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env_package should have a range of an Enum #2167

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sujaypatil96 opened this issue Aug 22, 2024 · 4 comments
Open

env_package should have a range of an Enum #2167

sujaypatil96 opened this issue Aug 22, 2024 · 4 comments

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@sujaypatil96
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The env_package slot in the schema should have the range of an Enum, with the list of permissible values constructed using the value of <EnvPackage> in https://www.ncbi.nlm.nih.gov/biosample/docs/packages/?format=xml (so we are aligned with NCBI as well)

@aclum
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aclum commented Aug 29, 2024

@mslarae13 @pkalita-lbl please comment on if you are okay with these proposed changes wrt submission portal. This will streamline the nmdc mongo to ncbi xml code. Otherwise we'll need a mapping table.

@turbomam
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I would also be open to the permissible values coming from MIxS Extensions, but am totally happy with @sujaypatil96's suggestion for the values NCBI calls <EnvPackage> on their submission specifications, and package in their downloadable Biosample XML records

@turbomam
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We need an official mapping between the NCBI namespace, the MIxS namespace, and any variable used in code like submission-schema and nmdc-server

@pkalita-lbl
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Broadly speaking that seems okay. As far as the submission portal is concerned, env_package is not a slot that we have users fill out for each sample metadata record. Instead it gets derived based on their choice in the Environmental Package screen:

image

The submission portal's frontend code already maintains a crazy mapping between human readable names and env_package values and submission-schema class names and more. If we could reduce (or at least not increase) the level of that craziness that would be nice.

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4 participants