test(e2e): added basic smoke test making sure everything starts OK (#31)

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ permissions: read-all
 
 jobs:
   build:
-    uses: miracum/.github/.github/workflows/standard-build.yaml@e86b05b914141334811d43d0973c95cec61bb729 # v1.4.6
+    uses: miracum/.github/.github/workflows/standard-build.yaml@f9d64a7dbe928557fde9f96defa3e372bc0eaf21 # v1.6.1
     permissions:
       contents: read
       id-token: write
@@ -26,8 +26,79 @@ jobs:
     secrets:
       github-token: ${{ secrets.GITHUB_TOKEN }}
 
+  test:
+    name: run k8s smoke test
+    runs-on: ubuntu-22.04
+    if: ${{ github.event_name == 'pull_request' }}
+    needs:
+      - build
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+
+      - name: Create KinD cluster
+        uses: helm/kind-action@99576bfa6ddf9a8e612d83b513da5a75875caced # v1.9.0
+        with:
+          cluster_name: kind
+
+      - name: Download image
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        with:
+          name: ${{ needs.build.outputs.image-slug }}
+          path: /tmp
+
+      - name: Load image into KinD
+        run: |
+          kind load image-archive /tmp/image.tar
+
+      - name: List images in cluster
+        run: docker exec kind-control-plane crictl images
+
+      - name: Install test chart
+        env:
+          IMAGE_TAG: ${{ needs.build.outputs.image-version }}
+        run: |
+          helm dep up tests/k8s
+
+          # start by first installing the Strimzi and Prometheus operators
+          helm upgrade --install \
+            --set "stream-processors.enabled=false" \
+            --set "stream-processors.processors.obds-to-fhir.container.image.tag=${IMAGE_TAG}" \
+            --wait \
+            --timeout=10m \
+            obds-to-fhir-test \
+            tests/k8s
+
+          # install the actual obds-to-fhir stream processor
+          helm upgrade --install \
+            --set "stream-processors.enabled=true" \
+            --set "stream-processors.processors.obds-to-fhir.container.image.tag=${IMAGE_TAG}" \
+            --wait \
+            --timeout=10m \
+            obds-to-fhir-test \
+            tests/k8s
+
+      - name: Run Helm test to make sure everything started correctly
+        run: |
+          helm test obds-to-fhir-test
+
+      - name: Print cluster logs
+        if: always()
+        run: |
+          kubectl cluster-info dump -o yaml | tee kind-cluster-dump.txt
+
+      - name: Upload cluster dump
+        if: always()
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
+        with:
+          name: kind-cluster-dump.txt
+          path: |
+            kind-cluster-dump.txt
+
   lint:
-    uses: miracum/.github/.github/workflows/standard-lint.yaml@e86b05b914141334811d43d0973c95cec61bb729 # v1.4.6
+    uses: miracum/.github/.github/workflows/standard-lint.yaml@f9d64a7dbe928557fde9f96defa3e372bc0eaf21 # v1.6.1
     permissions:
       contents: read
       pull-requests: write
@@ -41,7 +112,7 @@ jobs:
       github-token: ${{ secrets.GITHUB_TOKEN }}
 
   release:
-    uses: miracum/.github/.github/workflows/standard-release.yaml@e86b05b914141334811d43d0973c95cec61bb729 # v1.4.6
+    uses: miracum/.github/.github/workflows/standard-release.yaml@f9d64a7dbe928557fde9f96defa3e372bc0eaf21 # v1.6.1
     needs:
       - build
     permissions:

.github/workflows/schedule.yaml

@@ -10,7 +10,7 @@ permissions: read-all
 
 jobs:
   schedule:
-    uses: miracum/.github/.github/workflows/standard-schedule.yaml@e86b05b914141334811d43d0973c95cec61bb729 # v1.4.6
+    uses: miracum/.github/.github/workflows/standard-schedule.yaml@f9d64a7dbe928557fde9f96defa3e372bc0eaf21 # v1.6.1
     permissions:
       contents: read
       issues: write

