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NMDC Submission: f85fd516-b378-449c-a6bc-184aa96de715 #697

Closed JamesTessmer closed 4 months ago

JamesTessmer commented 5 months ago

Submitter: Montana Smith, 0000-0002-8683-0050 Submission ID: f85fd516-b378-449c-a6bc-184aa96de715 Has data been generated: Yes PI name: Montana Smith PI orcid: My ORCID Status: Submitted -Pending Review Data types: mg-jgi, mg-lr-jgi, mt-jgi, mp-emsl, mb-emsl, nom-emsl, mg, mt, mp, mb, nom Sample type:soil Number of samples:5 NCBI ID: NCBI GOLD ID: GOLD Alternative IDs/Names: Alternative

mslarae13 commented 5 months ago

Test 1 @JamesTessmer I included the JGI and EMSL IDs that are added in the Multi-Omics data step but I don't see them here?

mslarae13 commented 5 months ago

@ james for the data types

mg-jgi, mg-lr-jgi, mt-jgi, mp-emsl, mb-emsl, nom-emsl these are because of the boxes I check in the multiomics data step

mg, mt, mp, mb, nom these are because of the selections I made in the analysis / data type column in the metadata?

JamesTessmer commented 5 months ago

@mslarae13 Ah I misunderstood. I thought the issue should have either NCBI/Gold OR EMSL/JGI And not have both. This is an easy change to an if statement. Just to double check do you want all 4 always present?

mslarae13 commented 5 months ago

all present if populated. yes... gold and ncbi are only relevant if data has already been generated but regardless of ig data has or has not been generated, if DOE UF was used the JGI/EMSL ID should show

JamesTessmer commented 5 months ago

For the data types, I have the code grabbing everything in the omicsProcessingTypes from the multi-omics form. I'm not sure how all the values for that are populated. Do you only want a subset of those values or for them to be broken up into different sections?

JamesTessmer commented 5 months ago

That should be an easy fix for the IDs, I can probably get a PR with a working change for that wednesday or thursday.

JamesTessmer commented 5 months ago

@mslarae13 Where did you include the JGI and EMSL IDs? The alternative Names/ID field? update: No i see that the alternative names/ID are included. I'm a little lost, when I'm testing this now I don't see a place to put the JGI and EMSL IDs.

mslarae13 commented 5 months ago

@JamesTessmer

Here

Screenshot 2024-05-15 at 2 54 24 PM

When the user selected "No data has not yet been generated", the JGI and EMSL IDs show. see here https://github.com/microbiomedata/issues/issues/698#:~:text=JGI%20IDs%3A%20JGI%20ID%20new%0AEMSL%20IDs%3A%20EMSL%20New%20ID

mslarae13 commented 4 months ago

testing