Add "JGI - metagenomics - long read" class to submission schema

microbiomedata / submission-schema

https://microbiomedata.github.io/submission-schema/

MIT License

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Add "JGI - metagenomics - long read" class to submission schema #168

Closed bmeluch closed 6 months ago

bmeluch commented 9 months ago

Due in Dev Feb 23rd

Part of the effort to make the submission portal accommodate JGI user projects.

The current "JGI MG" tab was created based on short read data. Long read data will use the same slots, with the difference being that dna_absorb1 and dna_absorb2 are required. (See https://github.com/microbiomedata/issues/issues/433)

This will require creating a new JGI metagenomics long reads class and submission portal tab (https://github.com/microbiomedata/issues/issues/413#issuecomment-1847996488).

turbomam commented 9 months ago

Hi @bmeluch

Can you say more about the difference between a "tab" and a class? Where could I find "JGI MG" in the submission schema? I did the following search and I don't think I'm finding anything with that name.

https://github.com/search?q=repo%3Amicrobiomedata%2Fsubmission-schema+JGI+MG&type=code

"JGI MG - long reads" would be an unusual name for a class

bmeluch commented 9 months ago

@turbomam yes good call, the class name shouldn't have been in quotes it was just describing the idea for the class.

"JGI MG" is from here https://github.com/microbiomedata/submission-schema/blob/main/schemasheets/tsv_in/classes.tsv line 11, as well as from the tab name that displays in the submission portal (see below).

I'm proposing to change the one line "JgiMgInterface" to two lines, "JgiMgSrInterface" and "JgiMgLrInterface" to distinguish short and long read data.

If my understanding is correct, the interface classes (e.g. "SoilInterface") correspond to sample types, and sample types selected in setting up a submission determine the tabs that appear in the last step of the submission portal (example photos).

mslarae13 commented 8 months ago

@bmeluch are you currently working on this, or waiting on something?

mslarae13 commented 8 months ago

@pkalita-lbl I checked with @bmeluch. She feels like she's done about all she can here. Would you have some time to either take this on and wrap it up or help guide her to close this out?

We think the remaining things to happen are UI updates.

[ ] Update the UI to show the additional / update the metagenomics- long and -short
[ ] Update version / prod to show the 2 interface tabs

mslarae13 commented 8 months ago

Technically, schema is updated. UI needs updated. Should this be a separate issue?

pkalita-lbl commented 8 months ago

Yeah I can take over from here. Don't worry about a new issue for right now I'll make one for myself if needed. I'll add myself as an assignee and add this to the next sprint so I don't lose track of it.

mslarae13 commented 7 months ago

Need confirmation on additional analysis type. Then into submission schema. Rescheduled for March 8th in dev

pkalita-lbl commented 7 months ago

Reopening until the submission portal work is also done.

pkalita-lbl commented 6 months ago

Still in progress, awaiting review on this PR which upgrades the submission-schema version.

ssarrafan commented 6 months ago

It looks like there is a validation issue on the linked PR. Moving this to the next sprint.
@bmeluch @pkalita-lbl if this isn't high priority we can move it to the post-GSP sprint. Let me know.

pkalita-lbl commented 6 months ago

Just waiting on final code review here. Moving to next sprint in case it doesn't happen today.