chore(deps): update all non-major dependencies (#279)

* chore(deps): update all non-major dependencies * reformated snapshot * fix formatting * updated dockerfile and java to 21 * chore(deps): updates for camle 4.6 * enable stats * set routePolicyLevel * updated dev config --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: chgl <chgl@users.noreply.github.com>
miracum · Jun 5, 2024 · f412a22 · f412a22
1 parent 9754067
commit f412a22
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diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json
@@ -3,7 +3,7 @@
   "isRoot": true,
   "tools": {
     "csharpier": {
-      "version": "0.28.1",
+      "version": "0.28.2",
       "commands": ["dotnet-csharpier"]
     }
   }

diff --git a/charts/recruit/Chart.lock b/charts/recruit/Chart.lock
@@ -13,6 +13,6 @@ dependencies:
   version: 13.2.27
 - name: fhir-pseudonymizer
   repository: oci://ghcr.io/miracum/charts
-  version: 0.6.7
-digest: sha256:1d17c0e7a0e6040f97910e0c2fa7ba0a56b3ff3baa54c6e87f47ebd50777b18d
-generated: "2024-04-20T16:17:22.133627066Z"
+  version: 0.6.8
+digest: sha256:3a21e8062c517b7bd1ea1a1ce80f8e1116dd29af418bd09dbf3a48e743c6659f
+generated: "2024-05-30T20:48:03.146838977Z"
diff --git a/charts/recruit/Chart.yaml b/charts/recruit/Chart.yaml
@@ -37,7 +37,7 @@ dependencies:
     condition: postgresql.enabled
   - condition: fhir-pseudonymizer.enabled
     name: fhir-pseudonymizer
-    version: 0.6.7
+    version: 0.6.8
     repository: oci://ghcr.io/miracum/charts
 # x-release-please-start-version
 version: 10.1.11

diff --git a/charts/recruit/values.yaml b/charts/recruit/values.yaml
@@ -677,7 +677,7 @@ curl: # +doc-gen:ignore
   image:
     registry: docker.io
     repository: curlimages/curl
-    tag: 8.7.1@sha256:25d29daeb9b14b89e2fa8cc17c70e4b188bca1466086907c2d9a4b56b59d8e21
+    tag: 8.8.0@sha256:73e4d532ea62d7505c5865b517d3704966ffe916609bedc22af6833dc9969bcd
 
 broadseaAtlasdb:
   # -- whether to deploy the OHDSI Broadsea Atlasdb (<https://github.com/OHDSI/Broadsea-Atlasdb>)

diff --git a/docker-compose/docker-compose.probe.yaml b/docker-compose/docker-compose.probe.yaml
@@ -1,6 +1,6 @@
 services:
   health-probes:
-    image: docker.io/curlimages/curl:8.7.1@sha256:25d29daeb9b14b89e2fa8cc17c70e4b188bca1466086907c2d9a4b56b59d8e21
+    image: docker.io/curlimages/curl:8.8.0@sha256:73e4d532ea62d7505c5865b517d3704966ffe916609bedc22af6833dc9969bcd
     ipc: private
     security_opt:
       - "no-new-privileges:true"

diff --git a/docker-compose/docker-compose.staging.yaml b/docker-compose/docker-compose.staging.yaml
@@ -1,6 +1,6 @@
 services:
   traefik:
-    image: docker.io/library/traefik:2.11.2@sha256:c6f6001dd1fc09fb0ae47ad2198102c40a8d9586c02d6040d561fd4fb7e91f45
+    image: docker.io/library/traefik:v2.11.3@sha256:d7862e301ff8ca47529f687c7cb08cf1dbb4d0690cd8524cfc76673b8cbd92c7
     restart: unless-stopped
     ipc: none
     security_opt:
@@ -102,7 +102,7 @@ services:
       - "traefik.http.routers.ohdsi-atlas.entrypoints=web"
 
