From 54ddd1eba531efc662e16bc613b3de778d6f2ed5 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 28 Feb 2024 22:05:30 +0100
Subject: [PATCH] fix annotator after updating RDF version to 3.0

---
 .github/workflows/ruby-unit-tests.yml | 2 ++
 Gemfile.lock                          | 3 ++-
 lib/ncbo_annotator.rb                 | 6 ++++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
index 2e5c21cb..5829a11a 100644
--- a/.github/workflows/ruby-unit-tests.yml
+++ b/.github/workflows/ruby-unit-tests.yml
@@ -15,6 +15,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+      - name: create config.rb file
+        run: cp config/config.test.rb config/config.rb
       - name: Set up solr configsets
         run: ./test/solr/generate_ncbo_configsets.sh
       - name: Install Dependencies
diff --git a/Gemfile.lock b/Gemfile.lock
index bed91370..601f57a8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: cd5bc312bd3acd2ff056a87a6f37b5419f3444dc
+  revision: cb03c4888cc95006e653eb70dd29ee69901dd6cd
   branch: development
   specs:
     goo (0.0.2)
@@ -196,6 +196,7 @@ GEM
 
 PLATFORMS
   x86_64-darwin-23
+  x86_64-linux
 
 DEPENDENCIES
   addressable (~> 2.8.0)
diff --git a/lib/ncbo_annotator.rb b/lib/ncbo_annotator.rb
index 64a84105..d7b4fa79 100644
--- a/lib/ncbo_annotator.rb
+++ b/lib/ncbo_annotator.rb
@@ -733,11 +733,13 @@ def redis_last_mgrep_restart_default_timestamp()
       def create_term_entry(redis, instance_prefix, ontResourceId, resourceId, label_type, val, semanticTypes)
         begin
           # NCBO-696 - Remove case-sensitive variations on terms in annotator dictionary
-          val.upcase!()
+          val = val.dup.upcase
         rescue ArgumentError => e
+          binding.pry
+          val = val.dup
           # NCBO-832 - SCTSPA Annotator Cache building error (UTF-8)
           val = val.encode('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '')
-          val.upcase!()
+          val = val.upcase
         end
 
         # exclude single-character or empty/null values