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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Fixed

  • Improve disambiguation of properties in QuotedEntityChecker #1226
  • Skip "non-robot" columns in templates for the purposes of axiom annotations #1216
  • Add missing filter for deprecated in lowercase_definition check #1220
  • Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations #1223

1.9.7 - 2024-10-30

Fixed

  • Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. #1121

Changed

  • Update Whelk to 1.2.1 #1221
  • Treat raw IRI as an OWLClass in logical template cells #1211

1.9.6 - 2024-05-28

Added

  • Added option to input template strings from external file #1152

Changed

  • Updated duplicate_exact_syonym report query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types #1179
  • Extend --drop-axiom-annotations option to support value-specific removal of axiom annotations #1193
  • Add --enforce-obo-format, --exclude-named-classes and --include-subclass-of features to relax command #1060, #1183
  • Updated obographs to version 0.3.1
  • Updated OWL API to 3.5.29. This includes a major update to OBO Format which now supports IDSPACE declarations (non-OBO Foundry prefixes).
  • Updated Elk to version 0.6.0, see here.

Fixed

  • '--annotate-with-source true' does not work with extract --method subset #1160
  • Fix how Template adds entities to the QuotedEntityChecker #1104
  • merge and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies #1171
  • Handle IRIs that are not entities in export #1168
  • Fix integration tests #1181
  • robot repair is fixed to be more flexible, to enable partial repairs #1194
  • Invalid Xrefs test has been fixed to recognise invalid CURIEs correctly #1127
  • Fix issue with correctly determining base entities #1108

1.9.5 - 2023-09-20

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
  • Add --drop-axiom-annotations option to drop axiom annotations in remove and filter #1023

Changed

1.9.4 - 2023-05-23

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

1.9.3 - 2023-02-16

Added

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

1.9.2 - 2023-02-09

Changed

  • Upgrade OWLAPI to 4.5.24 #1086

Fixed

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

1.9.1 - 2022-10-28

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

1.9.0 - 2022-06-16

Added

Fixed

  • Fix OBOGraphs by updating guava #1009

1.8.4 - 2022-06-10

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

1.8.3 - 2021-12-16

Changed

Fixed

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

1.8.2 - 2021-12-02

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

1.8.1 - 2021-01-27

Fixed

1.8.0 - 2021-01-27

Added

  • Add measure command #774
  • Added 'strict' mode for loading ontologies in #788
  • Add --allow-missing-entities option in rename command #793
  • Add html-list format option to export in #703

Changed

  • Explanations for inconsistent and unsatisfiable classes in explain #779

Fixed

  • Allow case-insensitive "SubClasses" in export header #802

1.7.2 - 2020-11-18

Changed

  • Update to whelk 1.0.4
  • Run query on existing TDB dataset (instead of ontology input) in #792
  • Improved error messages for template parse errors in #796

Fixed

1.7.1 - 2020-10-22

Added

Fixed

1.7.0 - 2020-07-31

Added

Changed

  • Updated obographs from 0.0.8 to 0.2.1 #657

Fixed

  • Fix filtering axioms with multiple axiom selectors #644
  • Fix comparator method for sorting empty strings with export in #654
  • Fix releasing dataset after exception when running report with --tdb true #659
  • Reduced time spent loading datasets for query in #666
  • Fix writing JSON format to use OutputStream with convert in #671
  • Fix IRI resolution for template in #689
  • Fix MIREOT extract on overlapping class/individual entity for #709 in #710
  • Fix issue with --add-prefixes option in #715

1.6.0 - 2020-03-04

Added

  • Add collapse command #578
  • Add support for anonymous class assertions in template in #630
  • Add maven plugin to update OBO context #608
  • Add more efficient mode for reduce when only considering named classes #619

Changed

  • Switch whitespace queries to regex #606
  • Update nucleus import for tests #597

Fixed

  • Fix warning when term is in imports (extract command) #625
  • Fix index out of bounds error in extract #617
  • Use URIs to fix resource path issues #603

1.5.0 - 2019-11-28

Added

1.4.3 - 2019-09-12

Fixed

1.4.2 - 2019-09-11

Added

Changed

  • Follow redirects for gzipped input IRIs #537

Fixed

1.4.1 - 2019-06-27

Added

Changed

Fixed

  • Fix invalid reference errors for OWL built-ins #455
  • Fix import handling for SPARQL UPDATE #471
  • Fix remove/filter for terms not in ontology #507

1.4.0 - 2019-03-14

Added

Changed

  • Made improvements to the built-in reports #438

1.3.0 - 2019-01-18

Added

1.2.0 - 2018-12-06

Added

  • Add remove command for removing axioms from an ontology
  • Add filter command for copying selected axioms to a new ontology
  • Add --use-graphs true option for query allows queries over imports as named graphs #158
  • Add --labels option to diff command #363
  • Add support for gzipped files #371

Changed

  • Breaking Change: We have upgraded from Apache Jena 2.13.0 to 3.8.0 #314, which involves the renaming of several packages and changes to the return types of QueryOperation. One other change we've noted is that the new Jena adds fewer xsd:string datatypes than the previous version.
  • Upgrade to OWLAPI 4.5.6 sometimes changes the ordering of elements in RDFXML format, causing spurious differences in line order when comparing output from previous versions of ROBOT. But note that Protege5.5 uses the same version of the OWLAPI so orderings should be consistent between the two.

1.1.0 - 2018-08-04

Added

  • Add report command
  • Add --collapse-import-closure option for merge: When true (the default) all imports will be merged and all owl:import statements will be removed. Possible breaking change: In previous versions of ROBOT, owl:import statements were not removed. #275
  • Add global --catalog FILE option #274
  • Add --check option for convert allows conversion of more OBO-format files
  • Add --include-annotations option for merge allows better control of ontology annotations #277
  • Add --copy-ontology-annotations option for extract in #319
  • Add --dump-unsatisfiable option for reason #174

Fixed

  • improved error messages, linking to ROBOT website #246

1.0.0 - 2018-02-08

First official release of ROBOT!