   fhir:
-    image: docker.io/hapiproject/hapi:v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce
+    image: docker.io/hapiproject/hapi:v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b
     restart: unless-stopped
     cap_drop:
       - ALL

diff --git a/docs/development/contributing.md b/docs/development/contributing.md
@@ -75,3 +75,22 @@ From the `/src/list` directory, run:
 ```sh
 docker build -t ghcr.io/miracum/recruit/list:local .
 ```
+
+## Skaffold
+
+You can also directly build and deploy to a Kubernetes cluster for development:
+
+Create a KinD cluster and install NGINX Ingress
+
+```sh
+kind create cluster --config=hack/k8s/kind-with-ingress-config.yaml
+kubectl apply -f https://raw.githubusercontent.com/kubernetes/ingress-nginx/master/deploy/static/provider/kind/deploy.yaml
+```
+
+Run `skaffold dev`:
+
+```sh
+helm dep up ../charts/recruit/
+
+skaffold dev
+```
diff --git a/src/.dockerignore b/src/.dockerignore
@@ -5,3 +5,4 @@ list/
 gradle/
 hack/
 tests/
+Dockerfile
diff --git a/src/Dockerfile b/src/Dockerfile
@@ -1,38 +1,33 @@
-FROM docker.io/library/gradle:8.7.0-jdk17@sha256:34362edcf64f346589c67384634e33e9e44314c6ef9a82d936335c9f8ca7b06c AS build
-WORKDIR /home/gradle/src
-ENV GRADLE_USER_HOME="/gradle"
-
-ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.30.0
+FROM docker.io/library/gradle:8.7.0-jdk21@sha256:afba668dbed80665ed2cee8b16010c51e9639be3424c3f897637701bdd89371b AS build
+WORKDIR /home/gradle/project
+ARG OPENTELEMETRY_JAVA_AGENT_VERSION=2.4.0
 RUN wget --quiet "https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar"
 
-COPY settings.gradle ./
-COPY config/ config/
-COPY buildSrc/ buildSrc/
-
-ARG MODULE_NAME=query
-COPY ${MODULE_NAME}/build.gradle ./${MODULE_NAME}/
-
-RUN gradle clean build --no-daemon || true
-
 COPY --chown=gradle:gradle . .
 
-RUN gradle ":${MODULE_NAME}:build" -x test --info && \
-    java -Djarmode=layertools -jar ${MODULE_NAME}/build/libs/*.jar extract --destination "${MODULE_NAME}/"
+ARG MODULE_NAME=query
+RUN --mount=type=cache,target=/home/gradle/.gradle/caches <<EOF
+gradle clean ":${MODULE_NAME}:build" -x test --info --no-daemon
+gradle jacocoTestReport --no-daemon
+java -Djarmode=layertools -jar ${MODULE_NAME}/build/libs/*.jar extract --destination "${MODULE_NAME}/"
+EOF
 
 FROM build AS test
 ENV TZ="UTC"
-RUN gradle ":${MODULE_NAME}:test" && \
-    gradle jacocoTestReport
+RUN <<EOF
+gradle ":${MODULE_NAME}:test"
+gradle jacocoTestReport
+EOF
 
-FROM gcr.io/distroless/java17-debian12:nonroot@sha256:4a7f6fa8773acd31ec9fd76bc3f0e0edf0d25f69ce3221471b9786e0774833bc
+FROM gcr.io/distroless/java21-debian12:nonroot@sha256:0ba7333a0fb7cbcf90b18073132f4f445870608e8cdc179664f10ce4d00964c2
 WORKDIR /app
 
-COPY --from=build /home/gradle/src/opentelemetry-javaagent.jar ./opentelemetry-javaagent.jar
+COPY --from=build /home/gradle/project/opentelemetry-javaagent.jar ./opentelemetry-javaagent.jar
 
