Merge pull request #1185 from VisLab/add_examples

Worked on making script logging more uniform

Author: VisLab

hed/cli/cli.py

@@ -191,7 +191,9 @@ def validate():
     is_flag=True,
     help="Disable all logging output",
 )
+@click.pass_context
 def validate_bids_cmd(
+    ctx,
     data_path,
     error_limit,
     errors_by_file,
@@ -244,7 +246,8 @@ def validate_bids_cmd(
         args.append("-x")
         args.extend(exclude_dirs)
 
-    validate_bids_main(args)
+    result = validate_bids_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @validate.command(
@@ -354,7 +357,9 @@ def validate_bids_cmd(
     is_flag=True,
     help="Disable all logging output",
 )
+@click.pass_context
 def validate_hed_string_cmd(
+    ctx,
     hed_string,
     schema_version,
     definitions,
@@ -395,14 +400,16 @@ def validate_hed_string_cmd(
     if verbose:
         args.append("-v")
 
-    validate_string_main(args)
+    result = validate_string_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @schema.command(name="validate")
 @click.argument("schema_path", type=click.Path(exists=True), nargs=-1, required=True)
 @click.option("--add-all-extensions", is_flag=True, help="Always verify all versions of the same schema are equal")
 @click.option("-v", "--verbose", is_flag=True, help="Enable verbose output")
-def schema_validate_cmd(schema_path, add_all_extensions, verbose):
+@click.pass_context
+def schema_validate_cmd(ctx, schema_path, add_all_extensions, verbose):
     """Validate HED schema files.
 
     This command validates HED schema files for correctness, checking structure,
@@ -434,13 +441,15 @@ def schema_validate_cmd(schema_path, add_all_extensions, verbose):
     if verbose:
         args.append("-v")
 
-    validate_schemas_main(args)
+    result = validate_schemas_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @schema.command(name="convert")
 @click.argument("schema_path", type=click.Path(exists=True), nargs=-1, required=True)
 @click.option("--set-ids", is_flag=True, help="Set/update HED IDs in the schema")
-def schema_convert_cmd(schema_path, set_ids):
+@click.pass_context
+def schema_convert_cmd(ctx, schema_path, set_ids):
     """Convert HED schema between formats (TSV, XML, MEDIAWIKI, JSON).
 
     This command converts HED schema files between different formats while
@@ -467,14 +476,16 @@ def schema_convert_cmd(schema_path, set_ids):
     if set_ids:
         args.append("--set-ids")
 
-    convert_main(args)
+    result = convert_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @schema.command(name="add-ids")
 @click.argument("repo_path", type=click.Path(exists=True))
 @click.argument("schema_name")
 @click.argument("schema_version")
-def schema_add_ids_cmd(repo_path, schema_name, schema_version):
+@click.pass_context
+def schema_add_ids_cmd(ctx, repo_path, schema_name, schema_version):
     """Add HED IDs to a schema.
 
     This command adds unique HED IDs to schema elements that don't have them,
@@ -498,7 +509,8 @@ def schema_add_ids_cmd(repo_path, schema_name, schema_version):
 
     args = [repo_path, schema_name, schema_version]
 
-    add_ids_main(args)
+    result = add_ids_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @cli.group()
@@ -613,8 +625,19 @@ def extract():
     is_flag=True,
     help="Suppress log output to stderr; only applicable when --log-file is used (logs go only to file)",
 )
+@click.pass_context
 def extract_bids_sidecar_cmd(
-    data_path, suffix, value_columns, skip_columns, log_level, log_file, log_quiet, output_file, verbose, exclude_dirs
+    ctx,
+    data_path,
+    suffix,
+    value_columns,
+    skip_columns,
+    log_level,
+    log_file,
+    log_quiet,
+    output_file,
+    verbose,
+    exclude_dirs,
 ):
     """Extract a sidecar template from a BIDS dataset.
 
