1.1.28

This release backports refactors for the R linear model so that we can truly make org.rosuda.REngine optional.

1.1.27

Use local installation of rJava and Rserve.

• make org.rosuda.REngine dependencies native
• update dependencies

1.1.26

Add fully R-compatible implementations of make.names and make.unique.

Update Mockito to 5.17.0.

1.1.22

This should probably be a new minor release, but the 1.2.0 series is development is already underway, but not yet quite ready for prime time.

In brief:

• rewritten the ontology indexing from scratch using Lucene directly
• add support for stemming exclusions
• better isolate implementation of Jena-based ontology services
• update Jena to 2.13.0
• dropped jena-larq and jena-arq dependencies
• include subproperties when looking for restrictions to use for inferring parents/children
• simplify baseCode configuration
• update dependencies

1.1.16

• add support for ontology imports
• fix a bug with getChildren() and getParents() returning all terms from additional properties when direct is true
• include scores in search results
• include resources for MEDIC and NIF ontologies
• introduce JSR-305 annotations to mark the ontology API's nullability
• use temporary directory for caching ontologies if ontology.cache.dir is unset
• include OBO alternative labels in search index

Note: These release notes also include changes from 1.1.15.

1.1.13

• introduce OntologyService.getParents and OntologyService.getChildren as super-optimized strategy for gathering the parent and child terms of a set of ontology terms
• consistently exclude owl:Thing and owl:Nothing when listing parents and children terms
• cache all restrictions involving additional properties to make listing of parents and children efficient
• exclude deprecated terms when searching and listing parents/children by default and add an option to keep them
• move Jena-specific code under ubic.basecode.ontology.jena
• standardize how ontology resources are displayed and compared
• use owl:deprecated, OBO's ObsoleteClass and ObsoleteProperty to mark properties as obsolete

1.1.12

• fix a NPE when converting a term with a null URI
• remove cobertura to make our build compatible with Java 11 and forward

1.1.11

• drastically reduce memory usage of OntologyService by using OntModel's capabilities for retrieving resources by URIs instead of caching them
• add a new OntologyService interface to ease extension
• add proper support for part of and fix inference for proper part of
• use OWL_MEM_TRANS_INF consistently and remove parameters on OntologyLoader to configure the ontology spec
• suppress JenaException raised if the initialization thread is interrupted
• exclude transitive icu4j dependency from Jena which is old and breaks H2 database

1.1.5

This is a small patch release that add support for list in configuration values using , as a delimiter.

1.1.3

This release introduces checked exception for the ontology search and handling of missing values in ebayes implementation.