mirror of
https://github.com/chanzuckerberg/cellxgene.git
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af3c6e1d8e
* split out config * add tests for base and app config, refactor client config out of app config * refactor default config retrieval * create config test class and helper functions * move default_config into server to fix import issue
134 lines
4.4 KiB
Python
134 lines
4.4 KiB
Python
from os import path
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import click
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from server.converters.h5ad_data_file import H5ADDataFile
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@click.command(
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name="convert",
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short_help="Converts an H5AD dataset to the CXG format.",
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help="Converts an H5AD dataset to the CXG format. The CXG format is a cellxgene-private data format "
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"that has performance and access characteristics amenable to a multi-dataset, multi-user serving "
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"environment. You will be able to launch the cellxgene using the `cellxgene launch` command as "
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"usually with the generated CXG file.",
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)
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@click.argument(
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"input-file", nargs=1, type=click.Path(exists=True, dir_okay=False),
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)
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@click.option(
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"-o",
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"--output-directory",
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help="Name of the output CXG directory. If not provided, will default to be the input filename with a "
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"CXG extension.",
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)
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@click.option(
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"-b",
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"--backed",
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help="When true, loads the H5AD in file backed mode. This will cause the conversion to be slower, "
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"but will use less memory.",
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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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@click.option(
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"-t",
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"--title",
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help="Human readable dataset title that will be included as metadata about the CXG file. If omitted, "
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"the dataset title will be the filename.",
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)
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@click.option(
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"-a",
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"--about",
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help="A fully qualified URL that provides more information about the dataset and will be included as "
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"metadata about the CXG file.",
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)
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@click.option(
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"-s",
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"--sparse-threshold",
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help="If the dataset's percent of non-zero values falls belows the specified threshold, then the X "
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"array of the dataset will be sparse. Since the default value is 0.0, the default will be to "
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"convert to dense array.",
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default=0.0,
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show_default=True,
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)
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@click.option(
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"--obs-names",
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help="Name to a column in the obs dataframe that will be used as the index for the dataframe instead of "
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"the one designated by the dataframe generated-index.",
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)
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@click.option(
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"--var-names",
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help="Name to a column in the var dataframe that will be used as the index for the dataframe instead of "
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"the one designated by the dataframe generated-index.",
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)
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@click.option(
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"--disable-custom-colors",
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help="When set, conversion process will not extract scanpy-compatible category colors from the H5AD file.",
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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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@click.option(
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"--disable-corpora-schema",
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help="When set, conversion process will neither extract nor store Corpora schema information. See "
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"https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/corpora_schema.md for more "
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"information.",
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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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@click.option(
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"--overwrite",
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help="When set to true, will overwrite the output file if the output file already exists.",
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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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@click.help_option("--help", "-h", help="Show this message and exit.")
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def convert_to_cxg(
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input_file,
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output_directory,
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backed,
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title,
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about,
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sparse_threshold,
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obs_names,
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var_names,
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disable_custom_colors,
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disable_corpora_schema,
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overwrite,
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):
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"""
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Convert a dataset file into CXG.
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"""
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h5ad_data_file = H5ADDataFile(
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input_file, backed, title, about, obs_names, var_names, use_corpora_schema=not disable_corpora_schema
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)
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# Get the directory that will hold all the CXG files
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cxg_output_container = get_output_directory(input_file, output_directory, overwrite)
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h5ad_data_file.to_cxg(
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cxg_output_container, sparse_threshold, convert_anndata_colors_to_cxg_colors=not disable_custom_colors
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)
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def get_output_directory(input_filename, output_directory, should_overwrite):
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"""
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Get the name of the CXG output directory to be created/populated during the dataset conversion.
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"""
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if output_directory and (not path.isdir(output_directory) or (path.isdir(output_directory) and should_overwrite)):
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if output_directory.endswith(".cxg"):
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return output_directory
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return output_directory + ".cxg"
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if output_directory and path.isdir(output_directory) and not should_overwrite:
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raise click.BadParameter(
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f"Output directory {output_directory} already exists. If you'd like to overwrite, then run the command "
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f"with the --overwrite flag."
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)
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return path.splitext(input_filename)[0] + ".cxg"
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