MOLGENIS - for scientific data: management, exploration, integration and analysis.
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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):
Published by tommydeboer over 2 years ago
This release increases the REST API v2 upload limit to 5000 (was 1000).
Published by tommydeboer over 2 years ago
This release contains a Spring Framework upgrade to mitigate CVE-2022-22965
Published by tommydeboer over 2 years ago
This release contains a Spring Framework upgrade to mitigate CVE-2022-22965
Published by tommydeboer over 2 years ago
This release requires a complete reindexing, even if you've already installed a previous MOLGENIS 10.0.x
#9386 Search-all slow, inconsistent with previous versions and in some cases completely broken
Published by tommydeboer over 2 years ago
Fix #9376 Molgenis no longer waits for Elasticsearch to be up
Published by fdlk over 2 years ago
*=q=searchterm
) in a way that combines searches on the individual attributes and the individual attributes of references (1 level deep)elasticsearch.transport.addresses
to elasticsearch.hosts
.network.host
setting, since by default it restricts traffic to the localhost.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.
molgenis-math
helper) (docs - look for "Math helpers")The new release of the frontend contains various features and fixes in the forms.
Published by jelmerveen almost 3 years ago
Published by tommydeboer almost 3 years ago
Published by sidohaakma about 3 years ago
Published by fdlk about 3 years ago
Builds and runs on JDK 17. This impacts developers as well as system administrators.
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 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.
Molgenis 9.1 still runs on Apache Tomcat 9, but now needs JDK version 17.
Check: ansible playbook.
Published by fdlk about 3 years ago
#9310: User manager cannot edit user details
Published by MaxPostema about 3 years ago
Published by MaxPostema about 3 years ago
Published by MaxPostema about 3 years ago
Published by MaxPostema about 3 years ago
Published by MaxPostema about 3 years ago
Published by fdlk about 3 years ago
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
$('sample_type').value() && $('sample_type').value().indexOf('6')>-1
{sample_type} contains '6'
Fields that are hidden because the visibleExpression evaluates to false are automagically nullable.
nullable | visible |
---|---|
{status}!='SUBMITTED' or {job}!='researcher' |
{job}='researcher' |
{age} <= 17 or !{driversLicence} |
{age} > 17 and {driversLicence} |
nullable | visible |
---|---|
{status}!='SUBMITTED' |
{job}='researcher' |
false |
{age} > 17 and {driversLicence} |
NOT NULL
constraint if the nullable
boolean attribute is false
(unchanged)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. 🆕null
(unchanged)true
(unchanged)false
) 🆕nullable
(without the expression) set to true
then
nullableExpression
must be empty (unchanged) andvisibleExpression
must be empty 🆕<server URL>/plugin/dataexplorer/module/entitiesreport?entity=sys_md_Attribute
Published by sidohaakma over 3 years ago
Published by sidohaakma over 3 years ago