Infra: upgrade ncbo_annotator to Ruby 3.2 and Minitest 6

[mdorf]

Overview

This PR upgrades ncbo_annotator to Ruby 3.2 and Minitest 6, while aligning it with the updated OntoPortal dependency stack.

Unlike other repositories in this synchronization effort, ncbo_annotator has not significantly diverged from the AgroPortal implementation. The two codebases were previously synchronized in agroportal/ncbo_annotator#28, and only minimal changes have been introduced on the AgroPortal side since then.

As a result, this PR does not perform a full codebase alignment. Instead, it focuses on runtime modernization, dependency updates, and targeted compatibility fixes required to integrate with the synchronized OntoPortal stack.

The only notable AgroPortal-specific changes since the last synchronization are:

• Introduction of lemmatizer support (NOT included in this PR)
• A fix for compatibility with the RDF 3.x gem (included in this PR)

Prerequisites

This PR depends on the following updates:

• Sync: align ncbo/sparql-client with the AgroPortal codebase sparql-client#10
• Sync: align ncbo/goo with the AgroPortal codebase goo#176
• Sync: align ncbo/ontologies_linked_data with the AgroPortal codebase ontologies_linked_data#266

Notable Changes

• Ruby 3.2 upgrade

  • Updates runtime from Ruby 3.1.x to 3.2.x
  • Aligns Docker and local development environments

• Migration to Minitest 6

  • Replaces legacy MiniTest usage with Minitest::Test
  • Updates test setup (minitest/autorun, lifecycle hooks, reporters)
  • Adjusts Rake::TestTask configuration

• Alignment with updated OntoPortal dependency stack

  • Updates dependencies to use synchronized versions of:
    • goo
    • ontologies_linked_data
    • sparql-client

• RDF 3.x compatibility fixes

  • Incorporates updates required for compatibility with the RDF 3.x gem
  • Includes fixes adapted from AgroPortal

• Virtuoso graph handling fix

  • Prevents incorrect processing of graph URIs during hierarchy expansion
  • Ensures only ontology-related graphs are considered

• Configuration initialization fix

  • Ensures runtime overrides are applied after default configuration is loaded

• Test stability improvements

  • Fixes backend-specific inconsistencies (e.g., Virtuoso vs 4store)
  • Ensures deterministic ordering in results
  • Resolves edge-case test failures

• OntoPortal testkit integration

  • Adds .ontoportal-testkit.yml and CI workflow
  • Standardizes test execution across environments

• Dependency updates

  • Adds json-ld and jwt to support the updated stack

[codecov-commenter]

Codecov Report

❌ Patch coverage is 84.61538% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.21%. Comparing base (ff42df5) to head (9da3081).
⚠️ Report is 4 commits behind head on develop.

Files with missing lines	Patch %	Lines
lib/ncbo_annotator.rb	81.81%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #47      +/-   ##
===========================================
+ Coverage    79.17%   79.21%   +0.03%     
===========================================
  Files            9        9              
  Lines          658      659       +1     
===========================================
+ Hits           521      522       +1     
  Misses         137      137              

Flag	Coverage Δ
ag	79.21% <84.61%> (?)
fs	79.21% <84.61%> (?)
gd	79.21% <84.61%> (?)
unittests	79.21% <84.61%> (+0.03%)	⬆️
vo	79.21% <84.61%> (?)

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