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DataHarmonizer's linkml-datastructure branch doesn't use our validation rules #104

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Tracked by #105
turbomam opened this issue Apr 7, 2022 · 5 comments · Fixed by #115
Closed
Tracked by #105

DataHarmonizer's linkml-datastructure branch doesn't use our validation rules #104

turbomam opened this issue Apr 7, 2022 · 5 comments · Fixed by #115

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@turbomam
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turbomam commented Apr 7, 2022

Validation rules currently come from the validation_converter sheet and are processed by sheets_and_friends/converters/linkml2dataharmonizer.py

That gets bypassed when we use DataHarmonizer's linkml-datastructure branch, which takes our nmdc_dh.yaml as input

see also cidgoh/DataHarmonizer#290

@turbomam turbomam changed the title our validation rules aren't making it into interfaces built with DataHarmonizer's linkml-datastructure branch DataHarmonizer's linkml-datastructure branch doesn't use our validation rules Apr 7, 2022
@turbomam
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“{float} {unit}”

string serialization is interpolation where the things in curly brackets are slots

@turbomam
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turbomam commented Apr 12, 2022

full_name: string_serialization: “{given} {family}”

intent is to assemble/serialize a string from smaller value components

means that things with a full_name must also have a given value and a familyvalue

But we have erroneously put what should be MIxS structured patterns into string_serialization slots

@turbomam
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turbomam commented Apr 12, 2022

structured pattern: intent is to validate (reuse of smaller validation components)

@sujaypatil96
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On course to make a PR which adds pattern property to the slots in the NMDC schema generated from sheets_and_friends.

@turbomam
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@sujaypatil96 @ssarrafan I see some good developments for this issue in #115, but I don't think I understand how to use it. I have added some discussion about this to the dh_testing README

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