Migration guide

From 7.x to 8.0.x

There are a few major changes in the migration from 7.x to 8.x.

• The PostgreSQL version was 9.6 and is now 11.0.1

• We're transitioning the filestore to Minio, but the old filestore is still in use.

Operational requirements

There are a few services you need to migrate data from.

• PostgreSQL

  • for 7.x PostgreSQL 9.6

  • for 8.x PostgreSQL 11.0.1

• FileStore

  • for 7.x /srv/molgenis/data

  • for 8.x /home/molgenis/data

• Configuration

  • for 7.x /srv/molgenis/molgenis-server.properties

  • for 8.x /home/molgenis/molgenis-server.properties

PostgreSQL

Go to a terminal and dump your database using (as root-user):

cd /tmp/
pg_dump molgenis > molgenis.sql

Load you database using on the new server (as root-user):

Be sure you drop the database before you load the customer database.

cd /tmp/
psql molgenis < molgenis.sql

FileStore

Go to a terminal and tar you files into an archive (as root-user):

cd /home/molgens/
tar -pzcvf /tmp/molgenis.tar.gz /data

Restore the filestore on the new server (as root-user):

cd /home/molgenis
mv data data_backup
tar -pxvzf molgenis.tar.gz

note: if you use our Ansible playbook to deploy MOLGENIS you have to do the following steps:

• execute: chmod -R 770 /home/molgenis

Configuration

Go to a terminal and tar you files into an archive (as root-user):

cd /tmp/
cp /home/molgenis/molgenis-server.properties .

Restore the filestore on the new server (as root-user):

cd /tmp/
cp molgenis-server.properties /home/molgenis/ .

You need to add additional properties to make the deployment work with MOLGENIS 8.0.x

MINIO_ACCESS_KEY=molgenis
MINIO_SECRET_KEY=molgenis

EMX models and other configuration

The following changes require manual actions (if applicable for your application):

• MREF as labels are not allowed anymore. You should use template expressions. Please check: template expressions.

  • You can migrate the database first and if you encounter the following error

    Error:
      Conversion failure in entity type [#name#] attribute [#name#]; No converter found capable of converting from type [org.molgenis.data.support.DynamicEntity] to type [java.lang.String]

    You can fix these attributes in the Metadata Manager by editing the expression of the mentioned attribute.

• If users or groups were giving special permissions on the Settings Manager Plugin, these permissions should be set again for the replacement Settings Plugin. The plugin itself is replaced automatically.