CHANGELOG.md

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

1.7.2 - 2020-11-18

Changed

• Update to whelk 1.0.4

Fixed

• Fix blank node subjects in report in #767
• Fixed IRI handling for template in #783

1.7.1 - 2020-10-22

Added

• Add Whelk OWL reasoner in [#730]
• Add validate command #691
• Add --errors <path> option to template in #713
• Add new formats to report: HTML, JSON, and XLSX #699
• Add --fail-on-violation <bool> option to [verify] in #738

Fixed

• Handle empty template property charactersitics in #719
• Fix referencing properties by CURIE in export in #722
• Fix validate --write-all true in #726
• Fix reported row number in validate error tables in #727
• Fix equivalent class rendering for template in #728
• Fix ontology IRI rendering for report in #739

1.7.0 - 2020-07-31

Added

• Add export command #481
• Add JSON format to export in #645
• Add Excel format to export in #646
• Add --create-tdb <true/false> option to query in #685

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

• Add new python command, allowing ROBOT to be controlled from Python using Py4j.
• Add internal/external selectors for remove/filter in #570
• Add language selectors for remove/filter in #574
• Add tautologies and structural-tautologies selectors for remove/filter in #579
• Add catalog options for right-side of diff in #584

1.4.3 - 2019-09-12

Fixed

• Fix excessive logging, #567 and #374

1.4.2 - 2019-09-11

Added

• Update repair to migrate annotations #510
• Allow use of Jena TDB for report in #558
• Add --exclude-tautologies option for reason in #560

Changed

• Follow redirects for gzipped input IRIs #537

Fixed

• Fix bug with imported axioms #523
• Fix index out of bounds for report --print in #546
• Fix stack overflow in remove/filter in #547
• Fix query when chaining with --input-iri #555
• Fix template bug with equivalent classes #559
• Fix template bug with nested annotation #564

1.4.1 - 2019-06-27

Added

• Add --tdb true option to query for Jena TDB on-disk storage #475
• Add IRI pattern matching to remove/filter in #448
• Add --signature option to remove/filter, improve docs #484
• Add more output options to diff in #461
• Allow specified prefixes for output #488

Changed

• Made major update to template command #403

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

• Add rename command #419, allowing you to replace lists of old IRIs with new IRIs
• Add SPARQL Update support #352, but note the warning in the 'Update' section of the documentation at http://robot.obolibrary.org/query
• Add --annotate-with-source option for extract in #392
• Add --intermediates option for extract #441
• Add --individuals option for extract #385
• Add new selectors for remove and filter: domain and range #427, ontology #452

Changed

• Made improvements to the built-in reports #438

1.3.0 - 2019-01-18

Added

• Add explain command, contributed by Jim Balhoff

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!