schrodinger.application.bb_database.bb_arg_utils module

Does argument parsing and validation for bb_database_driver.py.

Copyright Schrodinger LLC, All Rights Reserved.

schrodinger.application.bb_database.bb_arg_utils.BB_TASK

alias of schrodinger.application.bb_database.bb_arg_utils.BBTask

exception schrodinger.application.bb_database.bb_arg_utils.BBValidationError

Bases: Exception

Used to simplify error passing in argument validation code.

schrodinger.application.bb_database.bb_arg_utils.add_build_args(subparsers: argparse._SubParsersAction) → None

Add arguments for TASK.BUILD.

schrodinger.application.bb_database.bb_arg_utils.add_describe_args(subparsers: argparse._SubParsersAction) → None

Add arguments for TASK.DESCRIBE.

schrodinger.application.bb_database.bb_arg_utils.add_jobcontrol_args(parser: argparse.ArgumentParser, task: str) → None

Adds the ‘Job Control Options’ argument group to the supplied parser. Note that -HOST, -TMPDIR, -JOBNAME and -NOJOBID are all removed from the command line before reaching the parser, so these arguments are provided here only for the benefit of the help message. See -run_in_foreground for important information about running bb_database within a workflow.

schrodinger.application.bb_database.bb_arg_utils.add_key_file_args(parser: argparse.ArgumentParser) → None

Adds the ‘Key File Options’ argument group to the supplied parser.

schrodinger.application.bb_database.bb_arg_utils.add_optional_args_group(parser: argparse.ArgumentParser) → argparse._ArgumentGroup

Adds an ‘Optional Arguments’ argument group to the supplied parser with a standard -h, –help message and returns the argument group.

schrodinger.application.bb_database.bb_arg_utils.add_qsplit_args(subparsers: argparse._SubParsersAction) → None

Add arguments for TASK.QSPLIT.

schrodinger.application.bb_database.bb_arg_utils.add_qrun_args(subparsers: argparse._SubParsersAction) → None

Add arguments for TASK.QRUN.

schrodinger.application.bb_database.bb_arg_utils.get_key_files(bbkeys: str) → list[str]

Returns key file names based on the bbkeys argument.

schrodinger.application.bb_database.bb_arg_utils.get_parser() → argparse.ArgumentParser

Creates argparse.ArgumentParser with supported command line options.

schrodinger.application.bb_database.bb_arg_utils.get_slice_limits(s: str) → tuple[int, int]

Returns slice limits parsed from a string of the form <min>:<max>, where either limit may be missing, in which case None is returned for the limt. Raises a ValueError if exactly one colon is not present, if <min> >= <max> or if a non-numeric limit is provided.

schrodinger.application.bb_database.bb_arg_utils.validate_bbkeys(args: argparse.Namespace) → None

Raises a BBValidationError if args.bbkeys is invalid.

schrodinger.application.bb_database.bb_arg_utils.validate_build_args(args: argparse.Namespace) → None

Raises a BBValidationError if the TASK.BUILD arguments are invalid.

schrodinger.application.bb_database.bb_arg_utils.validate_dbpath(dbpath: str) → None

Raises a BBValidationError if dbpath has the wrong extension or is not an absolute path.

schrodinger.application.bb_database.bb_arg_utils.validate_qrun_args(args: argparse.Namespace) → None

Raises a BBValidationError if the TASK.QRUN arguments are invalid.

schrodinger.application.bb_database.bb_arg_utils.validate_qsplit_args(args: argparse.Namespace) → None

Raises a BBValidationError if the TASK.QSPLIT arguments are invalid.

schrodinger.application.bb_database.bb_arg_utils.validate_slice_limits(s: str)

Raises a BBValidation error if the provided slice specification is invalid.

schrodinger.application.bb_database.bb_arg_utils.validate_args(args: argparse.Namespace) → tuple[bool, str]

Checks the validity of parsed command line arguments at startup time, and returns a tuple of validity and a non-empty error message if not valid.