Merge branch 'development' into feature/migrate-attrbiutes-metadata-t…

…o-scheme-file

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: f9b73ce6b6fac92bffd0a2a1b9dc9ba9266acf79
+  revision: c3456c45c12ed92d4a3ae43cac7c1d4cdbf290b6
   branch: development
   specs:
     goo (0.0.2)
@@ -32,15 +32,15 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.1)
+    addressable (2.8.4)
       public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
     bcrypt (3.1.18)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
-    connection_pool (2.3.0)
+    connection_pool (2.4.0)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     date (3.3.3)
@@ -123,8 +123,8 @@ GEM
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
-    parallel (1.22.1)
-    parser (3.2.1.1)
+    parallel (1.23.0)
+    parser (3.2.2.1)
       ast (~> 2.4.1)
     pony (1.13.1)
       mail (>= 2.0)
@@ -143,9 +143,9 @@ GEM
       addressable (>= 2.2)
     redis (5.0.6)
       redis-client (>= 0.9.0)
-    redis-client (0.14.0)
+    redis-client (0.14.1)
       connection_pool
-    regexp_parser (2.7.0)
+    regexp_parser (2.8.0)
     request_store (1.5.1)
       rack (>= 1.4)
     rest-client (2.1.0)
@@ -156,17 +156,17 @@ GEM
     rexml (3.2.5)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.48.1)
+    rubocop (1.50.2)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.2.0.0)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.26.0, < 2.0)
+      rubocop-ast (>= 1.28.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.27.0)
+    rubocop-ast (1.28.0)
       parser (>= 3.2.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -183,13 +183,13 @@ GEM
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
-    thin (1.8.1)
+    thin (1.8.2)
       daemons (~> 1.0, >= 1.0.9)
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
     timeout (0.3.2)
-    tzinfo (0.3.61)
+    tzinfo (0.3.62)
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
@@ -199,7 +199,6 @@ GEM
 
 PLATFORMS
   x86_64-darwin-21
-  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 4)
@@ -233,4 +232,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.3.15
+   2.3.23

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -21,7 +21,9 @@ class OntologySubmission < LinkedData::Models::Base
       include SKOS::RootsFetcher
 
       FILES_TO_DELETE = ['labels.ttl', 'mappings.ttl', 'obsolete.ttl', 'owlapi.xrdf', 'errors.log']
+      FOLDERS_TO_DELETE = ['unzipped']
       FLAT_ROOTS_LIMIT = 1000
+      FILE_SIZE_ZIPPING_THRESHOLD = 100 * 1024 * 1024 # 100MB
 
       model :ontology_submission, scheme: File.join(__dir__, '../../../config/schemes/ontology_submission.yml'),
                                   name_with: ->(s) { submission_id_generator(s) }
@@ -178,8 +180,8 @@ class OntologySubmission < LinkedData::Models::Base
       attribute :ontology, type: :ontology, enforce: [:existence]
 
       # Hypermedia settings
-      embed :contact, :ontology, :metrics
-      embed_values :submissionStatus => [:code], :hasOntologyLanguage => [:acronym]
+      embed :contact, :ontology
+      embed_values :submissionStatus => [:code], :hasOntologyLanguage => [:acronym], :metrics => [:classes, :individuals, :properties]
       serialize_default :contact, :ontology, :hasOntologyLanguage, :released, :creationDate, :homepage,
                         :publication, :documentation, :version, :description, :status, :submissionId
 
