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Make the SSSOM/T ruleset future-proof. #3440

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Nov 29, 2024
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There is one particular bit of syntax that is currently used in the SSSOM/T ruleset that I would like to disallow in the upcoming version of SSSOM/Java. Specifically, the dereferencing of a variable enclosed in angled brackets, as in:

  "... and (<%TAXREL> some NCBITaxon:????)"

It should either be %TAXREL (no angled brackets, preferred form as it is more readable) or <%{TAXREL}> (angled brackets + variable name enclosed in curly brackets — cumbersome, but more consistent throughout SSSOM/T).

The first form is already allowed with current versions of SSSOM-Java, so we can switch to it immediately without breaking anything. And this will ensure nothing will also break when the upcoming SSSOM-Java will land in the ODK.

There is one particular bit of syntax that is currently used in the
SSSOM/T ruleset that I would like to disallow in the upcoming version of
SSSOM/Java. Specifically, the dereferencing of a variable enclosed in
angled brackets, as in:

  "... and (<%TAXREL> some NCBITaxon:????)"

It should either be "%TAXREL" (no angled brackets, preferred form as it
is more readable) or "<%{TAXREL}>" (angled brackets + variable name
enclosed in curly brackets).

The first form is already allowed with current versions of SSSOM-Java,
so we can switch to it immediately without breaking anything.
@gouttegd gouttegd self-assigned this Nov 28, 2024
@gouttegd gouttegd requested a review from matentzn November 28, 2024 23:27
@gouttegd gouttegd added tech bridge-files Issues related to the generation of bridge files from Uberon to other ontologies. labels Nov 28, 2024
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LGTM based on your explanations!

@gouttegd gouttegd merged commit 99ecf28 into master Nov 29, 2024
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@gouttegd gouttegd deleted the futureproof-sssomt-ruleset branch November 29, 2024 16:47
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2 participants