Migration Guide

All migrations of webKnossos are documented in this file.

This project adheres to Calendar Versioning 0Y.0M.MICRO. User-facing changes are documented in the changelog.


  • Postgres Evolutions:

19.04.0 - 2019-04-01

  • Redis is now needed for the tracingstore module. Make sure to install redis in your setup and adapt the config keys tracingstore.redis.address and tracingstore.redis.port.

  • To ensure that the existing behavior for loading data is preserved ("best quality first" as opposed to the new "progressive quality" default) execute: update webknossos.user_datasetconfigurations set configuration = configuration || jsonb '{"loadingStrategy":"BEST_QUALITY_FIRST"}'. See #3801 for additional context.

  • The config parameter application.title has been added. Make sure to set a title for your instance.

  • The assets URLs now include assets/ again, if you link to assets directly, please update the paths (e.g. in postgres organizations.logoUrl)

Postgres Evolutions:

19.03.0 - 2019-03-04

  • The config paramters application.authentication.enableDevAutoVerify and application.authentication.enableDevAutoAdmin have been removed. To enable automatic verification for user signup, set the organization’s new enableAutoVerify field to true in the database.

Postgres Evolutions:

19.02.0 - 2019-02-04

  • WebKnossos has a publication gallery now. There is no public interface to create publications yet, but instead those need to be inserted into the database directly. Publications and additional dataset properties that are displayed in the gallery as well, can be inserted as follows:

    insert into webknossos.publications(_id, publicationDate, imageUrl, title, description) values('5c3c9ec895010095014759fd', NOW(), '<LINK_TO_IMAGE>', '<TITLE>', '<DESCRIPTION>');
    update webknossos.datasets set _publication = '5c3c9ec895010095014759fd', details='{"species":"<e.g. Mouse>", "brain-region":"<e.g. cortex>", "acquisition":"<e.g. Raw CLSM data>"}' where _id = '<DATASET_ID>' ;

Postgres Evolutions:

19.01.0 - 2019-01-14

Postgres Evolutions:

18.12.0 - 2018-11-26

  • If additional dataset directories were watched using the config key additionalFolders, those symlinks are no longer updated. Consider setting up additional datastores for these directories respectively.

Postgres Evolutions:

18.11.0 - 2018-10-29

  • Some config keys have changed, if you overwrite them in your setup, please adapt: the oxalis prefix is renamed to webKnossos so the new keys are webKnossos.user.time.tracingPauseInSeconds, webKnossos.tasks.maxOpenPerUser, webKnossos.newOrganizationMailingList as well as datastore.webKnossos.uri, datastore.webKnossos.secured, datastore.webKnossos.pingIntervalMinutes for the data store.

  • There is now a separate module for the tracingstore, the datastore is no longer responsible for saving tracings. This module can run as a standalone application, or as a module of webKnossos locally. It is recommended that you choose the option that was previously also in place for datastores. In case of a standalone datastore, the local one needs to be disabled in application.conf: tracingstore.enabled = false and play.modules.disabled += "com.scalableminds.braingames.datastore.TracingStoreModule – and in either case, the adress of the tracingstore (localhost or remote) needs to be inserted in the db in webknossos.tracingStores.

  • The FossilDB version has changed from 0.1.10 to 0.1.14.

  • The FossilDB needs to be run with an additional column family volumeUpdates.

  • If your setup overwrites the config key play.http.router to disable the local datastore, change it to "noDS.Routes" (or "noDS.noTS.Routes" to also disable the local tracingstore).

Postgres Evolutions:

18.10.0 - 2018-09-22

Postgres Evolutions:

Configuration Changes:

  • some keys in application.conf have changed, if you overwrite them in your setup, please adapt: application.secret is now play.http.secret.key, postgres.* is now slick.db.*

  • Logger configuration has been simplified. Webknossos no longer comes with multiple logger config xmls, so if your setup selected a specific one of these, that needs to be removed (or a custom file needs to be supplied). Same for standalone datastore.

Data Migrations:

  • Use tools/volumeAddFallbackLayer.py to add a fallback segmentation layer to existing volume tracing zip files (also compare CHANGELOG.md).

18.09.0 - 2018-08-20

Postgres Evolutions:

18.08.0 - 2018-07-23

Postgres Evolutions:

18.07.0 - 2018-07-05

First release