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Deploy Production-ready Aidbox to Kubernetes

Production-ready infrastructure

Key infrastructure elements:

  • Cluster configuration — Node pool and tooling

  • Database — Cloud or self-managed database

  • Aidbox — Aidbox installation

  • Logging — Сollect application and cluster logs

  • Monitoring — Сollect, alert, and visualize cluster and application metrics

  • Security — Vulnerability scanning and policy management

Cluster configuration and tooling

Recommended Kubernetes cluster configuration:

  • Small and medium workloads — 3 nodes X 4 VCPU 16 GB RAM

  • Huge workloads — 3 nodes X 8 VCPU X 64 GB RAM

Toolkit required for development and deployment:

  • AWS, GCP, AZURE - Cloud provider CLI and SDK. Depends on your cloud provider:

  • Kubectl - connection and cluster management

  • Helm - Kubernetes package manager

  • Lens - Kubernetes IDE

Optional - Development and Delivery tooling:

  • Terraform - Infrastructure automation tool

  • Grafana tanka - configuration utility for your Kubernetes

  • Argo CD - GitOps delivery and management

  • Flux - set of continuous and progressive delivery solutions for Kubernetes

Database

Managed solution

Aidbox supports all popular managed Postgresql databases. Supported versions - 13 and higher. See more details in this article — Run Aidbox on managed PostgreSQL.

Self-managed solution

For a self-managed solution, we recommend use AidboxDB image . This image contains all required extensions, backup tool, and pre-build replication support. Read more information in the documentation — AidboxDB.

First step — create volume

Persistent Volume
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: db-master-data
  namespace: prod
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 300Gi
  # depend on your cloud provider. Use SSD volumes
  storageClassName: managed-premium

Next - create all required configs, like postgresql.conf, required container parameters and credentials.

postgresql.conf
apiVersion: v1
kind: ConfigMap
metadata:
  name: db-pg-config
  namespace: prod
data:
  postgres.conf: |-
    listen_addresses = '*'
    shared_buffers = '2GB'
    max_wal_size = '4GB'
    pg_stat_statements.max = 500
    pg_stat_statements.save = false
    pg_stat_statements.track = top
    pg_stat_statements.track_utility = true
    shared_preload_libraries = 'pg_stat_statements'
    track_io_timing = on
    wal_level = logical
    wal_log_hints = on
    archive_command = 'wal-g wal-push %p'
    restore_command = 'wal-g wal-fetch %f %p'
db-config Configmap
apiVersion: v1
kind: ConfigMap
metadata:
  name: db-config
  namespace: prod
data:
  PGDATA: /data/pg
  POSTGRES_DB: postgres
db-secret Secret
apiVersion: v1
kind: Secret
metadata:
  name: db-secret
  namespace: prod
type: Opaque
data:
  POSTGRES_PASSWORD: cG9zdGdyZXM=
  POSTGRES_USER: cG9zdGdyZXM=

Now we can create a database StatefulSet

Db Master StatefulSet
apiVersion: apps/v1
kind: StatefulSet
metadata:
  name: prod-db-master
  namespace: prod
spec:
  replicas: 1
  serviceName: db
  selector:
    matchLabels:
      service: db
  template:
    metadata:
      labels:
        service: db
    spec:
      volumes:
        - name: db-pg-config
          configMap:
            name: db-pg-config
            defaultMode: 420
        - name: db-dshm
          emptyDir:
            medium: Memory
        - name: db-data
          persistentVolumeClaim:
            claimName: db-master-data
      containers:
        - name: main
          image: healthsamurai/aidboxdb:14.2
          ports:
            - containerPort: 5432
              protocol: TCP
          envFrom:
            - configMapRef:
                name: db-config
            - secretRef:
                name: db-secret
          volumeMounts:
            - name: db-pg-config
              mountPath: /etc/configs
            - name: db-dshm
              mountPath: /dev/shm
            - name: db-data
              mountPath: /data
              subPath: pg

Create master database service

Database Service
apiVersion: v1
kind: Service
metadata:
  name: db
  namespace: prod
spec:
  ports:
    - protocol: TCP
      port: 5432
      targetPort: 5432
  selector:
    service: db

Replica installation contains all the same steps but required additional configuration

Replica DB config
apiVersion: v1
kind: ConfigMap
metadata:
  name: db-replica
  namespace: prod
data:
  PG_ROLE: replica
  PG_MASTER_HOST: db-master
  PG_REPLICA: streaming_replica_streaming
  PGDATA: /data/pg
  POSTGRES_DB: postgres

For backups and WAL archivation we are recommended cloud-native solution WAL-G. You can find full information about configuration and usage on documentation page.

  • Configure storage access — WAL-G can store backups in S3, Google Cloud Storage, Azure, or a local file system.

  • Recommended backup policy — Full backup every week, incremental backup every day.

Alternative solutions

A set of tools to perform HA PostgreSQL with fail and switchover, automated backups.

  • Patroni — A Template for PostgreSQL HA with ZooKeeper, ETCD or Consul.

  • Postgres operator — The Postgres Operator delivers an easy to run HA PostgreSQL clusters on Kubernetes.

Aidbox

First of all, you need to get Aidbox license on Aidbox user portal

Create ConfigMap with all required config and database connection

Aidbox ConfigMap
apiVersion: v1
kind: ConfigMap
metadata:
  name: aidbox
  namespace: prod
data:
  AIDBOX_BASE_URL: https://my.box.url
  AIDBOX_BOX_ID: aidbox
  AIDBOX_FHIR_VERSION: 4.0.1
  AIDBOX_PORT: '8080'
  AIDBOX_STDOUT_PRETTY: all
  BOX_INSTANCE_NAME: aidbox
  BOX_METRICS_PORT: '8765'
  PGDATABASE: aidbox
  PGHOST: db.prod.svc.cluster.local   # database address
  PGPORT: '5432'                      # database port
Aidbox Secret
apiVersion: v1
kind: Secret
metadata:
  name: aidbox
  namespace: prod
data:
  AIDBOX_ADMIN_ID: <admin_login>
  AIDBOX_ADMIN_PASSWORD: <admin_password>
  AIDBOX_CLIENT_ID: <root_client_id>
  AIDBOX_CLIENT_SECRET: <root_client_password>
  AIDBOX_LICENSE: <JWT-LICENSE>    # JWT license from aidbox user portal
  PGPASSWORD: <db_password>        # database password
  PGUSER: <db_user>                # database username

Aidbox Deployment

Aidbox Deployment
apiVersion: apps/v1
kind: Deployment
metadata:
  name: aidbox
  namespace: prod
spec:
  replicas: 2
  selector:
    matchLabels:
      service: aidbox
  template:
    metadata:
      labels:
        service: aidbox
    spec:
      containers:
        - name: main
          image: healthsamurai/aidboxone:latest
          ports:
            - containerPort: 8080
              protocol: TCP
            - containerPort: 8765
              protocol: TCP
          envFrom:
            - configMapRef:
                name: aidbox
            - secretRef:
                name: aidbox
          livenessProbe:
            httpGet:
              path: /health
              port: 8080
              scheme: HTTP
            initialDelaySeconds: 20
            timeoutSeconds: 10
            periodSeconds: 10
            successThreshold: 1
            failureThreshold: 12
          readinessProbe:
            httpGet:
              path: /health
              port: 8080
              scheme: HTTP
            initialDelaySeconds: 20
            timeoutSeconds: 10
            periodSeconds: 10
            successThreshold: 1
            failureThreshold: 6
          startupProbe:
            httpGet:
              path: /health
              port: 8080
              scheme: HTTP
            initialDelaySeconds: 20
            timeoutSeconds: 5
            periodSeconds:  5
            successThreshold: 1
            failureThreshold: 4

All additional information about HA Aidbox configuration you can find in this article — HA Aidbox

