v7.1.0

What's Changed

• re-enable newrelic integration by @alexskr in #211
• Enforce slice-based access control on individual ontology endpoints by @alexskr in #209
• fix: /documentation NameError from sinatra-contrib 4.2.1 namespace bug by @alexskr in #213

Full Changelog: v7.0.0...v7.1.0

v7.0.0

Overview

v7.0.0 is a major alignment release that brings ncbo/ontologies_api in line with the OntoPortal/AgroPortal codebase while preserving NCBO-specific behavior. It ships significant new API surface area, runtime and framework upgrades, and modernized test infrastructure.

Highlights

Key changes in this release include:

• major alignment of ontologies_api with the AgroPortal codebase
• new ontology search and ontology content search endpoints
• expanded search helper functionality, including improved language handling and metadata-based search options
• restoration of NCBO-specific search behavior that depended on the static Solr schema
• resource dereferencing support with content negotiation
• OAuth support in the API layer
• Ruby 3.2 compatibility updates
• Sinatra 4 routing and request-handling fixes
• OntoPortal testkit integration and related CI/test modernization
• additional NCBO-specific fixes not present in AgroPortal

Details

Search

• New endpoints for ontology search and ontology-content search
• search_helper improvements: improved language handling, metadata-based ontology search, better query construction and filtering
• Restoration of NCBO-specific search behavior that depended on the static Solr schema
• Fixes for oboId and notation search
• Converted the acronyms filter from Boolean to Term syntax to avoid "too many boolean clauses" errors; replaced additional boolean queries with term queries for Solr robustness

New API capabilities

• Resource dereferencing controller with content negotiation
• User OAuth authentication support in the API layer
• Solr admin endpoints
• Filtering and pagination on the submissions endpoint
• Support for returning unmapped attributes on properties

Runtime and framework compatibility

• Ruby 3.2 compatibility (target: 3.2.9)
• Sinatra 4.2.1 compatibility — routing fixes for Sinatra's change from route-objects to arrays, and related request-handling adjustments
• Fix for the JSON 3.0 "duplicate key creator" warning
• Local dev server swapped from shotgun to bundle exec rackup -E development -p 9393
• Removed the minitest-fail-fast gem (minitest 6 ships --fail-fast natively)
• Removed legacy Cube integration
• NewRelic integration was temporarily removed in this release pending re-integration

Test infrastructure

• Integration with the OntoPortal testkit (#204)
• Test ontology files synchronized with AgroPortal
• Home-controller tests added to validate the / routes
• test_search_models_controller/test_search_data re-enabled after it stabilized
• test_submissions_includes refactored; test_mappings_slices added to test_slices_helper
• Safeguards to disable security for test after_all calls so a failing test cannot leave security disabled for subsequent runs

NCBO-specific fixes

• Fixed @context not showing in the home API service call
• Fixed ontology filename handling in create_ontology
• Additional NCBO-specific fixes not present in the AgroPortal implementation

What's Changed

• Infra/ontoportal testkit integration by @alexskr in #204
• Sync: align ncbo/ontologies_api with the AgroPortal codebase by @mdorf in #205
• Develop → Master merge, release v7.0.0 by @mdorf in #210

Full Changelog: v6.8.2...v7.0.0

v6.8.2

Full Changelog: v6.8.1...v6.8.2

v6.8.1

What's Changed

• CI: Refactor deployment workflow by @alexskr in #201
• Ontology logs permissions fix by @mdorf in e3e983d

Full Changelog: v6.8.0...v6.8.1

v6.8.0

What's Changed

• Feature: Ontology Admin Endpoints for Logs and Submission Management by @mdorf in #196
• Refactor/tests stability and minitest style by @alexskr in #198 and #199

Full Changelog: v6.7.0...v6.8.0

v6.7.0

• Feature :url data type validation for restricting URIs to the HTTP schema.
  Implemented in in ncbo/goo#169 and ncbo/ontologies_linked_data#258) by @alexskr

v6.6.1

ontologies_linked_data

• Refactor archive extraction: require RubyZip v3+, add Zip Slip protections, sanitize .gz orig_name, and switch file extraction to streaming for memory savings by @alexskr

Full Changelog: ncbo/ontologies_linked_data@v6.6.0...v6.6.1

ontologies_api

Full Changelog: v6.6.0...v6.6.1

v6.6.0

What's Changed

• Feature: Enforce system-controlled attributes by @alexskr in #179

Full Changelog: v6.5.0...v6.6.0

v6.5.0

What's Changed

This update integrates enhanced SKOS (Simple Knowledge Organization System) support, originally developed by the AgroPortal team, into BioPortal codebase

• Feature: enhanced skos support in #192
  • Add collection, schemes and skos labels endpoints and tests
  • Update the instance controller to use the Instance model
  • Update classes to endpoint to order or filter by an attribute, scheme or collection
• fix: ensure notes creator is set to current user by @alexskr in #190

Full Changelog: v6.4.1...v6.5.0

v6.4.1

What's Changed

• Fix/notes controller creator assignment by @alexskr in #191

Full Changelog: v6.4.0...v6.4.1