feat(tube-chart): Added helm chart for tube

helm/tube/.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/

helm/tube/Chart.lock

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+dependencies:
+- name: postgresql
+  repository: https://charts.bitnami.com/bitnami
+  version: 11.2.6
+digest: sha256:8d81dea9e85adbdff90d46721aa22b33c4cf66282432d20bbfb7335b77a73eef
+generated: "2022-05-23T15:48:59.956941-05:00"

helm/tube/Chart.yaml

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+apiVersion: v2
+name: tube
+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.
+appVersion: 2022.05
+
+dependencies:
+  - name: "postgresql"
+    repository: https://charts.bitnami.com/bitnami
+    version: 11.2.6
+    condition: postgres.enabled

helm/tube/templates/NOTES.txt

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+{{ .Chart.Name }} has been deployed successfully.

helm/tube/templates/_helpers.tpl

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

helm/tube/templates/deployment.yaml

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+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: tube-deployment
+  labels:
+    {{- include "tube.labels" . | nindent 4 }}
+spec:
+  strategy:
+    type: RollingUpdate
+    rollingUpdate:
+      maxSurge: 1
+      maxUnavailable: 0
+  selector:
+    matchLabels:
+      {{- include "tube.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      labels:
+        {{- include "tube.labels" . | nindent 8 }}
+    spec:
+      volumes:
+        {{- toYaml .Values.volumes | nindent 8 }}
+      containers:
+        - name: tube
+          image: "quay.io/cdis/tube:2021.12"
+          imagePullPolicy: Always
+          ports:
+          - containerPort: 80
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          command: ["/bin/bash"]
+          args:
+            - "-c"
+            - |
+              python run_config.py
+              while true; do sleep 5; done
+          env:
+            {{- toYaml .Values.env | nindent 12 }}
+          volumeMounts:
+            {{- toYaml .Values.volumeMounts | 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 }}

helm/tube/templates/etl-mapping.yaml

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+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: etl-mapping
+data:
+   etlMapping.yaml: {{   .Values.etl_mapping | default "None" }}

helm/tube/templates/ingress.yaml

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+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "tube.fullname" . -}}
+{{- $svcPort := .Values.service.port -}}
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    {{- include "tube.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  {{- if .Values.ingress.tls }}
+  tls:
+    {{- range .Values.ingress.tls }}
+    - hosts:
+        {{- range .hosts }}
+        - {{ . | quote }}
+        {{- end }}
+      secretName: {{ .secretName }}
+    {{- end }}
+  {{- end }}
+  rules:
+    {{- range .Values.ingress.hosts }}
+    - host: {{ .host | quote }}
+      http:
+        paths:
+          {{- range .paths }}
+          - path: {{ .path }}
+            pathType: {{ .pathType }}
+            backend:
+              service: 
+                name: {{ $fullName }}
+                port: 
+                  number: {{ $svcPort }}
+          {{- end }}
+    {{- end }}
+  {{- end }}

helm/tube/templates/tests/test-connection.yaml

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+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "tube.fullname" . }}-test-connection"
+  labels:
+    {{- include "tube.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": test
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args: ['{{ include "tube.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never

helm/tube/test.yml

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+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: tube-deployment
+  labels:
+    helm.sh/chart: tube-0.1.0
+    app.kubernetes.io/name: tube
+    app.kubernetes.io/instance: tube
+    app.kubernetes.io/version: "2021.12"
+    app.kubernetes.io/managed-by: Helm
+spec:
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: tube
+      app.kubernetes.io/instance: tube
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: tube
+        app.kubernetes.io/instance: tube
+    spec:
+      automountServiceAccountToken: false
+      volumes:
+        - name: creds-volume
+          secret:
+            secretName: "peregrine-creds"
+        - name: etl-mapping
+          configMap:
+            name: etl-mapping
+        - name: fence-yaml
+          configMap:
+            name: fence
+      containers:
+        - name: tube
+          imagePullPolicy: Always
+          GEN3_TUBE_IMAGE
+          ports:
+          - containerPort: 80
+          env:
+          - name: DICTIONARY_URL
+            valueFrom:
+              configMapKeyRef:
+                name: manifest-global
+                key: dictionary_url
+          - name: HADOOP_URL
+            value: hdfs://spark-service:9000
+          - name: ES_URL
+            value: esproxy-service
+          - name: HADOOP_HOST
+            value: spark-service
+          - name: HADOOP_CLIENT_OPTS
+            value: -Xmx1g
+          - name: SPARK_EXECUTOR_MEMORY
+            value: 4g
+          - name: SPARK_DRIVER_MEMORY
+            value: 6g
+          volumeMounts:
+            - name: "creds-volume"
+              readOnly: true
+              mountPath: "/gen3/tube/creds.json"
+              subPath: creds.json
+            - name: "etl-mapping"
+              readOnly: true
+              mountPath: "/gen3/tube/etlMapping.yaml"
+              subPath: "etlMapping.yaml"
+            - name: "fence-yaml"
+              mountPath: "/gen3/tube/user.yaml"
+              subPath: user.yaml
+          resources:
+            limits:
+              cpu: 1
+              memory: 12Gi
+          command: ["/bin/bash" ]
+          args:
+            - "-c"
+            - |
+              python run_config.py
+              while true; do sleep 5; done
+      affinity:
+        podAntiAffinity:
+          preferredDuringSchedulingIgnoredDuringExecution:
+          - weight: 100
+            podAffinityTerm:
+              labelSelector:
+                matchExpressions:
+                - key: app
+                  operator: In
+                  values:
+                  - tube
+              topologyKey: "kubernetes.io/hostname"