Merge pull request #257 from ncbo/develop

Develop -> Master merge, release v6.6.1

Author: alexskr

Gemfile

@@ -14,11 +14,10 @@ gem 'omni_logger'
 gem 'pony'
 gem 'rack'
 gem 'rake', '~> 10.0'
+gem 'request_store'
 gem 'rest-client'
 gem 'rsolr'
-gem 'rubyzip', '~> 1.0'
-gem 'thin'
-gem 'request_store'
+gem 'thin', '~> 1.0' # compatibility version pin. thin should be replaced with webmoc
 
 
 # Testing

Gemfile.lock

@@ -41,7 +41,7 @@ PATH
       rack
       rack-test
       rsolr
-      rubyzip
+      rubyzip (~> 3.0)
 
 GEM
   remote: https://rubygems.org/
@@ -57,7 +57,7 @@ GEM
     ansi (1.5.0)
     ast (2.4.3)
     bcrypt (3.1.20)
-    bigdecimal (3.1.9)
+    bigdecimal (3.2.2)
     builder (3.3.0)
     childprocess (5.1.0)
       logger (~> 1.5)
@@ -92,12 +92,12 @@ GEM
       concurrent-ruby (~> 1.0)
     json (2.13.2)
     json_pure (2.8.1)
-    language_server-protocol (3.17.0.4)
+    language_server-protocol (3.17.0.5)
     launchy (3.1.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
       logger (~> 1.6)
-    libxml-ruby (5.0.3)
+    libxml-ruby (5.0.5)
     lint_roller (1.1.0)
     logger (1.7.0)
     macaddr (1.7.2)
@@ -111,7 +111,7 @@ GEM
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2025.0805)
+    mime-types-data (3.2025.0819)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -121,16 +121,16 @@ GEM
       powerbar
     mocha (2.7.1)
       ruby2_keywords (>= 0.0.5)
-    mock_redis (0.50.0)
+    mock_redis (0.51.0)
       redis (~> 5)
-    multi_json (1.15.0)
+    multi_json (1.17.0)
     net-ftp (0.3.8)
       net-protocol
       time
     net-http (0.6.0)
       uri
     net-http-persistent (2.9.4)
-    net-imap (0.4.21)
+    net-imap (0.4.22)
       date
       net-protocol
     net-pop (0.1.2)
@@ -140,14 +140,14 @@ GEM
     net-smtp (0.5.1)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.10)
+    oj (3.16.11)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
-    ostruct (0.6.1)
+    ostruct (0.6.3)
     parallel (1.27.0)
-    parser (3.3.8.0)
+    parser (3.3.9.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -169,9 +169,9 @@ GEM
       addressable (>= 2.2)
     redis (5.4.1)
       redis-client (>= 0.22.0)
-    redis-client (0.25.1)
+    redis-client (0.25.2)
       connection_pool
-    regexp_parser (2.10.0)
+    regexp_parser (2.11.2)
     request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
@@ -183,31 +183,31 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.75.4)
+    rubocop (1.79.2)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.9.3, < 3.0)
-      rubocop-ast (>= 1.44.0, < 2.0)
+      rubocop-ast (>= 1.46.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.44.1)
+    rubocop-ast (1.46.0)
       parser (>= 3.3.7.2)
       prism (~> 1.4)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
-    rubyzip (1.3.0)
+    rubyzip (3.0.1)
     simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
-    simplecov-cobertura (2.1.0)
+    simplecov-cobertura (3.0.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.13.1)
+    simplecov-html (0.13.2)
     simplecov_json_formatter (0.1.4)
     systemu (2.6.5)
     thin (1.8.2)
@@ -219,7 +219,7 @@ GEM
       date
     timeout (0.4.3)
     tzinfo (0.3.62)
-    unicode-display_width (3.1.4)
+    unicode-display_width (3.1.5)
       unicode-emoji (~> 4.0, >= 4.0.4)
     unicode-emoji (4.0.4)
     uri (1.0.3)
@@ -261,11 +261,10 @@ DEPENDENCIES
   rest-client
   rsolr
   rubocop
-  rubyzip (~> 1.0)
   simplecov
   simplecov-cobertura
   sparql-client!
-  thin
+  thin (~> 1.0)
 
 BUNDLED WITH
    2.6.3

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -391,7 +391,7 @@ def sanity_check
         end
 
         zip = zipped?
-        files =  LinkedData::Utils::FileHelpers.files_from_zip(self.uploadFilePath) if zip
+        files = LinkedData::Utils::FileHelpers.filenames_in_archive(uploadFilePath) if zip
 
         if not zip and self.masterFileName.nil?
           return true
@@ -423,7 +423,7 @@ def sanity_check
 
         elsif zip and not self.masterFileName.nil?
           #if zip and the user chose a file then we make sure the file is in the list.
-          files =  LinkedData::Utils::FileHelpers.files_from_zip(self.uploadFilePath)
+          files =  LinkedData::Utils::FileHelpers.filenames_in_archive(self.uploadFilePath)
           if not files.include? self.masterFileName
             if self.errors[:uploadFilePath].nil?
               self.errors[:uploadFilePath] = []