do not log + helm

.helm/adhoc/cert.yaml

@@ -0,0 +1,42 @@
+apiVersion: cert-manager.io/v1
+kind: Certificate
+metadata:
+  name: siibra-jugex-certificate
+spec:
+  isCA: false
+  commonName: siibra-jugex.apps.tc.humanbrainproject.eu
+  dnsNames:
+  - siibra-jugex.apps.tc.humanbrainproject.eu
+  issuerRef:
+    kind: ClusterIssuer
+    name: letsencrypt-production-issuer-1
+  privateKey:
+    algorithm: RSA
+    encoding: PKCS1
+    size: 2048
+  renewBefore: 120h0m0s
+  secretName: siibra-jugex-prod-secret
+  usages:
+  - server auth
+---
+
+apiVersion: cert-manager.io/v1
+kind: Certificate
+metadata:
+  name: neurogenpy-certificate
+spec:
+  isCA: false
+  commonName: ngpy.apps.hbp.eu
+  dnsNames:
+  - ngpy.apps.hbp.eu
+  issuerRef:
+    kind: ClusterIssuer
+    name: letsencrypt-production-issuer-1
+  privateKey:
+    algorithm: RSA
+    encoding: PKCS1
+    size: 2048
+  renewBefore: 120h0m0s
+  secretName: neurogenpy-prod-secret
+  usages:
+  - server auth

.helm/adhoc/configmap.yaml

@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: jugex-toolbox
+data:
+  SIIBRA_TOOLBOX_LOG_DIR: /siibra-tool-log
+  SIIBRA_TOOLBOX_DATA_DIR: /siibra-tool-data
+  SIIBRA_JURGEX_CELERY_BROKER: redis://redis:6379 
+  SIIBRA_JURGEX_CELERY_RESULT: redis://redis:6379
+  SIIBRA_CACHEDIR: /siibra-tool-data/tmp

.helm/adhoc/cron.yaml

@@ -0,0 +1,30 @@
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: cronjob-trim-old-log-usage
+spec:
+  # run two month
+  schedule: "41 1 */5 */2 *"
+  concurrencyPolicy: Replace
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          containers:
+          - name: cronjob-trim-old-log-usage
+            image: docker-registry.ebrains.eu/monitoring/kubectl:v1.29.2
+            imagePullPolicy: Always
+            command:
+            - /bin/ash
+            - -c
+            # delete all files over 30 days of modification date
+            - "find /siibra-tool-log -mindepth 1 -maxdepth 1 -mtime +30 -delete"
+            volumeMounts:
+              - mountPath: /siibra-tool-log
+                name: log-volume
+
+          restartPolicy: OnFailure
+          volumes:
+          - name: log-volume
+            persistentVolumeClaim:
+              claimName: log-volume-claim-2

.helm/adhoc/deployment.yaml

@@ -0,0 +1,60 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: redis
+spec:
+  progressDeadlineSeconds: 600
+  replicas: 1
+  revisionHistoryLimit: 10
+  selector:
+    matchLabels:
+      app: redis
+  strategy:
+    rollingUpdate:
+      maxSurge: 25%
+      maxUnavailable: 25%
+    type: RollingUpdate
+  template:
+    metadata:
+      labels:
+        app: redis
+    spec:
+      containers:
+      - image: docker-registry.ebrains.eu/monitoring/redis:alpine3.17
+        imagePullPolicy: IfNotPresent
+        livenessProbe:
+          exec:
+            command:
+            - redis-cli
+            - ping
+          failureThreshold: 3
+          periodSeconds: 30
+          successThreshold: 1
+          timeoutSeconds: 1
+        name: redis
+        ports:
+        - containerPort: 6379
+          protocol: TCP
+        readinessProbe:
+          exec:
+            command:
+            - redis-cli
+            - ping
+          failureThreshold: 3
+          periodSeconds: 10
+          successThreshold: 1
+          timeoutSeconds: 1
+        resources:
+          limits:
+            cpu: 200m
+            memory: 1Gi
+          requests:
+            cpu: 100m
+            memory: 128Mi
+        terminationMessagePath: /dev/termination-log
+        terminationMessagePolicy: File
+      dnsPolicy: ClusterFirst
+      restartPolicy: Always
+      schedulerName: default-scheduler
+      securityContext: {}
+      terminationGracePeriodSeconds: 30

.helm/adhoc/ingress.yaml

@@ -0,0 +1,33 @@
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: jugex-toolbox
+spec:
+  rules:
+  - host: siibra-jugex.apps.tc.humanbrainproject.eu
+    http:
+      paths:
+      - backend:
+          service:
+            name: jugex-toolbox
+            port:
+              number: 6001
+        path: /
+        pathType: ImplementationSpecific
+  - host: ngpy.apps.hbp.eu
+    http:
+      paths:
+      - backend:
+          service:
+            name: neurogenpy-toolbox
+            port:
+              number: 6001
+        path: /
+        pathType: ImplementationSpecific
+  tls:
+  - hosts:
+    - siibra-jugex.apps.tc.humanbrainproject.eu
+    secretName: siibra-jugex-prod-secret
+  - hosts:
+    - ngpy.apps.hbp.eu
+    secretName: neurogenpy-prod-secret

.helm/adhoc/pvc.yaml

@@ -0,0 +1,27 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  labels:
+    type: longhorn-pvc
+  name: data-volume-claim
+spec:
+  accessModes:
+  - ReadWriteMany
+  resources:
+    requests:
+      storage: 16Gi
+  storageClassName: longhorn-1
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  labels:
+    type: longhorn-pvc
+  name: log-volume-claim-2
+spec:
+  accessModes:
+  - ReadWriteMany
+  resources:
+    requests:
+      storage: 4Gi
+  storageClassName: longhorn-1

.helm/adhoc/service.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: Service
+metadata:
+  labels:
+    app: redis
+  name: redis
+spec:
+  ports:
+  - port: 6379
+    protocol: TCP
+    targetPort: 6379
+  selector:
+    app: redis
+  type: ClusterIP

.helm/deploy_neurogenpy.sh

@@ -0,0 +1,16 @@
+#! /bin/bash
+
+SERVER_IMG="docker-registry.ebrains.eu/siibra-toolbox/neurogenpy"
+WORKER_IMG="docker-registry.ebrains.eu/siibra-toolbox/neurogenpy"
+SERVER_TAG="server"
+WORKER_TAG="worker"
+
+helm install neurogenpy ./toolbox \
+    --set image.serverRepository=$SERVER_IMG \
+    --set image.workerRepository=$WORKER_IMG \
+    --set image.serverTag=$SERVER_TAG \
+    --set image.workerTag=$WORKER_TAG \
+    --set workerResources.limits.memory=4Gi \
+    --set envObj.NEUROGENPY_CELERY_BROKER=redis://redis:6379 \
+    --set envObj.NEUROGENPY_CELERY_RESULT=redis://redis:6379
+

.helm/toolbox/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

.helm/toolbox/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: toolbox
+description: A Helm chart for Kubernetes
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+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: 0.1.0
+
+# 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.
+# It is recommended to use it with quotes.
+appVersion: "0.0.2"

.helm/toolbox/templates/NOTES.txt

@@ -0,0 +1,22 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "toolbox.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "toolbox.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "toolbox.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "toolbox.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}

.helm/toolbox/templates/_helpers.tpl

@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "toolbox.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "toolbox.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "toolbox.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "toolbox.labels" -}}
+helm.sh/chart: {{ include "toolbox.chart" . }}
+{{ include "toolbox.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "toolbox.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "toolbox.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "toolbox.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "toolbox.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}