5.22.2

Enhancements

• Added a contributor's guide and code of conduct.
• Bundled a new version of the owlapi_wrapper:
  • Upgraded to version 4.5.18 of the OWL API
  • Fixed an issue that caused NoClassDefFoundError exceptions during parsing of some ontologies (ncbo/owlapi_wrapper#16)
• Fixed an issue that prevented the ability to run unit tests via Rake (f217cf6).

Full Changelog: v5.22.1...v5.22.2

5.22.1

• Fixed a bug that caused mapping submission IDs queries to fail in AllegroGraph (ncbo/ontologies_linked_data#120)
• Fixed a bug that prevented UMLS ontologies from processing in AllegroGraph (ncbo/bioportal-project#215)
• Fixed a security vulnerability

Full Changelog: v5.22.0...v5.22.1

5.21.0

Enhancements

• Further optimizations to the mapping counts generation job, including periodic 4store health checks (ncbo/ncbo_cron#40)
• Added incremental progress logging to the Annotator dictionary generation job (ncbo/ncbo_annotator#16)

Bug Fixes

• Repaired the 4store health status check API (ncbo/goo#112)

Full Changelog: v5.20.0...v5.21.0

5.20.0

Enhancements

• New CRON job that allows on-demand regeneration of total mapping counts and mapping count pairs (ncbo/ncbo_cron#37)
• Modified the nightly ontology pull process to clear application caches after completion of a full run (ncbo/ncbo_cron#38)

Bug Fixes

• Mapping counts generation script failed to properly count mappings between ontoloigies (ncbo/ontologies_linked_data#88)
• Reported mapping counts between ontologies were always higher than actual counts (ncbo/ontologies_linked_data#115)
• Incorrect mapping count statistics generated for some ontologies (ncbo/ontologies_linked_data#94)
• Empty pages in paged result sets (ncbo/ontologies_linked_data#66)

Full Changelog: v5.19.0...v5.20.0

5.19.0

Enhancements

• New CRON job that synchronizes the search index with master data stored in the triplestore (ncbo/ncbo_cron#34)
• Updated the test runner script to use a dockerized instance of Redis for unit test execution

Bug Fixes

• Fixed an issue where the test runner script always reported success, despite test failures (ncbo/ontologies_linked_data#111)
• Fixed a bug that prevented a refresh of the ontologies report from completing successfully (ncbo/ncbo_cron#35)

Full Changelog: v5.18.1...v5.19.0

5.18.0

Enhancements

• Bundled a new version of the owlapi_wrapper. Highlights include:
  • Upgraded the OWL API to version 4.5.17.
  • Expanded the allowed list of ontology file suffixes to include .n3, .nt, .nq, .skos, .rdf, and .rdfs.
• Implemented several scripts to allow an on-demand regeneration of the ontology admin report (ncbo/ncbo_cron#32), ontology analytics data (ncbo/ncbo_cron#19), and ontology ranking data (ncbo/ncbo_cron#31).

Bug Fixes

• Fixed a Redis deprecation warning (ncbo/sparql-client#3, ncbo/ncbo_annotator#12)

Full Changelog: v5.17.0...v5.18.0

5.17.0

Enhancements

• Implemented the ability to retrieve sorted ontology classes via the search endpoint (ncbo/bioportal-project#165), e.g.: http://data.bioontology.org/search?ontologies=NCIT&sort=prefLabel.
• Implemented the ability to retrieve sorted descendant classes via the subtree search endpoint (ncbo/bioportal-project#165), e.g.: http://data.bioontology.org/search?subtree_ontology=NCIT&subtree_root_id=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16275&sort=prefLabel
• Implemented a test runner script that uses dockerized versions of 4store and AllegroGraph for running test suites. Facilitates the ability to switch seamlessly between triplestores and triplestore versions when executing unit tests (ncbo/ontologies_linked_data#105). For usage instructions, type bundle exec ruby test/run_tests.rb --help.

Bug Fixes

• Fixed an issue that prevented paged calls from completing properly when running against AllegroGraph v7+ (ncbo/goo#106).
• Fixed an issue with a failing ontology properties test when running against AllegroGraph v7+ (ncbo/ontologies_linked_data#106).
• Fixed an issue that caused Zlib::GzipWriter runtime errors during ontology processing (ncbo/ontologies_linked_data#107).
• Removed a workaround to address a bug in AllegroGraph v6+ that caused certain SPARQL queries to fail (ncbo/goo#104). Issue was addressed in the AllegroGraph v7.0.1 release.
• Fixed an issue that caused runtime errors when running against Ruby 2.7.0 and 2.7.1 (#69).
• Fixed an issue where a search on term ID with exact match returned irrelevant results (#57).
• Fixed an issue where a call to the class descendants endpoint failed if properties were included (#54).

Full Changelog: v5.16.0...v5.17.0

5.16.0

Enhancements

• Full integration with the AllegroGraph semantic graph database; 4store backwards compatibility intact (ncbo/bioportal-project#122, ncbo/goo#100)

Bug Fixes

• Fixed an issue where AllegroGraph request chains break with existing Goo code (ncbo/goo#101)
• Fixed an issue where no parsed ontology records appeared in AllegroGraph after an ontology has been parsed (ncbo/goo#102)
• Fixed an issue with paging calls returning incorrect results in AllegroGraph (ncbo/goo#103)

Full Changelog: v5.14.0...v5.16.0

5.14.0

• Implemented performance enhancements for the class descendants call (metadatacenter/cedar-project#980).
• Included a new version of owlapi-wrapper (OWL API v4.5.13).
• Updated Solr to version 8.2.0.
• Modified password reset URLs to use secure protocol (ncbo/ontologies_linked_data#98).

Full Changelog: v5.13.0...v5.14.0

5.13.0

Bundled version 1.3.4 of the owlapi_wrapper that produces more descriptive error output to assist in troubleshooting / fixing ontology parsing issues, e.g.: ncbo/bioportal-project#111.