To verify that Aidbox started correctly you can check the logs:

kubectl logs -f <aidbox-pod-name>

Create the Aidbox k8s service

Aidbox service
apiVersion: v1
kind: Service
metadata:
  name: aidbox
  namespace: prod
spec:
  ports:
    - protocol: TCP
      port: 80
      targetPort: 8080
  selector:
    service: aidbox

Ingress

A Cluster must have an ingress controller Installed. Our recommendation is to use kubernetes Ingress NGINX Controller. As an alternative, you can use Traefic. More additional information about Ingress in k8s you can found in this documentation — Kubernetes Service Networking

Ingress NGINX controller

Ingress-nginx — is an Ingress controller for Kubernetes using NGINX as a reverse proxy and load balancer.

Install Ingress NGINX
helm upgrade \
  --install ingress-nginx ingress-nginx \
  --repo https://kubernetes.github.io/ingress-nginx \
  --namespace ingress-nginx --create-namespace

CertManager

To provide a secure HTTPS connection you can use paid SSL certificates, issued for your domain, or use LetsEncrypt-issued certificates. In case of using LetsEcrypt, we recommend install and configure Cert Manager Operator

Install Cert Manager
helm repo add jetstack https://charts.jetstack.io
helm repo update
helm install \
  cert-manager jetstack/cert-manager \
  --namespace cert-manager \
  --create-namespace \
  --version v1.10.0 \       # Or latest available version
  --set installCRDs=true

Configure Cluster Issuer:

apiVersion: cert-manager.io/v1
kind: ClusterIssuer
metadata:
  name: letsencrypt
spec:
  acme:
    email: hello@my-domain.com
    preferredChain: ''
    privateKeySecretRef:
      name: issuer-key
    server: https://acme-v02.api.letsencrypt.org/directory
    solvers:
      - http01:
          ingress:
            class: nginx  # Ingress class name

If you use Multibox image and want to use cert manger — you should configure DNS01 authorization to provide wildcard certificates

https://letsencrypt.org/docs/challenge-types/#dns-01-challenge

Ingress resource

Now you can create k8s Ingress for Aidbox deployment

Ingress
apiVersion: networking.k8s.io/v1
kind: Ingress
metadata:
  name: aidbox
  namespace: prod
  annotations:
    acme.cert-manager.io/http01-ingress-class: nginx
    cert-manager.io/cluster-issuer: letsencrypt
    kubernetes.io/ingress.class: nginx
spec:
  tls:
    - hosts:
        - my.box.url
      secretName: aidbox-tls
  rules:
    - host: my.box.url
      http:
        paths:
          - path: /
            pathType: ImplementationSpecific
            backend:
              service:
                name: aidbox
                port:
                  number: 80

Now you can test ingress

curl https://my.box.url

Logging

General logging & audit information can be found in this article — Logging & Audit

Aidbox supports integration with the following systems:

ElasticSearch integration

You can install ECK using official guide.

Configure Aidbox and ES integration

Aidbox ConfigMap
apiVersion: v1
kind: Secret
metadata:
  name: aidbox
  namespace: prod
data:
  ...
  AIDBOX_ES_URL = http://es-service.es-ns.svc.cluster.local
  AIDBOX_ES_AUTH = <user>:<password>
  ...

DataDog integration

Aidbox ConfigMap
apiVersion: v1
kind: Secret
metadata:
  name: aidbox
  namespace: prod
data:
  ...
  AIDBOX_DD_API_KEY: <Datadog API Key>
  ...

