MongoDB remove duplicate with millions of records

Working with Data
1

I’m trying to remove duplicates of documents, in the collection the collection have millions of records and duplicates data I assume have 100k records. I did use aggregation to delete those duplicates, but it is slow and is not ideal when we deploy it to prod. Is there a better and fast way to remove duplicates in a collection?

What I have tried so far:

db.mycollection.aggregate([
{"$match":{
  "create_date_audit":{
      $gte: ISODate('2022-07-25T18:27:56.084+00:00'),
      $lte: ISODate('2022-07-26T20:15:50.561+00:00')
  }
}},
{"$sort":{
  _id: -1
}},
{"$group":{
  _id: {
    notification_id: '$notifId',
    empId: '$empId',
    date: '$date'
  },
  dups: {
    $push: '$_id'
  },
  creationTimestamp: {
    $push: '$create_date'
  },
  count: {
    $sum: 1
  }
}},
{"$match":{
  _id: {
    $ne: null
  },
  count: {
    $gt: 1
  }
}},
{"$sort":{
  create_date: -1
}},
], { allowDiskUse: true }).forEach(function(doc) {    
    db.mycollection.deleteMany({_id : {doc.dups[0]});  
})```
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2

I don’t know better than your aggregation query, if this is a one-time process and you want to do this faster then I would suggest you can do this operation on your local machine in the MongoDB server after taking dump of the collection and you can restore it after the successful operation.

3

As mentioned by @turivishal, if this is a one-time process vs a regular use-case will most likely be different. So it would be nice to know.

For continuously preventing duplicates, you might want to create a unique index on notifId,empId and date.

I am not sure about your deleteMany. It looks like you might delete only one of the duplicates, because you are deleting _id:doc.dups[0]. It might not be an issue if you know you only have 1 duplicate. But the use of $push makes me think that you might have many.

The final $sort seems useless since you do not have a field named create_date after the $group stage.

To speedup a little bit, you might remove the count in your $group and $match on doc.dups[1] : { $exists : true }.

You do not seem to use the $group field creationTimestamp so you could remove the $push. Unless this is what you want to $sort as the last stage.

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