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microbiomedata / nmdc-aggregator

Scripts that periodically aggregate data related to KEGG search
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Update functional_agg to use workflow_execution_set #19

Closed mbthornton-lbl closed 1 month ago

mbthornton-lbl commented 1 month ago

This PR provides updates to the MetaGenomeFunctAgg class to make it compatible with the Berkley database schema:

Removes:

self.mgact_col = self.db.metagenome_annotation_activity_set
self.mtact_col = self.db.metatranscriptome_annotation_set

Updates the sweep function to look in workflow_execution_set filter by type Renames some variables and a function name to be more Berkleyish

eecavanna commented 1 month ago

Looks like this was not merged into main, but rather merged into 10-berkeley-update-generate_metap_aggpy.

I'll work on getting a container image built from that specific branch and deployed to the Berkeley environment on Spin.