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Port apply-geolocation-rules to augur curate #1491

Merged
merged 7 commits into from
Jun 26, 2024
Merged

Port apply-geolocation-rules to augur curate #1491

merged 7 commits into from
Jun 26, 2024

Commits on Jun 26, 2024

  1. Copy apply-geolocation-rules from nextstrain/ingest 

    Removed the executable permission and shebang since this file is no
longer expected to be called directly.

Copied from: <https://github.com/nextstrain/ingest/blob/c94d78d1f38b99e893007a76526f3d3824ecded0/apply-geolocation-rules>
    @victorlin
    victorlin committed Jun 26, 2024
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  2. Include copied script as augur curate apply-geolocation-rules 

    Added the minimum required changes to allow this subcommand to work:

- renamed the file to work as a python module (i.e. replace hyphens
  with underscores, add .py extension)

- added it as a subcommand of augur curate (after titlecase to be
  consistent with the order used in existing workflows)

- replaced the main entrypoint with register_parser() + run()

- hooked up to augur curate's argparse parser

- updated to work with JSON records directly (i.e. letting augur curate
  handle stdin/stdout)
    @victorlin
    victorlin committed Jun 26, 2024
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  3. Add tests 

    This does not test all functionality, but is better than no testing.
    @victorlin
    victorlin committed Jun 26, 2024
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  4. Use AugurError and print_err 

    To be consistent with the rest of the codebase.
    @victorlin
    victorlin committed Jun 26, 2024
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  5. Fix error message formatting

    @victorlin
    victorlin committed Jun 26, 2024
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  6. Update changelog

    @victorlin
    victorlin committed Jun 26, 2024
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  7. Add apply-geolocation-rules test

    @joverlee521 @victorlin
    joverlee521 authored and victorlin committed Jun 26, 2024
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