BioHPC

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Database

Where is the DB hosted

Our BioHPC database is hosted on cbsujohnson.biohpc.cornell.edu. Once you created a BioHPC account, you can ssh to the machine using

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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/.

How to backup/restore the DB

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

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mongorestore --uri=<target DB URI> --drop path-to-backup-folder/

AWS

Lambda

For every Lambda, make sure to do the following configuration in the Configuration tab.

• In Configuration - VPC, 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 enables the Lambda to access public Internet.
• In Configuration - Permissions, use lambda-ex as the Execution Role.

EC2

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.

1. When creating an instance, we reuse existing key pairs instead of creating new ones.
2. We retrieve our codebase using git instead of scp.