diff --git a/.github/ct/ct.yaml b/.github/ct/ct.yaml index f12b8da7..5bcdb803 100644 --- a/.github/ct/ct.yaml +++ b/.github/ct/ct.yaml @@ -9,10 +9,7 @@ validate-yaml: true check-version-increment: false chart-dirs: - charts -helm-extra-args: --timeout 300s upgrade: true skip-missing-values: true release-label: release -chart-repos: - - bitnami=https://charts.bitnami.com/bitnami release-notes-file: CHANGELOG.md diff --git a/.github/ct/install.yaml b/.github/ct/install.yaml index b9f70b25..f54a7a97 100644 --- a/.github/ct/install.yaml +++ b/.github/ct/install.yaml @@ -1,10 +1,7 @@ chart-dirs: - charts chart-repos: - - bitnami=https://charts.bitnami.com/bitnami - - chgl=https://chgl.github.io/charts - codecentric=https://codecentric.github.io/helm-charts - hapifhir=https://hapifhir.github.io/hapi-fhir-jpaserver-starter - - miracum=https://miracum.github.io/charts debug: true remote: origin diff --git a/.github/workflows/helm-lint.yaml b/.github/workflows/helm-lint.yaml index dcd87f7d..c04990d5 100644 --- a/.github/workflows/helm-lint.yaml +++ b/.github/workflows/helm-lint.yaml @@ -13,7 +13,7 @@ permissions: read-all jobs: lint: runs-on: ubuntu-22.04 - container: ghcr.io/chgl/kube-powertools:v1.23.7@sha256:9fbd9806165d2d62a555ada53d458cd9e1b6595787b69b688f235b1fdaaba141 + container: ghcr.io/chgl/kube-powertools:v2.1.28@sha256:74c2ec2b1ac6d33891aaca488d5732a61668039fb0ccf2b9c883ed3df9ec463a steps: - name: Add workspace as safe directory run: | @@ -24,6 +24,10 @@ jobs: with: fetch-depth: 0 + # via + - run: | + git branch "master" "origin/master" + - name: Check if documentation is up-to-date run: | generate-docs.sh diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index eda30bd8..17899d83 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -101,7 +101,7 @@ jobs: publish-kyverno-policies: name: publish kyverno policies runs-on: ubuntu-22.04 - container: ghcr.io/chgl/kube-powertools:v1.23.7@sha256:6d575cad3af3d4febf1789ba6c88b1fd80ba4b75ec792dbffba54868acb045e0 + container: ghcr.io/chgl/kube-powertools:v2.1.28@sha256:74c2ec2b1ac6d33891aaca488d5732a61668039fb0ccf2b9c883ed3df9ec463a continue-on-error: true steps: - name: Checkout diff --git a/.github/workflows/reset-chart-changelog-annotations.yaml b/.github/workflows/reset-chart-changelog-annotations.yaml index d29d138e..0d33bb34 100644 --- a/.github/workflows/reset-chart-changelog-annotations.yaml +++ b/.github/workflows/reset-chart-changelog-annotations.yaml @@ -13,7 +13,7 @@ jobs: reset-commit-and-push: name: reset changelog annotations, commit, and push runs-on: ubuntu-22.04 - container: ghcr.io/chgl/kube-powertools:v1.23.7@sha256:9fbd9806165d2d62a555ada53d458cd9e1b6595787b69b688f235b1fdaaba141 + container: ghcr.io/chgl/kube-powertools:v2.1.28@sha256:74c2ec2b1ac6d33891aaca488d5732a61668039fb0ccf2b9c883ed3df9ec463a permissions: contents: write steps: diff --git a/.github/workflows/yamllint.yaml b/.github/workflows/yamllint.yaml index 8682a7a1..5253ddf4 100644 --- a/.github/workflows/yamllint.yaml +++ b/.github/workflows/yamllint.yaml @@ -18,7 +18,7 @@ jobs: yamllint: runs-on: ubuntu-22.04 # contains yamllint - container: ghcr.io/chgl/kube-powertools:v1.23.7@sha256:9fbd9806165d2d62a555ada53d458cd9e1b6595787b69b688f235b1fdaaba141 + container: ghcr.io/chgl/kube-powertools:v2.1.28@sha256:74c2ec2b1ac6d33891aaca488d5732a61668039fb0ccf2b9c883ed3df9ec463a steps: - name: Checkout uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2 diff --git a/.polaris.yaml b/.polaris.yaml new file mode 100644 index 00000000..0419dbda --- /dev/null +++ b/.polaris.yaml @@ -0,0 +1,44 @@ +checks: + # reliability + deploymentMissingReplicas: ignore + priorityClassNotSet: ignore + tagNotSpecified: danger + pullPolicyNotAlways: ignore + readinessProbeMissing: danger + livenessProbeMissing: danger + metadataAndInstanceMismatched: ignore + pdbDisruptionsIsZero: warning + missingPodDisruptionBudget: ignore + topologySpreadConstraint: ignore + + # efficiency + cpuRequestsMissing: ignore + cpuLimitsMissing: ignore + memoryRequestsMissing: ignore + memoryLimitsMissing: ignore + + # security + automountServiceAccountToken: ignore + hostIPCSet: danger + hostPIDSet: danger + linuxHardening: danger + missingNetworkPolicy: ignore + notReadOnlyRootFilesystem: warning + privilegeEscalationAllowed: danger + runAsRootAllowed: danger + runAsPrivileged: danger + dangerousCapabilities: danger + insecureCapabilities: warning + hostNetworkSet: danger + hostPortSet: warning + tlsSettingsMissing: warning + sensitiveContainerEnvVar: ignore + sensitiveConfigmapContent: danger + clusterrolePodExecAttach: danger + rolePodExecAttach: danger + clusterrolebindingPodExecAttach: danger + rolebindingClusterRolePodExecAttach: danger + rolebindingRolePodExecAttach: danger + clusterrolebindingClusterAdmin: danger + rolebindingClusterAdminClusterRole: danger + rolebindingClusterAdminRole: danger diff --git a/.trivyignore b/.trivyignore index 20742b39..a30282ca 100644 --- a/.trivyignore +++ b/.trivyignore @@ -10,3 +10,7 @@ CVE-2023-34104 # Image user should not be 'root' # this is only used by the cypress image AVD-DS-0002 + +# this is disputed by multiple parties because it is not plausible that untrusted +# user input would reach the code location where injection must occur. +CVE-2023-39017 diff --git a/Taskfile.yaml b/Taskfile.yaml index d4a5a945..1f5be92c 100644 --- a/Taskfile.yaml +++ b/Taskfile.yaml @@ -14,12 +14,8 @@ tasks: helm-add-repos: cmds: - - helm repo add argo https://argoproj.github.io/argo-helm - - helm repo add bitnami https://charts.bitnami.com/bitnami - helm repo add codecentric https://codecentric.github.io/helm-charts - - helm repo add chgl https://chgl.github.io/charts - helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter - - helm repo add miracum https://miracum.github.io/charts helm-update-dependencies: cmds: @@ -32,11 +28,11 @@ tasks: - kind create cluster - kubectl create namespace recruit - | - helm upgrade --install argo-workflows argo/argo-workflows \ + helm upgrade --install argo-workflows oci://ghcr.io/argoproj/argo-helm/argo-workflows \ --create-namespace \ -n argo-workflows \ -f tests/chaos/argo-workflows-values.yaml \ - --version 0.22.14 + --version 0.33.2 e2e-k8s: cmds: diff --git a/charts/recruit/Chart.lock b/charts/recruit/Chart.lock index cfbfe38d..9d13a021 100644 --- a/charts/recruit/Chart.lock +++ b/charts/recruit/Chart.lock @@ -1,18 +1,18 @@ dependencies: - name: hapi-fhir-jpaserver repository: https://hapifhir.github.io/hapi-fhir-jpaserver-starter - version: 0.12.0 + version: 0.13.0 - name: mailhog repository: https://codecentric.github.io/helm-charts version: 5.2.3 - name: ohdsi repository: oci://ghcr.io/chgl/charts - version: 0.21.6 + version: 0.21.7 - name: postgresql repository: oci://registry-1.docker.io/bitnamicharts version: 12.5.6 - name: fhir-pseudonymizer repository: oci://ghcr.io/miracum/charts - version: 0.4.3 -digest: sha256:340ac69550eb491f3c517f0807be000c9bd3a5709b603f14695926a00a849544 -generated: "2023-06-26T12:54:56.791682743+02:00" + version: 0.5.3 +digest: sha256:8f44772ab433b66d1135c8b60ea921bf5018711dbc0052938a36b636aa783595 +generated: "2023-09-07T19:15:55.796403352Z" diff --git a/charts/recruit/Chart.yaml b/charts/recruit/Chart.yaml index 50d48030..881ccdde 100644 --- a/charts/recruit/Chart.yaml +++ b/charts/recruit/Chart.yaml @@ -22,7 +22,7 @@ dependencies: alias: fhirserver name: hapi-fhir-jpaserver repository: https://hapifhir.github.io/hapi-fhir-jpaserver-starter - version: 0.12.0 + version: 0.13.0 - condition: mailhog.enabled name: mailhog repository: https://codecentric.github.io/helm-charts @@ -30,14 +30,14 @@ dependencies: - condition: ohdsi.enabled name: ohdsi repository: oci://ghcr.io/chgl/charts - version: 0.21.6 + version: 0.21.7 - name: postgresql version: 12.5.6 repository: oci://registry-1.docker.io/bitnamicharts condition: postgresql.enabled - condition: