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How to migrate Oasis versions

Software versions

We distribute NOMAD as docker images that are available in our public docker registry. The a NOMAD image names looks like this:

The version tag (e.g. v1.2.0) follows semantic versioning (major.minor.patch). Images released under a version tag do not change. There are also variable tags like stable, latest, and develop. The image tag for recent feature branches use a encoded variant of the respective merge request name. It is generally the safes to use version tags.

Our semantic interpretation of "minor" is the following:

  • there are only additions to programming interfaces and config options
  • NOMAD will still operate on existing data, but the structure of newly processed data might change
  • minor version might introduce new features that are only available after certain actions migration steps.

A road-map for major features can be found on our homepage here. You'll find a detailed change log in the source code here.

Configuration versions

Depending on the versions you need to update your docker-compose or NOMAD configuration. This might be necessary for breaking changes, or advisable to activate new features. Therefore, it is important to understand that the installations files that run NOMAD (e.g. docker-compose.yaml or nomad.yaml) are independent of the NOMAD image and they won't automatically change just because you use a new image.

We will list respective changes and guides under migration steps below.

Data versions

Different version of NOMAD might represent data differently. For example, the definition of the search index, database schema, file system layout, or internal file formats might change. For such changes, we might offer a migration period, where NOMAD supports two different data representations at the same time. However, eventually this requires some migration of the existing data. This might be necessary for breaking changes (or because an old representation is deprecated) or advisable because a new representation offers new features. Therefore, it is important to understand that the used NOMAD software and data are independent things. Using a new image, does not change the data in your installation.

We will list respective changes and guides under migration steps below.

Using a new version

To use a different version of NOMAD, it can be as simple as swapping the tag in the docker-compose services that use the nomad images (i.e. app and worker). Depending on the version change, further steps might be necessary:

  • for patch releases no further actions should be necessary
  • for minor releases some additional actions might be required to unlock new features
  • for major releases breaking changes are likely and further actions will be required

For changing the minor or major version, please check the migration steps below.

Migration steps

to 1.2.2

We upgraded the Jupyterhub version used for NORTH from 1.0.2 to 4.0.2. By default the Jupyterhub database is persisted in the nomad_oasis_north container. If you want to keep the database (e.g. to not loose any open tools), you will have to upgrade the database. Update the NOMAD docker image version and restart the Oasis like this:

docker compose down
docker compose pull
docker copmose run north python -m jupyterhub upgrade
docker compose up -d

Alternatively, you can delete the nomad_oasis_north container and start with a fresh database. Make sure that all north tools are stopped and removed.

docker compose down
docker rm nomad_oasis_north
docker compose pull
docker compose up -d

to 1.2.0

  • We introduced the plugin mechanism. There are now more options to control which schemas and parsers are available in your installation. By default all the existing and shipped schemas and parsers are enabled. See also here.

  • We changed the archive file format. Re-processing might yield better performance.

  • Parsers are now using a different workflow model and the UI now includes a workflow card on the overview page of entries with workflows for the new model. Re-processing all data will enable this feature for old data. Any analysis build on the old workflow model, might not work for new data.

  • We introduce the log-transfer service. This is currently an opt-in feature.

from 0.8.x to 1.x

Between versions 0.10.x and 1.x we needed to change how archive and metadata data is stored internally in files and databases. This means you cannot simply start a new version of NOMAD on top of the old data. But there is a strategy to adapt the data. This should work for data based on NOMAD >0.8.0 and <= 0.10.x.

The overall strategy is to create a new mongo database, copy all information, and then reprocess all data for the new version.

First, shutdown the OASIS and remove all old containers.

docker compose stop
docker compose rm -f

Update your config files (docker-compose.yaml, nomad.yaml, nginx.conf) according to the latest documentation (see above). Make sure to use index and database names that are different. The default values contain a version number in those names, if you don't overwrite those defaults, you should be safe.

Make sure you get the latest images and start the OASIS with the new version of NOMAD:

docker compose pull
docker compose up -d

If you go to the GUI of your OASIS, it should now show the new version and appear empty, because we are using a different database and search index now.

To migrate the data, we created a command that you can run within your OASIS' NOMAD application container. This command takes the old database name as an argument, it will copy all data from the old mongodb to the current one. The default v8.x database name was nomad_fairdi, but you might have changed this to nomad_v0_8 as recommended by our old Oasis documentation.

docker exec -ti nomad_oasis_app bash -c 'nomad admin upgrade migrate-mongo --src-db-name nomad_v0_8'
docker exec -ti nomad_oasis_app bash -c 'nomad admin uploads reprocess'

Now all your data should appear in your OASIS again. If you like, you can remove the old index and database:

docker exec nomad_oasis_elastic bash -c 'curl -X DELETE http://elastic:9200/nomad_fairdi'
docker exec nomad_oasis_mongo bash -c 'mongo nomad_fairdi --eval "printjson(db.dropDatabase())"'