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Migration Guide (Released)

All migrations of WEBKNOSSOS are documented in this file. See MIGRATIONS.unreleased.md for the changes which are not yet part of an official release.

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

24.04.0 - 2024-03-25

Commits

  • WKW datasets can now only be read if they have a header.wkw file in their mag directories. If specific datasets can no longer be loaded, consider adding such a file. Backend logging should show according error message. #7528
  • Content Security Policy (CSP) settings are now relaxed by default. To keep stricter CSP rules, add them to your specific application.conf. #7589
  • The way the segment index is stored for nd-annotations has been changed (#7411). Annotations with old segment indices should be archived if they do not contain relevant data. The following SQL query can be used:
UPDATE webknossos.annotations_ SET state = 'Finished' WHERE _id IN  (SELECT DISTINCT a._id AS nd_annotations_id FROM webknossos.annotations_ AS a INNER JOIN webknossos.datasets AS d ON a._dataset = d._id INNER JOIN webknossos.dataset_layer_additionalaxes AS dla ON d._id = dla._dataset)
  • WEBKNOSSOS now uses Java 21 (up from Java 11). #7599
  • NodeJS version 18+ is required for snapshot tests with ShadowDOM elements from Antd v5. #7522
  • Email verification is disabled by default. To enable it, set webKnossos.user.emailVerification.activated to true in your application.conf. #7620 #7621
  • New dependency draco/libdraco-dev needs to be installed when deploying without docker and for local development.
  • Config block braintracing is now unused and can be removed. #7693

Postgres Evolutions:

24.02.3 - 2024-02-22

Commits

24.02.2 - 2024-02-15

Commits

24.02.1 - 2024-02-15

Commits

24.02.0 - 2024-01-26

Commits

  • The config setting play.http.secret.key (secret random string) now requires a minimum length of 32 bytes.
  • If your setup contains webknossos-workers, postgres evolution 110 introduces the column supportedJobCommands. This needs to be filled in manually for your workers. Currently available job commands are compute_mesh_file, compute_segment_index_file, convert_to_wkw, export_tiff, find_largest_segment_id, infer_nuclei, infer_neurons, materialize_volume_annotation, render_animation. #7463
  • If your setup contains webknossos-workers, postgres evolution 110 introduces the columns maxParallelHighPriorityJobs and maxParallelLowPriorityJobs. Make sure to set those values to match what you want for your deployment. #7463
  • If your setup contains webknossos-workers, you may want to add the new available worker job compute_segment_index_file to the supportedJobCommands column of one or more of your workers. #7493
  • The WEBKNOSSOS api version has changed to 6. The isValidNewName route for datasets now returns 200 regardless of whether the name is valid or not. The body contains a JSON object with the key "isValid". #7550
  • If your setup contains ND datasets, run the python3 script at tools/migrate-axis-bounds/migration.py on your datastores to update the datasource-properties.jsons of the ND datasets.
  • With the upgrade to Play 3 and the migration to pekko, configuration keys using akka need to be changed. For the default configuration this results in the following changes:
    • akka.requestTimeout → pekko.requestTimeout
    • akka.actor.default-dispatcher → pekko.actor.default-dispatcher

Postgres Evolutions:

23.12.0 - 2023-11-27

Commits

  • If your deployment starts FossilDB separately, make sure to upgrade to version 0.1.27 (build master__484). Note that with the upgraded version, the database contents are automatically migrated. A downgrade to an older FossilDB version is not possible afterwards (creating an additional backup of the FossilDB data directory is advised)
  • WEBKNOSSOS now sets the Content-Security-Policy (CSP) HTTP response header restricting which dynamic resources are allowed to load. Please update the application.conf - play.filters.csp.directives key if you'd like to change the default CSP. The default CSP is suited for WEBKNOSSOS development. For production follow the comments next to the respective directives in the application.conf, i.e. remove 'unsafe-inline' from the script-src, remove ws://localhost:9002 from the connect-src, add the URLs of all external datastores to the connect-src, and add the host domain to the connect-src. #7367 and #7450

23.11.0 - 2023-10-24

Commits

  • The datastore/isosurface configuration key was renamed to `datastore/adHocMesh.
  • In order to enable segment statistics for existing volume annotations (without fallback segmentation), a user with superuser rights can call a migration route during a downtime. This will transform all volume annotation layers that qualify (cross organization). This will take some time, results will be logged by WEBKNOSSOS to stdout. The trigger route is curl -X PATCH "<domain>/api/annotations/addSegmentIndicesToAll?parallelBatchCount=16" -H 'X-Auth-Token: <token>' with the parallelBatchCount parameter controlling the parallelity of the migration (e.g. number of cpu cores of the tracingstore server). This action is designed to be idempotent.

