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CLI prints thousands of disease normalization failures to console #435

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jsstevenson opened this issue Sep 30, 2024 · 0 comments
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bug Something isn't working priority:medium Medium priority

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@jsstevenson
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When running updates via the CLI, tons and tons of disease normalization failure lines get printed to stdout:

Failed to normalize disease term: Wrist Fractures
Failed to normalize disease term: wrist fracture
Failed to normalize disease term: mesh:D007718
Failed to normalize disease term: EFO:0009507
Failed to normalize disease term: Knee Injuries
Failed to normalize disease term: knee injury
 13%|████▎                           | 324539/2431025 [04:07<25:45, 1363.31it/s]Failed to normalize disease term: mesh:D058533
 13%|████▎                           | 326418/2431025 [04:09<23:59, 1462.28it/s]Failed to normalize disease term: mesh:D011030
Failed to normalize disease term: HP:0002107
Failed to normalize disease term: mesh:D016657
 14%|████▎                           | 328544/2431025 [04:10<24:49, 1411.52it/s]Failed to normalize disease term: mesh:D000077299
Failed to normalize disease term: mesh:D018784
Failed to normalize disease term: EFO:1001753
Failed to normalize disease term: Abdominal Abscess
Failed to normalize disease term: mesh:D017192

This probably has to do with the way click intersects with the logging module. We should definitely be logging these warnings but shouldn't be printing them.

@jsstevenson jsstevenson added priority:medium Medium priority bug Something isn't working labels Sep 30, 2024
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