diff --git a/docs/_navbar.md b/docs/_navbar.md index 09fbae6ac..12b325e9c 100644 --- a/docs/_navbar.md +++ b/docs/_navbar.md @@ -16,4 +16,6 @@ * [ds-dictionaries](https://github.com/lifecycle-project/ds-dictionaries/blob/master/README.md) - * [Armadillo 2 to 3 migration guide](/migration-guide-2-to-3.md#instructions-for-migrating-a-2x-armadillo-to-3x "Armadillo 2 to 3 migration guide") \ No newline at end of file + * [Migration from 2 to 3](/upgrade-2-3.md) + + * [Release test (R)](/release-test.md) diff --git a/docs/_sidebar.md b/docs/_sidebar.md index 9870f3a3a..abbc11d08 100644 --- a/docs/_sidebar.md +++ b/docs/_sidebar.md @@ -3,7 +3,8 @@ - [Configure](/ops/configuring.md) - [UI](/ui.md#armadillo-user-interface "Armadillo 3 UI") - [FAQ](/faq.md) - - [Armadillo 2 to 3 migration guide](/migration-guide-2-to-3.md#instructions-for-migrating-a-2x-armadillo-to-3x "Armadillo 2 to 3 migration guide") + - [Migration from 2 to 3](/upgrade-2-3.md) + - [Release test (R)](/release-test.md) - External sites - [DsMolgenisArmadillo](https://github.com/molgenis/molgenis-r-datashield/blob/master/README.md) - [MolgenisArmadillo](https://molgenis.github.io/molgenis-r-armadillo/) diff --git a/docs/migration-guide-2-to-3.md b/docs/migration-guide-2-to-3.md deleted file mode 100644 index 646081388..000000000 --- a/docs/migration-guide-2-to-3.md +++ /dev/null @@ -1,138 +0,0 @@ -# Instructions for migrating a 2.x Armadillo to 3.x -The release of Armadillo 3.0 introduces some breaking changes. These instructions will guide you -through the steps needed to migrate your old Armadillo service to the new version. - -## Configuration -This section is about changes in the `application.yml` configuration file. For a full -example you can look at [the application.yml in the code](/armadillo/src/main/resources/application.yml). - -### OIDC -Besides accepting JWTs from a trusted authentication provider, you can now enable OIDC authentication. -This will make it possible for admins to log in with their institute account in the UI. - -To enable this, add the following properties: - -``` -spring: - security: - oauth2: - client: - registration: - molgenis: - client-id: - client-secret: -``` - -### Armadillo Settings -The `datashield` property has been renamed to `armadillo`, and some new settings have been -introduced: - -``` -armadillo: - oidc-permission-enabled: false - oidc-admin-user: user@yourinstitute.org - docker-management-enabled: true -``` - -These settings are explained in more detail below. - -#### OIDC Permission Enabled -By default, roles and permissions are managed in Armadillo itself. However, you can still accept -roles from your authentication provider by setting `oidc-permission-enabled` to `true`. This is -not recommended. - -#### OIDC Admin User -You can configure a default OIDC admin user by setting the `oidc-admin-user` property. Armadillo -will add this user when the application starts. This admin will then immediately be able to login -with their institute account. - -#### Docker Management Enabled -Armadillo can manage the Docker containers used for profiles. To enable, set `docker-management-enabled` -to `true`. Keep in mind that Armadillo needs to be able to access a local Docker instance. - -### Profiles -Profiles can now be created and managed at runtime in the UI or via the profiles API. However, -it is still possible to configure one or more profiles, which will be created for you when -the application starts. - -Before 3.0, profiles and R environments had to be defined separately: - -``` -rserve: - environments: - - name: default - host: localhost - port: 6311 - -datashield: - profiles: - - name: default - environment: default - whitelist: - - dsBase - options: - datashield: - seed: 342325352 -``` - -This is no longer the case. You now have to configure everything inside a profile: - -``` -armadillo: - profiles: - - name: default - image: datashield/armadillo-rserver - host: localhost - port: 6311 - whitelist: - - dsBase - options: - datashield: - seed: 342325352 -``` - -Note that the root `datashield` property has been renamed to `armadillo`. - -Also note the `image` property: this one is optional and only necessary when you have enabled -[Docker Management](#docker-management). The image should be an image available on DockerHub. - -### Storage -You can now choose where Armadillo should store data: on a MinIO server (like before) or on the local file system. - -If you want to keep using MinIO, you don't need to change anything. The old configuration will still work: - -``` -minio: - url: http://localhost - port: 9000 - access-key: - secret-key: -``` - -To use the local file system, set the following parameter: - -``` -storage: - root-dir: -``` - -MinIO has precedence over local file storage, so keep that in mind when you have both configured. - -## Migrating users and data - -Since users and permissions are now managed in Armadillo instead of the authentication server, this -information needs to be migrated. And if you choose to host the data on the local file system -instead of a MinIO server, the data needs to be migrated as well. For both scenarios we have migration -scripts. - -### User migration script: Fusion Auth to Armadillo -To migrate users from Fusion Auth to Armadillo, you can use the script found [here](/scripts/migrate-auth.py). -More information on how to run it can be found in the script or by calling it with the `-h` flag. Make -sure Armadillo is NOT running when you run the script. After the script is done you need to start -Armadillo and it will automatically create the projects based on the folders that were copied. - -### Data migration script: MinIO to local file system -To migrate data from MinIO to the local file system, you can use the script found [here](/scripts/migrate-minio.py). -More information on how to run it can be found in the script or by calling it with the `-h` flag. Make -sure Armadillo is running when you run the script. -