23.10.2 - 2023-09-26

Commits

23.10.1 - 2023-09-22

Commits

23.10.0 - 2023-09-21

Commits

Postgres Evolutions:

23.09.0 - 2023-08-29

Commits

  • Postgres Evolution 105 (see below) adds email verification and sets the emails of all existing users as verified. To set all email addresses as unverified, execute this query:
UPDATE webknossos.multiUsers SET isEmailVerified = false;

  • When interacting with webknossos via the python library, make sure you update to the latest version, as the task and project api have changed. Compare webknossos-libs#930. #7220

  • If you have OIDC authentication set up, you can now remove the config keys singleSignOn.openIdConnect.publicKey and singleSignOn.openIdConnect.publicKeyAlgorithm, as the server’s public key is now automatically fetched. #7267

Postgres Evolutions:

23.08.0 - 2023-07-24

Commits

Postgres Evolutions:

23.07.0 - 2023-06-20

Commits

  • FossilDB needs to be opened with new additional column family volumeSegmentIndex.

Postgres Evolutions:

23.06.0 - 2023-05-30

Commits

  • FossilDB needs to be opened with new additional column families editableMappingsInfo, editableMappingsAgglomerateToGraph, editableMappingsSegmentToAgglomerate.
  • For instances with existing editable mapping (a.k.a supervoxel proofreading) annotations: To keep those annotations alive, a python migration has to be run with access to your tracingstore’s FossilDB. It is recommended to do this during a webknossos downtime to avoid data loss. It needs python 3.8+ and the pip packages installable by pip install grpcio-tools grpcio-health-checking. Run it with python tools/migrate-editable-mappings/migrate-editable-mappings.py -v -w -o localhost:7155. Omit -o for a faster migration but no access to older versions of the editable mappings. The migration is idempotent.
  • The datastore now needs brotli. For Debian-based systems, this can be installed with apt-get install libbrotli1.
  • New FossilDB version 0.1.23 (master__448 on Dockerhub) is required, compare FossilDB PR.

Postgres Evolutions:

None.

23.05.2 - 2023-05-08

Commits

Postgres Evolutions:

None.

23.05.1 - 2023-05-02

Commits

Postgres Evolutions:

None.

23.05.0 - 2023-04-25

Commits

  • The config key features.isDemoInstance was renamed to features.isWkorgInstance (only needs to be adapted for the main wkorg instance). #6941

Postgres Evolutions:

None.

23.04.2 - 2023-04-14

Commits

Postgres Evolutions:

None.

23.04.1 - 2023-04-06

Commits

Postgres Evolutions:

None.

23.04.0 - 2023-03-27

Commits

Postgres Evolutions:

23.03.1 - 2023-03-14

Commits

  • WEBKNOSSOS now requires at least Java 11 (up from Java 8). #6869

Postgres Evolutions:

None.

23.03.0 - 2023-02-28

Commits

  • WEBKNOSSOS now requires Node.js not only for development and building, but also for execution. The prebuilt Docker images already contain this dependency. If you're using these, nothing needs to be changed. #6803
  • Requires Voxelytics worker version 23.02.xx for long-running jobs. #6838

Postgres Evolutions:

23.02.1 - 2023-02-07

Commits

Postgres Evolutions:

None.

23.02.0 - 2023-02-01

Commits

  • WEBKNOSSOS requires Loki instead of Elasticsearch for Voxelytics logging now. Please update the application.conf: Remove voxelytics.elasticsearch.index, rename voxelytics.elasticsearch to voxelytics.loki, and update voxelytics.loki.uri. #6770

Postgres Evolutions:

23.01.0 - 2023-01-03

Commits

  • Bulk task creation now needs the taskTypeId, the task type summary will no longer be accepted. If you have scripts generating CSVs for bulk task creation, they should not output task type summaries. #6640

Postgres Evolutions:

22.12.0 - 2022-11-24

Commits

Postgres Evolutions:

None.

