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update_r_packages: kill the stuck processes, and exit immediately if nothing changed in the SVN repository and the argument was 'install'. See https://support.d4science.org/issues/10272

This commit is contained in:
Andrea Dell'Amico 2017-11-08 18:54:18 +01:00
parent f11655bb1b
commit 5b50d86b9e
1 changed files with 23 additions and 4 deletions
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27
R/templates/update_r_packages.sh.j2
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@ -1,4 +1,8 @@
#!/bin/bash #!/bin/bash
#
# TODO: kill an old process if it is running from too much time (12 hours?)
# using something like ps -o etimes= -p "$PROCNUM"
#
export PATH="$PATH:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin" export PATH="$PATH:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin"
@ -19,6 +23,9 @@ R_PKGS_SVN_DIR=RPackagesManagement
R_PKGS_SVN_URL={{ r_package_updater_subversion_repo }} R_PKGS_SVN_URL={{ r_package_updater_subversion_repo }}
R_PKGS_SVN_BASE_DIR={{ r_packages_svn_base_dir }} R_PKGS_SVN_BASE_DIR={{ r_packages_svn_base_dir }}
R_PKGS_FILES_PREFIX={{ r_packages_svn_files_prefix }} R_PKGS_FILES_PREFIX={{ r_packages_svn_files_prefix }}
SVN_UPDATE_STATUS=
# In seconds. 60*60*6=21600s (6h)
UPDATER_PROCESS_MAX_RUNTIME=21600
# - debian packages list format: # - debian packages list format:
# one package per line # one package per line
DEB_PKGS_SKIP=0 DEB_PKGS_SKIP=0
@ -65,7 +72,6 @@ function fail() {
exit 1 exit 1
} }
function init_env() { function init_env() {
if [ -f $LOCK_FILE ] ; then if [ -f $LOCK_FILE ] ; then
OLDPROC=$( cat $LOCK_FILE ) OLDPROC=$( cat $LOCK_FILE )
@ -73,8 +79,15 @@ function init_env() {
RETVAL=$? RETVAL=$?
if [ $RETVAL -eq 0 ] ; then if [ $RETVAL -eq 0 ] ; then
logger "update_r_packages: $OLDPROC_RUNNING" logger "update_r_packages: $OLDPROC_RUNNING"
logger "update_r_packages: another process is running, exiting." OLDPROC_RUNNING_TIME=$( ps -o etimes= -p ${PROCNUM} )
exit 0 if [ $OLDPROC_RUNNING_TIME > $UPDATER_PROCESS_MAX_RUNTIME ] ; then
logger "update_r_packages: process $OLDPROC_RUNNING got stuck, killing it"
kill -9 $OLDPROC_RUNNING
cleanup
else
logger "update_r_packages: another process is running, exiting."
exit 0
fi
else else
logger "update_r_packages: lock file exist but the process not. Continuing." logger "update_r_packages: lock file exist but the process not. Continuing."
rm -fr $TMP_FILES_DIR rm -fr $TMP_FILES_DIR
@ -119,7 +132,8 @@ function get_data_files_from_svn() {
if [ -d $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR ] ; then if [ -d $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR ] ; then
logger "update_r_packages: SVN update" logger "update_r_packages: SVN update"
cd $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR cd $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR
svn update >/dev/null 2>&1 SVN_UPDATE_OP=$( svn update | tail -1 | grep Updated >/dev/null 2>&1 )
SVN_UPDATE_STATUS=$?
else else
cd $R_PKGS_SVN_BASE_DIR cd $R_PKGS_SVN_BASE_DIR
logger "update_r_packages: first SVN checkout." logger "update_r_packages: first SVN checkout."
@ -198,6 +212,11 @@ get_args
init_env init_env
if [ $R_PKGS_FROM_SVN == 'True' ] ; then if [ $R_PKGS_FROM_SVN == 'True' ] ; then
get_data_files_from_svn get_data_files_from_svn
if [ $SVN_UPDATE_STATUS -ne 0 -a "$ACTION" == "install" ] ; then
logger "update_r_packages: nothing new to install from SVN, exiting"
cleanup
exit 0
fi
else else
get_data_files get_data_files
fi fi