All migrations of webKnossos are documented in this file.
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additionalFolders, those symlinks are no longer updated.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.
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.newOrganizationMailingList as well as
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
The FossilDB version has changed from
The FossilDB needs to be run with an additional column family
If your setup overwrites the config key
play.http.router to disable the local datastore, change it to
"noDS.noTS.Routes" to also disable the local tracingstore).
some keys in
application.conf have changed, if you overwrite them in your setup, please adapt:
application.secret is now
postgres.* is now
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.
tools/volumeAddFallbackLayer.py to add a fallback segmentation layer to existing volume tracing zip files (also compare CHANGELOG.md).
To clean up half-deleted tasks as caused by this bug, run
update webknossos.annotations set isDeleted = true where _id in (select a._id from webknossos.annotations_ a join webknossos.tasks t on a._task = t._id where t.isDeleted and a.typ == 'Task')
Add email addresses for notifications about new users and about task overtime to the
webknossos.organizations entries in the Postgres database (previously in