22.11.2 - 2022-11-10

Commits

Postgres Evolutions:

None.

22.11.1 - 2022-10-27

Commits

Postgres Evolutions:

None.

22.11.0 - 2022-10-24

Commits

Postgres Evolutions:

None.

22.10.0 - 2022-09-27

Commits

  • To use the Voxelytics reporting features in webKnossos, the config field features.voxelyticsEnabled needs to be set to true. When also using the logging features, an Elasticsearch instance needs to be running and configured in the config field voxelytics.elasticsearch.uri.

Postgres Evolutions:

22.09.0 - 2022-08-25

Commits

  • webKnossos requires node 16 now. #6350
  • Removed the foreign datastore feature. If you have any foreign datastores registered in your webKnossos, running this upgrade may result in undefined behavior. #6392

Postgres Evolutions:

22.08.0 - 2022-07-20

Commits

  • Postgres evolution 83 (see below) introduces unique and url-safe constraints for annotation layer names. If the database contains entries violating those new constraints, they need to be fixed manually, otherwise the evolution will abort:

    • change null names to the front-end-side defaults:

      update webknossos.annotation_layers set name = 'Volume' where name is null and typ = 'Volume'
update webknossos.annotation_layers set name = 'Skeleton' where name is null and typ = 'Skeleton'

    • find annotations with multiple layers, make unique manually

      select _annotation, name from webknossos.annotation_layers where _annotation in (select s._annotation from
(select _annotation, count(_annotation) from webknossos.annotation_layers where typ = 'Volume' group by _annotation order by count(_annotation) desc limit 1000) as s
where count > 1) and typ = 'Volume' order by _annotation

    • find layers with interesting names, manually remove spaces and special characters

      select * from webknossos.annotation_layers where not name ~* '^[A-Za-z0-9\-_\.]+$'

Postgres Evolutions:

  • 083-unique-layer-names.sql Note: Note that this evolution introduces constraints which may not be met by existing data. See above for manual steps

22.07.0 - 2022-06-28

Commits

  • FossilDB now has to be started with two new additional column families: editableMappings,editableMappingUpdates. Note that this upgrade can not be trivially rolled back, since new rocksDB column families are added and it is not easy to remove them again from an existing database. In case webKnossos needs to be rolled back, it is recommended to still keep the new column families in FossilDB. #6195

Postgres Evolutions:

22.06.1 - 2022-06-16

Commits

Postgres Evolutions:

22.06.0 - 2022-05-27

Commits

  • Note that the datastore API version has changed to 2.0. If you use webknossos-connect alongside your webKnossos instance, you will need to upgrade that one as well, compare webknossos-connect#129. #6159

Postgres Evolutions:

22.05.1 - 2022-04-29

Commits

Postgres Evolutions:

22.05.0 - 2022-04-26

Commits

Postgres Evolutions:

22.04.0 - 2022-03-22

Commits

22.03.0 - 2022-02-21

Commits

  • The config field googleAnalytics.trackingId needs to be changed to GA4 measurement id, if used.

Postgres Evolutions:

22.02.0 - 2022-01-24

Commits

Postgres Evolutions:

22.01.0 - 2022-01-04

Commits

  • The datastore now also needs access to a Redis database. New config fields datastore.redis.address and datastore.redis.port are required. Note that this Redis instance may be the same one the tracingstore uses, but does not have to be.

Postgres Evolutions:

21.11.0 - 2021-11-30

  • The docker files now place the webKnossos installation under /webknossos instead of /srv/webknossos. All mounts, most importantly /srv/webknossos/binaryData, need to be changed accordingly.
  • The entrypoint of the docker files have changed. Therefore, any existing docker-compose.yml setups need to be adapted. In most cases, only the entrypoint: bin/webknossos lines need to be removed (if existant).
  • To receive Slack notifications about slow bucket requests, overwrite slackNotifications.uri in the webknossos-datastore config.
  • If your setup includes a webknossos-worker, it needs to be updated to the latest version (PR https://github.com/scalableminds/webknossos-worker/pull/70)

Postgres Evolutions:

21.10.0 - 2021-11-08

Postgres Evolutions:

21.09.0 - 2021-10-01

  • For webknossos.org: Change publicDemoDatasetUrl in the features-block within application.conf to be an actionable URL. For example, append /createExplorative/hybrid?fallbackLayerName=segmentation to the URL so that a new annotation is created if a user clicks on Open a Demo Dataset in the dashboard.

