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I did a domain wide update for users where I work last week using a CSV created from our HR system.
As Jay mentioned above after calling the CSV you then need to say which fields in the CSV need to be used for which fields.
It gets a bit "messy" when doing managers and departments etc. as they're a little buried!
The API reference gives some pointers: https://github.com/taers232c/GAMADV-XTD3/wiki/Users
To update those 3 fields you need to do:
gam csv <source.csv> gam update user "~Email" relations manager "~Manager's email" organization department "~Department" costcenter "~Cost Center"
You may need to update the various field references for the CSV to suit whatever is in your sheet. Double-quotes might also not be needed, I use them on my own Mac as zsh complains otherwise ;P
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Mark Skrzypczyk