
+      repository.save_file(tmp_path, determine_path(iri, :fullpath),
+                           message, user)
     end
 
     def determine_locid(external_iri)

lib/uri_fetcher.rb

@@ -26,9 +26,7 @@ def produce_response_body(response, write_file=nil)
     if write_file
       File.open(write_file.to_s, 'w') do |file|
         file.flock(File::LOCK_EX)
-        response.read_body do |chunk|
-          file.write chunk
-        end
+        file.write(response.read_body)
       end
       write_file
     else

spec/controllers/files_controller_spec.rb

@@ -90,7 +90,7 @@
             tmpfile.write('unchanged')
             tmpfile.close
 
-            repository.save_file_only(tmpfile, filepath, message, user)
+            repository.save_file(tmpfile, filepath, message, user, do_parse: false)
           end
 
           context "without validation error" do
@@ -159,7 +159,7 @@
           tmpfile.write('unchanged')
           tmpfile.close
 
-          repository.save_file_only(tmpfile, filepath, message, user)
+          repository.save_file(tmpfile, filepath, message, user, do_parse: false)
         end
 
         before do

spec/models/repository_directory_spec.rb

@@ -29,7 +29,7 @@
 
       let(:save_operation) do
         file = Tempfile.new('tempfile').path
-        repository.save_file_only(file, filepath, 'message', user)
+        repository.save_file(file, filepath, 'message', user, do_parse: false)
       end
 
       it 'should add a commit' do