slicer.org scripts

%etc%cron.d%spl

# Unlike any other crontab you don't have to run the 'crontab'
# command to install the new version when you edit this file
# and other files in /etc/cron.d
#
# These files also have username fields,
# which user crontabs do not - making this more flexible as a solution to put
# all your crons in one place.
#
# System cron is in /etc/crontab and you generally don't want to edit that file
                                                                                                                                                                                                                                                                     
SHELL=/bin/sh                                                                                                                                                                                                                                                        
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin                                                                                                                                                                                          
# set the MAILTO variable so that I get notices of this job                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
MAILTO=greg@equality-tech.com                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
####  FORMAT of cron NOTE the user field here                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
# minute hour dayofmonth month dayofweek user  command                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                
# fetch any upstream edits to the static content of slicer.org into DOC_ROOT discarding STDOUT                                                                                                                                                                  
*/5 * * * * root /var/www/slicer.org/bin/pull.github.sh > /dev/null
# */30 * * * * greg curl "https://issues.slicer.org/plugin.php?page=Source/import&id=all&api_key=<YOUR_API_KEY>"
 
# This job will keep MediaWiki happy
0 0 * * * root /usr/bin/php /var/www/slicer.org/www/w/maintenance/runJobs.php 2> /var/log/runJobs.log
10 0 * * * root /usr/bin/php /var/www/na-mic.org/www/w/maintenance/runJobs.php 2> /var/log/runJobs.log

#### Backup our databases every day 
15 04 * * * root /root/bin/backup.db.sh slicer_slicerWiki_wiki
20 04 * * * root /usr/bin/find /backups -mtime +15 -exec rm {} \;

#### Renew our LetsEncrypt certificates automatically every week because they expire every 90 days
#### Hitting their server when the cert is valid is not a problem
05 04 * * 1 root /opt/certbot/certbot-auto renew -q

%root%bin%backup.db.sh

#!/bin/bash
# @author Greg Rundlett <info@eQuality-Tech.com>
# This is a quick shell script to create a sql dump of your database.
# You may need to adjust the path of mysqldump, 
# or sudo apt-get install mysqldump  if it doesn't exist
# set -x # show execution
# set -v # show verbose

# To configure this script, 
# you could hardcode which database to backup
# DB=wiki
# We'll make it so you can pass the database name as the first parameter 
# to the script.  If no parameter is passed, we'll prompt you for the name
DB=$1
if [ $# -ne 1 ]; then 
  echo "Here are the current databases on the server"
  mysql -u root --batch --skip-column-names -e 'show databases;'
  echo "Enter the name of the database you want to backup"
  read DB
fi
# We'll use a location that is exported to the host, so that our backups are 
# accessible even if the virtual machine is no longer accessible.
# backupdir="/vagrant/mediawiki/backups";
backupdir="/backups";
if [ ! -d "$backupdir" ]; then
  mkdir -p "$backupdir";
fi

# we'll start with a default backup file named '01' in the sequence
backup="${backupdir}/dump-$(date +%F).$(hostname)-${DB}.01.sql";
# and we'll increment the counter in the filename if it already exists
i=1
filename=$(basename "$backup") # foo.txt (basename is everything after the last slash)
# shell parameter expansion see http://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html
extension=${filename##*.}    # .txt (filename with the longest matching pattern of *. being deleted)
file=${filename%.*}        # foo (filename with the shortest matching pattern of .* deleted)
file=${file%.*}        # repeat the strip to get rid of the counter
# file=${filename%.{00..99}.$extension} # foo (filename with the shortest matching pattern of .[01-99].* deleted)
while [ -f $backup ]; do
  backup="$backupdir/${file}.$(printf '%.2d' $(( i+1 ))).${extension}"
  i=$(( i+1 ))  # increments $i 
  # note that i is naked because $(( expression )) is arithmetic expansion in bash
done

backedup=$(/usr/bin/mysqldump "$DB" > "$backup")

/usr/bin/mysqldump "$DB" > "$backup" || ( echo "Something went wrong with the backup" && exit 1 )

verbose=false;

if $verbose; then
  echo "backup created successfully"
  ls -al "$backup";
  echo "A command such as"
  echo "mysql -u root $DB < $backup" 
  echo "will restore the database from the chosen sql dump file"
fi

%var%www%slicer.org%bin%pull.github.sh

#!/bin/sh

DOC_ROOT=/var/www/slicer.org/www
cd $DOC_ROOT
# we don't need to checkout the branch because we will only ever be on the branch
# git checkout gh-pages
git pull