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data_extract_cli.py
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data_extract_cli.py
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# -*- coding: utf-8 -*-
"""sup3r data extraction CLI entry points."""
import logging
import click
import sup3r
from sup3r import __version__
from sup3r.utilities import ModuleName
from sup3r.utilities.cli import AVAILABLE_HARDWARE_OPTIONS, BaseCLI
logger = logging.getLogger(__name__)
@click.group()
@click.version_option(version=__version__)
@click.option('-v', '--verbose', is_flag=True,
help='Flag to turn on debug logging. Default is not verbose.')
@click.pass_context
def main(ctx, verbose):
"""Sup3r Data Extraction Command Line Interface"""
ctx.ensure_object(dict)
ctx.obj['VERBOSE'] = verbose
@main.command()
@click.option('--config_file', '-c', required=True,
type=click.Path(exists=True),
help='sup3r data extract configuration json file.')
@click.option('-v', '--verbose', is_flag=True,
help='Flag to turn on debug logging. Default is not verbose.')
@click.pass_context
def from_config(ctx, config_file, verbose=False, pipeline_step=None):
"""Run sup3r data extraction from a config file.
Parameters
----------
ctx : click.pass_context
Click context object where ctx.obj is a dictionary
config_file : str
Filepath to sup3r data extraction json file.
verbose : bool
Flag to turn on debug logging. Default is not verbose.
pipeline_step : str, optional
Name of the pipeline step being run. If ``None``, the
``pipeline_step`` will be set to the ``module_name``,
mimicking old reV behavior. By default, ``None``.
"""
config = BaseCLI.from_config_preflight(ModuleName.DATA_EXTRACT, ctx,
config_file, verbose)
config["pipeline_step"] = pipeline_step
exec_kwargs = config.get('execution_control', {})
hardware_option = exec_kwargs.pop('option', 'local')
config_handler = config.get('handler_class', 'DataHandler')
HANDLER_CLASS = getattr(sup3r.preprocessing.data_handling, config_handler)
cmd = HANDLER_CLASS.get_node_cmd(config)
cmd_log = '\n\t'.join(cmd.split('\n'))
logger.debug(f'Running command:\n\t{cmd_log}')
if hardware_option.lower() in AVAILABLE_HARDWARE_OPTIONS:
kickoff_slurm_job(ctx, cmd, **exec_kwargs)
else:
kickoff_local_job(ctx, cmd)
def kickoff_local_job(ctx, cmd, pipeline_step=None):
"""Run sup3r data extraction locally.
Parameters
----------
ctx : click.pass_context
Click context object where ctx.obj is a dictionary
cmd : str
Command to be submitted in shell script. Example:
'python -m sup3r.cli data_extract -c <config_file>'
pipeline_step : str, optional
Name of the pipeline step being run. If ``None``, the
``pipeline_step`` will be set to the ``module_name``,
mimicking old reV behavior. By default, ``None``.
"""
BaseCLI.kickoff_local_job(ModuleName.DATA_EXTRACT, ctx, cmd, pipeline_step)
def kickoff_slurm_job(ctx, cmd, pipeline_step=None, alloc='sup3r',
memory=None, walltime=4, feature=None,
stdout_path='./stdout/'):
"""Run sup3r on HPC via SLURM job submission.
Parameters
----------
ctx : click.pass_context
Click context object where ctx.obj is a dictionary
cmd : str
Command to be submitted in SLURM shell script. Example:
'python -m sup3r.cli data_extract -c <config_file>'
pipeline_step : str, optional
Name of the pipeline step being run. If ``None``, the
``pipeline_step`` will be set to the ``module_name``,
mimicking old reV behavior. By default, ``None``.
alloc : str
HPC project (allocation) handle. Example: 'sup3r'.
memory : int
Node memory request in GB.
walltime : float
Node walltime request in hours.
feature : str
Additional flags for SLURM job. Format is "--qos=high"
or "--depend=[state:job_id]". Default is None.
stdout_path : str
Path to print .stdout and .stderr files.
"""
BaseCLI.kickoff_slurm_job(ModuleName.DATA_EXTRACT, ctx, cmd, alloc, memory,
walltime, feature, stdout_path, pipeline_step)
if __name__ == '__main__':
try:
main(obj={})
except Exception:
logger.exception('Error running sup3r data extraction CLI')
raise