Helm charts for Drugis

Troubleshooting

Recover a persistent volume

When you delete an application and delete the namespace the volume is still recoverable.

This will only work when a nfs-provisioner-retain StorageClass is chosen.

1. Navigate to the cluster level
2. Click "Storage" and then "Persistent Volumes"
3. Search for the name of the application e.g. "gemtc"
4. Copy the volume Name
5. On the cluster level you can fire up a terminal using Launch kubectl
6. Execute kubectl patch pv #volume-name# -p '{"spec":{"claimRef": null}}'

   Use the copied volume name, not volume claim name

7. Navigate to the project you want to deploy into
8. Navigate to "Resources" then "Workloads" then "Volumes"
9. Click on "Add Volume", give it a Name, select the correct Namespace and select Use existigin persistent volume
10. Search for the volume name and select it
11. Then redeploy the instance with an existing volume claim pointing to the one you just created.

Database recovery

IMPORTANT: be sure you save the database password! You will need it when you redeploy the instance. Copy the backup dump to the container.

rancher kubectl cp ~/backups/2022-01-13_test_jena_es_backup.n4.gz addis-jena-es:/tmp/. -n addis

Shell into the pod

rancher kubectl exec -it pod/addis-jena-es bash -n addis

Drop the existing database

dropdb database -U rootUser

Fill password for postgres root-user

Create the database again

createdb database -U applicationUser

Fill in password for application user and load the dump.

psql database -U applicationUser < /tmp/database-dump.sql

Jena recovery

Apache Jena 2.13 is needed Copy the backup dump to the container.

rancher kubectl cp ~/backups/2022-01-13_test_jena_es_backup.n4.gz addis-jena-es:/tmp/. -n addis

Shell into the pod

rancher kubectl exec -it pod/addis-jena-es bash -n addis

Get Apache Jena

wget http://archive.apache.org/dist/jena/binaries/apache-jena-2.13.0.zip

Unzip the archive

unzip apache-jena-2.13.0.zip

Remove the lock and cd to /

rm -rf /DB/ mkdir /DB/ cd /

To recover Jena you need the tdbloader command

/#jena-path#/bin/tdbloader --loc=DB /#backup-path#/$(date +%Y-%m-%d)_test_jena_es_backup.n4.gz

The --loc=DB is sub-directory location where you at.

Add docker registry secret

You can add a a registry to each project to be able to use the imagePullSecret value in the chart. This is needed for the Enterprise edition of the Addis platform.

1. Click on "Resources"
2. Click on "Secrets"
3. Click on "Registry secrets"
4. Select "Custom"
5. Fill in "https://registry.molgenis.org/repository/helm"
6. Fill in "Username" and "Password"