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This PR adds a `validate` command that can be used to validate Babel Outputs. At a minimum it reads through all output files, ensuring that they all exist, are non-empty and are in the right format. Most validations consist of summarizing pieces of information (unique types, unique prefixes) and writing them out in a format that can be used to compare outputs between runs, while others (see #14 for examples) test particular aspects of the file, in particular bugs that have crept into the Babel outputs previously that we can use to ensure that those bugs don't reappear.
The goal is to have a program that we can point at a Babel run that runs some basic tests on the generated files, including:
umls.txt
) only contains a single Biolink typeCHEBI:CHEBI:41423
as per RemoveCHEBI:CHEBI:41423
from PUBCHEM.COMPOUND:2662 results Babel#69)We're also tracking this in the Babel repository at TranslatorSRI/Babel#36
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