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microbiomedata / metadata-for-user-facility-template-transformations

CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
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EMSL metadata mapper is failing? #42

Closed mslarae13 closed 2 months ago

mslarae13 commented 2 months ago

I recently ran the MUTTs script to transform a metadata sheet to the EMSL format

poetry run python etl.py --submission d6293e5e-6fed-4705-ae1e-790749e2e094 --user-facility emsl --mapper input-files/emsl_header.json --unique-field samp_name --output test_2024-08_emsl.xlsx

The EMSL excel file that is output doesn't have any metadata. It has the headers, but the mapping from the NMDC submission to the EMSL headers seems to be broken.

sujaypatil96 commented 2 months ago

When using the EMSL mapper, we need to include the --header option, like below:

$ poetry run python etl.py --submission d6293e5e-6fed-4705-ae1e-790749e2e094 --user-facility emsl --mapper input-files/emsl_header.json --header --unique-field samp_name --output test_2024-08_emsl.xlsx
mslarae13 commented 2 months ago

To do: test with @sujaypatil96 's corrections to the command.

mslarae13 commented 2 months ago

adding --header fixed my problem