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ylepylep
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Merge pull request #5 from HumanBrainProject/feat_migration
feat: add helm deploy
2 parents 3215ef0 + 02e7084 commit 780baab

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‎.github/workflows/dockerimage.yaml

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name: '[build] docker image'
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env:
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DOCKER_REPO: docker-registry.ebrains.eu
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DOCKER_NAMESPACE: hbp-spatial-backend
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DOCKER_IMAGE: server
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DOCKER_TAG: latest
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DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
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DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
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on:
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push:
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branches:
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- main
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jobs:
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build-server-image:
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if: github.repository_owner == 'HumanBrainProject' and ${{ env.DOCKER_USERNAME != '' }} and ${{ env.DOCKER_PASSWORD != '' }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: 'Build and Push'
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run: |
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FULL_TAG=${{ env.DOCKER_REPO }}/${{ env.DOCKER_NAMESPACE }}/${{ env.DOCKER_IMAGE }}:${{ env.DOCKER_TAG }}
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echo FULL_TAG: $FULL_TAG
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docker build -t $FULL_TAG -f Dockerfile.server .
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echo Build successful
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echo Login
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docker login \
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-u '${{ env.DOCKER_USERNAME }}' \
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-P '${{ env.DOCKER_PASSWORD }}' \
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${{ env.DOCKER_REPO }}
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echo Login Successful
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echo Pushing image
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docker push $FULL_TAG
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echo Pushing image successful

‎.github/workflows/tox.yaml

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on: [push]
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jobs:
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build:
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runs-on: ubuntu-latest
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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# Python versions used in BrainVISA base images (i.e. Ubuntu LTS,
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# at the moment 18.04 and 20.04) + the latest stable Python version
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python-version: [ '3.10', '3.8', '3.6' ]
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python-version: [ '3.10', '3.8' ]
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os: ['ubuntu-latest']
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include:
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- python-version: '3.6'
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# see https://github.com/actions/setup-python/issues/355#issuecomment-1335042510
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os: 'ubuntu-20.04'
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}

‎.helm/README.md

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# Deploying to production
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This document is intended for a documentation on how hbp-spatial-backend can be deployed to a [kubernetes (k8s)](https://kubernetes.io/) cluster via [helm](https://helm.sh/).
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Whilst the helm chart is produced with a rancher installation at https://rancher.tc.humanbrainproject.eu/ , the concept should be applicable to other k8s installations.
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## Get started
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1/ Create resources listed in adhoc (they may need to be adjusted based on the cluster you are working on) with:
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```sh
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kubectl apply -f .helm/adhoc/*.yaml
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```
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2/ cp the static files needed to startup the service:
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```sh
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pod_name=$(kubectl get pod -l app=busy-box -o jsonpath="{.items[0].metadata.name}")
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for f in $(find /volatile/hbp-spatial-transformations-data/)
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do
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kubectl cp $f $pod_name:/static-data/${f#/volatile/hbp-spatial-transformations-data/}
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done
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```
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3/ Start application with `helm install prod .helm/hbp_spatial_backend`

‎.helm/adhoc/certificate.yaml

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apiVersion: cert-manager.io/v1
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kind: Certificate
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metadata:
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name: siibra-spatial-backend
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spec:
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commonName: siibra-spatial-backend.apps.tc.humanbrainproject.eu
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isCA: false
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dnsNames:
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- siibra-spatial-backend.apps.tc.humanbrainproject.eu
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issuerRef:
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kind: ClusterIssuer
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name: letsencrypt-production-issuer-1
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privateKey:
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algorithm: RSA
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encoding: PKCS1
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size: 2048
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renewBefore: 120h
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secretName: siibra-spatial-backend-secret
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usages:
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- server auth

‎.helm/adhoc/deployment-busybox.yaml

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apiVersion: apps/v1
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kind: Deployment
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metadata:
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name: busy-box
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labels:
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app: busy-box
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spec:
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replicas: 1
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selector:
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matchLabels:
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app: busy-box
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template:
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metadata:
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labels:
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app: busy-box
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spec:
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volumes:
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- name: data-volume
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persistentVolumeClaim:
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claimName: data-volume-claim
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containers:
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- name: busybox
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image: busybox:latest
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command: ["tail"]
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args: ["-f", "/dev/null"]
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resources:
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limits:
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cpu: 100m
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memory: 128Mi
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requests:
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cpu: 100m
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memory: 128Mi
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volumeMounts:
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- mountPath: /static-data
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name: data-volume

‎.helm/adhoc/pvc-data.yaml

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apiVersion: v1
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kind: PersistentVolumeClaim
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metadata:
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name: data-volume-claim
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labels:
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type: longhorn-pvc
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spec:
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# https://wiki.ebrains.eu/bin/view/Collabs/migration-faq/EBRAINS%20Kubernetes%20README/?srid=01ZnoA2n#HDownloadandconfigureyourkubeconfigfile
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storageClassName: longhorn-1
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resources:
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requests:
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storage: 40Gi
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accessModes:
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- ReadWriteMany

‎.helm/hbp_spatial_backend/.helmignore

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

‎.helm/hbp_spatial_backend/Chart.yaml

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apiVersion: v2
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name: hbp-spatial-backend
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description: A Helm chart for Kubernetes
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# A chart can be either an 'application' or a 'library' chart.
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#
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# Application charts are a collection of templates that can be packaged into versioned archives
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# to be deployed.
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#
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# Library charts provide useful utilities or functions for the chart developer. They're included as
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# a dependency of application charts to inject those utilities and functions into the rendering
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# pipeline. Library charts do not define any templates and therefore cannot be deployed.
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type: application
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# This is the chart version. This version number should be incremented each time you make changes
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# to the chart and its templates, including the app version.
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# Versions are expected to follow Semantic Versioning (https://semver.org/)
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version: 0.1.0
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# This is the version number of the application being deployed. This version number should be
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# incremented each time you make changes to the application. Versions are not expected to
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# follow Semantic Versioning. They should reflect the version the application is using.
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# It is recommended to use it with quotes.
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appVersion: "0.0.3"

‎.helm/hbp_spatial_backend/templates/NOTES.txt

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

‎.helm/hbp_spatial_backend/templates/_helpers.tpl

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

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