Fix incorrect logger calls (#1186)

chanzuckerberg · Jun 5, 2024 · 75fa725 · 75fa725
1 parent 5ac71a4
commit 75fa725
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/experiment_builder.py b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/experiment_builder.py
@@ -282,7 +282,7 @@ def get_obs_and_var(
             obs_column_names=CXG_OBS_COLUMNS_READ,
             var_column_names=CXG_VAR_COLUMNS_READ,
         ) as adata:
-            logging.debug(f"{dataset.dataset_id}/{spec.name} - found {adata.n_obs} cells")
+            logger.debug(f"{dataset.dataset_id}/{spec.name} - found {adata.n_obs} cells")
 
             # Skip this dataset if there are not cells after filtering
             if adata.n_obs == 0:

diff --git a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py
@@ -1111,7 +1111,7 @@ def validate(args: CensusBuildArgs) -> int:
     with create_dask_client(args, n_workers=n_workers, threads_per_worker=1, memory_limit=None) as client:
         assert all(r.result() for r in distributed.wait(validate_soma(args, client)).done)
         shutdown_dask_cluster(client)
-        logging.info("Validation complete.")
+        logger.info("Validation complete.")
 
     assert validate_consolidation(args)
     logger.info("Validating correct consolidation and vacuuming - complete")

diff --git a/tools/census_contrib/src/census_contrib/__main__.py b/tools/census_contrib/src/census_contrib/__main__.py
@@ -236,7 +236,7 @@ def load_qc_anndata(
 
 def create_qc_plots(config: Config, embedding: Path) -> None:
     if config.metadata.data_type == "var_embedding":
-        logging.info("Skipping QC plots for var embedding")
+        logger.info("Skipping QC plots for var embedding")
         return
 
     sc._settings.settings.autoshow = False

diff --git a/tools/perf_checker/perf_checker.py b/tools/perf_checker/perf_checker.py
@@ -42,18 +42,18 @@ def format_string(text: str) -> Any:
     formatted_first_profile = json.dumps(format_string(str(attr.asdict(first_profile))))
     formatted_curr_profile = json.dumps(format_string(str(attr.asdict(curr_profile))))
 
-    logging.info("****************************")
-    logging.info(f"Current time {curr_time} vs first time {first_time}")
-    logging.info("****************************")
-    logging.info(f"First profile: {formatted_first_profile}")
-    logging.info("****************************")
-    logging.info(f"Current profile: {formatted_curr_profile}")
-    logging.info("****************************")
-    logging.info(
+    logger.info("****************************")
+    logger.info(f"Current time {curr_time} vs first time {first_time}")
+    logger.info("****************************")
+    logger.info(f"First profile: {formatted_first_profile}")
+    logger.info("****************************")
+    logger.info(f"Current profile: {formatted_curr_profile}")
+    logger.info("****************************")
+    logger.info(
         f"TileDB version ver = first: {first_profile.tiledbsoma_version} curr: {curr_profile.tiledbsoma_version}"
     )
     if float(curr_time) > threshold * float(first_time):
         raise SystemExit(f"Major performance degradation detected on {args.command}")
 
     if threshold * float(curr_time) < float(first_time):
-        logging.info(f"Major performance increase detected on {args.command}")
+        logger.info(f"Major performance increase detected on {args.command}")