Update gold:Gs0114675 / nmdc:sty-11-8fb6t785 Deep subsurface shale (metagenomes)

microbiomedata / nmdc_automation

Prototype automation

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Update gold:Gs0114675 / nmdc:sty-11-8fb6t785 Deep subsurface shale (metagenomes) #166

Closed mbthornton-lbl closed 4 months ago

mbthornton-lbl commented 4 months ago

Omics Type(s): metagenomes Note: Study only goes to OmicsProcessing level.

Steps:

[x] Unset has_output for omics_processing records
[x] update-study

aclum commented 4 months ago

I've used queries:run to update has_output to an empty list on napa, dev, and prod. Unsetting did not work with the endpoint so @eecavanna and I opted to use $set with an empty list as an alternative.

eecavanna commented 4 months ago

Yes, that's my stance. I propose that we $set to [] for now (because the Runtime allows it) and then — after re-ID-ing takes place — as a separate endeavor, "clean up" those empty lists. To identify those empty lists later, someone can either (a) use any logs/records that the re-ID-ing tool generates or (b) use a Python notebook I wrote a few months ago to search the entire database for them (just took a few minutes when run on a NERSC machine).

ssarrafan commented 4 months ago

Appears active. Moving to new sprint for review. Please remove from sprint if not active.