xnat

Helm Chart for XNAT

Local Installation

Create a local cluster

Create a cluster into which the chart will be installed using your preferred method. For example, using kind:

kind create cluster --name xnat

Package the chart

To install a local copy of the chart, first create a package:

helm package --dependency-update chart

Install the chart

Install the packaged chart in the cluster with the following command:

helm install \
--set image.name=xnat-core
--set image.tag=0.0.1 \
--set imageCredentials.enabled=true \
--set imageCredentials.registry=ghcr.io \
--set imageCredentials.username=<GH_USERNAME> \
--set imageCredentials.password=<GH_PAT> \
--set postgresql.auth.password=xnat \
--namespace xnat-core \
--create-namespace \
xnat-core xnat-0.0.7.tgz

Note that omitting the namespace option and create-namespace flag will result in the resources being created in the default namespace.

Set image.tag to the version of the XNAT image you would like to use.

Create a PAT with read:packages scope. Use the PAT to set imageCredentials.password.

Set imageCredential.username to be your GitHub username.

Uninstall the chart

Uninstall the chart using the following command:

helm uninstall xnat-core -n xnat-core

Render the chart

The chart can be rendered using the default values with the following command:

helm template xnat-core ./xnat-0.0.7.tgz > build/chart.yaml

Parameters

Common parameters

Name	Description	Value
replicaCount	Number of replicas	1
image.pullPolicy	image pull policy	IfNotPresent
image.pullSecret	Name of secret used to pull image	""
image.registry	Image registry	ghcr.io
image.namespace	Image registry namespace	ucl-mirsg
image.name	Name of the image in the registry	""
image.tag	Image tag	latest
imageCredentials.enabled	Enable or disable image pull secret	false
imageCredentials.registry	Image registry	""
imageCredentials.username	Image registry username	""
imageCredentials.password	Image registry password	""
imageCredentials.email	Image registry email	""
nameOverride	Override name	""
fullnameOverride	Override fullname	""
serviceAccount.create	Specifies whether a service account should be created	true
serviceAccount.automount	Automatically mount a ServiceAccount's API credentials?	true
serviceAccount.annotations	Annotations to add to the service account	{}
serviceAccount.name	The name of the service account to use.	""
service.port	Service port	80
service.type	Service type	ClusterIP
service.targetPort	Service target port	8080
persistence.storageClass	Persistent volume storage class	nil
persistence.annotations	Persistent volume annotations	{}
volumes[0].name	XNAT node configuration Volume name	node-conf
volumes[1].name	XNAT archive Volume name	xnat-archive
volumes[1].accessModes	XNAT archive Volume access modes	["ReadWriteOnce"]
volumes[1].annotations	XNAT archive Volume annotations	{}
volumes[1].existingClaim	XNAT archive Volume existingClaim	nil
volumes[1].persistent	XNAT archive Volume persistent	true
volumes[1].size	XNAT archive Volume size	8Gi
volumes[1].storageClass	XNAT archive Volume storageClass	nil
volumes[2].name	XNAT instance configuration Volume name	xnat-config
volumes[2].secret.secretName	XNAT instance configuration Volume secret name	xnat-conf
volumes[3].name	XNAT OpenID configuration Volume name	xnat-openid-config
volumes[3].secret.secretName	XNAT OpenID configuration Volume secret name	openid-conf
volumes[4].name	XNAT prearchive Volume name	xnat-prearchive
volumes[4].accessModes	XNAT prearchive Volume access modes	["ReadWriteOnce"]
volumes[4].annotations	XNAT prearchive Volume annotations	{}
volumes[4].existingClaim	XNAT prearchive Volume existingClaim	nil
volumes[4].persistent	XNAT prearchive Volume persistent	true
volumes[4].size	XNAT prearchive Volume size	8Gi
volumes[4].storageClass	XNAT prearchive Volume storageClass	nil
volumeMounts[0].name	XNAT node configuration Volume name	node-conf
volumeMounts[0].mountPath	XNAT node configuration Volume mount path	/data/xnat/home/config/node-conf.properties
volumeMounts[0].subPath	XNAT node configuration Volume sub path	node-conf.properties
volumeMounts[1].name	XNAT archive Volume name	xnat-archive
volumeMounts[1].mountPath	XNAT archive Volume mount path	/data/xnat/archive
volumeMounts[1].subPath	XNAT archive Volume sub path	nil
volumeMounts[2].name	XNAT instance configuration Volume name	xnat-config
volumeMounts[2].mountPath	XNAT instance configuration Volume mount path	/data/xnat/home/config/xnat-conf.properties
volumeMounts[2].readOnly	XNAT instance configuration Volume read only	true
volumeMounts[2].subPath	XNAT instance configuration Volume sub path	xnat-conf.properties
volumeMounts[3].name	XNAT OpenID configuration Volume name	xnat-openid-config
volumeMounts[3].mountPath	XNAT OpenID configuration Volume mount path	/data/xnat/home/config/auth/openid-conf.properties
volumeMounts[3].readOnly	XNAT OpenID configuration Volume read only	true
volumeMounts[3].subPath	XNAT OpenID configuration Volume sub path	openid-conf.properties
volumeMounts[4].name	XNAT prearchive Volume name	xnat-prearchive
volumeMounts[4].mountPath	XNAT prearchive Volume mount path	/data/xnat/prearchive
volumeMounts[4].subPath	XNAT prearchive Volume sub path	nil

