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monarch-initiative / koza

Data transformation framework for LinkML data models
https://koza.monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
48 stars 4 forks source link

koza validate fails with skip_lines error #63

Closed kevinschaper closed 2 years ago

kevinschaper commented 3 years ago

It looks like some older parameters are getting used:

✗ poetry run koza validate --file monarch_ingest/zfin/gene_to_phenotype.yaml
Traceback (most recent call last):
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/bin/koza", line 8, in <module>
    sys.exit(main.typer_app())
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/typer/main.py", line 214, in __call__
    return get_command(self)(*args, **kwargs)
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/typer/main.py", line 500, in wrapper
    return callback(**use_params)  # type: ignore
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/koza/main.py", line 64, in validate
    validate_file(
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/koza/cli_runner.py", line 77, in validate_file
    reader = CSVReader(
  File "/Users/kschaper/Documents/Monarch/monarch-ingest/.venv/lib/python3.9/site-packages/koza/io/reader/csv_reader.py", line 94, in __init__
    self.reader = reader(io_str, *args, **kwargs)
TypeError: 'skip_lines' is an invalid keyword argument for this function