Skip to content
Compare
Choose a tag to compare

This release increases the REST API v2 upload limit to 5000 (was 1000).

Compare
Choose a tag to compare

This release contains a Spring Framework upgrade to mitigate CVE-2022-22965

Compare
Choose a tag to compare

This release contains a Spring Framework upgrade to mitigate CVE-2022-22965

Compare
Choose a tag to compare

This release requires a complete reindexing, even if you've already installed a previous MOLGENIS 10.0.x

Fixes

#9386 Search-all slow, inconsistent with previous versions and in some cases completely broken

Compare
Choose a tag to compare

Fixes

Fix #9376 Molgenis no longer waits for Elasticsearch to be up

Compare
Choose a tag to compare

Breaking changes

Elasticsearch 7.15.0

  • The Elasticsearch client is upgraded to high level REST client version 7.15.0.
  • The Elasticsearch backend needs to be version 7.x. Version 7.15 and up are supported on JDK 17.
  • Reimplements search on * attribute (*=q=searchterm) in a way that combines searches on the individual attributes and the individual attributes of references (1 level deep)
  • Switches to high-level REST client. The old tcp client is deprecated.

MOLGENIS configuration changes

  • The configuration property for Elasticsearch changes from elasticsearch.transport.addresses to elasticsearch.hosts.
  • The default server port changes from 9300 (native) to 9200 (http REST).

Elasticsearch configuration changes

Upgrading existing servers

To upgrade, you need to remove the existing Elasticsearch 5 installation, including the indices, and install a fresh Elasticsearch 7.x. Molgenis will recreate the indices when it boots.

Features

  • Admin endpoints for getting the value of a database sequence and deleting a sequence (docs)
  • Improved search behaviour of the mref filter in the Data Explorer
  • Template expressions now support simple math operations (with the molgenis-math helper) (docs - look for "Math helpers")

Bugfixes

  • #8505 Inconsistent search operator behaviour
  • Data Explorer 1 now has compounds visible by default

Frontend

The new release of the frontend contains various features and fixes in the forms.

f4b655c
Compare
Choose a tag to compare

Bugfixes

  • fix: enable auto id pattern scrambler
Compare
Choose a tag to compare

Features

  • You can now update your apps in the App Manager instead of having to remove and re-upload an app.
  • Configurable patterns for automatically generated identifiers that increment sequentially. Read more about it in the documentation
Compare
Choose a tag to compare

Bugfixes

  • #9335: Change password validation is broken
Compare
Choose a tag to compare

Breaking changes

JDK 17

Builds and runs on JDK 17. This impacts developers as well as system administrators.

Flavor

The exact distribution of the JDK does not matter. The flavor of the VM might actually make a difference. We test using the standard hotspot VM.

The build runs in a build container based on maven:3.8-openjdk-17-slim which in turn is based on openjdk:17-jdk-slim, which contains a JDK 17 from Oracle.

We base the molgenis/molgenis-app docker image based on tomcat:9-jdk17 which in turn is based on openjdk:17-jdk-bullseye, Debian Bullseye plus a JDK 17 from Oracle.

Developers

Developers needs to upgrade their JDK to version 17 and maven to 3.8.
If you run molgenis in docker, the base image has already been upgraded.

System administrators

Molgenis 9.1 still runs on Apache Tomcat 9, but now needs JDK version 17.

Check: ansible playbook.

Features

  • View and manage ownership through permissions API
  • Add tags in v2 api attribute response
  • Add data-row-permissions package as a stable app

Bugfixes

  • #9304 Log script output if the script fails
  • #9321 Occasional NPEs when an entity is updated and read simultaneously