Clean up dead/hosted code [zh2310] (#2430)

* Clean up dead/hosted code

* Remove schema conversion tool and related
* Remove cxg references
* Remove locust

* missed a spot

* Remove aws secret manager

* Merge branch 'main' into brodgers/2310/code-cleanup-v1

* cleanup merge

backend/server/cli/cli.py

@@ -3,7 +3,6 @@ import click
 from .launch import launch
 from .prepare import prepare
 from .upgrade import log_upgrade_check
-from .schema import schema_cli
 from .. import __version__
 
 
@@ -30,4 +29,3 @@ def cli(upgrade_check):
 
 cli.add_command(launch)
 cli.add_command(prepare)
-cli.add_command(schema_cli)

backend/server/cli/schema.py

@@ -1,72 +0,0 @@
-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)