basistest-cron.sh

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#! /bin/bash
##############################################################################
# @file  basistest-cron.sh
# @brief Script intended to be run as cron job to perform automated testing.
#
# This script sets up the environment for the actual master script which
# handles the automated testing. Further, it uses qsub to submit testing jobs
# to the configured SGE queue, with the SGE options as set in this script.
#
# Edit this script to change the settings of the automated testing.
# The default settings are the ones used for the cron job running on the
# cluster of our lab as the 'swtest' user.
#
# The configuration of automated tests is done in the configuration file
# for the basistest-master.sh. See value of conf variable below.
#
# Copyright (c) 2011 University of Pennsylvania. All rights reserved.<br />
# See https://www.cbica.upenn.edu/sbia/software/license.html or COPYING file.
#
# Contact: SBIA Group <sbia-software at uphs.upenn.edu>
#
# @ingroup Tools
##############################################################################


# constants used by the shflags.sh module
HELP_COMMAND='basistest-cron (BASIS)'
HELP_CONTACT='SBIA Group <sbia-software at uphs.upenn.edu>'
HELP_VERSION='version 1.2.3 (revision 2104)'
HELP_COPYRIGHT='Copyright (c) University of Pennsylvania. All rights reserved.
See https://www.rad.upenn.edu/sbia/software/license.html or COPYING file.'


# ----------------------------------------------------------------------------
## @brief Get real path of given file or directory.
#
# @note This function was substituted by BASIS either for the string
#       \@BASIS_BASH_UTILITIES\@ or \@BASIS_BASH_FUNCTION_realpath\@.
#
# Example:
# @code
# exec_dir=`realpath $0`
# @endcode
#
# @param [in] path File or directory path.
#
# @returns Canonical path.
#
# @sa http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script
function realpath
{
    local path=$1

    local linkdir=''
    local symlink=''

    while [ -h ${path} ]; do
        # 1) change to directory of the symbolic link
        # 2) change to directory where the symbolic link points to
        # 3) get the current working directory
        # 4) append the basename
        linkdir=$(dirname -- "${path}")
        symlink=$(readlink ${path})
        path=$(cd "${linkdir}" && cd $(dirname -- "${symlink}") && pwd)/$(basename -- "${symlink}")
    done

    echo -n "$(cd -P -- "$(dirname "${path}")" && pwd -P)/$(basename -- "${path}")"
}

readonly _SBIA_BASIS_BASISTEST_CRON_DIR="$(dirname -- "$(realpath "$(cd -P -- "$(dirname -- "${BASH_SOURCE}")" && pwd -P)/$(basename -- "$BASH_SOURCE")")")"
source "${_SBIA_BASIS_BASISTEST_CRON_DIR}/../lib/basis.sh" || exit 1


# ============================================================================
# constants
# ============================================================================

get_executable_directory _EXEC_DIR  && readonly _EXEC_DIR
get_executable_name      _EXEC_NAME && readonly _EXEC_NAME

# ============================================================================
# settings
# ============================================================================

## @brief Whether to use SGE or not.
sge=1

## @brief SGE queue; set to '' to not specify any.
queue='centos5'

## @brief Mail address for SGE notifications; set to '' to disable notifications.
mail=''

## @brief Output file for test log; used for -o and -e option of qsub.
log='/sbia/home/swtest/var/log/basistest-$JOB_ID.log'

## @brief Maximum number of days for which log files should be kept.
max_log_mtime=7

## @brief Configuration file; configure the automated tests here, see <tt>basistestd -h</td>.
conf='/sbia/home/swtest/etc/basistest.conf'

## @brief Schedule file; note that this file is created/updated by the testing daemon.
schedule='/sbia/home/swtest/var/run/basistest.schedule'

## @brief CTest script.
#
# Has to be given with full path because SGE copies the slave script which
# looks for the CTest script relative to its own location.
ctest="${_EXEC_DIR}/../share/cmake/basistest.ctest"

