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ENH: Adds NCBI api-key option #203

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@mikerobeson mikerobeson commented Sep 4, 2024

Attempts to fix #145, by adding the --p-api-key option to both get-ncbi-data and get-ncbi-data-protein. It does this by appending api_key to the _entrez_params dictionary so that it is available for all NCBI requests.

To do:

  • Test code
    • I could use help on the best way to write test code for this...
    • Might test reading in a mock api-key?

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Going to close this PR as it is clear that NCBI requests are not the rate-limiting step. At least for the purposes being used here. This was confirmed after several rounds of testing. There was no difference in overall run time when downloading marker gene data from NCBI, with or without the api-key.

@mikerobeson mikerobeson deleted the ncbi-api-key branch September 15, 2024 18:57
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Use NCBI API keys in get-ncbi-data command
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