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Preserve prefixes from loaded ontology.#1106

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jamesaoverton merged 5 commits intomasterfrom
issue-1101
May 11, 2023
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Preserve prefixes from loaded ontology.#1106
jamesaoverton merged 5 commits intomasterfrom
issue-1101

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@balhoff
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@balhoff balhoff commented Mar 28, 2023 •
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Resolves #1101.

  • 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

This change gets the document format used to load the ontology, and sets it as the prefix manager for the document format being used to save the ontology.

balhoff and others added 2 commits March 28, 2023 10:32
@balhoff
Preserve prefixes from loaded ontology.
4c15eae
@gouttegd
Add a test case for conservation of prefixes.
61a1c1f 
Add a test to ensure that prefixes initially present in an ontology are
preserved when the ontology is saved through IOHelper.
This was referenced Mar 28, 2023
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@matentzn
Merge pull request #1107 from gouttegd/issue-1101-test
b3f3e91 
Add a test case for conservation of prefixes.
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matentzn approved these changes Apr 6, 2023
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I tested this on 4 different ontologies and 12 different file variants. I am convinced it does what we need it to do.

Thank you @balhoff, @gouttegd!

This was referenced Apr 28, 2023
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jamesaoverton commented May 11, 2023

I'm getting some weirdness in the diffs. In some cases the xmlns and xml:base attributes of the root rdf:RDF element use the Ontology IRI of the previousOntology even though I'm setting a new Ontology IRI with robot annotate. So I get diffs like this:

diff views-old/NIAID-GSC-BRC.owl views/NIAID-GSC-BRC.owl
2,3c2,3
< <rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/NIAID-GSC-BRC.owl#"
<      xml:base="http://purl.obolibrary.org/obo/obi/NIAID-GSC-BRC.owl"
---
> <rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi.owl#"
>      xml:base="http://purl.obolibrary.org/obo/obi.owl"
diff views-old/obi.obo views/obi.obo
3c3
< date: 11:05:2023 11:17
---
> date: 11:05:2023 14:28
diff views-old/obi.owl views/obi.owl
2,3c2,3
< <rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi.owl#"
<      xml:base="http://purl.obolibrary.org/obo/obi.owl"
---
> <rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/obi_merged.owl#"
>      xml:base="http://purl.obolibrary.org/obo/obi/obi_merged.owl"

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balhoff commented May 11, 2023

I think we might want to tweak this a little to not replace the default namespace. See OBOFoundry/COB#234 (review)

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balhoff commented May 11, 2023

@jamesaoverton I've pushed a commit which should fix your issue.

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jamesaoverton commented May 11, 2023

It does. Thanks!

@jamesaoverton jamesaoverton merged commit 26a6999 into master May 11, 2023
@jamesaoverton jamesaoverton deleted the issue-1101 branch May 11, 2023 21:20
@balhoff balhoff mentioned this pull request May 24, 2023
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@allenbaron allenbaron mentioned this pull request Dec 1, 2023
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ROBOT convert is stripping prefixes

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@balhoff @jamesaoverton @matentzn @gouttegd