Features

• Users need to agree to a Privacy Policy when logging in. This feature can be turned off in Settings > Authentication Settings

• Changes to the FAIR module to support the new specification of the FDP.
  In the EMX file, some tags have been deleted (e.g., the ones from r3d ontology) or replaced and some others have been
  added (e.g. some fdp-o specific terms such as fdp-o:MetadataService).
  Also, in the model two attributes have been added to the FDP entities (Metadata, Catalog, Dataset and Distribution):

  • hasMemberRelation, to specify the IRI of the property of the entity that contains children of the FDP Resource
  • directContainerTitle, a string with the title of the LDP DirectContainer with the navigation information for the Resource

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

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

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

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

Fixes

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

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

• If your Elasticsearch server does not run on localhost, you need to configure the server's network.host setting, since by default it restricts traffic to the localhost.

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.

Bugfixes

• fix: enable auto id pattern scrambler

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

Bugfixes

• #9335: Change password validation is broken

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

Bugfixes

#9310: User manager cannot edit user details

Breaking changes

expressions

New and easier to use and read expression language replaces JS MagmaScript in EMX nullable, visible and validation expressions. JS MagmaScript is still the expression language in the Mapping Service.

This means that all expressions in your data models need to be rewritten. This should be fairly straightforward, but contact us if you need help

before

$('sample_type').value() && $('sample_type').value().indexOf('6')>-1

after

{sample_type} contains '6'

invisible fields are nillable

Fields that are hidden because the visibleExpression evaluates to false are automagically nullable.

before (EMX)

after (EMX)

the nitty gritty details

• The database only writes a NOT NULL constraint if the nullable boolean attribute is false (unchanged)
• In EMX, if nullable is set to false, and a visibleExpression is set, writes the false to the nullableExpression instead, so the value does not get a NOT NULL constraint. 🆕
• When validating an attribute value, the nullable expression constraint is violated if
  • the value is null (unchanged)
  • the nullable expression is present and does not evaluate to true (unchanged)
  • not (the visible expression is present and evaluates to false) 🆕
• If an attribute has value nullable (without the expression) set to true then
  • nullableExpression must be empty (unchanged) and
  • visibleExpression must be empty 🆕

Features

• When creating an entity type in the Metadata Manager, you can set a custom ID.
• View model documentation in old data-explorer by selecting attributes <server URL>/plugin/dataexplorer/module/entitiesreport?entity=sys_md_Attribute
• New form settings: enable/disable the N/A option for nullable categoricals, booleans and enums.
• Allow update of entity types through EMX

Bugfixes

• #9243 Improved error handling on unsupported RSQL operators in REST APIs.
• #9265: Template expressions escape their values
• #9262: Disabled user with OIDC user mapping can still log in
• #9269: Error if OIDC roles path is missing in ID token and user info
• #9276: Part of page is hidden behind header
• #9279: Set default request encoding in multipart form to utf-8
• #9290: Get returned to the login screen when authenticating using OIDC
• #9292: Auto generated dates not working in compound
• #9300 : the menu will now calculate the space it needs