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Fix #60 #61

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merged 1 commit into from
Sep 3, 2024
Merged

Fix #60 #61

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18 changes: 9 additions & 9 deletions src/kg_bioportal/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,9 @@ def main(verbose: int, quiet: bool):


@main.command()
@click.option("output_dir", "-o", required=True, default="data/raw")
@click.option("--output_dir", "-o", required=True, default="data/raw")
@click.option(
"api_key",
"--api_key",
"-k",
required=False,
type=str,
Expand Down Expand Up @@ -66,34 +66,34 @@ def get_ontology_list(output_dir, api_key) -> None:

@main.command()
@click.option(
"ontologies",
"--ontologies",
"-d",
required=False,
type=str,
)
@click.option(
"ontology_file",
"--ontology_file",
"-f",
required=False,
type=click.Path(exists=True),
)
@click.option("output_dir", "-o", required=True, default="data/raw")
@click.option(
"snippet_only",
"--snippet_only",
"-x",
is_flag=True,
default=False,
help="Download only the first 5 kB of each (uncompressed) source, for testing and file checks [false]",
)
@click.option(
"ignore_cache",
"--ignore_cache",
"-i",
is_flag=True,
default=False,
help="ignore cache and download files even if they exist [false]",
)
@click.option(
"api_key",
"--api_key",
"-k",
required=False,
type=str,
Expand Down Expand Up @@ -154,8 +154,8 @@ def download(


@main.command()
@click.option("input_dir", "-i", default="data/raw", type=click.Path(exists=True))
@click.option("output_dir", "-o", default="data/transformed")
@click.option("--input_dir", "-i", default="data/raw", type=click.Path(exists=True))
@click.option("--output_dir", "-o", default="data/transformed")
def transform(input_dir, output_dir) -> None:
"""Transforms all ontologies in the input directory to KGX nodes and edges.

Expand Down
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