Merge pull request #120 from fxusyd/xnat1.8.7-multinode

Xnat1.8.7 with multinode xnat support
Australian-Imaging-Service · May 30, 2023 · 3f34fc3 · 3f34fc3
2 parents f4367c6 + b28283a
commit 3f34fc3
Show file tree

Hide file tree

Showing 4 changed files with 38 additions and 16 deletions.
diff --git a/releases/xnat/Chart.yaml b/releases/xnat/Chart.yaml
@@ -15,18 +15,18 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 1.1.5
+version: 1.1.6
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
-appVersion: 1.8.4.1
+appVersion: 1.8.7.1
 
 dependencies:
 - name: postgresql
-  version: "~10.16.2"
-  repository: "https://charts.bitnami.com/bitnami"
+  version: "10.16.2"  # posgresql app version 11.14.0
+  repository: "https://raw.githubusercontent.com/bitnami/charts/archive-full-index/bitnami"
   condition: postgresql.enabled
 - name: xnat-web
-  version: 1.1.5
+  version: 1.1.6
   condition: xnat-web.enabled
diff --git a/releases/xnat/charts/xnat-web/Chart.yaml b/releases/xnat/charts/xnat-web/Chart.yaml
@@ -15,9 +15,9 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 1.1.5
+version: 1.1.6
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
-appVersion: 1.8.4.1
+appVersion: 1.8.7.1
diff --git a/releases/xnat/charts/xnat-web/templates/statefulset.yaml b/releases/xnat/charts/xnat-web/templates/statefulset.yaml
@@ -35,6 +35,13 @@ spec:
             {{- toYaml .Values.securityContext | nindent 12 }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
+          {{- $request := trimSuffix "Mi" .Values.resources.requests.memory }}
+          {{- $nonheap := trimSuffix "Mi" .Values.nonheapmem }}
+          env:
+            - name: CATALINA_OPTS
+              value: -Xms{{ sub $request $nonheap }}m -Xmx{{ sub $request $nonheap }}m -Dxnat.home=/data/xnat/home
+            - name: timezone
+              value: {{ .Values.timezone }}
           ports:
             - name: http
               containerPort: 8080
@@ -45,10 +52,14 @@ spec:
               port: http
             failureThreshold: {{ .Values.probes.liveness.failureThreshold }}
             periodSeconds: {{ .Values.probes.liveness.periodSeconds }}
+            timeoutSeconds: {{ .Values.probes.liveness.timeoutSeconds }}
           readinessProbe:
             httpGet:
               path: /app/template/Login.vm#!
               port: http
+            failureThreshold: {{ .Values.probes.readiness.failureThreshold }}
+            periodSeconds: {{ .Values.probes.readiness.periodSeconds }}
+            timeoutSeconds: {{ .Values.probes.readiness.timeoutSeconds }}
           startupProbe:
             httpGet:
               path: /app/template/Login.vm#!
@@ -120,6 +131,7 @@ spec:
               for plugin in ${plugins[@]}; do
                 cp -r --preserve=mode,timestamps ${XNAT_HOME}/plugins/${plugin}-* /HOME-PLUGINS || true
               done
+              echo "node.id=$HOSTNAME" > /XNAT_HOME/config/node-conf.properties
           volumeMounts:
             - name: tomcat
               mountPath: /TOMCAT

diff --git a/releases/xnat/charts/xnat-web/values.yaml b/releases/xnat/charts/xnat-web/values.yaml
@@ -65,17 +65,20 @@ ingress:
   #    hosts:
   #      - chart-example.local
 
-resources: {}
+resources:
   # We usually recommend not to specify default resources and to leave this as a conscious
   # choice for the user. This also increases chances charts run on environments with little
   # resources, such as Minikube. If you do want to specify resources, uncomment the following
-  # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
-  # limits:
-  #   cpu: 100m
-  #   memory: 128Mi
-  # requests:
-  #   cpu: 100m
-  #   memory: 128Mi
+  # lines, adjust them as necessary, and remove the curly braces after 'resources:'
+  requests:
+    cpu: 250m
+    memory: 4000Mi
+  limits:
+    cpu: 250m
+    memory: 4000Mi
+
+# nonheapmem is recommended to be set at 40-50% of the request/limit memory for XNAT
+nonheapmem: 2000Mi
 
 autoscaling:
   enabled: false
@@ -221,4 +224,11 @@ probes:
     periodSeconds: 10
   liveness:
     failureThreshold: 1
-    periodSeconds: 10
+    periodSeconds: 10
+    timeoutSeconds: 5
+  readiness:
+    failureThreshold: 1
+    periodSeconds: 10
+    timeoutSeconds: 3
+
+timezone: ""