Monitoring

For monitoring our recommendation is to use kube prometheus stack

helm repo add prometheus-community https://prometheus-community.github.io/helm-charts
helm repo update
helm install prometheus prometheus-community/kube-prometheus-stack

Create Aidbox metrics service

apiVersion: v1
kind: Service
metadata:
  name: aidbox-metrics
  namespace: prod
  labels:
    operated: prometheus
spec:
  ports:
    - protocol: TCP
      port: 80
      targetPort: 8765
  selector:
    service: aidbox

Create ServiceMonitor config for scrapping metrics data

ServiceMonitor
apiVersion: monitoring.coreos.com/v1
kind: ServiceMonitor
metadata:
  labels:
    app.kubernetes.io/component: metrics
    release: kube-prometheus
    serviceMonitorSelector: aidbox
  name: aidbox
  namespace: kube-prometheus
spec:
  endpoints:
    - honorLabels: true
      interval: 10s
      path: /metrics
      targetPort: 8765
    - honorLabels: true
      interval: 60s
      path: /metrics/minutes
      targetPort: 8765
    - honorLabels: true
      interval: 10m
      path: /metrics/hours
      targetPort: 8765
  namespaceSelector:
    any: true
  selector:
    matchLabels:
      operated: prometheus

Or you can directly specify the Prometheus scrapers configuration

global:
  external_labels:
    monitor: 'aidbox'
scrape_configs:
  - job_name: aidbox
    scrape_interval: 5s
    metrics_path: /metrics
    static_configs:
      - targets: [ 'aidbox-metrics.prod.svc.cluster.local:8765' ]

  - job_name: aidbox-minutes
    scrape_interval: 30s
    metrics_path: /metrics/minutes
    static_configs:
      - targets: [ 'aidbox-metrics.prod.svc.cluster.local:8765' ]

  - job_name: aidbox-hours
    scrape_interval: 1m
    scrape_timeout: 30s                     
    metrics_path: /metrics/hours
    static_configs:
      - targets: [ 'aidbox-metrics.prod.svc.cluster.local:8765' ]

Alternative solutions

  • VictoriaMetrics — High Performance Open Source Time Series Database.

  • Thanos — highly available Prometheus setup with long term storage capabilities.

  • Grafana Mimir — highly available, multi-tenant, long-term storage for Prometheus.

Export the Aidbox Grafana dashboard

Aidbox metrics has integration with Grafana, which can generate dashboards and upload them to Grafana — Grafana Integration

Additional monitoring

System monitoring:

  • node exporter — Prometheus exporter for hardware and OS metrics exposed by *NIX kernels

  • kube state metrics — is a simple service that listens to the Kubernetes API server and generates metrics about the state of the objects

  • cadvisor — container usage metrics

PostgreSQL monitoring:

  • pg_exporter — Prometheus exporter for PostgreSQL server metrics

Alerting

Alerting rules allow you to define alert conditions based on Prometheus expression language expressions and to send notifications about firing alerts to an external service.

Alert rules

Alert for long-running HTTP queries with P99 > 5s in 5m interval

alert: SlowRequests
for: 5m
expr: histogram_quantile(0.99, sum (rate(aidbox_http_request_duration_seconds_bucket[5m])) by (le, route, instance)) > 5
labels: {severity: ticket}
annotations:
  title: Long HTTP query execution
  metric: '{{ $labels.route }}'
  value: '{{ $value | printf "%.2f" }}'

Alert delivery

Alert manager template for Telegram

global:
  resolve_timeout: 5m
  telegram_api_url: 'https://api.telegram.org/'
route:
  group_by: [alertname instance]
  # Default receiver
  receiver: <my-ops-chat>
  routes:
  # Mute watchdog alert
  - receiver: empty
    match: {alertname: Watchdog}
receivers:
- name: empty
- name: <my-ops-chat>
  telegram_configs:
  - chat_id: <chat-id>
    api_url: https://api.telegram.org
    parse_mode: HTML
    message: |-
      <b>[{{ .CommonLabels.instance }}] {{ .CommonLabels.alertname }}</b>
      {{ .CommonAnnotations.title }}
      {{ range .Alerts }}{{ .Annotations.metric }}: {{ .Annotations.value }}
      {{ end }}
    bot_token: <bot-token>

All other integrations you can find on AlertManager documentation page.

Additional tools

  • Embedded Grafana alerts

  • Grafana OnCall

Security

Vulnerability and security scanners:

Kubernetes Policy Management:

Advanced:

  • Datree — k8s resources linter

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Last updated

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