MongoDB Virtual Machines (VM) hosting

This section is for the dfttk users who want to host their MongoDB by themselves.

MongoDB is one of the most popular document-oriented databases under the banner of NoSQL database. The schema-free implementation of MongoDB eliminates the prerequisites of defining a fixed structure required by the SQL database.

In computing, a virtual machine (VM) is an emulation of a computer system. Virtual machines are based on computer architectures and provide functionality of a physical computer. Their implementations may involve specialized hardware, software, or a combination. See https://en.wikipedia.org/wiki/Virtual_machine

Our MongoDB databases are currently by Penn State’s VM hosting service that provides cost-effective, reliable VM for departments, colleges, and research units at Penn State University.

In our case, we have changed the default tcp port from 27017 into 27018 due to historical reason

VM operation

Connect your VM by ssh (ssh youruserid@146.186.149.69 in our case). One should use VPN if you have firewall for your system

• To add user to your VM linux system

  Run the follwing command under Linux

sudo adduser newuser
usermod -aG sudo newuser #add admin user to your VM

Note on adding other users to access the VM. In order to add other users to access the VM from the Morpheus portal you would need to add them to the VM. For the VM itself you would need to add their user ID to the /etc/security/access.conf file and if they need sudo access you would need to add their ID to the /etc/sudoers.d/sudo-users file as well.

MongoDB operation

• MongoDB installation

  Run the follwing command

apt update
apt install mongodb

More information about installing and configuring MongoDB 3.6 is available here: https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/

If you would like the most recent version of MongoDB (4.4), please reference this guide for installation and configuration instructions for Ubuntu 18.04: https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/. #Note: In step 2 of the link listed above, please reference the command for Ubuntu 18.04 (Bionic)

Additional configuration info for MongoDB 4.4 can be found here: https://www.digitalocean.com/community/tutorials/how-to-install-mongodb-on-ubuntu-18-04-source

• Start mongdb service

mongod --bind_ip_all -port 27018 &

• Shut down mongdb service

db.adminCommand( { shutdown: 1 } )

For more details on MongodB user management, see https://docs.mongodb.com/manual/tutorial/enable-authentication/

• Connect to MongoDB by port 27018 for management

mongod -port 27018

• Quit from MongoDB

  hit Ctrl+d

• Create admin user for mongdb

After connected to your mongoDB by mongo -port 27018, input the following lines

use admin
db.createUser(
  {
    user: "admin",
    pwd: "xxxxxxxxx", // xxxxxxxx is the admin password of your choice
    roles: [ { role: "userAdminAnyDatabase", db: "admin" }, "readWriteAnyDatabase" ]
  }
)

• Create general user

Connect to your mongoDB as admin user by

mongo --port 27018 --authenticationDatabase "admin" -u "admin" -p

followed by inputting the following lines

use userid-fws
db.createUser({user: "userid", pwd: "B5nRcUvoCZ92", roles: [{role: "dbOwner", db: "userid-fws"}]})
use userid-results
db.createUser({user: "userid", pwd: "BeFihJ2mrKGm", roles: [{role: "dbOwner", db: "userid-results"}]})
db.createUser({user: "userid-ro", pwd: "QIvaUT9ca6H8", roles: [{role: "read", db: "userid-results"}]})

These lines can be produced by dfttk by run a python code named mongodb_user.py which can be downlonded from https://github.com/PhasesResearchLab/dfttk/tree/master/dfttk/scripts After download the code, one can run it by

python mongodb_user.py

The run will prompt the MongoDB system manager to input an userid for the user. After you input userid and hit enter, one gets the above outputs in the screen.

Meanwhile, a file named db.json in the JSON format containing something similiar to the following lines which should be sent to the MongoDB user.

{
    "database": "userid-results",
    "collection": "tasks",
    "admin_user": "userid",
    "admin_password": "BeFihJ2mrKGm",
    "readonly_user": "userid-ro",
    "readonly_password": "QIvaUT9ca6H8",
    "host": "146.186.149.69",
    "port": 27018,
    "aliases": {}
}

The MongoDB user should save this data in a json file named db.json under the path dfttk/config that created by dfttk config -mp -aci command.

• Remove user

db.removeUser(username)

• Check if mongodb is running, use

ps -ef | grep mongo