From bc905f4cfa7eb70955e411eaf8126996f30e41dc Mon Sep 17 00:00:00 2001
From: Trent Smith <1429913+Bento007@users.noreply.github.com>
Date: Tue, 3 Dec 2024 11:19:15 -0800
Subject: [PATCH] fix: clean up the cli (#1108)

---
 cellxgene_schema_cli/cellxgene_schema/cli.py  | 37 +++++++++----------
 .../cellxgene_schema/validate.py              |  4 --
 2 files changed, 18 insertions(+), 23 deletions(-)

diff --git a/cellxgene_schema_cli/cellxgene_schema/cli.py b/cellxgene_schema_cli/cellxgene_schema/cli.py
index 33fce82b6..1254a7ba1 100644
--- a/cellxgene_schema_cli/cellxgene_schema/cli.py
+++ b/cellxgene_schema_cli/cellxgene_schema/cli.py
@@ -1,7 +1,10 @@
+import logging
 import sys
 
 import click
 
+logger = logging.getLogger("cellxgene_schema")
+
 
 @click.group(
     name="schema",
@@ -9,11 +12,13 @@
     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():
-    pass
+@click.option("-v", "--verbose", help="When present will set logging level to debug", is_flag=True)
+def schema_cli(verbose):
+    logging.basicConfig(level=logging.ERROR)
+    logger.setLevel(logging.DEBUG if verbose else logging.INFO)
 
 
-@click.command(
+@schema_cli.command(
     name="validate",
     short_help="Check that an h5ad follows the cellxgene data integration schema.",
     help="Check that an h5ad follows the cellxgene data integration schema. If validation fails this command will "
@@ -31,27 +36,25 @@ def schema_cli():
     type=click.Path(exists=False, dir_okay=False, writable=True),
 )
 @click.option("-i", "--ignore-labels", help="Ignore ontology labels when validating", is_flag=True)
-@click.option("-v", "--verbose", help="When present will set logging level to debug", is_flag=True)
-def schema_validate(h5ad_file, add_labels_file, ignore_labels, verbose):
+def schema_validate(h5ad_file, add_labels_file, ignore_labels):
     # Imports are very slow so we defer loading until Click arg validation has passed
-
-    print("Loading dependencies")
+    logger.info("Loading dependencies")
     try:
         import anndata  # noqa: F401
     except ImportError:
         raise click.ClickException("[cellxgene] cellxgene-schema requires anndata") from None
 
-    print("Loading validator modules")
+    logger.info("Loading validator modules")
     from .validate import validate
 
-    is_valid, _, _ = validate(h5ad_file, add_labels_file, ignore_labels=ignore_labels, verbose=verbose)
+    is_valid, _, _ = validate(h5ad_file, add_labels_file, ignore_labels=ignore_labels)
     if is_valid:
         sys.exit(0)
     else:
         sys.exit(1)
 
 
-@click.command(
+@schema_cli.command(
     name="remove-labels",
     short_help="Create a copy of an h5ad without portal-added labels",
     help="Create a copy of an h5ad without portal-added labels.",
@@ -61,24 +64,24 @@ def schema_validate(h5ad_file, add_labels_file, ignore_labels, verbose):
 def remove_labels(input_file, output_file):
     from .remove_labels import AnnDataLabelRemover
 
-    print("Loading dependencies")
+    logger.info("Loading dependencies")
     try:
         import anndata  # noqa: F401
     except ImportError:
         raise click.ClickException("[cellxgene] cellxgene-schema requires anndata") from None
 
-    print(f"Loading h5ad from {input_file}")
+    logger.info(f"Loading h5ad from {input_file}")
     adata = anndata.read_h5ad(input_file)
     anndata_label_remover = AnnDataLabelRemover(adata)
     if not anndata_label_remover.schema_def:
         return
-    print("Removing labels")
+    logger.info("Removing labels")
     anndata_label_remover.remove_labels()
-    print(f"Labels have been removed. Writing to {output_file}")
+    logger.info(f"Labels have been removed. Writing to {output_file}")
     anndata_label_remover.adata.write(output_file, compression="gzip")
 
 
-@click.command(
+@schema_cli.command(
     name="migrate",
     short_help="Convert an h5ad to the latest schema version.",
     help="Convert an h5ad from the previous to latest minor schema version. No validation will be "
@@ -94,9 +97,5 @@ def migrate(input_file, output_file, collection_id, dataset_id):
     migrate(input_file, output_file, collection_id, dataset_id)
 
 
-schema_cli.add_command(schema_validate)
-schema_cli.add_command(migrate)
-schema_cli.add_command(remove_labels)
-
 if __name__ == "__main__":
     schema_cli()
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
index 434983bc0..4f92ef053 100644
--- a/cellxgene_schema_cli/cellxgene_schema/validate.py
+++ b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -2130,10 +2130,6 @@ def validate(
 
     # Perform validation
     start = datetime.now()
-    if verbose:
-        logging.basicConfig(level=logging.DEBUG)
-    else:
-        logging.basicConfig(level=logging.INFO, format="%(message)s")
     validator = Validator(
         ignore_labels=ignore_labels,
     )