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Installing MongoDB Community Version

On Ubuntu

On MacOS

On Windows

Directories and Files (config, logs, data)

These are the default locations for some important mongodb files.

On Ubuntu

  • config file : /etc/mongod.conf
  • log directory : /var/log/mongodb
  • data directotry : /var/lib/mongodb

On MacOS Intel Processor

  • config file : /usr/local/etc/mongod.conf
  • log directory : /usr/local/var/log/mongodb
  • data directotry : /usr/local/var/mongodb

On MacOS M1 Processor

  • config file : /opt/homebrew/etc/mongod.conf
  • log directory : /opt/homebrew/var/log/mongodb
  • data directory : /opt/homebrew/var/mongodb

To start/stop/restart the MongoDB daemon

When running as a service, the default config file will be used

On Ubuntu

  • $ sudo systemctl start mongod
  • $ sudo systemctl stop mongod
  • $ sudo systemctl restart mongod

On MacOS

  • $ brew services start mongodb/brew/mongodb-community
  • $ brew services stop mongodb/brew/mongodb-community
  • $ brew services restart mongodb/brew/mongodb-community

To manually start MongoDB with a custom config file

For MacOS Intel Processors

  • $ mongod --config /usr/local/etc/mongod.conf --fork

For MacOS M1 processors

  • $ mongod --config /opt/homebrew/etc/mongod.conf --fork
  • NOTE: This could be useful when needing to run a test database with separate log files and data directory. Or we could use the same log files and the same data directory and instead just create a new database covizu_test within the Mongo application.

To open the Command Line Tool for MongoDB a.k.a mongosh

  • $ mongosh

Database Authorization

  • By default MongoDB does not seem to enable any authorization. Meaning anyone can connect to our database on port:27017 and CRUD our data.
  • However, it might be different for you. When trying to open the cli if you get an error that looks like this
Current Mongosh Log ID:	63fc56344c05787dbf853d87
Connecting to:mongodb://127.0.0.1:27017/?directConnection=true&serverSelectionTimeoutMS=2000&appName=mongosh+1.7.1
MongoNetworkError: connect ECONNREFUSED 127.0.0.1:27017

then it probably means your MongoDB has locked you out. You need to disable authorization.

  • To enable/disable authorization, open the afore-mentioned mongod.conf configuraiton file.
  • Add (remove) the following lines to the bottom of the config file to enable (disable) authorization
security:
  authorization: enabled

NOTE : That whitespace between authorization: and enabled might be crucial.

  • After editing those lines, restart the MongoDB daemon.
  • To confirm that you've succesfully enabled(disabled) authorization, open mongosh without any auth token.
    • $ mongosh
  • Switch to the admin database
    • $ use admin
  • View all the databases
    • $ show databases
  • If MongoDB prints out something like this then you've succesfully disabled (unsuccesfully enabled) authentication.
admin> show databases
admin     180.00 KiB
config    108.00 KiB
local     120.00 KiB
  • If instead, MongoDB prints out something like this then you've succesfully enabled (unsuccesfully disabled) authentication.
admin> show databases
MongoServerError: command listDatabases requires authentication

Creating user accounts

  • On first install, we need to create a admin account, and a covizu acccount (readonly). To do so, first disable authorization in the mongod.conf configuration file
  • Then ensure that your .env.dev or .env.prod file contains the environment variables for the following
DATA_FOLDER='data'
ADMIN_USERNAME='admin'
ADMIN_PASSWORD='supersecretpassword'
COVIZU_USERNAME='covizu'
COVIZU_PASSWORD='supersecretpassword'
DB_URL='localhost:27017'

  • Before creating the user accounts, first we check for any existing user accounts of the same name as our ADMIN_USERNAME or COVIZU_USERNAME. Run the following nodejs script.

    • $ npm run delete-users

  • To confirm that there are no user accounts with conflicting names open the mongosh

    • $ mongosh
    • test> use admin
    • test> show users

  • After deleting any existing user accounts, run the following script

    • $ npm run create-users

  • Once your user accounts are created, edit the config file to enable authorization and restart the service.

Populating the database

  • If you haven't already, obtain the following data files from our main server at https://filogeneti.ca/covizu/data/:
  • timetree.nwk
  • dbstats.json
  • clusters.json and save your local copies under covizu/data/.
  • To import these data files into our MongoDB database run the following script
    • $ npm run update-db1
  • This will create our primary database and import the JSON/text records into it.
  • Once the import script has finished executing, start the server by executing the following script
    • $ npm run start-db1
  • Navgiate your browser to localhost:8001 to verify that it works.
  • If that went well, then run the next script to setup our secondary database
    • $ npm run update-db2
  • After executing the import script, start the server with a connection to the secondary database
    • $ npm run start-db2

Updating the database

  • To update the database, first obtain the new data files from https://filogeneti.ca/covizu/data and replace the files in covizu/data
  • If your node server is currently using the primary (secondary) database then update the secondary (primary) database
    • $ npm run update-db2 ($ npm run update-db1)
  • After updating the secondary (primary) database, close the currently running server which is still serving data from the primary(secondary) database and restart the server with a connection to the secondary (primary) database
    • $ npm run start-db2 ($ npm run start-db1)
  • On the next batch of new data, update the primary (secondaary) database and restart the node server with a connection to the primary (secondary) database

Some useful mongosh shell commands

  • To open mongo CLI in non-authenticated mode

    • $ mongosh

  • To open mongo CLI as an admin

    • $ mongosh --username admin --authenticationDatabase admin

  • To view all users

    • Connect as admin ()
    • use admin
    • show users

  • To delete an existing user "myusername"

    • Connect as admin
    • use admin
    • show users
    • db.dropUser('myusername')

  • To view all collections within a database "mydatabase"

    • Connect as admin
    • use mydatabase
    • show collections

  • To drop the database "mydatabase"

    • Connect as admin
    • use mydatabase
    • db.dropDatabase()

  • To drop the collection "mycollection" with the database "mydatabase"

    • Connect as admin
    • use mydatabase
    • db.mycollection.drop()