launching and config updates

[turbomam]

fixes #1613

• apply nmdc-schema standards for launching, configuring and writing to db_tool.py  #1613

[turbomam]

@mbthornton-lbl do you see how I am launching this now with the extract-study wrapper and configuring it with local/.env via --env_file?

If so, are you willing to merge this into your branch?

[turbomam]

@mbthornton-lbl reported seeing

ValueError: No such slot host_disease_stat as an attribute of Biosample ancestors or as a slot definition in the schema

after doing some reasonable due diligence:

poetry run gen-doc -d docs --template-directory src/doc-templates src/schema/nmdc.yaml

That's because building just about anything locally for the nmdc-schema (including gen-doc), may require a one-time clearing and regeneration of src/schema/mixs.yaml with

make mixs-yaml-clean src/schema/mixs.yaml 

Once you have done that in any given environment, it shouldn't be necessary to keep doing it. And the need to do it at all will be removed by

• DO NOT MERGE YET change MIxS import to 6.2 #1386