XNAT Database parameters

Name	Description	Value
postgresql.enabled	Enable or disable the PostgreSQL deployment	true
postgresql.auth.database	PostgreSQL database name	xnat
postgresql.auth.username	PostgreSQL username	xnat
postgresql.auth.password	PostgreSQL password. Make sure to override this.	xnat
postgresql.auth.postgresPassword	PostgreSQL password. Make sure to override this.	postgres
postgresql.image.tag	PostgreSQL image tag	14.17.0-debian-12-r2
postgresql.primary.resources.requests.cpu	CPU request	1
postgresql.primary.resources.requests.memory	Memory request	4000Mi
postgresql.primary.resources.limits.cpu	CPU limit	2
postgresql.primary.resources.limits.memory	Memory limit	4000Mi

XNAT Web parameters

Name	Description	Value
web.siteUrl	Site URL	""
web.auth.openid.clientId	OpenID client ID	""
web.auth.openid.clientSecret	OpenID client secret	""
web.auth.openid.accessTokenUri	OpenID access token URI	""
web.auth.openid.userAuthUri	OpenID user authentication URI	""
web.auth.openid.link	OpenID link	""
web.podAnnotations	Annotations to add to the web pod	{}
web.podLabels	Labels to add to the web pod	{}
web.podSecurityContext.runAsUser	Pod security context runAsUser	1000
web.securityContext	Pod security context	{}
web.ingress.enabled	Enable or disable the ingress deployment	false
web.ingress.className	Ingress class name	""
web.ingress.annotations	Ingress annotations	{}
web.ingress.hosts[0].host	Ingress host	chart-example.local
web.ingress.hosts[0].paths[0].path	Ingress path	/
web.ingress.hosts[0].paths[0].pathType	Ingress path type	ImplementationSpecific
web.ingress.tls	Ingress TLS	[]
web.resources.limits.cpu	CPU and memory limits	2
web.resources.limits.memory	Memory limits	4000Mi
web.resources.requests.cpu	CPU and memory requests	1
web.resources.requests.memory	Memory requests	4000Mi
web.livenessProbe.failureThreshold	Liveness probe failure threshold	1
web.livenessProbe.httpGet.path	Liveness probe httpGet path	/app/template/Login.vm#!
web.livenessProbe.httpGet.port	Liveness probe httpGet port	http
web.livenessProbe.periodSeconds	Liveness probe period seconds	10
web.livenessProbe.timeoutSeconds	Liveness probe timeout seconds	5
web.readinessProbe.failureThreshold	Readiness probe failure threshold	1
web.readinessProbe.httpGet.path	Readiness probe httpGet path	/app/template/Login.vm#!
web.readinessProbe.httpGet.port	Readiness probe httpGet port	http
web.readinessProbe.periodSeconds	Readiness probe period seconds	10
web.readinessProbe.timeoutSeconds	Readiness probe timeout seconds	3
web.startupProbe.failureThreshold	Startup probe failure threshold	15
web.startupProbe.httpGet.path	Startup probe httpGet path	/app/template/Login.vm#!
web.startupProbe.httpGet.port	Startup probe httpGet port	http
web.startupProbe.periodSeconds	Startup probe period seconds	10
web.startupProbe.initialDelaySeconds	Startup probe initial delay seconds	20
web.autoscaling.enabled	Enable or disable the autoscaling	false
web.autoscaling.minReplicas	Minimum number of replicas	1
web.autoscaling.maxReplicas	Maximum number of replicas	100
web.autoscaling.targetCPUUtilizationPercentage	Target CPU utilisation percentage	80
web.nodeSelector	Node selector	{}
web.tolerations	Tolerations to add to the web pod	[]
web.affinity	Affinity to add to the web pod	{}