Add data-dashboard-backend

README.md

@@ -407,7 +407,7 @@ If installed, to upgrade `timescaledb`, uncomment the `production.yaml` line `ti
 ```shell
 kubectl delete secrets timescaledb-postgresql
 kubectl delete statefulsets timescaledb-postgresql
-helmfile -f helmfile.d/20-grafana.yaml apply
+helmfile -f helmfile.d/20-dashboard.yaml apply
 ```
 
 If installed, to upgrade `radar-upload-postgresql`, uncomment the `production.yaml` line `radar_upload_postgresql.primary.existingClaim: "data-radar-upload-postgresql-postgresql-0"`. Then run

bin/generate-secrets

@@ -68,6 +68,7 @@ insert_secret ".management_portal.oauth_clients.radar_redcap_integrator.client_s
 insert_secret ".management_portal.oauth_clients.radar_fitbit_connector.client_secret"
 insert_secret ".management_portal.oauth_clients.radar_appconfig.client_secret"
 insert_secret ".management_portal.oauth_clients.radar_push_endpoint.client_secret"
+insert_secret ".management_portal.oauth_clients.radar_data_dashboard_backend.client_secret"
 
 insert_secret \
   ".radar_appserver_postgresql.global.postgresql.auth.postgresPassword" \

charts/data-dashboard-backend/.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/

charts/data-dashboard-backend/Chart.yaml

@@ -0,0 +1,22 @@
+apiVersion: v2
+appVersion: "0.1.0"
+name: data-dashboard-backend
+description: API for data in the data dashboard
+version: 0.1.6
+sources: ["https://github.com/thehyve/radar-data-dashboard-backend"]
+deprecated: false
+type: application
+home: "https://radar-base.org"
+maintainers:
+  - email: keyvan@thehyve.nl
+    name: Keyvan Hedayati
+    url: https://www.thehyve.nl
+  - email: nivethika@thehyve.nl
+    name: Nivethika Mahasivam
+    url: https://www.thehyve.nl/experts/nivethika-mahasivam
+  - email: bastiaan@thehyve.nl
+    name: Bastiaan de Graaf
+    url: https://www.thehyve.nl/experts/bastiaan-de-graaf
+  - email: pim@thehyve.nl
+    name: Pim van Nierop
+    url: https://www.thehyve.nl/experts/pim-van-nierop

