Our BioHPC database is hosted on cbsujohnson.biohpc.cornell.edu. Once you created a BioHPC account, you can ssh to the machine using
ssh <your NetID>@cbsujohnson.biohpc.cornell.edu |
Then, if you run docker1 ps, you can see the Docker container of our database
This container is created and run by Zack, one of our previous team members, and the script he used is located at /workdir/ztb5/mongo/.
Currently, the backup is done by a Cron job that executes the script /home/ts864/mongoDbBackup/dumpJob.sh at 4:00 AM every day. The content of the script is provided below
# Scheduled to run daily at 4am. # Captures and stores the current state of the database. mongodump --uri="mongodb://mongodbuser:2TQFTnrQYb2yQFhYqnCUGxesurPISnXwhsFHyfP2cr4ILQeUk1@cbsujohnson.biohpc.cornell.edu:8001/?authSource=admin&readPreference=primary&appname=MongoDB%20Compass&ssl=false" \ -o=/home/ts864/mongoDbBackup/dumpData/dump-$(date +%Y-%m-%d) # Deletes backups created more than and including 7 days ago. find /home/ts864/mongoDbBackup/dumpData/dump-* -mtime +7 -delete |
It is scheduled using command crontab -e. The backups are stored in a /home directory because BioHPC automatically backups home directories nightly.
To restore the backups to a target DB, run the following command
mongorestore --uri=<target DB URI> --drop path-to-backup-folder/ |
In order to allow Lambdas to access public Internet, for every Lambda make sure to use cu-cals-johnson-lab-vpc for VPC and use both cu-cals-johnson-lab-subnet-private-1 and cu-cals-johnson-lab-subnet-private-2 for subnets. This can be done during the creation of a new Lambda or in the Configuration tab of an existing Lambda.
The EC2 instances used for deploying backend services are created following the procedure starting from step 3 of this tutorial (https://medium.com/@umairnadeem/deploy-to-aws-using-docker-compose-simple-210d71f43e67) with the following modifications.