.gitignore

@@ -59,3 +59,5 @@ bin
 fhirpkg.lock.json
 
 *.received.fhir.json
+
+tests/k8s/**/charts

.prettierignore

@@ -1 +1,2 @@
 src/test/java/snapshots/**
+tests/k8s/**/templates

.yamllint → .yamllint.yml

@@ -1,7 +1,9 @@
 ---
-
 extends: default
 
 rules:
   document-start: disable
   line-length: disable
+
+ignore: |
+  tests/k8s/**/templates

build.gradle

@@ -31,6 +31,8 @@ dependencies {
 	implementation 'org.apache.kafka:kafka-streams'
 	implementation 'org.springframework.cloud:spring-cloud-stream'
 	implementation 'org.springframework.cloud:spring-cloud-stream-binder-kafka-streams'
+	implementation "org.springframework.boot:spring-boot-starter-actuator"
+	implementation "org.springframework.boot:spring-boot-starter-web"
 	implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${hapiVersion}"
 	implementation 'io.micrometer:micrometer-registry-prometheus:1.12.2'
 	implementation 'io.micrometer:micrometer-core:1.12.2'

deploy/docker-compose.dev.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   oracle2:
-    image: docker.miracum.org/oracle/database:19.3.0-se2
+    image: harbor.miracum.org/oracle/database:19.3.0-se2
     hostname: oracle2
     ports:
       - "1521:1521"
@@ -39,21 +39,6 @@ services:
     depends_on:
       - zoo1
 
-  kafka-rest-proxy:
-    image: confluentinc/cp-kafka-rest:7.5.3@sha256:a4558632cad6c4eedd8bc340a30277ab020b4fd97444844df1be0dbf9061782d
-    hostname: kafka-rest-proxy
-    ports:
-      - "8082:8082"
-    environment:
-      # KAFKA_REST_ZOOKEEPER_CONNECT: zoo1:2181
-      KAFKA_REST_LISTENERS: http://0.0.0.0:8082/
-      KAFKA_REST_SCHEMA_REGISTRY_URL: http://kafka-schema-registry:8081/
-      KAFKA_REST_HOST_NAME: kafka-rest-proxy
-      KAFKA_REST_BOOTSTRAP_SERVERS: PLAINTEXT://kafka1:19092
-    depends_on:
-      - zoo1
-      - kafka1
-
   kafka-connect:
     image: confluentinc/cp-kafka-connect:7.5.3@sha256:e6bc1b88b43a23de290da574b0bbc06135b0005ecb9cac0c95155d3ff50f283a
     hostname: kafka-connect
@@ -80,7 +65,6 @@ services:
     depends_on:
       - zoo1
       - kafka1
-      - kafka-rest-proxy
 
   akhq:
     image: tchiotludo/akhq:0.24.0

src/main/resources/application.yml

@@ -165,3 +165,20 @@ spring:
       key-store-password: ${SSL_KEY_STORE_PASSWORD}
     producer:
       compression-type: gzip
+
+management:
+  endpoint:
+    health:
+      show-details: always
+      probes:
+        enabled: true
+        add-additional-paths: true
+  endpoints:
+    web:
+      exposure:
+        include: "health,prometheus"
+  health:
+    livenessstate:
+      enabled: true
+    readinessstate:
+      enabled: true

tests/k8s/Chart.lock

@@ -0,0 +1,12 @@
+dependencies:
+- name: stream-processors
+  repository: oci://ghcr.io/miracum/charts
+  version: 1.6.1
+- name: strimzi-kafka-operator
+  repository: oci://quay.io/strimzi-helm
+  version: 0.40.0
+- name: kube-prometheus-stack
+  repository: oci://ghcr.io/prometheus-community/charts
+  version: 57.0.3
+digest: sha256:c3e7f5ed93a6ac74b481eacebb57b683a410808b4c2be3f41436914e3b0d1a82
+generated: "2024-03-18T15:26:37.617325079+01:00"