@@ -467,6 +469,25 @@ def delete_old_submission_files
         submission_files.push(csv_path)
         submission_files.push(parsing_log_path) unless parsing_log_path.nil?
         FileUtils.rm(submission_files, force: true)
+
+        submission_folders = FOLDERS_TO_DELETE.map { |f| File.join(path_to_repo, f) }
+        submission_folders.each {|d| FileUtils.remove_dir(d) if File.directory?(d)}
+      end
+
+      def zip_submission_uploaded_file
+        self.bring(:uploadFilePath) if self.bring?(:uploadFilePath)
+
+        return self.uploadFilePath if zipped?
+        return self.uploadFilePath if self.uploadFilePath.nil? || self.uploadFilePath.empty?
+
+
+        return self.uploadFilePath if File.size(self.uploadFilePath) < FILE_SIZE_ZIPPING_THRESHOLD
+
+
+        old_path = self.uploadFilePath
+        new_path = Utils::FileHelpers.zip_file(old_path)
+        FileUtils.rm(old_path, force: true)
+        new_path
       end
 
       # accepts another submission in 'older' (it should be an 'older' ontology version)
@@ -1004,6 +1025,25 @@ def archived?
         return ready?(status: [:archived])
       end
 
+      def archive_submission
+        self.submissionStatus = nil
+        status = LinkedData::Models::SubmissionStatus.find("ARCHIVED").first
+        add_submission_status(status)
+
+        # Delete everything except for original ontology file.
+        ontology.bring(:submissions)
+        submissions = ontology.submissions
+        unless submissions.nil?
+          submissions.each { |s| s.bring(:submissionId) }
+          submission = submissions.sort { |a, b| b.submissionId <=> a.submissionId }[0]
+          # Don't perform deletion if this is the most recent submission.
+          if self.submissionId < submission.submissionId
+            delete_old_submission_files
+            self.uploadFilePath = zip_submission_uploaded_file
+          end
+        end
+      end
+
       ################################################################
       # Possible options with their defaults:
       #   process_rdf       = false
@@ -1072,21 +1112,7 @@ def process_submission(logger, options = {})
           status = nil
 
           if archive
-            self.submissionStatus = nil
-            status = LinkedData::Models::SubmissionStatus.find("ARCHIVED").first
-            add_submission_status(status)
-
-            # Delete everything except for original ontology file.
-            ontology.bring(:submissions)
-            submissions = ontology.submissions
-            unless submissions.nil?
-              submissions.each { |s| s.bring(:submissionId) }
-              submission = submissions.sort { |a, b| b.submissionId <=> a.submissionId }[0]
-              # Don't perform deletion if this is the most recent submission.
-              if (self.submissionId < submission.submissionId)
-                delete_old_submission_files
-              end
-            end
+            archive_submission
           else
             if process_rdf
               # Remove processing status types before starting RDF parsing etc.

lib/ontologies_linked_data/monkeypatches/object.rb

@@ -337,6 +337,8 @@ def embed_goo_objects_just_values(hash, attribute, value, options, &block)
   end
 
   def add_goo_values(goo_object, embedded_values, attributes_to_embed, options, &block)
+    return if goo_object.nil?
+
     if attributes_to_embed.length > 1
       embedded_values_hash = {}
       attributes_to_embed.each do |a|

lib/ontologies_linked_data/security/access_control.rb

@@ -57,12 +57,12 @@ def access_for_all?
     def read_restricted_based_on?(based_on)
       if based_on.is_a?(Proc)
         instance_to_base_on = based_on.call(self)
-        restricted = instance_to_base_on.read_restricted?
+        restricted = instance_to_base_on ? instance_to_base_on.read_restricted?  : false
       elsif based_on.is_a?(LinkedData::Models::Base)
         restricted = based_on.read_restricted?
       elsif based_on.is_a?(Symbol)
         instance_to_base_on = based_on.send(based_on)
-        restricted = instance_to_base_on.read_restricted?
+        restricted =  instance_to_base_on ? instance_to_base_on.read_restricted?  : false
       else
         restricted = false
       end

lib/ontologies_linked_data/serializer.rb

@@ -84,7 +84,9 @@ def self.response(options = {})
     end
 
     def self.serialize(type, obj, params, request)
-      lang = params['lang'] || params['language']|| Goo.main_languages.first
+
+      lang = self.get_language(params)
+
       only = params['display'] || []
       only = only.split(',') unless only.is_a?(Array)
       all = only[0] == 'all'
@@ -106,5 +108,11 @@ def self.print_stacktrace?
       end
     end
 