charts/data-dashboard-backend/README.md

@@ -0,0 +1,67 @@
+# data-dashboard-backend
+
+![Version: 0.1.1](https://img.shields.io/badge/Version-0.1.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 0.1.0](https://img.shields.io/badge/AppVersion-0.1.0-informational?style=flat-square)
+
+API for data in the data dashboard
+
+**Homepage:** <https://radar-base.org>
+
+## Maintainers
+
+| Name | Email | Url |
+| ---- | ------ | --- |
+| Keyvan Hedayati | <keyvan@thehyve.nl> | <https://www.thehyve.nl> |
+| Joris Borgdorff | <joris@thehyve.nl> | <https://www.thehyve.nl/experts/joris-borgdorff> |
+| Nivethika Mahasivam | <nivethika@thehyve.nl> | <https://www.thehyve.nl/experts/nivethika-mahasivam> |
+
+## Source Code
+
+* <https://github.com/IMI-H2O/outcomes-dashboard>
+
+## Prerequisites
+* Kubernetes 1.17+
+* Kubectl 1.17+
+* Helm 3.1.0+
+
+## Values
+
+| Key | Type | Default                                            | Description |
+|-----|------|----------------------------------------------------|-------------|
+| replicaCount | int | `2`                                                | Number of replicas to deploy |
+| image.repository | string | `"quay.io/imi-h2o/data-dashboard-backend"`         | docker image repository |
+| image.pullPolicy | string | `"Always"`                                         | image pull policy |
+| image.tag | string | `"dev"`                                            |  |
+| imagePullSecrets | list | `[]`                                               | Docker registry secret names as an array |
+| nameOverride | string | `""`                                               | String to partially override fullname template with a string (will prepend the release name) |
+| fullnameOverride | string | `""`                                               | String to fully override fullname template with a string |
+| podSecurityContext | object | `{}`                                               | Configure pod's Security Context |
+| securityContext | object | `{}`                                               | Configure container's Security Context |
+| service.type | string | `"ClusterIP"`                                      | Kubernetes Service type |
+| service.port | int | `9000`                                             | data-dashboard-backend port |
+| ingress.enabled | bool | `true`                                             | Enable ingress controller resource |
+| ingress.className | string | `""`                                               | Ingress class name |
+| ingress.annotations | object | check values.yaml                                  | Annotations that define default ingress class, certificate issuer |
+| ingress.path | string | `"/api($                                           |/)(.*)"` | Path within the url structure |
+| ingress.pathType | string | `"ImplementationSpecific"`                         |  |
+| ingress.hosts | list | `["localhost"]`                                    | Hosts to accept requests from |
+| ingress.tls.secretName | string | `"radar-base-tls"`                                 | TLS Secret Name |
+| resources | object | `{}`                                               |  |
+| autoscaling.enabled | bool | `false`                                            | Enable horizontal autoscaling |
+| autoscaling.minReplicas | int | `1`                                                |  |
+| autoscaling.maxReplicas | int | `100`                                              |  |
+| autoscaling.targetCPUUtilizationPercentage | int | `80`                                               |  |
+| nodeSelector | object | `{}`                                               | Node labels for pod assignment |
+| tolerations | list | `[]`                                               | Toleration labels for pod assignment |
+| affinity | object | `{}`                                               | Affinity labels for pod assignment |
+| existingSecret | string | `""`                                               |  |
+| javaOpts | string | `"-Xmx550m"`                                       | Standard JAVA_OPTS that should be passed to this service |
+| managementPortal.url | string | `"http://management-portal:8080/managementportal"` | ManagementPortal URL |
+| managementPortal.clientId | string | `"data_dashboard_backend"`                         | ManagementPortal OAuth 2.0 client ID, having grant type client_credentials |
+| managementPortal.clientSecret | string | `"secret"`                                         | ManagementPortal OAuth 2.0 client secret |
+| path | string | `"/api"`                                           |  |
+| score | object | Diabetes score calculation table configurations    | Where to find lookup tables for score calculations, and how to calculate them. |
+| jdbc.driver | string | `"org.postgresql.Driver"`                          | JDBC Driver to connect to the database. |
+| jdbc.url | string | `"jdbc:postgresql://postgresql:5432/outcomes"`     | JDBC Connection url of the database. |
+| jdbc.user | string | `"radarbase"`                                      | Username of the database |
+| jdbc.password | string | `"password"`                                       | Password of the user |
+| jdbc.dialect | string | `"org.hibernate.dialect.PostgreSQLDialect"`        | Hibernate dialect to use for JDBC Connection |

charts/data-dashboard-backend/README.md.gotmpl

@@ -0,0 +1,18 @@
+{{ template "chart.header" . }}
+{{ template "chart.deprecationWarning" . }}
+
+{{ template "chart.badgesSection" . }}
+
+{{ template "chart.description" . }}
+
+{{ template "chart.homepageLine" . }}
+
+{{ template "chart.maintainersSection" . }}
+
+{{ template "chart.sourcesSection" . }}
+
+{{ template "common.prerequisites" . }}
+
+{{ template "chart.requirementsSection" . }}
+
+{{ template "chart.valuesSection" . }}

charts/data-dashboard-backend/templates/NOTES.txt

@@ -0,0 +1,20 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host }}{{ $.Values.path }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "data-dashboard-backend.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "data-dashboard-backend.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "data-dashboard-backend.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 "data-dashboard-backend.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://127.0.0.1:9000 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 9000:$CONTAINER_PORT
+{{- end }}

charts/data-dashboard-backend/templates/_helpers.tpl

@@ -0,0 +1,73 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "data-dashboard-backend.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 "data-dashboard-backend.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 "data-dashboard-backend.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Get the password secret.
+*/}}
+{{- define "data-dashboard-backend.secretName" -}}
+{{- if .Values.existingSecret }}
+    {{- printf "%s" .Values.existingSecret -}}
+{{- else -}}
+    {{- printf "%s" (include "data-dashboard-backend.fullname" .) -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Return true if a secret object should be created
+*/}}
+{{- define "data-dashboard-backend.createSecret" -}}
+{{- if .Values.existingSecret }}
+{{- else if .Values.existingSecret -}}
+{{- else -}}
+    {{- true -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Common labels
+*/}}
+{{- define "data-dashboard-backend.labels" -}}
+helm.sh/chart: {{ include "data-dashboard-backend.chart" . }}
+{{ include "data-dashboard-backend.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "data-dashboard-backend.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "data-dashboard-backend.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}

