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biolink / biolink-model-toolkit

A collection of useful python functions for looking up information and working with the Biolink Model
https://biolink.github.io/biolink-model-toolkit/
BSD 3-Clause "New" or "Revised" License
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initialization time is too slow #91

Closed sierra-moxon closed 1 year ago

sierra-moxon commented 1 year ago

We've had two reports that BMT initialization is slow. One user reports that it is intermittent, and the other finds it fairly frequently to be too slow on initialization.

One possibility is that resolving the LinkML:types import is intermittently slow, but we need to investigate.

cmungall commented 1 year ago

https://github.com/linkml/linkml/issues/1012

sierra-moxon commented 1 year ago

I refactored the toolkit method to depend on linkml SchemaView instead of generating a schema-view like object itself. This removes the direct linkml dependency from BMT. We now depend only on linkml-runtime. Next step is to test what initialization looks like with this refactoring.

sierra-moxon commented 1 year ago

I'm going to close this as fixed, please reopen if it still seems too slow to initialize