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Improve validation of Auspice JSONs #621

Merged
merged 3 commits into from
Oct 21, 2020
Merged

Improve validation of Auspice JSONs #621

merged 3 commits into from
Oct 21, 2020

Commits on Oct 15, 2020

  1. [schema] allow nodes with a single child in Auspice JSONs

    Auspice has no problem rendering (internal) nodes with a single
    child (we use this in our SARS-CoV-2 build to encode travel
    history). This updates the schema so that such builds pass.
    jameshadfield committed Oct 15, 2020
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  2. [validate] duplicate node names are now a fatal error

    Auspice (v2) JSONs are not allowed to have duplicate names (it causes
    Auspice to crash). This modifies the vlidate functionality so that it
    identifies this (previously there was no warning).
    jameshadfield committed Oct 15, 2020
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Commits on Oct 20, 2020

  1. Add unit tests for ensure_no_duplicate_names

    Adds minimal tests for validation of no duplicate names. Instead of
    mocking up the tree JSON directly, these tests build a minimal BioPython
    tree and use augur's own tree-to-JSON function to make the more verbose
    JSON structure expected by the validation function.
    huddlej committed Oct 20, 2020
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