+    def self.get_language(params)
+      lang = params['lang'] || params['language'] ||  Goo.main_languages&.first.to_s || 'en'
+      lang = lang.split(',').map {|l| l.downcase.to_sym}
+      return lang.length == 1 ? lang.first : lang
+    end
+
   end
 end

lib/ontologies_linked_data/serializers/json.rb

@@ -6,8 +6,11 @@ class JSON
       CONTEXTS = {}
 
       def self.serialize(obj, options = {})
+
+
         hash = obj.to_flex_hash(options) do |hash, hashed_obj|
           current_cls = hashed_obj.respond_to?(:klass) ? hashed_obj.klass : hashed_obj.class
+          result_lang = self.get_languages(get_object_submission(hashed_obj), options[:lang]) if result_lang.nil?
 
           # Add the id to json-ld attribute
           if current_cls.ancestors.include?(LinkedData::Hypermedia::Resource) && !current_cls.embedded? && hashed_obj.respond_to?(:id)
@@ -27,7 +30,7 @@ def self.serialize(obj, options = {})
               hash["links"].merge!(generate_links_context(hashed_obj)) if generate_context?(options)
             end
           end
-          
+
           # Generate context
           if current_cls.ancestors.include?(Goo::Base::Resource) && !current_cls.embedded?
             if generate_context?(options)
@@ -40,13 +43,35 @@ def self.serialize(obj, options = {})
             context = {"@context" => context_hash}
             hash.merge!(context)
           end
-          hash['@context']['@language'] = options[:lang] if hash['@context']
+          hash['@context']['@language'] = result_lang if hash['@context']
         end
         MultiJson.dump(hash)
       end
 
       private
 
+      def self.get_object_submission(obj)
+        obj.class.attributes.include?(:submission) ? obj.submission : nil
+      end
+
+      def self.get_languages(submission, user_languages)
+        result_lang = user_languages
+
+        if submission
+          submission.bring :naturalLanguage
+          languages = get_submission_languages(submission.naturalLanguage)
+          # intersection of the two arrays , if the requested language is not :all
+          result_lang = user_languages == :all ? languages : Array(user_languages) & languages
+          result_lang = result_lang.first if result_lang.length == 1
+        end
+
+        result_lang
+      end
+
+      def self.get_submission_languages(submission_natural_language = [])
+        submission_natural_language.map { |natural_language| natural_language["iso639"] && natural_language.split('/').last[0..1].to_sym }.compact
+      end 
+
       def self.type(current_cls, hashed_obj)
         if current_cls.respond_to?(:type_uri)
           # For internal class

lib/ontologies_linked_data/utils/file.rb

@@ -14,15 +14,7 @@ def initialize(gz)
           self.name = gz.orig_name
         end
       end
-
-      def self.gzip?(file_path)
-        file_path = file_path.to_s
-        unless File.exist? file_path
-          raise ArgumentError, "File path #{file_path} not found"
-        end
-        file_type = `file --mime -b #{Shellwords.escape(file_path)}`
-        return file_type.split(";")[0] == "application/x-gzip"
-      end
+
 
       def self.zip?(file_path)
         file_path = file_path.to_s
@@ -88,6 +80,21 @@ def self.unzip(file_path, dst_folder)
         extracted_files
       end
 
+      def self.zip_file(file_path)
+        return file_path if self.zip?(file_path)
+
+        zip_file_path = "#{file_path}.zip"
+        Zip::File.open(zip_file_path, Zip::File::CREATE) do |zipfile|
+          # Add the file to the zip
+          begin
+            zipfile.add(File.basename(file_path), file_path)
+          rescue Zip::EntryExistsError
+          end
+
+        end
+        zip_file_path
+      end
+
       def self.automaster?(path, format)
         self.automaster(path, format) != nil
       end