 ARG MODULE_NAME=query
-COPY --from=build /home/gradle/src/${MODULE_NAME}/dependencies/ ./
-COPY --from=build /home/gradle/src/${MODULE_NAME}/spring-boot-loader/ ./
-COPY --from=build /home/gradle/src/${MODULE_NAME}/application/ .
+COPY --from=build /home/gradle/project/${MODULE_NAME}/dependencies/ ./
+COPY --from=build /home/gradle/project/${MODULE_NAME}/spring-boot-loader/ ./
+COPY --from=build /home/gradle/project/${MODULE_NAME}/application/ ./
 
 USER 65532:65532
 EXPOSE 8080/tcp 8081/tcp

diff --git a/src/buildSrc/build.gradle b/src/buildSrc/build.gradle
@@ -15,8 +15,8 @@ repositories {
 }
 
 dependencies {
-    implementation 'org.springframework.boot:spring-boot-gradle-plugin:3.2.5'
-    implementation 'io.spring.gradle:dependency-management-plugin:1.1.4'
+    implementation 'org.springframework.boot:spring-boot-gradle-plugin:3.3.0'
+    implementation 'io.spring.gradle:dependency-management-plugin:1.1.5'
     implementation 'com.google.cloud.tools:jib-gradle-plugin:3.4.2'
     implementation 'com.diffplug.spotless:spotless-plugin-gradle:6.25.0'
     implementation 'io.freefair.gradle:lombok-plugin:8.6'

diff --git a/src/buildSrc/src/main/groovy/org.miracum.recruit.java-application-conventions.gradle b/src/buildSrc/src/main/groovy/org.miracum.recruit.java-application-conventions.gradle
@@ -26,7 +26,7 @@ plugins {
 
 task downloadOpenTelemetryJavaAgent(type: Download) {
     src 'https://github.com/open-telemetry/opentelemetry-java-instrumentation' +
-        '/releases/download/v1.25.1/opentelemetry-javaagent.jar'
+        '/releases/download/v2.4.0/opentelemetry-javaagent.jar'
     dest '../'
     overwrite false
 }
@@ -48,8 +48,8 @@ dependencies {
 
     implementation 'org.postgresql:postgresql:42.7.3'
 
-    implementation 'io.micrometer:micrometer-registry-prometheus:1.12.5'
-    implementation 'io.micrometer:micrometer-core:1.12.5'
+    implementation 'io.micrometer:micrometer-registry-prometheus:1.13.0'
+    implementation 'io.micrometer:micrometer-core:1.13.0'
 
     developmentOnly 'org.springframework.boot:spring-boot-devtools'
 
@@ -101,14 +101,14 @@ spotless {
 }
 
 checkstyle {
-    toolVersion '10.15.0'
+    toolVersion '10.17.0'
     configFile = file('../config/checkstyle/checkstyle.xml')
 }
 
 jib {
     from {
-        image = 'gcr.io/distroless/java17-debian11:nonroot' +
-            '@sha256:9ed1f1775ffbaad2ab63c9812ec836a0e2def28b53752192b01bc53ad6195c6e'
+        image = 'gcr.io/distroless/java21-debian12:nonroot' +
+            '@sha256:0ba7333a0fb7cbcf90b18073132f4f445870608e8cdc179664f10ce4d00964c2'
     }
     to {
         image = "ghcr.io/miracum/recruit/${project.name}:${project.version}"

diff --git a/src/buildSrc/src/main/groovy/org.miracum.recruit.java-common-conventions.gradle b/src/buildSrc/src/main/groovy/org.miracum.recruit.java-common-conventions.gradle
@@ -11,8 +11,8 @@ plugins {
 
 group = 'org.miracum.recruit'
 version = '10.1.11' // x-release-please-version
-sourceCompatibility = '17'
-targetCompatibility = '17'
+sourceCompatibility = '21'
+targetCompatibility = '21'
 
 repositories {
     // Use Maven Central for resolving dependencies.

