float_config.py

#!/usr/bin/env python3

import yaml

from snakemake.common import get_container_image

from float_utils import logger


class FloatConfig:
    _CONFIG_FILE = 'snakemake-float.yaml'
    _REQUIRED_KWARGS = {'work-dir', 'data-volumes'}
    _SUPPORTED_KWARGS = _REQUIRED_KWARGS.union({
        'job-prefix',
        'base-image',
        'cpu',
        'mem',
        'submit-extra'
    })

    def __init__(self, config_file=_CONFIG_FILE):
        self._parameters = {'base-image': get_container_image()}

        try:
            with open(config_file) as cf:
                kwargs = yaml.safe_load(cf)
        except OSError:
            logger.exception('Cannot open float config file')
            raise
        except yaml.YAMLError:
            logger.exception(f"Cannot load YAML: {self._CONFIG_FILE}")
            raise

        for kwarg in self._REQUIRED_KWARGS:
            if kwarg not in kwargs:
                msg = f"{config_file} missing required argument: '{kwarg}'"
                logger.error(msg)
                raise TypeError(msg)

        for kwarg in kwargs:
            if kwarg not in self._SUPPORTED_KWARGS:
                msg = f"{config_file} has unsupported argument: '{kwarg}'"
                logger.warning(msg)

        self._parameters.update(kwargs)

    def parameters(self):
        return self._parameters