## @brief Testing master script.
master="${_EXEC_DIR}/basistest-master"

## @brief Test execution command.
#
# Note: We use a fixed site name for the tests. This allows the test job to be
#       run on any compute node with the same system installation without
#       having CDash list submissions from these different notes as separate.
#       In particular, the numbers of how many tests are now succeeding compared
#       to previous runs, or how many are now failing would otherwise be confusing
#       when the tests are not regularly run at one and the same site, but
#       different sites which represent the same operating system and configuration.
slave="${_EXEC_DIR}/basistest-slave -v -S ${ctest} --args site=sbia-cluster-centos5,shared-source,shared-build"

# ============================================================================
# main
# ============================================================================

dry='false'

while [ $# -gt 0 ]; do
    case "$1" in
        -h|--help)
            echo "Usage:"
            echo "  ${_EXEC_NAME}"
            echo
            echo "Description:"
            echo "  This command should be run regularly by a cron job. It contains"
            echo "  all the fixed settings for the execution of the basistest master"
            echo "  command, which is simply executed by this command."
            echo
            echo "Optional arguments:"
            echo "  --dry   Dry run, i.e., do not actually invoke the test execution command."
            echo
            print_contact
            exit 0
            ;;

        --helpshort)
            echo "Usage:"
            echo "  ${_EXEC_NAME}"
            echo
            print_contact
            exit 0
            ;;

        --version)
            print_version 'basistest-cron'
            exit 0
            ;;

        --dry)
            dry='true';
            ;;

        *)
            echo "Invalid argument $1! See ${_EXEC_NAME} --help." 1>&2
            exit 1
            ;;
    esac
    shift
done

# source environment settings of test user
source /sbia/home/swtest/.bashrc || exit 1

# prepend test command by qsub command
if [ ${sge} -ne 0 ]; then
    tmpslave=$(mktemp -t 'basistest-XXXXXX')
    echo "#! /usr/bin/env bash" >> "${tmpslave}"
    echo "# temporarily generated by basistest-cron for submission to SGE" >> "${tmpslave}"
    echo "${slave} \"\$@\"" >> "${tmpslave}"
    submit='qsub -cwd'
    if [ ! -z "${queue}" ]; then submit="${submit} -l ${queue}"; fi
    if [ ! -z "${mail}" ];  then submit="${submit} -M ${mail} -m b -m e -m a"; fi
    if [ ! -z "${log}" ];   then submit="${submit} -o ${log} -j y"; fi
    slave="${submit} ${tmpslave}"
fi

# remove log files that are older than max_log_mtime (days)
if [ ! -z "${log}" ]; then
    log_dir=${log//\$JOB_ID/\*}
    log_dir_ok=0
    if [[ $(uname) == 'Darwin' ]]; then
        if [[ "${log_dir}" =~ ^/sbia/home/swtest/var/ ]]; then
            log_dir_ok=1
        fi
    else
        if [[ "${log_dir}" =~ '^/sbia/home/swtest/var/' ]]; then
            log_dir_ok=1
        fi
    fi
    if [ ${log_dir_ok} -eq 1 ]; then
        find ${log_dir} -mtime "+${max_log_mtime}" -exec rm -f '{}' ';' 2> /dev/null
    else
        echo "WARNING: Attempting to delete old log files from directory other than /sbia/home/swtest/var/." 1>&2
        echo "WARNING: Skipping removal of any files. Update basistest-cron.sh to account for changed location of log files!" 1>&2
    fi
fi

# run actual testing master
if [ "$dry" == 'true' ]; then
    ${master} '--dry' -c "${conf}" -s "${schedule}" -t "${slave}"
else
    ${master} -c "${conf}" -s "${schedule}" -t "${slave}"
fi

# remove SGE submission script (SGE copied it already)
[ -n "${tmpslave}" ] && rm -f "${tmpslave}"