diff --git a/src/hack/docker-compose.yaml b/src/hack/docker-compose.yaml
@@ -1,6 +1,6 @@
 services:
   traefik:
-    image: docker.io/library/traefik:2.11.2@sha256:c6f6001dd1fc09fb0ae47ad2198102c40a8d9586c02d6040d561fd4fb7e91f45
+    image: docker.io/library/traefik:v2.11.3@sha256:d7862e301ff8ca47529f687c7cb08cf1dbb4d0690cd8524cfc76673b8cbd92c7
     restart: unless-stopped
     ipc: none
     security_opt:
@@ -23,7 +23,7 @@ services:
           memory: 128m
 
   fhir:
-    image: docker.io/hapiproject/hapi:v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce
+    image: docker.io/hapiproject/hapi:v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b
     restart: unless-stopped
     cap_drop:
       - ALL
@@ -270,7 +270,7 @@ services:
       OTEL_EXPORTER_JAEGER_ENDPOINT: "http://jaeger:14250"
 
   jaeger:
-    image: docker.io/jaegertracing/all-in-one:1.56.0@sha256:d2cd4c226624bdc116decd3106091b4df9882da8db42f8550293596cab79b8ea
+    image: docker.io/jaegertracing/all-in-one:1.57.0@sha256:8f165334f418ca53691ce358c19b4244226ed35c5d18408c5acf305af2065fb9
     ports:
       - "127.0.0.1:16686:16686"
       - "127.0.0.1:6831:6831/udp"

diff --git a/src/hack/k8s/kind-with-ingress-config.yaml b/src/hack/k8s/kind-with-ingress-config.yaml
@@ -0,0 +1,20 @@
+kind: Cluster
+apiVersion: kind.x-k8s.io/v1alpha4
+nodes:
+  - role: control-plane
+    kubeadmConfigPatches:
+      - |
+        kind: InitConfiguration
+        nodeRegistration:
+          kubeletExtraArgs:
+            node-labels: "ingress-ready=true"
+    extraPortMappings:
+      - containerPort: 80
+        hostPort: 80
+        protocol: TCP
+      - containerPort: 443
+        hostPort: 443
+        protocol: TCP
+
+# kind create cluster --config=hack/k8s/kind-with-ingress-config.yaml
+# kubectl apply -f https://raw.githubusercontent.com/kubernetes/ingress-nginx/master/deploy/static/provider/kind/deploy.yaml
diff --git a/src/hack/k8s/values-dev.yaml b/src/hack/k8s/values-dev.yaml
@@ -0,0 +1,96 @@
+list:
+  ingress:
+    enabled: true
+
+fhirserver:
+  postgresql:
+    auth:
+      # kics-scan ignore-line
+      postgresPassword: fhir
+
+query:
+  # run every minute
+  schedule: "* * * * *"
+  cohortSelectorLabels: []
+  shouldWaitForNotify: true
+  omop:
+    host: broadsea-atlasdb
+    port: 5432
+    database: postgres
+    username: postgres
+    # kics-scan ignore-line
+    password: mypass
+    resultsSchema: demo_cdm_results
+    cdmSchema: demo_cdm
+  webAPI:
+    dataSource: EUNOMIA
+  extraEnv:
+    - name: QUERY_WEBAPI_COHORT_CACHE_SCHEMA
+      value: webapi
+
+notify:
+  rules:
+    schedules:
+      everyMorning: "0 0 8 1/1 * ? *"
+    trials:
+      - acronym: "*"
+        subscriptions:
+          - email: "everything@example.com"
+
+      - acronym: "Demo new users of diclofenac"
+        accessibleBy:
+          users:
+            - "user1"
+            - "user.two@example.com"
+        subscriptions:
+          - email: "everyMorning@example.com"
+            notify: "everyMorning"
+          - email: "demo@example.com"
+
+ohdsi:
+  postgresql:
+    enabled: false
+  webApi:
+    db:
+      host: broadsea-atlasdb
+      port: 5432
+      database: "postgres"
+      username: "postgres"
+      # kics-scan ignore-line
+      password: "mypass"
+      schema: "webapi"
+    extraEnv:
+      - name: FLYWAY_BASELINEONMIGRATE
+        value: "true"
+      - name: FLYWAY_TABLE
+        value: schema_history
+      - name: flyway_baselineVersionAsString
+        value: "2.2.5.20180212152023"
+      - name: FLYWAY_BASELINEDESCRIPTION
+        value: "Base Migration"
+      - name: FLYWAY_LOCATIONS
+        value: "classpath:db/migration/postgresql"
+  cdmInitJob:
+    enabled: false
+  achilles:
+    schemas:
+      cdm: "demo_cdm"
+      vocab: "demo_cdm"
+      res: "demo_cdm_results"
+    sourceName: "EUNOMIA"
+  ingress:
+    enabled: true
+    hosts:
+      - host: recruit-ohdsi.127.0.0.1.nip.io
+
+broadseaAtlasdb:
+  enabled: true
+
+mailhog:
+  ingress:
+    enabled: true
+    hosts:
+      - host: recruit-mailhog.127.0.0.1.nip.io
+        paths:
+          - path: "/"
+            pathType: Prefix
diff --git a/src/list/Dockerfile b/src/list/Dockerfile
@@ -1,4 +1,4 @@
-FROM docker.io/library/node:20.12.2@sha256:844b41cf784f66d7920fd673f7af54ca7b81e289985edc6cd864e7d05e0d133c AS base
+FROM docker.io/library/node:20.14.0@sha256:ab71b9da5ba19445dc5bb76bf99c218941db2c4d70ff4de4e0d9ec90920bfe3f AS base
 WORKDIR /app
 
