MedBook

Parent repo for the MedBook project.

Getting started

# clone this repo
git clone https://github.com/UCSC-MedBook/MedBook
cd MedBook

# initialize and update all submodules
./init.sh

# set up the required environmental variables
# NOTE: on medbook.io these are stored in a file: `source ~/set_up_environment.sh`
export MONGO_URL=mongodb://mongo/MedBook
export MAIL_URL="smtp://EMAIL:[email protected]"
export WORLD_URL="medbook.io" # URL where this instance will be deployed

# start all the apps
docker-compose up

The last line (docker-compose up) assumes you have a seperate box for the mongo database. To run mongo as a docker image, call ./startDev.sh.

Setting up cBioPortal

# move the sql db to where you can restore it from
mv dump.sql /mnt/mysql-dump

# start the mysql container (as well as the other apps)
docker-compose up

# connect to the sql database and restore from dump.sql
docker exec -it mysql /bin/bash

# restore from dump.sql from within the docker container (uncompressed)
mysql -h localhost -u cbio -pP@ssword1;
use cbioportal; # `CREATE DATABASE CBIOPORTAL` if it doesn't exist already
source /mysql-dump/dump.sql;

# restore from dump.sql.gz within the docker container (compressed)
zcat /mysql-dump/dump_new.sql.gz | mysql -h localhost -u cbio -pP@ssword1 cbioportal

Backups

Backups are created every day at 3:30 am. Currently backups are not deleted, and we will run out of space for backups around October 20th.

The backup files are stored here: backup.medbook.io:/backups. /backups is a 500gb volume mounted using Azure. The production box has ssh access to backups.medbook.io if access needs to be granted to other machines.

Manually creating a backup

~/MedBook/scripts/create_backup.sh will create a backup from mongo and /filestore.

A couple notes/gotchas:

• Backups are named as follows: backup.[hostname].[year]-[month]-[day]_[hour]-[minute]-[second]
• Backups on the production machine run at /backup (a mounted disk) so there's enough space to dump and compress the database.
• When a backup is run on the production machine (HOSTNAME="medbook-prod") the backup is restored on staging as part of the backup script.
• The mongo host is assumed to be localhost except for on medbook-prod (medbook.io) and medbook-staging-2 (staging.medbook.io), where the hostname is hardcoded as mongo and mongo-staging respectively.
• Anyone can create a backup from any machine, so long as they have scp access to backup.medbook.io. This could be useful if someone had run a migration and wanted to share the migrated data with someone.

Manually restoring from a backup

~/MedBook/scripts/restore_from_backup.sh [backup name] will restore from the specified backup. Do not include .tgz in the backup name.

The restore command deletes everything in the mongo database as well as /filestore and then replaces it with the backup's data.

Currently the only way to view stored backups is by sshing into backup.medbook.io. On that box, the backups are stored at /backups.

Technically, all apps should be stopped before restoring from a backup. Currently, they aren't stopped on staging when we restore at ~4 am because no one is using staging at that time and it hasn't caused any problems yet. Problems could arise if a user created objects (or created a new user) before the new mongo data was restored, which would cause the mongorestore command to fail.