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README.md

Deployment instructions for TESK

Helm chart and config to deploy the TESK service. Tested with Helm v3.0.0.

Usage

First you must create a namespace in Kubernetes in which to deploy TESK. In development clusters such as Minikube it is fine to use the default namespace. The command below creates all deployments in the context of this namespace. How the namespace is created depends on the cluster, so it is not documented here.

To deploy the application:

  • modify values.yaml
  • If you are installing the FTP storage backend (and will not use .netrc file for FTP credentials) and/or OIDC client, create a secrets.yaml file. You need to fill up the username and password of the ftp account that will be potentially used to exchange I/O with a workflow manager such as cwl-tes. If you activated authentication (auth.mode == 'auth' in values.yaml), optionally you may activate the OICD client in the Swagger UI as well (you need to register the client by your OIDC provider). To do so, supply the client_id and client_secret values obtained during the client registration, otherwise the auth section must be removed.
ftp:
  username: <username>
  password: <password>

auth:
  client_id: <client_id>
  client_secret: <client_secret>

  • If you're using s3 as your storage option, do not forget to add the necessary config and credentials files (see here) under a folder named s3-config (charts/tesk/s3-config).

  • If you are installing the FTP storage backend and want to use .netrc file for FTP credentials, place the .netrc in the ftp folder. There is a template in the folder.

  • Finally execute:

$ helm upgrade --install tesk-release . -f secrets.yaml -f values.yaml

then you can check it all went as expected:

$ helm list -n tesk
NAME	        NAMESPACE  REVISION	UPDATED                                 	STATUS  	CHART     	APP VERSION
tesk-release	tesk	     16      	2020-05-14 11:38:45.521995325 +0300 EEST	deployed	tesk-0.1.0	dev

The first time running this command, the chart will be installed. Afterwards, it will apply any change in the chart.

IMPORTANT: In kubernetes, if you want to install TESK in a namespace different than default, it must be specified by using -n <namespace>, so the final command would be something like this:

$ helm upgrade -n tesk --install tesk-release . -f secrets.yaml -f values.yaml

Note: If you're running Helm 3, you might need to also use the --create-namespace option, as non-existent namespaces do not get created by default (see this).

Description of values

See values.yaml for default values.

Key Type Description
host_name string FQDN to expose the application
storageClass string Name of a user preferred storage class (default is empty)
storage string Can be either 'openstack' or 's3'
tesk.image string container image (including the version) to be used to run TESK API
tesk.port integer
tesk.taskmaster_image_version string the version of the image to be used to run TESK Taskmaster Job
tesk.taskmaster_filer_image_version string the version of the image to be used to run TESK Filer Job
tesk.executor_retries int The number of retries on error - actual task compute (executor)
tesk.filer_retries int The number of retries on error while handling I/O (filer)
tesk.debug boolean Activates the debugging mode
tesk.securityContext.enabled boolean Enable securityContext
transfer.wes_base_path string
transfer.tes_base_path string
transfer.pvc_name string
auth.mode string Can be 'noauth' to disable authentication, or 'auth' to enable it
auth.env_subgroup string Can be 'EBI' or 'CSC'
service.type string Can be 'NodePort' or 'ClusterIp' or 'LoadBalancer'
service.node_port integer Only used if service.type is 'NodePort', specifies the port
ftp.classic_ftp_secret String The name of a secret to store FTP credentials as keys. If empty, the old-style FTP secret is not created
ftp.netrc_secret String The name of a secret to store FTP credentials as a netrc file. If empty, the netrc FTP secret is not created
ftp.hostip string IP of the endpoint of the ftp as seen by containers in K8s (only needed, if in need of a DNS entry for locally installed FTP server)
ingress.rules boolean Apply or not the ingress rule
ingress.ingressClassName string Name of the Ingress Class
ingress.path string
ingress.tls_secret_name string If no TLS secret name configured, TLS will be switched off. A template can be found at deployment/tls_secret_name.yml-TEMPLATE. If you are using cert-manager the secret will be created automatically.
ingress.annotations string Annotations for the ingress rules