MongoDB 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 hosted 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 installation/configuration

These are the one time setup steps for MongoDB:

Assuming you are on Ubuntu and using the apt package manager:

apt update
apt install mongodb

This may be an outdated MongoDB. To follow the best security practices and get the latest features, you should install something more recent. More information about installing and configuring MongoDB 3.6 is available here: https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/

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

More broadly, the MongoDB security checklist should be followed. Critically, you should enable access control and set up an authentication database and credentials for at least one administrator.

Some key things to configure in /etc/mongodb.conf:

Set the path of the database to the correct location. You may need to sudo chown mongodb /path/to/database for permissions to work
Add the public IP of the server to bind_ip setting so it reads like 127.0.0.1,XXX.XXX.XXX.XX for your server’s IP XXX.XXX.XXX.XX.
Set a non-standard port if you want one
Enable authentication (assuming you enabled authentication and set up an administrator database and user)

MongoDB operation

Managing the MongoDB service

This section assumes that you already have your VM set up and your are managing it under linux environment.

The MongoDB server is managed by a systemd service that is managed through systemctl. Common commands are:

Check status of mongodb service:
```
sudo systemctl status mongodb
```
Start mongodb service:
```
sudo systemctl start mongodb
```
Shut down mongodb service:
```
sudo systemctl stop mongodb
```
Restart mongodb service (if it’s already running):
```
sudo systemctl restart mongodb
```

Connecting to the MongoDB server console

This section deals with your MongoDB database management to locally or remotely operate on it. This is to say you are going to manage your database from your local computer by mongo or mongosh.

#note mongosh by MongoDB Shell is the quickest way to connect, configure, query, and work with your MongoDB database

Create admin user for mongodb

These are the one time setup steps for MongoDB:

With access control enabled, ensure you have a user with userAdmin or userAdminAnyDatabase role in the admin database. This user can administrate user and roles such as: create users, grant or revoke roles from users, and create or modify customs roles.

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

Connect to the instance by open another terminal in your VM and connect a mongo shell to the instance:
```
mongod --port 27018
```

after the prompt “>” input:

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

Re-start the MongoDB instance with access control
1. Shut down the mongod instance
2. Exit the mongo shell by run the command exit or give an EOF (Ctrl+D)
3. Start the mongod with access control enabled by
adding the security.authorization configuration file setting

security: authorization: enabled

or If you start the mongod from the command line

mongod --auth --port 27018

Create general user

Assuming the service is running and configured with authentication (see above), Connect to your mongoDB as admin user locally by:

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

or remotelly by:

mongo 146.186.149.69:27018 --authenticationDatabase admin -u <admin username> -p <admin password>

or remotelly use mongosh by:

mongosh --username <admin username> --password --authenticationDatabase admin --host 146.186.149.69 --port 27018

followed by inputting the following lines after the prompt “>”:

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)
```