 COPY package.json ./

diff --git a/src/list/frontend/deploy/docker-compose.dev.yml b/src/list/frontend/deploy/docker-compose.dev.yml
@@ -2,7 +2,7 @@ version: "3.9"
 
 services:
   fhir:
-    image: docker.io/hapiproject/hapi:v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce
+    image: docker.io/hapiproject/hapi:v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b
     environment:
       HAPI_FHIR_VALIDATION_REQUESTS_ENABLED: "true"
       HAPI_FHIR_SUBSCRIPTION_RESTHOOK_ENABLED: "true"
@@ -14,7 +14,7 @@ services:
       - 8082:8080
 
   loader:
-    image: docker.io/curlimages/curl:8.7.1@sha256:25d29daeb9b14b89e2fa8cc17c70e4b188bca1466086907c2d9a4b56b59d8e21
+    image: docker.io/curlimages/curl:8.8.0@sha256:73e4d532ea62d7505c5865b517d3704966ffe916609bedc22af6833dc9969bcd
     command: >
       sh -c "curl -X POST -H 'Content-Type:application/fhir+json' --retry-connrefused --connect-timeout 30 --max-time 60 --retry 5 --retry-delay 15 --data '@/data/sample-record-1.json' http://fhir:8080/fhir &&
              curl -X POST -H 'Content-Type:application/fhir+json' --retry-connrefused --connect-timeout 30 --max-time 60 --retry 5 --retry-delay 15 --data '@/data/sample-record-2.json' http://fhir:8080/fhir &&
@@ -26,7 +26,7 @@ services:
       - fhir
 
   jaeger:
-    image: docker.io/jaegertracing/all-in-one:1.56@sha256:d2cd4c226624bdc116decd3106091b4df9882da8db42f8550293596cab79b8ea
+    image: docker.io/jaegertracing/all-in-one:1.57@sha256:8f165334f418ca53691ce358c19b4244226ed35c5d18408c5acf305af2065fb9
     environment:
       COLLECTOR_OTLP_ENABLED: "true"
     ports:
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,3 +5,4 @@ list/ @@
     gradle/
     hack/
     tests/
+    Dockerfile