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[ancestral, translate] node data validation improvements #1440

Merged
merged 5 commits into from
Mar 19, 2024
Merged

[ancestral, translate] node data validation improvements #1440

merged 5 commits into from
Mar 19, 2024

Commits on Mar 19, 2024

  1. Fix quoting typo 

    'q' is not a valid formatting type for python (it's a snakemake feature)
    @jameshadfield
    jameshadfield committed Mar 19, 2024
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  2. node data reading: skip validation when asked to 

    NodeDataFile (called by NodeDataReader, which is called by
read_node_data) no longer attempts JSON validation when the requested
validation mode is SKIP.
    @jameshadfield
    jameshadfield committed Mar 19, 2024
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  3. [ancestral, translate] validate output node-data 

    By leveraging the existing validation designed for reading node-data
files we not only validate against the annotation schema but also
perform other sanity checks on the node-data structure for which a
schema does not (yet) exist.

As part of this we add a `--validation-mode` argument following `augur
export v2` which allows users to skip validation of the output node-data
and (translate only) skip validation of the input node-data.
    @jameshadfield
    jameshadfield committed Mar 19, 2024
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  4. Validation mode warn no longer exits code 2 

    The help message for `--validation-mode` is very specific:

> 'error' mode causes a non-zero exit status if any validation checks
> failed, while 'warn' does not.

In the actual implementation however we would print an error and exit
with code 2 for any validation check _except_ the augur version check.
Now, for `ValidationMode.WARN` we catch these errors and turn them into
warnings such that augur can exit code 0 as specified.

Note that during validation, any non-ValidationError exception will be
be fatal even in `WARN`. An example of this would be errors loading the
schema itself. See the following review comment for more:
<#1440 (comment)>
    @jameshadfield
    jameshadfield committed Mar 19, 2024
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  5. changelog

    @jameshadfield
    jameshadfield committed Mar 19, 2024
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