tests/k8s/Chart.yaml

@@ -0,0 +1,18 @@
+apiVersion: v2
+name: obds-to-fhir-test
+type: application
+description: Simple smoke test for deploying obds-to-fhir on K8s.
+deprecated: false
+kubeVersion: ">= 1.21.0"
+dependencies:
+  - name: kube-prometheus-stack
+    repository: oci://ghcr.io/prometheus-community/charts
+    version: 57.0.3
+  - name: stream-processors
+    repository: oci://ghcr.io/miracum/charts
+    version: 1.6.1
+  - name: strimzi-kafka-operator
+    repository: oci://quay.io/strimzi-helm
+    version: 0.40.0
+version: 0.0.0
+appVersion: 0.0.0

tests/k8s/templates/kafka-cluster.yaml

@@ -0,0 +1,49 @@
+apiVersion: kafka.strimzi.io/v1beta2
+kind: KafkaNodePool
+metadata:
+  name: dual-role
+  labels:
+    strimzi.io/cluster: obds-to-fhir-kafka
+spec:
+  replicas: 1
+  roles:
+    - controller
+    - broker
+  storage:
+    type: jbod
+    volumes:
+      - id: 0
+        type: persistent-claim
+        size: 8Gi
+        deleteClaim: false
+---
+apiVersion: kafka.strimzi.io/v1beta2
+kind: Kafka
+metadata:
+  name: obds-to-fhir-kafka
+  annotations:
+    strimzi.io/node-pools: enabled
+    strimzi.io/kraft: enabled
+spec:
+  kafka:
+    version: 3.7.0
+    metadataVersion: 3.7-IV4
+    listeners:
+      - name: tls
+        port: 9093
+        type: internal
+        tls: true
+    config:
+      offsets.topic.replication.factor: 1
+      transaction.state.log.replication.factor: 1
+      transaction.state.log.min.isr: 1
+      num.partitions: 1
+      auto.create.topics.enable: true
+      default.replication.factor: 1
+      log.cleanup.policy: compact
+      # 30 MiB
+      message.max.bytes: 31457280
+      # https://kafka.apache.org/documentation/#brokerconfigs_compression.type
+      compression.type: gzip
+  entityOperator:
+    userOperator: {}

tests/k8s/templates/tests/test-connection.yaml

@@ -0,0 +1,48 @@
+{{- $streamProcessorsFullName := (include "stream-processors.fullname" (index .Subcharts "stream-processors")) -}}
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ .Release.Name }}-test-connection"
+  annotations:
+    helm.sh/hook: test-success
+spec:
+  restartPolicy: Never
+  containers:
+    - name: probe-health-endpoint
+      image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
+      imagePullPolicy: IfNotPresent
+      command: ["curl", "--fail-with-body"]
+      args: ["http://{{ $streamProcessorsFullName }}-obds-to-fhir-metrics:8080/actuator/health"]
+      {{- with $.Values.restrictedContainerSecurityContext }}
+      securityContext:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tests.resources }}
+      resources:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      livenessProbe:
+        exec:
+          command: ["true"]
+      readinessProbe:
+        exec:
+          command: ["true"]
+    - name: probe-metrics-endpoint
+      image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
+      imagePullPolicy: IfNotPresent
+      command: ["curl", "--fail-with-body"]
+      args: ["http://{{ $streamProcessorsFullName }}-obds-to-fhir-metrics:8080/actuator/prometheus"]
+      {{- with $.Values.restrictedContainerSecurityContext }}
+      securityContext:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tests.resources }}
+      resources:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      livenessProbe:
+        exec:
+          command: ["true"]
+      readinessProbe:
+        exec:
+          command: ["true"]