Scripts.WorkflowScripts.Workflow_utils module

Scripts.WorkflowScripts.Workflow_utils.run_command(command, error_message='Command failed', working_dir=None)

Run a shell command and exit on failure.

Parameters:

• command – The shell command to execute (string).

• error_message – Message to display if the command fails.

• working_dir – Optional working directory in which to run the command.

Raises:

SystemExit – Exits with code 1 if the command fails.

Scripts.WorkflowScripts.Workflow_utils.run_python_script(script_path, args=None, error_message='Python script failed', working_dir=None)

Execute a Python script with the current interpreter and optional arguments.

Parameters:

• script_path – Path to the Python script to run.

• args – List of arguments to pass to the script (defaults to []).

• error_message – Message to display if execution fails.

• working_dir – Optional working directory in which to run the script.

Raises:

SystemExit – Exits with code 1 if the script execution fails.

Scripts.WorkflowScripts.Workflow_utils.get_databank_paths(NMLDB_ROOT_PATH)

Retrieve relevant paths from databank.

Parameters:

NMLDB_ROOT_PATH – Root path of the database repository.

Returns:

Dictionary mapping descriptive keys to full paths of databank components.

Return type:

dict

Scripts.WorkflowScripts.Workflow_utils.delete_info_file(info_file_path)

Delete an information file at the specified path, warning on failure.

Parameters:

info_file_path – Path to the info file to be removed.

Raises:

OSError – Prints a warning if the file cannot be deleted.