diff --git a/clpipe/bids_validator.py b/clpipe/bids_validator.py index 76338ae2..14ab2e33 100644 --- a/clpipe/bids_validator.py +++ b/clpipe/bids_validator.py @@ -45,11 +45,6 @@ def bids_validate( ) sys.exit(1) - # batch_manager = BatchManager( - # config.batch_config_path, output_directory=log_dir, debug=debug - # ) - # batch_manager.update_mem_usage(DEFAULT_MEMORY_USAGE) - batch_manager = JobManagerFactory.get( batch_config=config.batch_config_path, output_directory=log_dir, @@ -57,9 +52,6 @@ def bids_validate( mem_use=DEFAULT_MEMORY_USAGE ) - # Not sure what this is doing tbh - config.bids_validation.bids_validator_image - singularity_string = SINGULARITY_CMD_TEMPLATE if verbose: logger.debug("Verbose mode: on") @@ -70,31 +62,20 @@ def bids_validate( singularity_string.format( validatorInstance=config.bids_validation.bids_validator_image, bidsDir=bids_dir, - bindPaths=batch_manager.config["SingularityBindPaths"], + bindPaths=batch_manager.config.singularity_bind_paths, ) ) logger.info("Validation complete.") else: - # batch_manager.addjob( - # Job( - # "BIDSValidator", - # singularity_string.format( - # validatorInstance=config.bids_validation.bids_validator_image, - # bidsDir=config.fmriprep.bids_directory, - # bindPaths=batch_manager.config["SingularityBindPaths"], - # ), - # ) - # ) - batch_manager.addjob( - "BIDSValidator", + batch_manager.add_job( + STEP_NAME, singularity_string.format( validatorInstance=config.bids_validation.bids_validator_image, bidsDir=config.fmriprep.bids_directory, - bindPaths=batch_manager.config["SingularityBindPaths"], + bindPaths=batch_manager.config.singularity_bind_paths, ) ) - # batch_manager.compilejobstrings() if submit: logger.info("Running BIDS validation in batch mode.") batch_manager.submit_jobs()