Fix: Enhance zipped submissions support - follow up

lib/ontologies_linked_data/utils/file.rb

@@ -1,6 +1,7 @@
 require 'net/http'
 require 'uri'
 require 'zip'
+require 'zlib'
 require 'tmpdir'
 
 module LinkedData
@@ -20,7 +21,7 @@ def self.gzip?(file_path)
         raise ArgumentError, "File path #{file_path} not found" unless File.exist? file_path
 
         file_type = `file --mime -b #{Shellwords.escape(file_path)}`
-        file_type.split(';')[0] == 'application/x-gzip'
+        file_type.split(';')[0] == 'application/gzip' || file_type.split(';')[0] == 'application/x-gzip'
       end
 
       def self.files_from_zip(file_path)
@@ -30,15 +31,22 @@ def self.files_from_zip(file_path)
         end
 
         files = []
-        Zip::File.open(file_path) do |zipfile|
-          zipfile.each do |file|
-            if not file.directory?
-              if not file.name.split('/')[-1].start_with? '.' #a hidden file in __MACOSX or .DS_Store
+        if gzip?(file_path)
+          Zlib::GzipReader.open(file_path) do |file|
+            files << file.orig_name unless File.directory?(file) || file.orig_name.split('/')[-1].start_with?('.') # a hidden file in __MACOSX or .DS_Store
+          end
+        elsif zip?(file_path)
+          Zip::File.open(file_path) do |zip_files|
+            zip_files.each do |file|
+              unless file.directory? || file.name.split('/')[-1].start_with?('.') # a hidden file in __MACOSX or .DS_Store
                 files << file.name
               end
             end
           end
+        else
+          raise StandardError, "Unsupported file format: #{File.extname(file_path)}"
         end
+
         return files
       end
 
@@ -52,21 +60,20 @@ def self.unzip(file_path, dst_folder)
         if gzip?(file_path)
           Zlib::GzipReader.open(file_path) do |gz|
             File.open([dst_folder, gz.orig_name].join('/'), "w") { |file| file.puts(gz.read) }
-            extracted_files << GzipFile.new(gz)
+            extracted_files << gz
           end
-        else
+        elsif zip?(file_path)
           Zip::File.open(file_path) do |zipfile|
             zipfile.each do |file|
               if file.name.split('/').length > 1
-                sub_folder = File.join(dst_folder,
-                                      file.name.split('/')[0..-2].join('/'))
-                unless Dir.exist?(sub_folder)
-                  FileUtils.mkdir_p sub_folder
-                end
+                sub_folder = File.join(dst_folder, file.name.split('/')[0..-2].join('/'))
+                FileUtils.mkdir_p sub_folder unless Dir.exist?(sub_folder)
               end
-              extracted_files << file.extract(File.join(dst_folder,file.name))
+              extracted_files << file.extract(File.join(dst_folder, file.name))
             end
           end
+        else
+          raise StandardError, "Unsupported file format: #{File.extname(file_path)}"
         end
         extracted_files
       end

test/models/test_ontology_submission.rb

@@ -81,6 +81,13 @@ def test_automaster_from_zip
     assert_equal nil, LinkedData::Utils::FileHelpers.automaster(zipfile, ".obo")
   end
 
+  def test_is_gzip
+    gzipfile = "./test/data/ontology_files/BRO_v3.2.owl.gz"
+    zipfile = "./test/data/ontology_files/evoc_v2.9.zip"
+    assert LinkedData::Utils::FileHelpers.gzip?(gzipfile)
+    refute LinkedData::Utils::FileHelpers.gzip?(zipfile)
+  end
+
   def test_duplicated_file_names
 
     acronym = "DUPTEST"
@@ -501,6 +508,43 @@ def test_submission_parse_zip
     puts "#{ctr} classes with no label"
   end
 
+  def test_submission_parse_gzip
+    skip if ENV["BP_SKIP_HEAVY_TESTS"] == "1"
+
+    acronym = "BROGZ"
+    name = "BRO GZIPPED"
+    ontologyFile = "./test/data/ontology_files/BRO_v3.2.owl.gz"
+    id = 11
+
+    LinkedData::TestCase.backend_4s_delete
+
+    ont_submission = LinkedData::Models::OntologySubmission.new({submissionId: id})
+    refute ont_submission.valid?
+    assert_equal 4, ont_submission.errors.length
+    upload_file_path = LinkedData::Models::OntologySubmission.copy_file_repository(acronym, id, ontologyFile)
+    ont_submission.uploadFilePath = upload_file_path
+    owl, bro, user, contact = submission_dependent_objects("OWL", acronym, "test_linked_models", name)
+    ont_submission.released = DateTime.now - 4
+    ont_submission.hasOntologyLanguage = owl
+    ont_submission.prefLabelProperty = RDF::URI.new("http://bioontology.org/projects/ontologies/radlex/radlexOwl#Preferred_name")
+    ont_submission.ontology = bro
+    ont_submission.contact = [contact]
+    assert ont_submission.valid?
+    ont_submission.save
+    parse_options = {process_rdf: true, reasoning: true, index_search: false, run_metrics: false, diff: false}
+    begin
+      tmp_log = Logger.new(TestLogFile.new)
+      ont_submission.process_submission(tmp_log, parse_options)
+    rescue StandardError => e
+      puts "Error, logged in #{tmp_log.instance_variable_get("@logdev").dev.path}"
+      raise e
+    end
+
+    assert ont_submission.ready?({status: [:uploaded, :rdf, :rdf_labels]})
+    read_only_classes = LinkedData::Models::Class.in(ont_submission).include(:prefLabel).read_only
+    refute read_only_classes.empty?
+  end
+
   def test_download_ontology_file
     begin
       server_port = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports