Local api infra (#107)

* Add basic api local k8s deployment * Update readme * action test to see if worth doing * Authenticate to ghcr with github.actor? * Increase timeout? * Add more timeout * more timeout * Move helm chart out of local * Fix helm chart path * Remove ghcr secret because api image is public * Larger minikube cluster * Move deploy to a single helm install instead of using helmsman. WIP failing tests * Replace docker compose local setup with minikube * Update readme * Cleanup docker compose-related files * Fix chat lint * Increase application start timeout... * Add debug * Add api logs to debug action * Add missing environment :) * Re-add docker compose * Update image to the one that gets auto-built * Fix tag * Fix helm test api test runner image
BioImage-Archive · Jun 12, 2024 · 702d908 · 702d908
1 parent 1e9a3a4
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diff --git a/.github/workflows/api_kube.yaml b/.github/workflows/api_kube.yaml
@@ -0,0 +1,81 @@
+name: Lint and Test Charts
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  helm-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with: 
+          fetch-depth: 0
+
+      - name: Install chart-testing
+        uses: helm/[email protected]
+
+      - run: helm repo add bitnami https://charts.bitnami.com/bitnami
+
+      - name: Run chart-testing (lint)
+        run: ct lint --charts ./api/helm-chart --debug
+
+  api-test:
+    runs-on: ubuntu-latest
+    environment:
+      name: test
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with: 
+          fetch-depth: 0
+
+      - uses: azure/[email protected]
+      - uses: azure/setup-kubectl@v3
+
+      - name: Start minikube - if this breaks on local do a 'minikube delete'
+        id: minikube
+        uses: medyagh/setup-minikube@master
+        with:
+          cpus: 4
+          memory: 4G # 'wait' below times out on Actions with 2G
+          start-args: '--force'
+
+      - run: helm repo add bitnami https://charts.bitnami.com/bitnami
+
+      - name: Get helm dependencies
+        run: helm dependency build ./api/helm-chart
+
+      - name: Start everything
+        run: |
+          helm install bia-api-local ./api/helm-chart \
+            --set "api_env.mongoRootUser=${{ vars.MONGO_INITDB_ROOT_USERNAME }}" \
+            --set "api_env.mongoRootPassword=${{ secrets.MONGO_INITDB_ROOT_PASSWORD }}" \
+            --set "api_env.jwtSecretKey=${{ secrets.JWT_SECRET_KEY }}" \
+            --set "api_env.userCreateSecretToken=${{ secrets.USER_CREATE_SECRET_TOKEN }}" \
+            --set "mongodb.enabled=true" \
+            --set "mongodb.auth.rootUser=${{ vars.MONGO_INITDB_ROOT_USERNAME }}" \
+            --set "mongodb.auth.rootPassword=${{ secrets.MONGO_INITDB_ROOT_PASSWORD }}"
+
+      - name: Wait for api to start and health-check
+        run: kubectl wait --for=condition=ready pod -l app.kubernetes.io/name=api --timeout=180s
+
+      - name: Run tests
+        run: helm test bia-api-local --logs
+
+      - name: List pods for CI minikube debug
+        run: |
+          kubectl get pods
+          kubectl describe pods -l app.kubernetes.io/name=api
+          kubectl logs -l app.kubernetes.io/name=api
+        if: ${{ failure() }}
+
+      - name: Cleanup
+        run: |
+          minikube delete
+        if: ${{ always() }}
diff --git a/api/.gitignore b/api/.gitignore
@@ -62,4 +62,6 @@ env
 # Project-specific
 ####
 .env
-.venv
+.venv
+
+helm-chart/charts
diff --git a/api/helm-chart/.helmignore b/api/helm-chart/.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/
diff --git a/api/helm-chart/Chart.lock b/api/helm-chart/Chart.lock
@@ -0,0 +1,6 @@
+dependencies:
+- name: mongodb
+  repository: https://charts.bitnami.com/bitnami
+  version: 15.4.3
+digest: sha256:59add6e9bcbda9f7e6d374adf69b03c7d28f0f1ca6660d734a86b2bb3b5b7f41
+generated: "2024-05-29T16:21:49.346169347+01:00"
diff --git a/api/helm-chart/Chart.yaml b/api/helm-chart/Chart.yaml
@@ -0,0 +1,18 @@
+apiVersion: v2
+name: api
+description: A Helm chart for the BioImage Archive api
+maintainers:
+  - name: LA  # Liviu Anita
+    email: [email protected]
+
+type: application
+
+version: 0.1.0
+
+appVersion: "0.1.0"
+
+dependencies:
+  - name: mongodb
+    version: 15.4.3
+    repository: https://charts.bitnami.com/bitnami
+    condition: mongodb.enabled
diff --git a/api/helm-chart/templates/NOTES.txt b/api/helm-chart/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 "api.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "api.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "api.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 "api.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 }}
