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loinc / comp-loinc

Computational LOINC in OWL.
MIT License
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Improve performance of saving outputs #75

Open joeflack4 opened 3 weeks ago

joeflack4 commented 3 weeks ago

Overview

The biggest performance bottleneck in builds is saving outputs, done by the LinkML OWLDumper.

Sub-tasks

Additional info

Based on my investigation so far, it seems that the OWLDumper.to_ontology_document() step of our save_to_owl(). This creates a OntologyDocument object. Once that's done, it saves writes via f.write(str(document)), but this step seems fast.

ShahimEssaid commented 3 weeks ago

I did some profiling. There is a utility "underscore" function that does about 3 regex substitutions. About 30% of the time is spent there alone.

Sent from mobile

On Mon, Sep 16, 2024, 7:30 PM Joe Flack @.***> wrote:

Overview

The biggest performance bottleneck in builds is saving outputs, done by the LinkML OWLDumper. Sub-tasks

  • Performance profiling

Additional info

Based on my investigation so far, it seems that the OWLDumper.to_ontology_document() step of our save_to_owl(). This creates a OntologyDocument object. Once that's done, it saves writes via f.write(str(document)), but this step seems fast.

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