Postgres Evolutions:

21.08.0 - 2021-08-26

Commits No migrations necessary.

21.07.0 - 2021-07-21

  • Consider setting defaultToLegacyBindings to true in application.conf if you want that new users use the classic controls by default.
  • To make the classic mouse bindings the default for existing users and task types execute the following (adapt true to false if you want the opposite):
-- Activate legacy bindings for all users
UPDATE webknossos.users
SET userconfiguration = jsonb_set(
        userconfiguration,
        array['useLegacyBindings'],
        to_jsonb('true'::boolean))

-- Recommend legacy bindings for users when starting a new task
UPDATE webknossos.tasktypes
SET recommendedconfiguration = jsonb_set(
        recommendedconfiguration,
        array['useLegacyBindings'],
        to_jsonb('true'::boolean))
  • The health check at api/health does not longer include checking data/health and tracings/health if the respective local modules are enabled. Consider monitoring those routes separately.
  • Run as sql: UPDATE webknossos.tasktypes SET recommendedconfiguration = recommendedconfiguration - 'highlightHoveredCellId'; to avoid invalid recommended configurations in existing task types. This was added later as evolution 75, but should be run already here (note that it is idempotent).

Postgres Evolutions:

21.06.0 - 2021-06-01

Postgres Evolutions:

21.05.1 - 2021-05-05

  • The config keys in application.conf were restructured. If you overwrite any of them for your config, please adapt to the new structure, according to the table below. If you run any stand-alone datastores or tracingstores, make sure to update their config files as well.
old key new key notes
http.address removed used by play, default is 0.0.0.0, you can still overwrite it if necessary
actor.defaultTimeout removed was already unused
js.defaultTimeout removed was already unused
akka.loggers removed was already unused
application.name removed was already unused
application.branch removed was already unused
application.version removed was already unused
application.title webKnossos.tabTitle
application.insertInitialData webKnossos.sampleOrganization.enabled
application.insertLocalConnectDatastore removed feature removed, insert manually instead
application.authentication.defaultuser.email webKnossos.sampleOrganization.user.email
application.authentication.defaultUser.password webKnossos.sampleOrganization.user.password
application.authentication.defaultUser.token webKnossos.sampleOrganization.user.token
application.authentication.defaultUser.isSuperUser webKnossos.sampleOrganization.user.isSuperUser
application.authentication.ssoKey webKnossos.user.ssoKey
application.authentication.inviteExpiry webKnossos.user.inviteExpiry
webKnossos.user.time.tracingPauseInSeconds webKnossos.user.time.tracingPause type changed from Int to FiniteDuration, add seconds
webKnossos.query.maxResults removed was already unused
user.cacheTimeoutInMinutes webKnossos.cache.user.timeout type changed from Int to FiniteDuration, add minutes
tracingstore.enabled removed info contained in play.modules.enabled
datastore.enabled removed info contained in play.modules.enabled
datastore.webKnossos.pingIntervalMinutes datastore.webKnossos.pingInterval type changed from Int to FiniteDuration, add minutes
braingames.binary.cacheMaxSize datastore.cache.dataCube.maxEntries
braingames.binary.mappingCacheMaxSize datastore.cache.mapping.maxEntries
braingames.binary.agglomerateFileCacheMaxSize datastore.cache.agglomerateFile.maxFileHandleEntries
braingames.binary.agglomerateCacheMaxSize datastore.cache.agglomerateFile.maxSegmentIdEntries
braingames.binary.agglomerateStandardBlockSize datastore.cache.agglomerateFile.blockSize
braingames.binary.agglomerateMaxReaderRange datastore.cache.agglomerateFile.cumsumMaxReaderRange
braingames.binary.loadTimeout removed was already unused
braingames.binary.saveTimeout removed was already unused
braingames.binary.isosurfaceTimeout datastore.isosurface.timeout type changed from Int to FiniteDuration, add seconds
braingames.binary.isosurfaceActorPoolSize datastore.isosurface.actorPoolSize
braingames.binary.baseFolder datastore.baseFolder
braingames.binary.agglomerateSkeletonEdgeLimit datastore.agglomerateSkeleton.maxEdges
braingames.binary.changeHandler.enabled datastore.watchFileSystem.enabled
braingames.binary.tickerInterval datastore.watchFileSystem.interval type changed from Int to FiniteDuration, add minutes
mail.enabled removed now enabled if mail.host is non-empty
jobs.username jobs.user
braintracing.active braintracing.enabled
braintracing.url braintracing.uri
airbrake.apiKey removed was already unused
airbrake.ssl removed was already unused
airbrake.enabled removed was already unused
airbrake.endpoint removed was already unused
slackNotifications.url slackNotifications.uri
google.analytics.trackingId googleAnalytics.trackingId
operatorData webKnossos.operatorData

