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Updating to OWLAPI 4.5.24#1005

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hkir-dev wants to merge 10 commits intoontodev:masterfrom
hkir-dev:owlapi-4.5.22
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Updating to OWLAPI 4.5.24#1005
hkir-dev wants to merge 10 commits intoontodev:masterfrom
hkir-dev:owlapi-4.5.22

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@hkir-dev hkir-dev commented May 24, 2022 •
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Resolves owlapi#1004

  • docs/ have been added/updated
  • tests have been added/updated
  • mvn verify says all tests pass
  • mvn site says all JavaDocs correct
  • CHANGELOG.md has been updated

Changes Summary:

  • Backward compatibility checking maven plugin (com.github.siom79.japicmp) ignoreMissingClassesByRegularExpressions parameter added in robot-core/pom.xml. Owlapi 4.5.22 uses a newer version of the rio-api: sesame-rio-api-2.7.16.jar -> rdf4j-rio-api-2.4.2.jar. Plugin is raising "Could not load 'org.openrdf.rio.RDFHandlerException'" exception, but that class renamed to org.eclipse.rdf4j.rio.RDFHandlerException now.
  • Owlapi Manchester syntax parsing logic changed to prevent illegal punning: owlapi#851. Property punning between properties is illegal, but punning of a property name and class name or individual name is allowed. QuotedEntityChecker.getOWLDataProperty, getOWLObjectProperty and getOWLClass was causing illegal punning exception when called without a reference ontology. Added if controls to prevent exception.
  • Axiom annotations using undeclared annotation properties are now getting parsed in 4.5.22 (inferring type from usage), updated the test files accordingly. Example case: oboInOwl:date_retrieved not declared in edit.owl
  • DLExpressivityChecker.Construct changed in the new owlapi, accordingly OntologyMetrics and MeasureOperationTest updated

@hkir-dev hkir-dev requested a review from matentzn May 24, 2022 15:52
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beckyjackson approved these changes May 25, 2022
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Everything looks OK to me and I ran some tests on my machine. I confirmed that it resolves the template issue in #609, which is cool!

@hkir-dev hkir-dev mentioned this pull request May 30, 2022
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@matentzn matentzn mentioned this pull request Jun 14, 2022
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@jamesaoverton jamesaoverton added this to the 1.10.0 milestone Jun 14, 2022
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balhoff commented Oct 13, 2022

Ready to merge?

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jamesaoverton commented Oct 13, 2022

I would like the latest ROBOT and Protege to use the same OWLAPI version. They are working on a new Protege release here: protegeproject/protege#1072. That seems to be going well, but I'd like to wait and see for a bit longer.

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hkir-dev commented Jan 17, 2023 •
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OWL API 4.5.24 has been released and Protege 5.6.0 will use this version.

INCATools/ontology-development-kit#770 (comment)

OWL API 4.5.24 has been released with the fix (the tag is not yet visible on GitHub, but the artifact is available on Maven Central).
I’ve rebuilt the 5.6.0-beta-2 release of Protégé with the new version.

Updated current PR accordingly.

@hkir-dev hkir-dev changed the title Updating to OWLAPI 4.5.22 Updating to OWLAPI 4.5.24 Jan 17, 2023
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jamesaoverton commented Feb 8, 2023

@hkir-dev I want to merge this, but I'm still uncomfortable with the large number of changes to the examples: I don't understand all the new <owl:Axiom>s.

Why am I so nervous? We've worked very, very hard to build trust with our users, and I don't want to jeopardize that. This OWLAPI update is going to cause significant churn in git diffs. We'll communicate that as clearly as possible to our users, but essentially we'll be asking people to just ignore the big diffs and trust that we haven't broken their stuff.

The examples are the core of our automated test suite. They're what convinces me that we aren't breaking things. So I need to fully understand all the changes.

  1. I understand the changes to the code -- they're small and look good
  2. I understand why xsd:string datatypes are disappearing from the examples, and that's good
  3. I don't understand where all the <owl:Axiom>s are coming from, or why they're necessary

Are you testing that OBO-format output is including axiom annotations properly? If so, could we just update a few of the tests, and not all of them?

If all these new <owl:Axioms> come from new behaviour in the OWLAPI, then there's something major that I don't understand.

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hkir-dev commented Feb 9, 2023 •
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Just to save our Slack discussion:
There is an OWLAPI behaviour change regarding this issue: owlcs/owlapi#875
OWLAPI was used to ignore axiom annotations if the annotation property is not declared. Now, with the new version, it automatically declares the property and persists the related axiom annotations.
It seems that some of our test files have such undeclared properties and with the new OWLAPI release these axioms are starting to reappear in the output files. We need to test in detail to ensure all those axioms are valid.

jamesaoverton added a commit that referenced this pull request Feb 9, 2023
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Update to OWLAPI 4.5.24, building on #1005
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jamesaoverton commented Feb 9, 2023

Thanks @hkir-dev for all your work on this. I updated the examples in #1085, and created a new PR #1086 to apply your changes more cleanly.

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Merge pull request #1086 from ontodev/owlapi-4.5.24
60d46f6 
Update to OWLAPI 4.5.24, building on #1005
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OWLAPI Writers add xsd:string randomly.

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