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Data migration for dictyBase

This is a source repository for docker image to run dictyBase data migration tasks. The docker container setup is based on radial topology.

Usage

The migration task is run using kubernetes. Kubernetes can be run both locally(dev version) and in google compute engine. For both the cases, kubectl command line client need to be installed.

Local

  • Install docker compose.
  • Clone this repository and start up a single node kubernetes cluster.
$_> docker-compose -f k8s-local.yml
  • Go the kubernetes folder.
$_> cd spoke-postgresql/kubernetes/k8s-local
  • Create a persistent volume and a volume claim. For this to work /mnt/docker/database folder need to exist, if not alter the configuration accordingly in the volume.json file.
$_> kubectl create -f volume.json; kubectl create -f claim.json

The above with create a 25G of persistent volume and a 20G of persistent claim. To change any of the default parameter change the configurations accordingly.

  • Run the postgresql service and pod with replication controller. By default, the database will be initialized with 20G of disk space(from 20G persistent claim).
$_> kubectl create -f service.json; kubectl create -f pod.json

Google compute engine

  • Download latest kubernetes and untar it.
  • Setup all prerequisites for google compute engine to run the cluster.
  • Go to untar kubernetes folder and start the cluster.
$_> cd kubernetes
$_> cluster/kube-up.sh
  • Create a GCE disk named 'database-disk'.
$_> gcloud compute disks create --size 30GB database-disk.

The disk size cannot be below 25GB.

  • Create volume and claim.
$_> kubectl create -f volume.json; kubectl create -f claim.json
  • To create secrets, copy the example_secrets.json to secrets.json (any other name will also work) and fill up all the seven fields. All fields need to be base64 encoded.
$_> kubectl create -f secrets.json
  • Now start the postgresql database server service and pod.
$_> kubectl create -f service.json; kubectl create -f pod-pvc-secret.json