diff --git a/api/helm-chart/templates/_helpers.tpl b/api/helm-chart/templates/_helpers.tpl
@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "api.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 "api.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 "api.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "api.labels" -}}
+helm.sh/chart: {{ include "api.chart" . }}
+{{ include "api.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "api.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "api.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "api.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "api.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}
diff --git a/api/helm-chart/templates/deployment.yaml b/api/helm-chart/templates/deployment.yaml
@@ -0,0 +1,59 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "api.fullname" . }}
+spec:
+  selector:
+    matchLabels:
+      {{- include "api.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      labels:
+        {{- include "api.labels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          image: "ghcr.io/bioimage-archive/bia-integrator-api:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /v1/search/studies?limit=1
+              port: http
+            initialDelaySeconds: 10
+            failureThreshold: 10
+            periodSeconds: 60
+          readinessProbe:
+            httpGet:
+              path: /v1/openapi.json
+              port: http
+            initialDelaySeconds: 10
+            failureThreshold: 10
+            periodSeconds: 60
+          env:
+            - name: DB_NAME
+              value: {{ .Values.api_env.dbName }}
+            - name: JWT_SECRET_KEY
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: jwtSecretKey
+            - name: USER_CREATE_SECRET_TOKEN
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: userCreateSecretToken
+            - name: MONGO_CONNSTRING
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: mongoConnstring
diff --git a/api/helm-chart/templates/ingress.yaml b/api/helm-chart/templates/ingress.yaml
@@ -0,0 +1,61 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "api.fullname" . -}}
+{{- $svcPort := .Values.service.port -}}
+{{- if and .Values.ingress.className (not (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion)) }}
+  {{- if not (hasKey .Values.ingress.annotations "kubernetes.io/ingress.class") }}
+  {{- $_ := set .Values.ingress.annotations "kubernetes.io/ingress.class" .Values.ingress.className}}
+  {{- end }}
+{{- end }}
+{{- if semverCompare ">=1.19-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: networking.k8s.io/v1
+{{- else if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: networking.k8s.io/v1beta1
+{{- else -}}
+apiVersion: extensions/v1beta1
+{{- end }}
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    {{- include "api.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  {{- if and .Values.ingress.className (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion) }}
+  ingressClassName: {{ .Values.ingress.className }}
+  {{- end }}
+  {{- 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 }}
+            {{- if and .pathType (semverCompare ">=1.18-0" $.Capabilities.KubeVersion.GitVersion) }}
+            pathType: {{ .pathType }}
+            {{- end }}
+            backend:
+              {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+              service:
+                name: {{ $fullName }}
+                port:
+                  number: {{ $svcPort }}
+              {{- else }}
+              serviceName: {{ $fullName }}
+              servicePort: {{ $svcPort }}
+              {{- end }}
+          {{- end }}
+    {{- end }}
+{{- end }}
diff --git a/api/helm-chart/templates/secrets.yaml b/api/helm-chart/templates/secrets.yaml
@@ -0,0 +1,9 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: {{ include "api.fullname" . }}
+type: Opaque
+stringData:
+  mongoConnstring: "mongodb://{{ .Values.api_env.mongoRootUser }}:{{ .Values.api_env.mongoRootPassword }}@{{ .Values.api_env.mongoHost }}:27017"
+  jwtSecretKey: {{ .Values.api_env.jwtSecretKey }}
+  userCreateSecretToken: {{ .Values.api_env.userCreateSecretToken }}
diff --git a/api/helm-chart/templates/service.yaml b/api/helm-chart/templates/service.yaml
@@ -0,0 +1,11 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "api.fullname" . }}
+  labels:
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+  selector:
+    {{- include "api.selectorLabels" . | nindent 4 }}
-Original file line number
+Diff line change
@@ Expand Up / @@ -62,4 +62,6 @@ env @@
     # Project-specific
     ####
     .env
-    .venv
+    .venv
+    helm-chart/charts