helmchart to deploy clowder2 in kubernetes

.gitignore

@@ -55,3 +55,6 @@ dist
 
 # keycloak mounted volume
 scripts/keycloak/data/*
+
+# ignore clowder chart deps
+charts/clowder2/charts

charts/README.md

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+# Clowder 2
+
+This depends on some subcharts, make sure to have them installed if you plan on modifying the helm chart:
+
+```bash
+helm repo add bitnami https://charts.bitnami.com/bitnami
+helm dep build
+```
+
+The chart has some common values, if you want to run this on your local machine you can use the following values (*.clowder2.ncsa.cloud is an DNS record that points to 127.0.0.1):
+
+```yaml
+minio:
+  ingress:
+    hostname: minio.clowder2.ncsa.cloud
+  apiIngress:
+    hostname: minio.clowder2.ncsa.cloud
+
+rabbitmq:
+  ingress:
+    hostname: rabbitmq.clowder2.ncsa.cloud
+```
+
+Now you can install (or upgrade) clowder using:
+```bash
+helm upgrade --install --namespace clowder2 --create-namespace --values local.yaml clowder2 .
+```
+
+
+
+# Docker Desktop
+
+You will need an ingress controller, I like Traefik as my ingress controller. You install this with:
+
+```bash
+helm install --namespace traefik --create-namespace traefik traefik/traefik
+```
+
+If you want to enable the dashboard, you need the following file (dashboard.yaml):
+
+```yaml
+apiVersion: traefik.containo.us/v1alpha1
+kind: IngressRoute
+metadata:
+  name: dashboard
+spec:
+  entryPoints:
+    - web
+  routes:
+    - match: Host(`traefik.clowder2.ncsa.cloud`)
+      kind: Rule
+      services:
+        - name: api@internal
+          kind: TraefikService
+```
+
+and apply it using:
+
+```bash
+kubectl -n traefik apply -f dashboard.yaml
+```
+

charts/clowder2/.helmignore

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+# 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/

charts/clowder2/Chart.lock

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+dependencies:
+- name: mongodb
+  repository: https://charts.bitnami.com/bitnami
+  version: 12.1.31
+- name: minio
+  repository: https://charts.bitnami.com/bitnami
+  version: 11.10.3
+- name: rabbitmq
+  repository: https://charts.bitnami.com/bitnami
+  version: 10.3.6
+- name: elasticsearch
+  repository: https://charts.bitnami.com/bitnami
+  version: 19.4.2
+- name: keycloak
+  repository: https://charts.bitnami.com/bitnami
+  version: 10.1.2
+digest: sha256:0c0e022885173885dfd6097d9a39dc22082515c41b93cda8cf9756a5d019a84f
+generated: "2022-09-30T15:19:12.308156-05:00"

charts/clowder2/Chart.yaml

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+apiVersion: v2
+type: application
+
+# Information about clowder.
+name: clowder2
+icon: https://isda.ncsa.illinois.edu/~kooper/charts/images/clowder.png
+home: https://clowderframework.org/
+description: >
+  Open Source Data Management for Long Tail Data. Clowder is a customizable and
+  scalable data management framework to support any data format and multiple
+  research domains.
+
+# 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: "main"
+
+# List of people that maintain this helm chart.
+maintainers:
+  - name: Rob Kooper
+    email: [email protected]
+  - name: Chen Wang
+    email: [email protected]
+
+# location of source code
+sources:
+  - https://github.com/clowder-framework/clowder2
+
+# Dependencies for clowder. Some of the dependencies are only installed if they
+# are enabled.
+dependencies:
+  - name: mongodb
+    version: ~12
+    repository: https://charts.bitnami.com/bitnami
+    condition: mongodb.enabled
+  - name: minio
+    version: ~11
+    repository: https://charts.bitnami.com/bitnami
+    condition: minio.enabled
+  - name: rabbitmq
+    version: ~10
+    repository: https://charts.bitnami.com/bitnami
+    condition: rabbitmq.enabled
+  - name: elasticsearch
+    version: ~19
+    repository: https://charts.bitnami.com/bitnami
+    condition: elasticsearch.enabled
+  - name: keycloak
+    version: ~10
+    repository: https://charts.bitnami.com/bitnami
+    condition: keycloak.enabled

charts/clowder2/dashboard.yaml

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+# dashboard.yaml
+apiVersion: traefik.containo.us/v1alpha1
+kind: IngressRoute
+metadata:
+  name: dashboard
+spec:
+  entryPoints:
+    - web
+  routes:
+    - match: Host(`traefik.clowder2.ncsa.cloud`) && (PathPrefix(`/dashboard`) || PathPrefix(`/api`))
+      kind: Rule
+      services:
+        - name: api@internal
+          kind: TraefikService

charts/clowder2/templates/NOTES.txt

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+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 }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.frontend.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "clowder2.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.frontend.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "clowder2.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "clowder2.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.frontend.service.port }}
+{{- else if contains "ClusterIP" .Values.frontend.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "clowder2.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 }}

charts/clowder2/templates/_helpers.tpl

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+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "clowder2.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 "clowder2.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 "clowder2.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "clowder2.labels" -}}
+helm.sh/chart: {{ include "clowder2.chart" . }}
+{{ include "clowder2.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "clowder2.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "clowder2.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "clowder2.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "clowder2.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

charts/clowder2/templates/backend/deployment.yaml

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+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "clowder2.fullname" . }}-backend
+  labels:
+    {{- include "clowder2.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: {{ include "clowder2.name" . }}-backend
+      app.kubernetes.io/instance: {{ .Release.Name }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        app.kubernetes.io/name: {{ include "clowder2.name" . }}-backend
+        app.kubernetes.io/instance: {{ .Release.Name }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "clowder2.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: backend
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.backend.image.repository }}:{{ .Values.backend.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.backend.image.pullPolicy }}
+          env:
+            - name: WEB_CONCURRENCY
+              value: "4"
+            - name: MINIO_SERVER_URL
+              value: {{ include "clowder2.name" . }}-minio-headless:9000
+            - name: MONGODB_URL
+              value: mongodb://{{ include "clowder2.name" . }}-mongodb:27017
+            - name: CLOWDER2_URL
+              value: http://{{ .Values.hostname }}
+            - name: auth_base
+              value: $(CLOWDER2_URL)
+            - name: auth_url
+              value: $(CLOWDER2_URL)/keycloak/realms/clowder/protocol/openid-connect/auth?client_id=clowder2-backend&response_type=code
+            - name: oauth2_scheme_auth_url
+              value: http://{{ include "clowder2.name" .}}-keycloak-headless:8080/keycloak/realms/clowder/protocol/openid-connect/auth?client_id=clowder2-backend&response_type=code
+            - name: auth_register_url
+              value: $(CLOWDER2_URL)/keycloak/realms/clowder/protocol/openid-connect/registrations?client_id=clowder2-backend&response_type=code
+            - name: auth_token_url
+              value: http://{{ include "clowder2.name" .}}-keycloak-headless:8080/keycloak/realms/clowder/protocol/openid-connect/token
+            - name: auth_server_url
+              value: http://{{ include "clowder2.name" .}}-keycloak-headless:8080/keycloak/
+            - name: keycloak_base
+              value: $(CLOWDER2_URL)/api
+            - name: frontend_url
+              value: $(CLOWDER2_URL)
+            - name: elasticsearch_url
+              value: http://{{ include "clowder2.name" . }}-elasticsearch:9200
+          ports:
+            - name: http
+              containerPort: 80
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: http
+          readinessProbe:
+            httpGet:
+              path: /
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}