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microbiomedata / sheets_and_friends

Enhance a LinkML model with imported and optionally modified slots
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modifications_long tab in sheets_and_friends configuration sheet not being applied to multi-view DH #171

Closed mslarae13 closed 1 year ago

mslarae13 commented 1 year ago

The modifications_long tab in sheets_and_friends configurations like sheets-for-nmdc-submission-schema_MLS define modifications that should be made to MIxS terms before they are included in the submission schema, or any DataHarmonizer built from it.

The modification are applied by the artifacts/nmdc_submission_schema.yaml rule in the Makefile, which calls the modifications_and_validation script.

It appears that modifications are not being applied anymore. We're not sure when that started. Note that sheets_and_friends can apply different modifications on a class-by-class basis. _In fact, the modifications were applied by specifying a slot_usage for each slot in each class, which lead to the enormous file sizes in the past._

For example, modification_long says that samp_store_temp's description should be changed from the MIxS specified value of "Temperature at which sample was stored, e.g. -80 degree Celsius" to the modified value of 'Temperature at which the sample was stored (degrees are assumed)'.

This was successful in commit d93ce72be9bf96af6316e01dfdd947cb2983d3c0

Recently @mslarae13 added modifications for more terms like fire, be we don't have as much history about whether that was ever applied sucessfully.

Criteria for completion

mslarae13 commented 1 year ago

We will discuss on 02/14 at SubPort squad meeting @pkalita-lbl , @turbomam

mslarae13 commented 1 year ago

When you make changes to sheets-and-friends the main branch needs the Feb 3rd was the last time artifacts were made.

Need to make an SOP or ?? for the protocol for updating the sheets_and_friends

For GSP: When schema freeze is over, merge / update to Montana's sheets_and_friends file, remake the make file, and push these slot updates to the submission portal

NOT for GSP: Develop a better way of tracking, merging, and resolving the schema updates that happen in sheets-and-friends for the Submission Portal

pkalita-lbl commented 1 year ago

This issue refers to issues around the shared Google sheet. That is no longer being used in favor of TSV files checked into https://github.com/microbiomedata/submission-schema. I think it's safe to close this one.