@@ -643,7 +666,8 @@ def extract_bids_sidecar_cmd(
         args.append("-x")
         args.extend(exclude_dirs)
 
-    extract_main(args)
+    result = extract_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 @extract.command(
@@ -781,7 +805,9 @@ def extract_bids_sidecar_cmd(
     is_flag=True,
     help="Suppress log output to stderr; only applicable when --log-file is used (logs go only to file)",
 )
+@click.pass_context
 def extract_tabular_summary_cmd(
+    ctx,
     data_path,
     name_prefix,
     name_suffix,
@@ -834,7 +860,8 @@ def extract_tabular_summary_cmd(
     if verbose:
         args.append("-v")
 
-    extract_summary_main(args)
+    result = extract_summary_main(args)
+    ctx.exit(result if result is not None else 0)
 
 
 def main():

hed/scripts/extract_tabular_summary.py

@@ -45,6 +45,7 @@
 from hed import _version as vr
 from hed.tools.util.io_util import get_file_list
 from hed.tools.analysis.tabular_summary import TabularSummary
+from hed.scripts.script_utils import setup_logging
 
 
 def get_parser():
@@ -338,57 +339,6 @@ def format_output(summary, args):
         return json.dumps(output_dict, indent=4)
 
 
-def setup_logging(args):
-    """Configure logging based on command line arguments.
-
-    Parameters:
-        args (argparse.Namespace): Parsed command line arguments.
-
-    Returns:
-        logging.Logger: Configured logger instance.
-    """
-    # Determine log level
-    log_level = args.log_level.upper() if args.log_level else "WARNING"
-    if args.verbose:
-        log_level = "INFO"
-
-    # Configure logging format
-    log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-    date_format = "%Y-%m-%d %H:%M:%S"
-
-    # Clear any existing handlers from root logger
-    root_logger = logging.getLogger()
-    for handler in root_logger.handlers[:]:
-        root_logger.removeHandler(handler)
-
-    # Set the root logger level
-    root_logger.setLevel(getattr(logging, log_level))
-
-    # Create formatter
-    formatter = logging.Formatter(log_format, datefmt=date_format)
-
-    # File handler if log file specified
-    if args.log_file:
-        file_handler = logging.FileHandler(args.log_file, mode="w", encoding="utf-8")
-        file_handler.setLevel(getattr(logging, log_level))
-        file_handler.setFormatter(formatter)
-        root_logger.addHandler(file_handler)
-
-    # Console handler (stderr) unless explicitly quieted and file logging is used
-    if not args.log_quiet or not args.log_file:
-        console_handler = logging.StreamHandler(sys.stderr)
-        console_handler.setLevel(getattr(logging, log_level))
-        console_handler.setFormatter(formatter)
-        root_logger.addHandler(console_handler)
-
-    logger = logging.getLogger("extract_tabular_summary")
-    logger.info(f"Starting tabular summary extraction with log level: {log_level}")
-    if args.log_file:
-        logger.info(f"Log output will be saved to: {args.log_file}")
-
-    return logger
-
-
 def main(arg_list=None):
     """Main entry point for the script.
 
@@ -406,7 +356,15 @@ def main(arg_list=None):
     args = parser.parse_args(arg_list)
 
     # Setup logging
-    logger = setup_logging(args)
+    setup_logging(args.log_level, args.log_file, args.log_quiet, args.verbose, False)
+    logger = logging.getLogger("extract_tabular_summary")
+    effective_level = logging.getLevelName(logger.getEffectiveLevel())
+    logger.info(
+        f"Starting tabular summary extraction with effective log level: {effective_level} "
+        f"(requested: {args.log_level}, verbose={'on' if args.verbose else 'off'})"
+    )
+    if args.log_file:
+        logger.info(f"Log output will be saved to: {args.log_file}")
 
     try:
         # Extract the summary

hed/scripts/hed_convert_schema.py

@@ -72,12 +72,12 @@ def convert_and_update(filenames, set_ids):
     return 0
 
 
-def main():
+def main(arg_list=None):
     parser = argparse.ArgumentParser(description="Update other schema formats based on the changed one.")
     parser.add_argument("filenames", nargs="*", help="List of files to process")
     parser.add_argument("--set-ids", action="store_true", help="Add missing HED ids")
 
