What additional sample types should be available for EMSL metadata submission via NMDC

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What additional sample types should be available for EMSL metadata submission via NMDC #417

Closed mslarae13 closed 7 months ago

mslarae13 commented 1 year ago

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RACI

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Responsible: @mslarae13
Accountable: @mslarae13
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Describe the the task?

[x] Identify additional sample types for NMDC submission for EMSL samples
[x] microbiomedata/nmdc-schema#1335
[x] Add slots / update NMDC submission schema for expanded EMSL samples
[x] remove env package slot & fill in this slot in DB using the package that is checked
[x] microbiomedata/submission-schema#183
[x] microbiomedata/nmdc-server#1154

Criteria for completion

Additional sample types are available for NMDC metadata submission for EMSL sample submission

Estimate people time

Completion Date (Goal)

10/6
Rescheduled 02/09

Target Sprint Start & End Dates

Start: 9/11
End: 02/09

Tag Blocker/Contingent upon issues

[Tagg issues]

mslarae13 commented 1 year ago

@brynnz22 , @pkalita-lbl , @bmeluch please break into / link smaller issues

mslarae13 commented 1 year ago

Delayed, initial thoughts plant-associated sediment water pore water

Currently have soil & water extracted soil (let's get rid of this)

Do we need to limit the environmental package (should change this to extension) selection at step 5

mslarae13 commented 1 year ago

Identification of sample types complete. @bmeluch is working on inventorying /checking slots. Bea, can you create an issue for this work?

mslarae13 commented 12 months ago

Part of https://github.com/microbiomedata/issues/issues/444

mslarae13 commented 11 months ago

Decision, skip pore-water... should a user complete soil or water metadata is VERY unclear and records in NCBI are all over the place. This should likely be a MIxS extension first.

ssarrafan commented 10 months ago

@mslarae13 is this issue still 'in progress'? Or should it be moved to backlog?

mslarae13 commented 10 months ago

@ssarrafan advice on the best way to manage the inprogess of super issues? This is in progress cuz it's the full picture, but the individual broken out work is linked (super issue)

ssarrafan commented 10 months ago

@ssarrafan advice on the best way to manage the inprogess of super issues? This is in progress cuz it's the full picture, but the individual broken out work is linked (super issue)

I think leaving it in the squad board and then adding the related active issues to the current sprint would be great.

mslarae13 commented 7 months ago

This looks done! Submitting a separate ticket for validating or limiting sample type options. This is a future problem. https://github.com/microbiomedata/nmdc-server/issues/1185