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IMP: updating GTDB url selection - #271
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mikerobeson
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VinzentRisch
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Sep 29, 2026
VinzentRisch
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Hey @mikerobeson
I ran the download with all three urls and it all works fine.
See some comments below.
| 'data from European servers. \'world-wide-asia\' will ' | ||
| 'download data from Asian-Pacific servers. and ' | ||
| '\'australia\' will download from Australian servers. ' | ||
| 'Choose the server that is best for your reagion.'}, |
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| 'Choose the server that is best for your reagion.'}, | |
| 'Choose the server that is best for your region.'}, |
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| def _assemble_queries(version='232.0', | ||
| def _assemble_queries(db_url, |
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| def _assemble_queries(db_url, | |
| def _assemble_queries(db_url='world-wide-europe', |
I would set 'world-wide-europe' as default. It is recommended for worldwide downloads on the website and will work anywhere. If there is no default a user always has to set it themselves for a parameter that does not matter that much because the download is quick anyway.
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Description
This PR replaces
--p-url-typewith--p-db-url. GTDB no longer usesPrimaryandMirroras their url options. They now suggest the options outlined here.I've currently made this a required parameter, and the user needs to select one of the following url options:
world-wide-europeworld-wide-asiaaustraliaI was considering setting
world-wide-europeas the default. But that might defeat the purpose... 🤷 I am open to suggestions.Contains updated and newly added new unit tests.
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