charts/data-dashboard-backend/templates/configmap.yaml

@@ -0,0 +1,26 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ template "data-dashboard-backend.fullname" . }}
+  labels:
+    app: {{ template "data-dashboard-backend.name" . }}
+    chart: {{ template "data-dashboard-backend.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+data:
+  dashboard.yml: |
+    service:
+      baseUri: http://0.0.0.0:9000{{ .Values.path }}
+      advertisedBaseUri: null
+      enableCors: true
+    auth:
+      managementPortal:
+        url: {{ .Values.managementPortal.url }}
+        clientId: {{ .Values.managementPortal.clientId }}
+        clientSecret: {{ .Values.managementPortal.clientSecret }}
+      jwtResourceName: res_data_dashboard_backend
+    database:
+      url: {{ .Values.jdbc.url }}
+      user: {{ .Values.jdbc.user }}
+      password: {{ .Values.jdbc.password }}
+      dialect: {{ .Values.jdbc.dialect }}

charts/data-dashboard-backend/templates/deployment.yaml

@@ -0,0 +1,93 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "data-dashboard-backend.fullname" . }}
+  labels:
+    {{- include "data-dashboard-backend.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "data-dashboard-backend.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      annotations:
+        checksum/configmap: {{ include (print $.Template.BasePath "/configmap.yaml") . | sha256sum }}
+        checksum/secrets: {{ include (print $.Template.BasePath "/secrets.yaml") . | sha256sum }}
+      {{- range $key, $value := .Values.podAnnotations }}
+        {{ $key }}: {{ $value | quote }}
+      {{- end }}
+      labels:
+        {{- include "data-dashboard-backend.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          args:
+            - "/etc/data-dashboard-backend/dashboard.yml"
+          env:
+          - name: DATABASE_URL
+            valueFrom:
+              secretKeyRef:
+                name: {{ template "data-dashboard-backend.secretName" . }}
+                key: databaseUrl
+          - name: DATABASE_USER
+            valueFrom:
+              secretKeyRef:
+                name: {{ template "data-dashboard-backend.secretName" . }}
+                key: databaseUser
+          - name: DATABASE_PASSWORD
+            valueFrom:
+              secretKeyRef:
+                name: {{ template "data-dashboard-backend.secretName" . }}
+                key: databasePassword
+          ports:
+            - name: http
+              containerPort: 9000
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /api/health
+              port: http
+              httpHeaders:
+                - name: Accept
+                  value: application/json
+          readinessProbe:
+            httpGet:
+              path: /api/health
+              port: http
+              httpHeaders:
+                - name: Accept
+                  value: application/json
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          volumeMounts:
+            - name: config
+              mountPath: /etc/data-dashboard-backend/
+      volumes:
+        - name: config
+          configMap:
+            name: {{ include "data-dashboard-backend.fullname" . }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}

charts/data-dashboard-backend/templates/hpa.yaml

@@ -0,0 +1,28 @@
+{{- if .Values.autoscaling.enabled }}
+apiVersion: autoscaling/v2beta1
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "data-dashboard-backend.fullname" . }}
+  labels:
+    {{- include "data-dashboard-backend.labels" . | nindent 4 }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "data-dashboard-backend.fullname" . }}
+  minReplicas: {{ .Values.autoscaling.minReplicas }}
+  maxReplicas: {{ .Values.autoscaling.maxReplicas }}
+  metrics:
+    {{- if .Values.autoscaling.targetCPUUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: cpu
+        targetAverageUtilization: {{ .Values.autoscaling.targetCPUUtilizationPercentage }}
+    {{- end }}
+    {{- if .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: memory
+        targetAverageUtilization: {{ .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    {{- end }}
+{{- end }}