use flock for scheduled task

stanstrup · Jun 24, 2019 · f89956b · f89956b
1 parent 948aa61
commit f89956b
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/setup/Dockerfile b/setup/Dockerfile
@@ -75,7 +75,7 @@ COPY ./setup /srv/shiny-server/QC4Metabolomics/setup/
 
 
 FROM base AS process
-##### Scheduled jobs ######################################################
+##### Scheduled jobs ##########################################################
 RUN apt-get update && \
 	apt-get install  -y \
 	\
@@ -84,7 +84,7 @@ RUN apt-get update && \
 
 
 RUN R -e "BiocManager::install('bnosac/cronR')"
-RUN R -e "library(cronR);cmd <- cron_rscript('/srv/shiny-server/QC4Metabolomics/setup/scheduled_tasks.R', rscript_log = '/var/log/QC_cron.log');cron_add(cmd, frequency = '*/1 * * * *', id = 'QC_processing', description = 'Process files every 1 minute')"
+RUN R -e "library(cronR);cmd <- cron_rscript('/srv/shiny-server/QC4Metabolomics/setup/scheduled_tasks.sh', cmd = '/bin/bash', rscript_log = '/var/log/QC_cron.log');cron_add(cmd, frequency = '*/1 * * * *', id = 'QC_processing', description = 'Process files every 1 minute')"
 ###############################################################################
 
 

diff --git a/setup/scheduled_tasks.R b/setup/scheduled_tasks.R
@@ -1,3 +1,5 @@
+message("====================================================\nRunning scheduled tasks at: ", Sys.time(), "\n====================================================")
+
 setwd("/srv/shiny-server/QC4Metabolomics/")
 source(".Rprofile")
 

diff --git a/setup/scheduled_tasks.sh b/setup/scheduled_tasks.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+[ "${FLOCKER}" != "$0" ] && exec env FLOCKER="$0" flock -n "$0" "$0" "$@" || :
+
+/usr/local/bin/Rscript '/srv/shiny-server/QC4Metabolomics/setup/scheduled_tasks.R'