Postgres Evolutions:

21.05.0 - 2021-04-22

  • Instances with long-running jobs only: the tiff_cubing job was renamed to convert_to_wkw. For old jobs to be listed properly, execute sql update webknossos.jobs set command = 'convert_to_wkw' where command = 'tiff_cubing';

Postgres Evolutions:

21.04.0 - 2021-03-22

Postgres Evolutions:

21.03.0 - 2021-02-24

  • Support for KNOSSOS cubes data format was removed. Use the webKnossos cuber tool to convert existing datasets saved as KNOSSOS cubes.
  • Multi-organization instances only: user experience domains are now separated per organization. After postgres evolution 64 (see below), make sure to move existing experience domains to the correct organization in the database. (The evolution just selects any one from the database).

Postgres Evolutions:

21.02.1 - 2021-02-03

Commits No migrations necessary.

21.02.0 - 2021-01-20

  • 060-multiusers.sql (Note that its reversion can only be performed if there are no multiple users per multiuser yet)

21.01.0 - 2020-12-21

No migrations necessary.

20.12.0 - 2020-11-23

  • As volume annotations in arbitrary magnifications are now supported and the behavior of magnification restrictions of tasks has changed (allow full zoom, but disable tools unless in correct magnification), you may want to restrict all volume and hybrid task types to mag 1 to achieve the old behavior (mag1-only). NOTE: This query has to be executed BEFORE evolution 59 is performed.
update webknossos.tasktypes
set settings_allowedmagnifications = '{"min":1,"max":1,"shouldRestrict":true}'
where (tracingtype = 'volume' or tracingtype = 'hybrid')
and (settings_allowedmagnifications is null or settings_allowedmagnifications::json->>'shouldRestrict'='false');

Postgres Evolutions:

20.11.0 - 2020-10-26

20.10.0 - 2020-09-21

No migrations necessary.

20.09.0 - 2020-08-20

No migrations necessary.

20.08.0 - 2020-07-20

Postgres Evolutions:

20.07.0 - 2020-06-29

No migrations necessary.

20.06.0 - 2020-05-25

Postgres Evolutions:

20.05.0 - 2020-05-05

  • The optional defaultOrganization attribute from the features block in application.conf is not used anymore and can be removed. #4559

20.04.0 - 2020-03-23

  • Default interval for detecting new/deleted datasets on disk (braingames.binary.changeHandler.tickerInterval in the config) has been reduced from 10 to 1 minute. If you relied on the value being 10 minutes, you have to set it explicitly now.

Postgres Evolutions:

20.03.0 - 2020-02-27

No migrations necessary.

20.2.0 - 2020-01-27

Postgres Evolutions:

20.1.0 - 2020-01-08

  • The initial organization was renamed to sample_organization. Make sure to move the data over or to put a symlink in place.
  • The default operatorData was replaced. Make sure to update with valid information for public deployments.
  • The config uri has been refactored. Pairs of uri and secured have been replaced with just uri which now requires a http:// or https:// prefix.

Postgres Evolutions:

19.12.0 - 2019-11-25

No migrations necessary.

19.11.0 - 2019-10-28

Postgres Evolutions:

19.10.0 - 2019-09-30

Postgres Evolutions:

19.09.0 - 2019-08-28

No migrations necessary.

19.08.0 - 2019-07-29

No migrations necessary.

19.07.0 - 2019-07-01

Postgres Evolutions:

19.06.0 - 2019-05-27

No migrations necessary.

19.05.0 - 2019-04-29

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