コード例 #1
0
ファイル: do.py プロジェクト: zhangyupisa/bcbio-nextgen
def run(cmd,
        descr=None,
        data=None,
        checks=None,
        region=None,
        log_error=True,
        log_stdout=False,
        env=None):
    """Run the provided command, logging details and checking for errors.
    """
    if descr:
        descr = _descr_str(descr, data, region)
        logger.debug(descr)
    cmd_id = diagnostics.start_cmd(cmd, descr or "", data)
    try:
        logger_cl.debug(" ".join(
            str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks, log_stdout, env=env)
    except:
        diagnostics.end_cmd(cmd_id, False)
        if log_error:
            logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #2
0
ファイル: do.py プロジェクト: kenongit/bcbio-nextgen
def run(cmd, descr, data, checks=None):
    """Run the provided command, logging details and checking for errors.
    """
    if data:
        descr = "{0} : {1}".format(descr, data["name"][-1])
    logger.info(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        _do_run(cmd, checks)
    except:
        diagnostics.end_cmd(cmd_id, False)
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #3
0
def run(cmd, descr, data, checks=None):
    """Run the provided command, logging details and checking for errors.
    """
    if data:
        descr = "{0} : {1}".format(descr, data["name"][-1])
    logger.info(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        _do_run(cmd, checks)
    except:
        diagnostics.end_cmd(cmd_id, False)
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #4
0
ファイル: do.py プロジェクト: brentp/bcbio-nextgen
def run(cmd, descr, data=None, checks=None):
    """Run the provided command, logging details and checking for errors.
    """
    if data:
        descr = "{0} : {1}".format(descr, data["name"][-1])
    logger.debug(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        logger_cl.debug(" ".join(cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks)
    except:
        diagnostics.end_cmd(cmd_id, False)
        logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #5
0
ファイル: do.py プロジェクト: cauyrd/bcbio-nextgen
def run(cmd, descr, data=None, checks=None, region=None, log_error=True,
        log_stdout=False):
    """Run the provided command, logging details and checking for errors.
    """
    descr = _descr_str(descr, data, region)
    logger.debug(descr)
    cmd_id = diagnostics.start_cmd(cmd, descr, data)
    try:
        logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks, log_stdout)
    except:
        diagnostics.end_cmd(cmd_id, False)
        if log_error:
            logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #6
0
ファイル: do.py プロジェクト: MCowperthwaite/bcbio-nextgen
def run(cmd, descr, data=None, checks=None, region=None, log_error=True):
    """Run the provided command, logging details and checking for errors.
    """
    descr = _descr_str(descr, data, region)
    logger.debug(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        logger_cl.debug(" ".join(cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks)
    except:
        diagnostics.end_cmd(cmd_id, False)
        if log_error:
            logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #7
0
ファイル: do.py プロジェクト: yangjl/bcbio-nextgen
def run(cmd, descr, data, checks=None):
    """Run the provided command, logging details and checking for errors.
    """
    if data:
        descr = "{0} : {1}".format(descr, data["name"][-1])
    logger.debug(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        logger_cl.debug(
            " ".join(cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks)
    except:
        diagnostics.end_cmd(cmd_id, False)
        logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)
コード例 #8
0
def run(cmd, descr, data=None, checks=None, region=None, log_error=True,
        log_stdout=False):
    """Run the provided command, logging details and checking for errors.
    """
    descr = _descr_str(descr, data, region)
    logger.debug(descr)
    # TODO: Extract entity information from data input
    cmd_id = diagnostics.start_cmd(descr, data, cmd)
    try:
        logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
        _do_run(cmd, checks, log_stdout)
    except:
        diagnostics.end_cmd(cmd_id, False)
        if log_error:
            logger.exception()
        raise
    finally:
        diagnostics.end_cmd(cmd_id)