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[taxonomy] Update OWL ontology building process #788

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@apeteri apeteri commented Mar 28, 2021

This PR changes DelegateOntology so that the expression content of each OWL axiom reference set member is loaded directly, without splitting them into stated relationship fragments.

- Collect all stated relationships
- Collect non-IS A statement fragments extracted from OWL axioms
- Collect all stated axioms
- Parse and include OWL axioms as-is
- Generate an extra axiom on the fly for concepts that still have stated
relationships
@apeteri apeteri added the bug label Mar 28, 2021
@apeteri apeteri self-assigned this Mar 28, 2021
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Codecov Report

Merging #788 (f5631bb) into 7.x (68c727f) will increase coverage by 0.00%.
The diff coverage is 89.53%.

Impacted file tree graph

@@            Coverage Diff            @@
##                7.x     #788   +/-   ##
=========================================
  Coverage     58.90%   58.90%           
+ Complexity    12880    12873    -7     
=========================================
  Files          1777     1777           
  Lines         65623    65606   -17     
  Branches       6475     6466    -9     
=========================================
- Hits          38655    38648    -7     
+ Misses        23949    23943    -6     
+ Partials       3019     3015    -4     
Impacted Files Coverage Δ Complexity Δ
...snomed/reasoner/request/OntologyExportRequest.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
...owl/snomed/reasoner/ontology/DelegateOntology.java 59.79% <81.81%> (-2.17%) 66.00 <13.00> (-11.00)
...astore/index/taxonomy/ReasonerTaxonomyBuilder.java 57.54% <93.75%> (+0.99%) 53.00 <2.00> (-1.00) ⬆️
...snomed/datastore/index/taxonomy/InternalIdMap.java 76.92% <100.00%> (+0.60%) 11.00 <2.00> (+1.00)
...d/datastore/index/taxonomy/InternalIdMultimap.java 89.18% <100.00%> (+0.30%) 8.00 <1.00> (+1.00)
...med/datastore/index/taxonomy/ReasonerTaxonomy.java 94.28% <100.00%> (ø) 22.00 <3.00> (ø)
...nomed/reasoner/normalform/NormalFormGenerator.java 87.28% <100.00%> (+0.21%) 49.00 <2.00> (+2.00)
...med/reasoner/request/ClassificationJobRequest.java 75.36% <100.00%> (ø) 10.00 <0.00> (ø)
...nternational/snowowl/core/events/util/Promise.java 68.75% <0.00%> (-1.79%) 19.00% <0.00%> (ø%)
... and 6 more

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lgtm-com bot commented Mar 28, 2021

This pull request fixes 1 alert when merging f5631bb into 68c727f - view on LGTM.com

fixed alerts:

  • 1 for Dereferenced variable may be null

@nagyo nagyo self-requested a review April 6, 2021 13:25
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Further investigation is needed due to higher amount of classification results after applying the proposed changes

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apeteri commented May 8, 2021

Closing in favor of a future PR that incorporates these changes.

@apeteri apeteri closed this May 8, 2021
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3 participants