Add schema subcommand (#1939)

Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands.

The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema.

The second takes an h5ad and checks if it follows the schema version written into its metadata.

Both are currently marked as "experimental" as the primary intended users are still at CZI.

server/cli/cli.py

@@ -4,6 +4,7 @@ from .convert_to_cxg import convert_to_cxg
 from .launch import launch
 from .prepare import prepare
 from .upgrade import log_upgrade_check
+from .schema import schema_cli
 from .. import __version__
 
 
@@ -31,3 +32,4 @@ def cli(upgrade_check):
 cli.add_command(launch)
 cli.add_command(prepare)
 cli.add_command(convert_to_cxg)
+cli.add_command(schema_cli)

server/cli/schema.py

@@ -0,0 +1,72 @@
+import click
+
+from server.converters.schema import remix, validate
+
+
+@click.group(
+    name="schema",
+    subcommand_metavar="COMMAND <args>",
+    short_help="Apply and validate the cellxgene data integration schema to an h5ad file.",
+    context_settings=dict(max_content_width=85, help_option_names=["-h", "--help"]),
+)
+def schema_cli():
+    try:
+        import scanpy  # noqa: F401
+    except ImportError:
+        raise click.ClickException(
+            "[cellxgene] cellxgene schema requires scanpy"
+        )
+
+
+@click.command(
+    name="apply",
+    short_help="(experimental) Apply the cellxgene data integration schema to an h5ad.",
+    help="(experimental) Using a yaml file that describes schema values to insert or convert and in input "
+    "h5ad file, apply the schema changes and create a new, conforming h5ad.",
+)
+@click.option(
+    "--source-h5ad",
+    help="Input h5ad file.",
+    nargs=1,
+    required=True,
+    type=click.Path(exists=True, dir_okay=False),
+)
+@click.option(
+    "--remix-config",
+    help="Config yaml with information on how to apply the schema.",
+    nargs=1,
+    required=True,
+    type=click.Path(exists=True, dir_okay=False),
+)
+@click.option(
+    "--output-filename",
+    help="Filename for the new, schema-conforming h5ad file.",
+    required=True,
+    nargs=1
+)
+def schema_apply(source_h5ad, remix_config, output_filename):
+    remix.apply_schema(source_h5ad, remix_config, output_filename)
+
+
+@click.command(
+    name="validate",
+    short_help="(experimental) Check that an h5ad follows the cellxgene data integration schema.",
+)
+@click.argument(
+    "h5ad",
+    nargs=1,
+    type=click.Path(exists=True, dir_okay=False),
+)
+@click.option(
+    "--shallow",
+    help="When true, just check that the correct version information is present.",
+    default=False,
+    show_default=True,
+    is_flag=True,
+)
+def schema_validate(h5ad, shallow):
+    validate.validate(h5ad, shallow)
+
+
+schema_cli.add_command(schema_apply)
+schema_cli.add_command(schema_validate)