Upgrading the workspace

Some workspace version upgrades are not strictly drop in replacements and require action from the service admins. This document describes versions that need special treatment and what actions are required.


  • A working knowledge of the workspace service start up and shut down methods
  • A working knowledge of MongoDB, in particular creating indexes, viewing documents, and updating documents via the CLI.

Notes on index creation

The Workspace will build any new indexes in the foreground prior to starting to avoid possible data corruption and / or table scans. This startup time can be avoided by building the indexes in the background while the prior version of the service is running. However, indexes that must be altered - e.g. dropped and recreated - must be handled while all workspace services are down and no database writes are occurring.

Upgrading to version 0.1.0

  • Upgrading to version 0.1.0 from an earlier version is not supported.

Upgrading to version 0.2.0

  • The temp-dir parameter in the deploy.cfg file must be set.

Upgrading to version 0.5.0

  • Handle Service version b9de6991b851e9cd8fa9b5012db565f051e0894f+ is now required.
  • Handle Manager version 3e60998fc22bb331e51b189ae1b71ebd54e58b90+ is now required.
  • Shock version 0.9.6+ is now required.

Upgrading to version 0.8.0

  • Java 8 is now required.
  • A Dockerfile was added, using Tomcat rather than Glassfish as the application server.
  • Several index changes are required.
    • New indexes (build in the background on the prior version):
      • db.workspaceObjVersions.createIndex({savedby: 1}, {background: true})
      • db.workspaceObjVersions.createIndex({ws: 1, id: 1, ver: -1}, {unique: true, background: true})
    • Replaced indexes (shutdown all workspace servers)
      • db.workspaces.dropIndex({name: 1})
      • db.workspaces.createIndex({name: 1}, {sparse: true})

Upgrading to version 0.9.0

  • The configuration that was previously stored in the workspace MongoDB database has been moved to the deploy.cfg file. The new configuration parameters are mongodb-type-database, backend-type, backend-url, and backend-user. Correct values for these parameters can be determined for existing installations by examining the contents of the settings collection in the MongoDB workspace database (although note that shock and gridFS are now capitalized as Shock and GridFS).


Setting these values incorrectly can cause unexpected and undesired behavior, including data corruption.

  • Due to the configuration changes, the initialize.py script is no longer needed and has been removed.
  • The globus-url configuration parameter has been replaced by the auth2-service-url parameter.

Upgrading to version 0.11.0

Upgrading to version 0.12.0

Version 0.12.0 requires a database schema upgrade and is therefore more involved than prior upgrades.

Prior to attempting an upgrade note that:

  • MongoDB 3.6+ is required.
  • Shock is no longer supported as a data backend, and data must be transferred to an S3 compatible instance. This is a complicated process - please contact KBase for help.
  • The Sample service is no longer supported as a KBase dynamic service, only as a core service. As such, the sample-service-tag configuration key has been removed.
  • The SearchPrototypeEventHandlerFactory listener has been removed. It must be deactivated or removed from the configuration.
  • The MongoDB driver API has been updated from the 2.X driver legacy interface to the new interface introduced in the 3.0 driver. This change is invisible other than the sorted key in GridFS file documents has been moved to the new metadata field from the root of the document. Since the GridFS backend is not recommended for production use and no known productions installations exist, a schema updater for the GridFS backend is not provided.

Updating the schema

The schema upgrade has several steps.

  • While the prior workspace service version is running, add new indexes:
    • db.workspaceObjVersions.createIndex({tyname: 1, tymaj: 1, tymin: 1, ws: 1, id: 1, ver: -1}, {background: true})
    • db.workspaceObjVersions.createIndex({tyname: 1, tymaj: 1, ws: 1, id: 1, ver: -1}, {background: true})
    • db.workspaceObjVersions.createIndex({tyname: 1, ws: 1, id: 1, ver: -1}, {background: true})
    • The updater script (below) will create these indexes in the foreground if they do not already exist.
  • Create the updater script:
    • This requires the standard Workspace compilation dependencies such as ant and the JDK.
    • You may wish to leave the production installation alone and create a new 0.12.0 repo just for the upgrade, and then update the production installation when ready to switch to 0.12.0.
    • In the 0.12.0 workspace repo, run ant script.
  • While the prior workspace service version is running, run the updater script:
    • update_workspace_database_schema <path to deploy.cfg file for the service>
    • The script is non-destructive and will pick up where it left off if interrupted.
    • The script can be run multiple times against the database to ‘top off’ the changes prior to shutting down the workspace, minimizing downtime.
  • Shutdown the workspace and finish the ugrade.
    • No writes may occur to the database while the upgrade is in progress.
    • Run the updater script as above with the --complete option.


If database writes occur at this point, all database records may not be updated. This may cause errors or incorrect query results.


Once the upgrade is complete, versions of the Workspace prior to 0.12.0 will no longer run against the upgraded database.

  • Start up the 0.12.0 workspace.

  • Optional: if it is clear that a rollback to an earlier workspace version is not required, the old type index can be deleted. Do not perform this action until after the update is complete, as the updater depends on the index and will recreate it if it’s missing.

    • db.workspaceObjVersions.dropIndex({type: 1, chksum: 1})

Rolling back to an earlier version

If a rollback to an earlier version of the workspace is required:

  • Recreate the old type index (in the background) if it was deleted.
  • Shut down the 0.12.0 workspace.
  • The single document in the config collection has a schemaver key with a value of 2. Update that value to 1.
  • Start the older version of the workspace.

Upgrading to version 0.13.0

  • If used, Sample Service 0.1.1 is now required.