Merge pull request #4 from ElixirTeSS/master

Merge main developments into oai-pmh branch

Author: eilmiv

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -67,4 +67,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

Gemfile

@@ -2,7 +2,7 @@
 
 source 'https://rubygems.org'
 
-gem 'rails', '7.2.2.1'
+gem 'rails', '7.2.2.2'
 
 gem 'active_model_serializers'
 gem 'activerecord-session_store'

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ElixirTeSS/TeSS_RDF_Extractors
-  revision: c89fcad2a46ead316af14b270d26c6ba924646b6
+  revision: f9eee4621738c8fcaa9e0729e76a307fcd55650f
   branch: master
   specs:
     tess_rdf_extractors (1.1.0)
@@ -23,29 +23,29 @@ GEM
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actioncable (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
       zeitwerk (~> 2.6)
-    actionmailbox (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionmailbox (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       mail (>= 2.8.0)
-    actionmailer (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      actionview (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionmailer (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      actionview (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       mail (>= 2.8.0)
       rails-dom-testing (~> 2.2)
-    actionpack (7.2.2.1)
-      actionview (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionpack (7.2.2.2)
+      actionview (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       nokogiri (>= 1.8.5)
       racc
       rack (>= 2.2.4, < 3.2)
@@ -54,15 +54,15 @@ GEM
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
       useragent (~> 0.16)
-    actiontext (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actiontext (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionview (7.2.2.2)
+      activesupport (= 7.2.2.2)
       builder (~> 3.1)
       erubi (~> 1.11)
       rails-dom-testing (~> 2.2)
@@ -72,32 +72,32 @@ GEM
       activemodel (>= 4.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
-    activejob (7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activejob (7.2.2.2)
+      activesupport (= 7.2.2.2)
       globalid (>= 0.3.6)
-    activemodel (7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activemodel (7.2.2.2)
+      activesupport (= 7.2.2.2)
     activemodel-serializers-xml (1.0.3)
       activemodel (>= 5.0.0.a)
       activesupport (>= 5.0.0.a)
       builder (~> 3.1)
-    activerecord (7.2.2.1)
-      activemodel (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activerecord (7.2.2.2)
+      activemodel (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       timeout (>= 0.4.0)
     activerecord-session_store (2.0.0)
       actionpack (>= 5.2.4.1)
       activerecord (>= 5.2.4.1)
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 2.0.8, < 3)
       railties (>= 5.2.4.1)
-    activestorage (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activestorage (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       marcel (~> 1.0)
-    activesupport (7.2.2.1)
+    activesupport (7.2.2.2)
       base64
       benchmark (>= 0.3)
       bigdecimal
@@ -131,7 +131,7 @@ GEM
       erubi (>= 1.0.0)
       rack (>= 0.9.0)
       rouge (>= 1.0.0)
-    bigdecimal (3.2.2)
+    bigdecimal (3.2.3)
     bindata (2.5.0)
     bindex (0.8.1)
     binding_of_caller (1.0.0)
@@ -159,7 +159,7 @@ GEM
       openapi_parser (~> 1.0)
       rack (>= 1.5)
     concurrent-ruby (1.3.5)
-    connection_pool (2.5.3)
+    connection_pool (2.5.4)
     countries (5.6.0)
       unaccent (~> 0.3)
     country_select (8.0.2)
@@ -243,7 +243,7 @@ GEM
     icalendar (2.9.0)
       ice_cube (~> 0.16)
     ice_cube (0.16.4)
-    io-console (0.8.0)
+    io-console (0.8.1)
     irb (1.15.2)
       pp (>= 0.6.0)
       rdoc (>= 4.0.0)
@@ -279,7 +279,7 @@ GEM
       rack (>= 2.2, < 4)
       rdf (~> 3.3)
       rexml (~> 3.2)
-    json-ld-preloaded (3.3.1)
+    json-ld-preloaded (3.3.2)
       json-ld (~> 3.3)
       rdf (~> 3.3)
     json_schema (0.21.0)
@@ -351,7 +351,7 @@ GEM
       net-pop
       net-smtp
     marcel (1.0.4)
-    matrix (0.4.2)
+    matrix (0.4.3)
     maxmind-db (1.2.0)
