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Install with Helm

Prerequisites

Get CDCS dependencies

Add the bitnami repository to pull the charts of CDCS dependencies:

helm repo add bitnami https://charts.bitnami.com/bitnami

Then pull the charts:

helm dependency build

Quick Start

To install the CDCS and its dependencies, run the command below. By default, it will use the basic configuration from the values.yaml file provided with this repository. See options below to override the basic configuration with your own.

Install the Chart:

helm install -n [NAMESPACE] --create-namespace [RELEASE] [CHART]

Example:

helm install -n mdcs-test --create-namespace mdcs-helm-test .

Override the default values.yaml by linking to a new values file using the -f option:

helm install -n mdcs-test --create-namespace -f ./values.test.yaml mdcs-helm-test .

Override only specific fields of the values.yaml file, with the --set option:

helm install -n mdcs-test --create-namespace mdcs-helm-test . --set cdcs.imagePullPolicy=IfNotPresent

The CDCS container can be configured using environment variables. The complete list of environment variables can be found in the customized deployment section of the CDCS Docker documentation. These environment variables can be set in the file values.yaml.

Example:

cdcs:
  envs:
    - name: PROJECT_NAME
      value: "mdcs"

Once the chart is installed, you should get a message telling you how to access the web server, such as:

NAME: mdcs-helm-test
LAST DEPLOYED: [DATE]
NAMESPACE: mdcs-test
STATUS: deployed
REVISION: 1
NOTES:
1. The system has been deployed at the following URL:
  http://localhost

Once all the pods are properly started, go to the provided URL to access the system.

Create a Superuser

The superuser is the first user that will be added to the CDCS. This is the main administrator on the platform. Once it has been created, more users can be added using the web interface. Wait for the CDCS server to start, then run the following and enter the desired username, password and optional email:

HELM_RELEASE_NAMESPACE="[NAMESPACE]" &&\
HELM_RELEASE_NAME="[RELEASE]" &&\
CDCS_POD_NAME=$(kubectl get pod --namespace $HELM_RELEASE_NAMESPACE -l component=[COMPONENT] -o jsonpath='{.items[0].metadata.name}') &&\
kubectl exec -it --namespace $HELM_RELEASE_NAMESPACE $CDCS_POD_NAME -c [CONTAINER] -- python manage.py createsuperuser

Example:

HELM_RELEASE_NAMESPACE="mdcs-test" &&\
HELM_RELEASE_NAME="mdcs-helm-test" &&\
CDCS_POD_NAME=$(kubectl get pod --namespace $HELM_RELEASE_NAMESPACE -l component=cdcs-django -o jsonpath='{.items[0].metadata.name}') &&\
kubectl exec -it --namespace $HELM_RELEASE_NAMESPACE $CDCS_POD_NAME -c cdcs -- python manage.py createsuperuser

MongoDB Secrets

Passwords for MongoDB can be stored in a secret. To do so, MongoDB requires specific keys and changes to the values.yaml that will be described in this section.

Create a secret

First, to create a secret for MongoDB, copy the file mongo-secrets-example to a new file called mongo-secrets and set the two variables mongodb-root-password and mongodb-passwords:

Example:

mongodb-root-password=mongo_admin_pass
mongodb-passwords=mongo_pass

Create a secret from the environment file with the following command:

kubectl create secret generic [SECRET] --from-env-file=./config/mongo-secrets --namespace [NAMESPACE]

Example:

kubectl create secret generic mongodb --from-env-file=./config/mongo-secrets --namespace mdcs-test

Edit values.yaml

Then edit the values.yaml or your own override file, to use the secret:

  • Comment auth.passwords and auth.rootPassword
  • Uncomment existingSecret and put the name of the secret previously created.

Example:

auth:
#    passwords:
#      - mongo_pass
#    rootPassword: mongo_admin_pass
    # Set the name of the secret created by the previous command
    existingSecret: "mongodb"

Volumes

To use existing PVC, first create the PVC by following these instructions. Existing claims need to be created in the same namespace as the helm chart release. You can follow the instructions to create a namespace prior to creating the PVC.

Ingress TLS Secret

Instructions to create a TLS secret for ingress can be found at this link. Once the TLS secret has been created, it can be set using the following field of the values.yml file:

Example:

cdcs:
  ingress:
    tls:
      - secretName: "cdcs-cert"

Ingress Controller NodePort configurations (optional, bare metal only).

On bare metal configuration, follow these instructions to setup a specific port to access the application.

Replication

Django

Replication can be enabled for the Django web server by setting the cdcs.replicas field:

helm install -n [NAMESPACE] --create-namespace [RELEAE] [CHART] --set cdcs.replicas=[REPLICAS]

Example:

helm install -n mdcs-test --create-namespace mdcs-helm-test . --set cdcs.replicas=2

PostgreSQL

Read replicas can be enabled for the PostgreSQL databases by setting postgresql.architecture=replication and by configuring the postgresql.readReplicas fields:

The Django server needs to be properly configured to use the replicas. See the Django database routing documentation for more information.

Example:

helm install -n mdcs-test --create-namespace mdcs-helm-test . --set postgresql.architecture=replication --set postgresql.readReplicas.replicaCount=1

Uninstall the chart

To uninstall the chart, type the following command:

helm uninstall -n [NAMESPACE] [CHART]

Example:

helm uninstall -n mdcs-test mdcs-helm-test

Troubleshooting

MongoDB chart on ARM architectures

The bitnami helm chart for MongoDB is currently not supported on ARM-based chips (e.g. Apple M1).

PostgreSQL and Redis charts conflicts

The version of the bitnami chart for Redis required by the CDCS is not compatible with the version of the bitnami chart for PostgreSQL and needs to be downgraded (See comment in Chart.yml).