So, this is how to problem was solved.
Step 1:
We have installed the same version of MongoDB that was used in the server. For our case, the version was 4.0.10. We have used the following command to download the specific version:
sudo apt-get install -y mongodb-org=4.0.10 mongodb-org-server=4.0.10 mongodb-org-shell=4.0.10 mongodb-org-mongos=4.0.10 mongodb-org-tools=4.0.10
Step 2:
The version installed at step 1 was storing it’s data on /var/lib/mongodb. So, we started the MongoDB server using
mongod --dbpath /var/lib/mongodb
Step 3:
We have started the mongo terminal client using the command:
mongo
Step 4:
After entering into the client, we have created a new database using the command
use new_database
Step 5:
We have created a dummy collection inside our “new_database” using the command:
db.newCollection.insert({hi: "helo"})
Step 6:
We have checked the stats of our new collection using:
db.newCollectoin.stats()
Step 7:
From the output file generated at step 6, we have looked for the keyword “uri” to see under which .wt file, our “newCollection” collection is stored. The uri key in the output should look something like this:
"uri" : "statistics:table:collection-44--4912736618580810110",
Step 8:
We have kept a local copy of our server database at a location, let’s call it /home/user/old_database. Inside it, let’s say, there’s a .wt file called “collection-12–4912736618580810442.wt”. We copied this .wt file to our new .wt file that represents the “newCollection” collection. We used the command:
sudo cp /home/user/old_database/collection-12--4912736618580810442.wt /var/lib/collection-44--4912736618580810110.wt
Our intention is to make the new database consider the server .wt file as a distorted version of new databases’ .wt file.
Step 9:
We stopped the MongoDB client and server and run the repair command on our new database:
sudo mongod --dbpath /var/lib/mongodb --repair
Step 10:
After a successful repair, we have seen the exit code 0, as output of our command in line 9. So, we restarted the MongoDB server again, just like step 2:
mongod --dbpath /var/lib/mongodb
Step 11:
We started the mongo client again, choose the new_database again and looked at the collection like this:
db.newCollection.find({}).pretty()
Fortunately, we could see the old documents stored in one of the collections of our old_database.
Step 12:
We repeated steps 1 to 11 again for other .wt files in the old_database.
We have learned this technique from: Repairing MongoDB When WiredTiger.wt File is Corrupted | by Ido Ozeri | Medium
Hope this write-up will help some other teams in the future. Please don’t forget to keep regular backup as well 