Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)

* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands

backend/server/cli/schema.py

@@ -0,0 +1,72 @@
+import click
+
+from backend.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)