     method_source (1.1.0)
     mime-types (3.5.1)
@@ -375,14 +375,14 @@ GEM
       money (~> 6.13)
       railties (>= 3.0)
     msgpack (1.7.2)
-    multi_json (1.15.0)
+    multi_json (1.17.0)
     multi_xml (0.6.0)
     multipart-post (2.4.1)
     nested_form (0.3.2)
     net-http (0.6.0)
       uri
-    net-http-persistent (4.0.5)
-      connection_pool (~> 2.2)
+    net-http-persistent (4.0.6)
+      connection_pool (~> 2.2, >= 2.2.4)
     net-imap (0.5.8)
       date
       net-protocol
@@ -428,6 +428,7 @@ GEM
       validate_url
       webfinger (~> 2.0)
     orm_adapter (0.5.0)
+    ostruct (0.6.3)
     parallel (1.23.0)
     parser (3.2.2.3)
       ast (~> 2.4.1)
@@ -452,7 +453,7 @@ GEM
       activerecord (>= 6.1)
       i18n (>= 0.5.0)
       railties (>= 6.1.0)
-    public_suffix (6.0.1)
+    public_suffix (6.0.2)
     puma (6.5.0)
       nio4r (~> 2.0)
     pundit (2.3.1)
@@ -477,20 +478,20 @@ GEM
     rackup (1.0.1)
       rack (< 3)
       webrick
-    rails (7.2.2.1)
-      actioncable (= 7.2.2.1)
-      actionmailbox (= 7.2.2.1)
-      actionmailer (= 7.2.2.1)
-      actionpack (= 7.2.2.1)
-      actiontext (= 7.2.2.1)
-      actionview (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activemodel (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    rails (7.2.2.2)
+      actioncable (= 7.2.2.2)
+      actionmailbox (= 7.2.2.2)
+      actionmailer (= 7.2.2.2)
+      actionpack (= 7.2.2.2)
+      actiontext (= 7.2.2.2)
+      actionview (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activemodel (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       bundler (>= 1.15.0)
-      railties (= 7.2.2.1)
+      railties (= 7.2.2.2)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -512,9 +513,9 @@ GEM
       nested_form (~> 0.3)
       rails (>= 6.0, < 9)
       turbo-rails (>= 1.0, < 3)
-    railties (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    railties (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       irb (~> 1.13)
       rackup (>= 1.0.0)
       rake (>= 12.2)
@@ -525,10 +526,13 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rdf (3.3.2)
+    rdf (3.3.4)
       bcp47_spec (~> 0.2)
       bigdecimal (~> 3.1, >= 3.1.5)
       link_header (~> 0.0, >= 0.0.8)
+      logger (~> 1.5)
+      ostruct (~> 0.6)
+      readline (~> 0.0)
     rdf-aggregate-repo (3.3.0)
       rdf (~> 3.3)
     rdf-hamster-repo (3.3.0)
@@ -585,22 +589,24 @@ GEM
     rdf-turtle (3.3.0)
       ebnf (~> 2.4)
       rdf (~> 3.3)
-    rdf-vocab (3.3.2)
+    rdf-vocab (3.3.3)
       rdf (~> 3.3)
     rdf-xsd (3.3.0)
       rdf (~> 3.3)
       rexml (~> 3.2)
     rdoc (6.14.0)
       erb
       psych (>= 4.0.0)
+    readline (0.0.4)
+      reline
     recaptcha (5.15.0)
     redcarpet (3.6.0)
     redis (5.0.7)
       redis-client (>= 0.9.0)
     redis-client (0.16.0)
       connection_pool
     regexp_parser (2.8.1)
-    reline (0.6.1)
+    reline (0.6.2)
       io-console (~> 0.5)
     responders (3.1.1)
       actionpack (>= 5.2)
@@ -612,7 +618,7 @@ GEM
       netrc (~> 0.8)
     reverse_markdown (2.1.1)
       nokogiri
-    rexml (3.4.0)
+    rexml (3.4.2)
     rouge (4.1.3)
     rsolr (2.6.0)
       builder (>= 2.1.2)
@@ -746,13 +752,13 @@ GEM
     sxp (1.3.0)
       matrix (~> 0.4)
       rdf (~> 3.3)
-    temple (0.10.3)
+    temple (0.10.4)
     terrapin (0.6.0)
       climate_control (>= 0.0.3, < 1.0)
     terser (1.1.17)
       execjs (>= 0.3.0, < 3)
     thor (1.4.0)
-    tilt (2.6.0)
+    tilt (2.6.1)
     timeout (0.4.3)
     turbo-rails (2.0.11)
       actionpack (>= 6.0.0)
@@ -863,7 +869,7 @@ DEPENDENCIES
   puma
   pundit
   rack-cors
-  rails (= 7.2.2.1)
+  rails (= 7.2.2.2)
   rails-assets-clipboard (~> 1.5.12)!
   rails-assets-devbridge-autocomplete (~> 1.4.9)!
   rails-assets-eonasdan-bootstrap-datetimepicker (~> 4.17.42)!

app/controllers/workflows_controller.rb

@@ -24,7 +24,6 @@ def index
   # GET /workflows/1.json
   def show
     authorize @workflow
-    @skip_flash_messages_in_header = true # we will handle flash messages in the 'workflows' layout
     respond_to do |format|
       format.html { render layout: 'workflows' }
       format.json