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Allow extensions block in auspice config & dataset JSONs, add --skip-validation #865

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merged 3 commits into from
Mar 14, 2022

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Allows auspice config JSONs to define an "extensions" block which is
passed through unchanged to the dataset JSON. This is intended for use
by other applications (i.e. not auspice) and, as such, no schema for the
block is specified. Tests added & can be run via
`cram --shell=/bin/bash tests/functional/export_v2.t`

Closes #861
@jameshadfield jameshadfield requested review from corneliusroemer and a team March 10, 2022 23:53
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codecov bot commented Mar 10, 2022

Codecov Report

Merging #865 (29a9357) into master (e4fdf59) will decrease coverage by 0.02%.
The diff coverage is 0.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #865      +/-   ##
==========================================
- Coverage   34.31%   34.28%   -0.03%     
==========================================
  Files          41       41              
  Lines        5937     5942       +5     
  Branches     1518     1521       +3     
==========================================
  Hits         2037     2037              
- Misses       3818     3823       +5     
  Partials       82       82              
Impacted Files Coverage Δ
augur/export_v2.py 10.94% <0.00%> (-0.10%) ⬇️

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Looks great, thanks a lot!

Do you think I need to test? End to end test looks great. If it passes, it works.

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@huddlej huddlej left a comment

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This looks good, @jameshadfield. Do you want functional tests for an invalid JSON with and with the new --skip-validation flag to confirm that this functionality works as expected?

@jameshadfield jameshadfield force-pushed the feat/export-extensions branch from 7774e6e to c014fe6 Compare March 13, 2022 23:46
An appropriate warning is added to the argument, but this can be useful
in certain situations and can result in a large speed-up (it speeds
up generation of a large testing dataset from 2m27s to 8s).

As discussed in #861
@jameshadfield jameshadfield force-pushed the feat/export-extensions branch from c014fe6 to 29a9357 Compare March 13, 2022 23:48
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jameshadfield commented Mar 13, 2022

do you want functional tests for an invalid JSON with and with the new --skip-validation flag to confirm that this functionality works as expected?

Good idea! Added via b0c383b. Will merge once CI passes.

@jameshadfield jameshadfield merged commit 751549e into master Mar 14, 2022
@jameshadfield jameshadfield deleted the feat/export-extensions branch March 14, 2022 00:25
@victorlin victorlin added this to the Next release X.X.X milestone Mar 30, 2022
@corneliusroemer corneliusroemer changed the title Allow extensions block in auspice config & dataset JSONs Allow extensions block in auspice config & dataset JSONs, add --skip-validation Apr 25, 2022
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4 participants