Merge pull request #5 from HumanBrainProject/feat_migration

feat: add helm deploy

.github/workflows/dockerimage.yaml

@@ -0,0 +1,35 @@
+name: '[build] docker image'
+
+env:
+  DOCKER_REPO: docker-registry.ebrains.eu
+  DOCKER_NAMESPACE: hbp-spatial-backend
+  DOCKER_IMAGE: server
+  DOCKER_TAG: latest
+  DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+  DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
+
+on:
+  push:
+    branches:
+    - main
+jobs:
+  build-server-image:
+    if: github.repository_owner == 'HumanBrainProject' and ${{ env.DOCKER_USERNAME != '' }} and ${{ env.DOCKER_PASSWORD != '' }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: 'Build and Push'
+      run: |
+        FULL_TAG=${{ env.DOCKER_REPO }}/${{ env.DOCKER_NAMESPACE }}/${{ env.DOCKER_IMAGE }}:${{ env.DOCKER_TAG }}
+        echo FULL_TAG: $FULL_TAG
+        docker build -t $FULL_TAG -f Dockerfile.server .
+        echo Build successful
+        echo Login
+        docker login \
+          -u '${{ env.DOCKER_USERNAME }}' \
+          -P '${{ env.DOCKER_PASSWORD }}' \
+          ${{ env.DOCKER_REPO }}
+        echo Login Successful
+        echo Pushing image
+        docker push $FULL_TAG
+        echo Pushing image successful

.github/workflows/tox.yaml

@@ -3,13 +3,18 @@ name: '[tox]'
 on: [push]
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         # Python versions used in BrainVISA base images (i.e. Ubuntu LTS,
         # at the moment 18.04 and 20.04) + the latest stable Python version
-        python-version: [ '3.10', '3.8', '3.6' ]
+        python-version: [ '3.10', '3.8' ]
+        os: ['ubuntu-latest']
+        include:
+        - python-version: '3.6'
+          # see https://github.com/actions/setup-python/issues/355#issuecomment-1335042510
+          os: 'ubuntu-20.04'
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

.helm/README.md

@@ -0,0 +1,26 @@
+# Deploying to production
+
+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/).
+
+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.
+
+## Get started
+
+1/ Create resources listed in adhoc (they may need to be adjusted based on the cluster you are working on) with:
+
+```sh
+kubectl apply -f .helm/adhoc/*.yaml
+```
+2/ cp the static files needed to startup the service:
+
+```sh
+pod_name=$(kubectl get pod -l app=busy-box -o jsonpath="{.items[0].metadata.name}")
+
+for f in $(find /volatile/hbp-spatial-transformations-data/)
+do
+
+    kubectl cp $f $pod_name:/static-data/${f#/volatile/hbp-spatial-transformations-data/}
+done
+```
+
+3/ Start application with `helm install prod .helm/hbp_spatial_backend`

.helm/adhoc/certificate.yaml

@@ -0,0 +1,20 @@
+apiVersion: cert-manager.io/v1
+kind: Certificate
+metadata:
+  name: siibra-spatial-backend
+spec:
+  commonName: siibra-spatial-backend.apps.tc.humanbrainproject.eu
+  isCA: false
+  dnsNames:
+  - siibra-spatial-backend.apps.tc.humanbrainproject.eu
+  issuerRef:
+    kind: ClusterIssuer
+    name: letsencrypt-production-issuer-1
+  privateKey:
+    algorithm: RSA
+    encoding: PKCS1
+    size: 2048
+  renewBefore: 120h
+  secretName: siibra-spatial-backend-secret
+  usages:
+  - server auth

.helm/adhoc/deployment-busybox.yaml

@@ -0,0 +1,35 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: busy-box
+  labels:
+    app: busy-box
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: busy-box
+  template:
+    metadata:
+      labels:
+        app: busy-box
+    spec:
+      volumes:
+      - name: data-volume
+        persistentVolumeClaim:
+          claimName: data-volume-claim
+      containers:
+      - name: busybox
+        image: busybox:latest
+        command: ["tail"]
+        args: ["-f", "/dev/null"]
+        resources:
+          limits:
+            cpu: 100m
+            memory: 128Mi
+          requests:
+            cpu: 100m
+            memory: 128Mi
+        volumeMounts:
+        - mountPath: /static-data
+          name: data-volume

.helm/adhoc/pvc-data.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: data-volume-claim
+  labels:
+    type: longhorn-pvc
+spec:
+  # https://wiki.ebrains.eu/bin/view/Collabs/migration-faq/EBRAINS%20Kubernetes%20README/?srid=01ZnoA2n#HDownloadandconfigureyourkubeconfigfile
+  storageClassName: longhorn-1
+  resources:
+    requests:
+      storage: 40Gi
+  accessModes:
+    - ReadWriteMany

.helm/hbp_spatial_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/

.helm/hbp_spatial_backend/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: hbp-spatial-backend
+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: "0.0.3"

.helm/hbp_spatial_backend/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 "hbp_spatial_backend.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "hbp_spatial_backend.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "hbp_spatial_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 "hbp_spatial_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://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}

.helm/hbp_spatial_backend/templates/_helpers.tpl

@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "hbp_spatial_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 "hbp_spatial_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 "hbp_spatial_backend.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "hbp_spatial_backend.labels" -}}
+helm.sh/chart: {{ include "hbp_spatial_backend.chart" . }}
+{{ include "hbp_spatial_backend.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "hbp_spatial_backend.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "hbp_spatial_backend.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "hbp_spatial_backend.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "hbp_spatial_backend.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

.helm/hbp_spatial_backend/templates/configmap.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+data:
+  config.py: |
+    CORS_ORIGINS = '*'
+    PROXY_FIX = {
+        'x_for': 1,
+        'x_host': 1,
+        'x_port': 1,
+        'x_proto': 1,
+    }
+    DEFAULT_TRANSFORM_GRAPH = '/static-data/DISCO_20181004_sigV30_DARTEL_20181004_reg_x4/graph.yaml'
+kind: ConfigMap
+metadata:
+  name: siibra-spatial-backend
+  labels:
+    {{- include "hbp_spatial_backend.labels" . | nindent 4 }}

.helm/hbp_spatial_backend/templates/deployment.yaml

@@ -0,0 +1,72 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "hbp_spatial_backend.fullname" . }}
+  labels:
+    {{- include "hbp_spatial_backend.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "hbp_spatial_backend.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "hbp_spatial_backend.labels" . | nindent 8 }}
+	{{- with .Values.podLabels }}
+        {{- toYaml . | nindent 8 }}
+        {{- end }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "hbp_spatial_backend.serviceAccountName" . }}
+      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 }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /health
+              port: http
+          readinessProbe:
+            httpGet:
+              path: /health
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          {{- with .Values.volumeMounts }}
+          volumeMounts:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+      {{- with .Values.volumes }}
+      volumes:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}