mirror of
https://github.com/chanzuckerberg/cellxgene.git
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78c9d24ed4
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
73 lines
2.0 KiB
Python
73 lines
2.0 KiB
Python
import click
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from backend.czi_hosted.converters.schema import remix, validate
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@click.group(
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name="schema",
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subcommand_metavar="COMMAND <args>",
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short_help="Apply and validate the cellxgene data integration schema to an h5ad file.",
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context_settings=dict(max_content_width=85, help_option_names=["-h", "--help"]),
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)
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def schema_cli():
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try:
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import scanpy # noqa: F401
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except ImportError:
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raise click.ClickException(
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"[cellxgene] cellxgene schema requires scanpy"
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)
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@click.command(
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name="apply",
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short_help="(experimental) Apply the cellxgene data integration schema to an h5ad.",
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help="(experimental) Using a yaml file that describes schema values to insert or convert and in input "
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"h5ad file, apply the schema changes and create a new, conforming h5ad.",
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)
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@click.option(
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"--source-h5ad",
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help="Input h5ad file.",
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nargs=1,
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required=True,
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type=click.Path(exists=True, dir_okay=False),
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)
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@click.option(
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"--remix-config",
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help="Config yaml with information on how to apply the schema.",
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nargs=1,
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required=True,
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type=click.Path(exists=True, dir_okay=False),
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)
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@click.option(
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"--output-filename",
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help="Filename for the new, schema-conforming h5ad file.",
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required=True,
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nargs=1
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)
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def schema_apply(source_h5ad, remix_config, output_filename):
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remix.apply_schema(source_h5ad, remix_config, output_filename)
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@click.command(
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name="validate",
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short_help="(experimental) Check that an h5ad follows the cellxgene data integration schema.",
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)
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@click.argument(
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"h5ad",
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nargs=1,
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type=click.Path(exists=True, dir_okay=False),
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)
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@click.option(
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"--shallow",
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help="When true, just check that the correct version information is present.",
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default=False,
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show_default=True,
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is_flag=True,
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)
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def schema_validate(h5ad, shallow):
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validate.validate(h5ad, shallow)
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schema_cli.add_command(schema_apply)
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schema_cli.add_command(schema_validate)
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