Improve validation of Auspice JSONs #621
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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.
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).
Codecov Report
@@ Coverage Diff @@
## master #621 +/- ##
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+ Coverage 28.37% 28.64% +0.26%
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Files 39 39
Lines 5332 5342 +10
Branches 1306 1309 +3
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+ Hits 1513 1530 +17
+ Misses 3766 3756 -10
- Partials 53 56 +3
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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
approved these changes
Oct 20, 2020
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This improves
augur validate export-v2in two important ways:(1) Stops validation failing on trees with (internal) nodes with a single child. Such trees are allowed - in fact we use this ability for our nCoV trees to encode travel history!
(2) Trees with identical node names cause Auspice to crash, however they currently pass validation without any warnings. They now result in an error message such as:
cc @batson