Fix order of exported colorings from augur export v2 when color by metadata is used #1177
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Adds a functional test and mock data that should work where augur export includes the `--color-by-metadata` argument with a column named `custom_trait`. The resulting Auspice JSON should include the `custom_trait` as a node attribute for each tip and as a coloring that appears after the colorings explicitly defined in the Auspice config JSON. The original goal of this test was to confirm that "color by metadata" colorings disrupt the order of all colorings in the Auspice config JSON, but this test also reveals a separate potential bug where one of the node data annotations (`mutation_length`) that also appears in the metadata gets dropped completety from the Auspice JSON when the color by metadata argument is used.
huddlej
changed the title
Adds option to pretty-print DeepDiff output in functional tests and uses this option for a new test that has especially long diff output when the test fails where clearer printing helps with debugging.
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@huddlej it looks like maybe this was a proof-of-bug and can be closed? |
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I don't know if either of the bugs I mentioned above have been resolved or not. I can convert this into a proper issue at some point before closing this PR but probably not this week. |
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Description of proposed changes
Adds a functional test and mock data that should work where augur export includes the
--color-by-metadataargument with a column namedcustom_trait. The resulting Auspice JSON should include thecustom_traitas a node attribute for each tip and as a coloring that appears after the colorings explicitly defined in the Auspice config JSON.The original goal of this test was to confirm that "color by metadata" colorings disrupt the order of all colorings in the Auspice config JSON (a bug I encountered this morning in another project and wanted to confirm here), but this test also reveals a separate potential bug where one of the node data annotations (
mutation_length) that also appears in the metadata gets dropped completety from the Auspice JSON when the color by metadata argument is used.Testing
Checklist