biolink/kgx

kgx validate `-o` option writes an empty file, output goes to stderr rather than stdout

kevinschaper opened this issue · 0 comments

It looks like all of the validation output is going to stderr with or without the option specified, but the logging about the action is going to stdout - which is possibly reversed from what I would expect.

kgx validate -i tsv monarch-kg_nodes.tsv monarch-kg_edges.tsv 2> validate.txt
[KGX][__init__.py][    validate_wrapper] ERROR: kgx.validate() errors encountered... check the error log
  • -o should write the validation output
  • without -o specified, the validation output should be captured by > and the logging about the validation process should go to stderr.