-    args = parser.parse_args()
+    args = parser.parse_args(arg_list)
 
     filenames = args.filenames
     set_ids = args.set_ids

hed/scripts/hed_extract_bids_sidecar.py

@@ -35,6 +35,7 @@
 import sys
 from hed import _version as vr
 from hed.tools import BidsDataset
+from hed.scripts.script_utils import setup_logging
 
 
 def get_parser():
@@ -219,41 +220,14 @@ def main(arg_list=None):
     args = parser.parse_args(arg_list)
 
     # Setup logging configuration
-    log_level = args.log_level.upper() if args.log_level else "WARNING"
-    if args.verbose:
-        log_level = "INFO"
-
-    # Configure logging format
-    log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-    date_format = "%Y-%m-%d %H:%M:%S"
-
-    # Clear any existing handlers from root logger
-    root_logger = logging.getLogger()
-    for handler in root_logger.handlers[:]:
-        root_logger.removeHandler(handler)
-
-    # Set the root logger level - this is crucial for filtering
-    root_logger.setLevel(getattr(logging, log_level))
-
-    # Create and configure handlers
-    formatter = logging.Formatter(log_format, datefmt=date_format)
-
-    # File handler if log file specified
-    if args.log_file:
-        file_handler = logging.FileHandler(args.log_file, mode="w", encoding="utf-8")
-        file_handler.setLevel(getattr(logging, log_level))
-        file_handler.setFormatter(formatter)
-        root_logger.addHandler(file_handler)
-
-    # Console handler (stderr) unless explicitly quieted and file logging is used
-    if not args.log_quiet or not args.log_file:
-        console_handler = logging.StreamHandler(sys.stderr)
-        console_handler.setLevel(getattr(logging, log_level))
-        console_handler.setFormatter(formatter)
-        root_logger.addHandler(console_handler)
+    setup_logging(args.log_level, args.log_file, args.log_quiet, args.verbose, False)
 
     logger = logging.getLogger("extract_bids_sidecar")
-    logger.info(f"Starting BIDS sidecar extraction with log level: {log_level}")
+    effective_level = logging.getLevelName(logger.getEffectiveLevel())
+    logger.info(
+        f"Starting BIDS sidecar extraction with effective log level: {effective_level} "
+        f"(requested: {args.log_level}, verbose={'on' if args.verbose else 'off'})"
+    )
     if args.log_file:
         logger.info(f"Log output will be saved to: {args.log_file}")
 

hed/scripts/validate_bids.py

@@ -201,13 +201,19 @@ def main(arg_list=None):
 
     # Parse the arguments
     args = parser.parse_args(arg_list)
-    print(f"{str(args)}")
 
     # Set up logging
     setup_logging(args.log_level, args.log_file, args.log_quiet, args.verbose, args.no_log)
 
     logger = logging.getLogger("validate_bids")
-    logger.info(f"Starting BIDS validation with log level: {args.log_level}")
+    logger.debug("Parsed arguments: %s", args)
+    effective_level_name = logging.getLevelName(logger.getEffectiveLevel())
+    logger.info(
+        "Starting BIDS validation with effective log level: %s (requested: %s, verbose=%s)",
+        effective_level_name,
+        args.log_level,
+        "on" if args.verbose else "off",
+    )
     if args.log_file:
         logger.info(f"Log output will be saved to: {args.log_file}")
 

hed/scripts/validate_hed_string.py

@@ -98,6 +98,15 @@ def main(arg_list=None):
 
     import logging
 
+    logger = logging.getLogger("validate_hed_string")
+    effective_level_name = logging.getLevelName(logger.getEffectiveLevel())
+    logger.info(
+        "Starting HED string validation with effective log level: %s (requested: %s, verbose=%s)",
+        effective_level_name,
+        args.log_level,
+        "on" if args.verbose else "off",
+    )
+
     try:
         # Load schema (handle single version or list of versions)
         schema_versions = args.schema_version[0] if len(args.schema_version) == 1 else args.schema_version

hed/scripts/validate_schemas.py

@@ -19,9 +19,9 @@ def get_parser():
     return parser
 
 
-def main():
+def main(arg_list=None):
     parser = get_parser()
-    args = parser.parse_args()
+    args = parser.parse_args(arg_list)
 
     schema_files = sort_base_schemas(args.schema_files, args.add_all_extensions)
     issues = validate_all_schemas(schema_files)