reapply overwritten changes made in 629aa39

commit 629aa39
ncbo · May 10, 2024 · 91444a6 · 91444a6
1 parent d25ce99
commit 91444a6
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Showing 3 changed files with 8 additions and 7 deletions.
diff --git a/lib/ontologies_linked_data/diff/bubastis_diff.rb b/lib/ontologies_linked_data/diff/bubastis_diff.rb
@@ -37,11 +37,11 @@ class BubastisDiffCommand < DiffTool
       # 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(old_file_path, new_file_path)
+      def initialize(old_file_path, new_file_path, output_repo)
         @bubastis_jar_path = LinkedData.bindir + "/bubastis.jar"
         @input_fileOld = old_file_path
         @input_fileNew = new_file_path
-        @output_repo = File.expand_path(@input_fileNew).gsub(File.basename(@input_fileNew),'')
+        @output_repo = output_repo
         @file_diff_path = nil
         @java_heap_size = LinkedData.settings.java_max_heap_size
       end

diff --git a/...ntologies_linked_data/services/submission_process/operations/submission_diff_generator.rb b/...ntologies_linked_data/services/submission_process/operations/submission_diff_generator.rb
@@ -15,11 +15,13 @@ def diff(logger, older)
       # accepts another submission in 'older' (it should be an 'older' ontology version)
       def init_diff_tool(older)
         @submission.bring(:uploadFilePath)
-        older.bring(:uploadFilePath)
+        older.bring(:uploadFilePath) if older.bring? :uploadFilePath
 
         LinkedData::Diff::BubastisDiffCommand.new(
           File.expand_path(older.uploadFilePath),
-          File.expand_path(@submission.uploadFilePath))
+          File.expand_path(@submission.uploadFilePath),
+          @submission.data_folder
+        )
       end
 
       def process_diff(logger)
@@ -61,11 +63,10 @@ def process_diff(logger)
         end
       end
 
-
       def generate_diff(logger, diff_tool)
         begin
           @submission.bring_remaining
-          @submission.bring(:diffFilePath)
+          @submission.bring(:diffFilePath) if @submission.bring? :diffFilePath
 
           LinkedData::Diff.logger = logger
           @submission.diffFilePath = diff_tool.diff

diff --git a/...ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb b/...ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb
@@ -311,7 +311,7 @@ def process_rdf(logger, reasoning)
 
         status = LinkedData::Models::SubmissionStatus.find('OBSOLETE').first
         begin
-          generate_obsolete_classes(logger, file_path)
+          generate_obsolete_classes(logger, @submission.uploadFilePath.to_s)
           @submission.add_submission_status(status)
           @submission.save
         rescue Exception => e