v1.9.5

Added

• Updated ELK from 0.4.3 to 0.5.0. #999. This is an important change as ELK 0.5.0 is more complete than 0.4.3, which means that it will potentially uncover inferences, in particular unsatisfiable classes, which were not recognised by ELK 0.4.3.
• Add support for pluggable commands #1119

Changed

• Migrate to OWL API 4.5.26 to deal with broken turtle serialiser(#1129). #1135
• Improvements to export and report for XLSX format #1148

v1.9.4

Changed

• Speed up unsatisfiable object-property check on certain reasoners including HermiT #1100
• Update HermiT from 1.3.8.413 to 1.4.5.456 #1073

Fixed

• Preserve prefixes across ontology load and save #1101

v1.9.3

Added

• Subset method added to extract #1000

Changed

• Upgrade OWLAPI to 4.5.25 #1093

Fixed

• Restore logging details for CLI #1091
• Fix OBO Serialiser bug where built in vocabulary was introduced as annotation properties #1089
• Fix OBO Serialiser erroneous logging #1088

v1.9.2

Changed

• Upgrade OWLAPI to 4.5.24 #1086

Fixed

• Downgrade SnakeYaml to 1.31 #1071
• Don't check for disjoint annotation properties #1084

This ROBOT release synchronizes with Protégé 5.6.0 which has updated to OWL API 4.5.24. This version of OWL API includes several changes to some serializers (notably the OBO-format serializer), which will likely result in large diffs when ontology files are saved with this version of ROBOT or Protégé for the first time. To minimize the annoyance caused by such diffs, it is advised to:

• save your ontology with ROBOT 1.9.2 or Protégé 5.6.0 without introducing any changes to the logic or annotations, and commit the resulting ontology files; consider saving to OFN syntax and then OWL (RDF/XML) format, as explained in #1090
• once the ontology files have been saved once with ROBOT 1.9.2 or Protégé 5.6.0, avoid editing it again with older versions of ROBOT or Protégé.

v1.9.1 with ELK 0.5.0

This version of ROBOT includes a snapshot of ELK 0.5.0, based on #999. ELK 0.5.0 is more strict than ELK 0.4.3 that was previously included with ROBOT, and so ROBOT may report more logical problems such as unsatisfiable classes when using the new ELK. This pre-release is for testing with ELK 0.5.0 in ROBOT workflows.

v1.9.1

Added

• extract and merge should optionally inject provenance #977
• Checking for empty strings in addition to missing ones in missing_label.rq #1017
• Add "domain" and "range" support to export #1061

Fixed

• Fixed report serialization in JSON #1016
• Fix missing labels in diff output. #1026
• input IRI now takes catalog file into account #1030

v1.9.0

Added

• Add new command: expand #964

Fixed

• Fix OBOGraphs by updating guava #1009

v1.8.4

This ROBOT release drops support for Java 8. The minimum required version is now Java 11. If you see an error similar to the following, then you are probably still running Java 8:

/Users/james/Repositories/github/ontodev/robot/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java:[32,42] cannot access org.geneontology.obographs.core.io.OgJsonGenerator   
  bad class file: /Users/james/.m2/repository/org/geneontology/obographs/obographs-core/0.3.0/obographs-core-0.3.0.jar(org/geneontology/obographs/core/io/OgJsonGenerator.class)              
    class file has wrong version 55.0, should be 52.0                                                                                                                                         
    Please remove or make sure it appears in the correct subdirectory of the classpath.

Added

• Add --mapping option and support for label updates to rename #960

Changed

• Optimize memory usage for update queries using --temporary-file switch #978
• Allow any case builtin TYPE in template #971
• Sort report violations by rule name within level #955

Fixed

• Fix subClassOf cycles in related object selection #979
• Fix equivalent axioms in template #973

v1.8.3

Note that this is the last ROBOT release that supports Java 8. In future releases of ROBOT the minimum required version is Java 11.

Changed

• Replace log4j with logback #948 #953

Fixed

• Fix custom report queries #944
• Fix methods in Report object for ROBOT as a library #951

v1.8.2

Added

• Add links to query documentation for default rules in report #879
• Ability to restrict report to base ontology #872
• Add check for equivalent class with no genus to report #865
• Add check for illegal use of built-in vocabulary #867
• Add check for misused replaced-by annotation #869
• Add checks for undeclared synonymtype and subsettype #870
• Inferred axiom generators for domains and ranges #931

Changed

• Split equivalent class check #856
• Allow Dublin Core "terms" namespace (http://purl.org/dc/terms/) for description and title properties on ontology. #741
• Allow numbers in lowercase_definition check #866
• Blank nodes in report are now referred to as blank node rather than a random identifier #873
• Change behaviour of template --errors option without --force #929
• Fail hard on bad reason --equivalent-classes-allowed argument #938

Fixed

• Fix printing violations in report #823
• Fix handling of rdf:type in export #834
• Fix missing annotations from export #850
• Fail on unknown rule names in report #858
• Fix behaviour of --preserve-structure when using internal or external axiom selectors for remove or filter #816
• Fix duplicate_label_synonym #864
• Fix value rendering for entities in report #874
• Fix OBO serialisation issues when using --check false #896
• Fix merge --inputs patterns with parent directories #899
• Fix deprecated_class_reference report query #902
• Fix error handling for JSON conversion #907
• Fix handling of property chains when removing/filtering base axioms in #914
• Fix SPLIT unpacking in named individuals in template #924

Changed

• Do not allow malformed IRIs to be returned by IOHelper #882