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Improve reporting errors during validation of phenotypic feature in PhenotypeCreator. #113

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ielis opened this issue Dec 8, 2023 · 1 comment · Fixed by #128
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Improve reporting errors during validation of phenotypic feature in PhenotypeCreator. #113

ielis opened this issue Dec 8, 2023 · 1 comment · Fixed by #128
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@lnrekerle
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enhancement New feature or request
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Nice to have

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@ielis
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ielis commented Dec 8, 2023 •
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PhenotypeCreator can complain during creating Phenotypes if an HPO term cannot be found in the HPO version being used in analysis. Right now, we log term's absence and note that it will be ignored.
However, the user may be interested in fixing this but the log messages lack the necessary context.

The log message should include the individual ID to help the user fix the issue. However, we do not have that available within PhenotypeCreator and we may need to revise the PhenotypeCreator API to provide the context.
@ielis ielis added the enhancement New feature or request label Dec 8, 2023
@ielis ielis added this to the Nice to have milestone Dec 8, 2023
@ielis ielis mentioned this issue Dec 8, 2023
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ielis commented Dec 19, 2023

Related to #120

@lnrekerle lnrekerle self-assigned this Dec 19, 2023
This was referenced Jan 9, 2024
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@ielis ielis linked a pull request Jan 16, 2024 that will close this issue
Formalize handling and reporting of input errors #128
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