Compact all collections inside of a MongoDB database

compact.js

// This script loops though the list of collection names in a MongoDB and runs the compact operation on them
// Simply paste this into the Mongo shell

use testDbName;
db.getCollectionNames().forEach(function (collectionName) {
    print('Compacting: ' + collectionName);
    db.runCommand({ compact: collectionName });
});

If you want to execute the command on a secondary member of your replicaSet then you need to execute the following first:

rs.slaveOk();

https://docs.mongodb.com/manual/reference/method/rs.slaveOk/
That way you can avoid downtimes. Please note that the server won't be available for failover during that time.

FYI if you were prepared to take your database offline, you can run a repair that performs a compaction on all collections. This article covers the two approaches and discusses a rolling update which works great on MLab hosted databases https://dzone.com/articles/managing-disk-space-mongodb

@ST-DDT which server versions do these constraints apply to? (I mean that the secondary node won't be avail for failover?)

Can you please point me to the according documentation? Thanks :)

rs.slaveOk();

for actual versions must be:
rs.secondaryOK();

anyway thanks.

db.getCollectionNames returns views too 🙃

Returns an array containing the names of all collections and views

https://www.mongodb.com/docs/manual/reference/method/db.getCollectionNames/

If you want collection names only you need something like db.getCollectionInfos({ type: 'collection' }).map(v => v.name).filter(v => v != 'system.views')