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Update metadata section in Augur to Auspice #184

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joverlee521 opened this issue Jan 27, 2024 · 2 comments
Open

Update metadata section in Augur to Auspice #184

joverlee521 opened this issue Jan 27, 2024 · 2 comments
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documentation Improvements or additions to documentation

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@joverlee521
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Depends on release of nextstrain/augur#1384

Note the new option to use --metadata-columns to export metadata without needing to use as coloring in the "What metadata is exported" section of the "Augur to Auspice" docs.

What metadata is exported
-------------------------
Augur has two main types of “metadata” which we'll refer to as
“TSV-data” (provided with the ``--metadata`` argument) and “node-data”
which are JSONs provided via ``--node-data`` (see :doc:`data formats </reference/data-formats>` for more).
Typically, node-data information is automatically exported as a coloring whereas
TSV-data must be explicitly exported by requesting it as a coloring in the
auspice-config JSON. [#f3]_ Metadata is exported as a coloring if via the
following process:
- All key-value pairs specified in node-data JSONs, unless they match a
hardcoded-list of exclusions and special-cases (next section). This
has the effect that data provided in node-data JSONs will form a
coloring and thus be exported in the dataset JSON.
- Command-line provided colorings (not covered in this guide)
- Colorings specified in the ``auspice_config.json`` (see below)

@joverlee521 joverlee521 added the documentation Improvements or additions to documentation label Jan 27, 2024
@joverlee521
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Noting that I chatted with @kimandrews in our 1:1 today about the metadata_columns feature. It was pretty confusing for me to remember the distinction of colorings, filters, and metadata_columns in the Auspice config JSON and I'm the one who added the new feature 😅

@jameshadfield
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I find reading the description / $comment in the schema to be helpful. One day we'll turn these schemas into docs!

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