To avoid long loading times for new service sites.
Stop server from collecting more nanopubs:
$ docker-compose stop server
Wait a few seconds then make Virtuoso checkpoint:
$ docker-compose exec virtuoso isql-v EXEC=checkpoint
Stop all services:
$ docker-compose stop
Create zip files (might need sudo, and to prevent tar from aborting it might need to be enclosed in nohup ... &):
$ tar -czvf mongodb.tar.gz data/mongodb
$ tar --exclude=data/virtuoso/virtuoso.log --exclude=data/virtuoso/dumps --exclude=data/virtuoso/virtuoso.trx --exclude=data/virtuoso/.dba_pwd_set -czvf virtuoso.tar.gz data/virtuoso
Start the services again:
$ docker-compose start
Extract MongoDB in empty directory:
$ tar -xvzf mongodb.tar.gz
Remove lock files, if any (might need sudo):
$ rm -f data/mongodb/*.lock
Run MongoDB:
$ docker run -v $(pwd)/data/mongodb:/data/db -p 27017:27017 -d nanopub/mongo
Check journal ID (mongosh instead of mongo for newer versions; has to installed via apt install mongodb-org and installation sources added first):
$ mongo --eval "db.getSiblingDB('nanopub-server').getCollection('journal').find({'_id':'journal-id'});"
Set journal ID to 0:
$ mongo --eval "db.getSiblingDB('nanopub-server').getCollection('journal').findAndModify({'query':{'_id':'journal-id'},'update':{'_id':'journal-id','value':'0'}});"
Check again:
$ mongo --eval "db.getSiblingDB('nanopub-server').getCollection('journal').find({'_id':'journal-id'});"
Stopping MongoDB:
$ docker stop DOCKER-CONTAINER-ID
Remove lock files again, if any, and diagnostic data (might need sudo):
$ rm -f data/mongodb/*.lock
$ rm -rf data/mongodb/diagnostic.data
Making new archive (might need sudo):
$ tar -czvf mongodb0.tar.gz data/mongodb
Downloading and then unzipping:
$ tar -xvzf mongodb0.tar.gz
$ tar -xvzf virtuoso.tar.gz