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Update JGI Plate well description #580

Closed
Tracked by #587 ...
mslarae13 opened this issue Dec 30, 2022 · 8 comments
Closed
Tracked by #587 ...

Update JGI Plate well description #580

mslarae13 opened this issue Dec 30, 2022 · 8 comments
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backlog Issue not assigned to a sprint or not completed during a sprint. Needs to be reprioritized.

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@mslarae13
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Currently, the description for plate well is
"Required when 'plate' is selected for container type. Corner wells must be blank. For partial plates, fill by columns. Leave blank if the sample will be shipped in a tube."

Should be

"Required when 'plate' is selected for container type. Corner wells must be blank. For partial plates, fill by columns. Provide "NA" if the sample will be shipped in a tube."

Completion involves updating the schema and merging the change into main.

@mslarae13
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@turbomam
When the schema is updated, the submission portal schema updates, and an ingest (?) triggers the update to the submission portal. Right?

@mslarae13 mslarae13 moved this to 🔖 Ready in SubPort Squad Issues Jan 4, 2023
@mslarae13 mslarae13 moved this from 🔖 Ready to 🏗 In progress in SubPort Squad Issues Jan 4, 2023
@mslarae13 mslarae13 moved this from 🏗 In progress to 🔖 Ready in SubPort Squad Issues Jan 4, 2023
@mslarae13 mslarae13 mentioned this issue Jan 6, 2023
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@ssarrafan
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@mslarae13 @turbomam is this issue being actively worked on?

@ssarrafan
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Haven't heard back so removing from sprint

@ssarrafan ssarrafan added the backlog Issue not assigned to a sprint or not completed during a sprint. Needs to be reprioritized. label Jan 17, 2023
@turbomam
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This is a reasonable issue, but

Required when 'plate' is selected for container type. Corner wells must be blank. For partial plates, fill by columns. Provide "NA" if the sample will be shipped in a tube.

isn't a description. We should create an actual description and capture this kind of knowledge in comments.

Blank entries are allowed now so I wouldn't recommend entering 'NA'. In fact, I don't think NA will validate.

There's a DataHarmonizer issue to address an implementation that won't require this workaround at all. But I don't think there's any development on that yet. I haven't created the necessary rule in the schema yet either.

@turbomam
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turbomam commented Jan 23, 2023

I'm starting to work on this now. You're talking about slot dna_cont_well, right?

@turbomam
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@sujaypatil96 pointed out that the place that text appears in the Data Portal is in the Guidance, which sources its content from an element's description and comments!

@turbomam
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So my pet peeve about descriptions vs comments is irrelevant here!

@turbomam
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Comments and rules have been written to address this. Enforcement of the rules in DataHarmonizer has not been, but has been raised as an issue in the DataHarmonizer issue tracker.

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Labels
backlog Issue not assigned to a sprint or not completed during a sprint. Needs to be reprioritized.
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Status: ✅ SubPort 1 - Done
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