fhir-pseudonymizer.enabled name: fhir-pseudonymizer - version: 0.4.3 + version: 0.5.3 repository: oci://ghcr.io/miracum/charts # x-release-please-start-version version: 10.1.3 diff --git a/charts/recruit/README.md b/charts/recruit/README.md index b01a03d8..91074ed5 100644 --- a/charts/recruit/README.md +++ b/charts/recruit/README.md @@ -19,9 +19,6 @@ See [UPGRADING.md](./docs/UPGRADING.md) for information on breaking changes intr helm install recruit oci://ghcr.io/miracum/recruit/charts/recruit -n recruit ``` -> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/main/bitnami/postgresql#upgrading) -> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)). - ## Values | Key | Type | Default | Description | @@ -165,6 +162,7 @@ helm install recruit oci://ghcr.io/miracum/recruit/charts/recruit -n recruit | query.webAPI.auth.username | string | `""` | the username to login as. Note that this user needs permissions to query and generate cohorts | | query.webAPI.dataSource | string | `"CDS-CDMV5"` | name of the OMOP datasource used to generate the cohorts from. | | query.webAPI.url | string | `"http://example:8080/WebAPI"` | URL of the ATLAS WebAPI endpoint. Usually ends in /WebAPI. | +| tests.resources | object | `{}` | configure the test pods resource requests and limits | | waitForPostgresInitContainer | object | `{}` | | ## Configure Notifcation Rules diff --git a/charts/recruit/README.md.gotmpl b/charts/recruit/README.md.gotmpl index 67501649..82a66da1 100644 --- a/charts/recruit/README.md.gotmpl +++ b/charts/recruit/README.md.gotmpl @@ -19,9 +19,6 @@ See [UPGRADING.md](./docs/UPGRADING.md) for information on breaking changes intr helm install recruit oci://ghcr.io/miracum/recruit/charts/recruit -n recruit ``` -> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/main/bitnami/postgresql#upgrading) -> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)). - {{ template "chart.valuesSection" . }} ## Configure Notifcation Rules diff --git a/charts/recruit/templates/tests/check-all-health-probes.yaml b/charts/recruit/templates/tests/check-all-health-probes.yaml index 6e1b078b..5c84a8c5 100644 --- a/charts/recruit/templates/tests/check-all-health-probes.yaml +++ b/charts/recruit/templates/tests/check-all-health-probes.yaml @@ -21,13 +21,10 @@ spec: securityContext: {{- toYaml . | nindent 8 }} {{- end }} + {{- with .Values.tests.resources }} resources: - limits: - cpu: 50m - memory: 64Mi - requests: - cpu: 50m - memory: 64Mi + {{- toYaml . | nindent 8 }} + {{- end }} livenessProbe: exec: command: ["true"] @@ -45,13 +42,10 @@ spec: securityContext: {{- toYaml . | nindent 8 }} {{- end }} + {{- with .Values.tests.resources }} resources: - limits: - cpu: 50m - memory: 64Mi - requests: - cpu: 50m - memory: 64Mi + {{- toYaml . | nindent 8 }} + {{- end }} livenessProbe: exec: command: ["true"] @@ -69,13 +63,10 @@ spec: securityContext: {{- toYaml . | nindent 8 }} {{- end }} + {{- with .Values.tests.resources }} resources: - limits: - cpu: 50m - memory: 64Mi - requests: - cpu: 50m - memory: 64Mi + {{- toYaml . | nindent 8 }} + {{- end }} livenessProbe: exec: command: ["true"] diff --git a/charts/recruit/values.yaml b/charts/recruit/values.yaml index ae3c44cc..d27cd56b 100644 --- a/charts/recruit/values.yaml +++ b/charts/recruit/values.yaml @@ -669,9 +669,19 @@ curl: # +doc-gen:ignore image: registry: docker.io repository: curlimages/curl - tag: 8.1.2@sha256:fcf8b68aa7af25898d21b47096ceb05678665ae182052283bd0d7128149db55f + tag: 8.2.1@sha256:bb0843a1307b1aa73f65f24379d11dde881c16db62ba50810de0c64d48e740ed broadseaAtlasdb: # -- whether to deploy the OHDSI Broadsea Atlasdb () # currently only used by internal integration tests. See [./values-integrationtest.yaml](values-integrationtest.yaml) enabled: false + +tests: + # -- configure the test pods resource requests and limits + resources: {} + # limits: + # cpu: 100m + # memory: 128Mi + # requests: + # cpu: 100m + # memory: 128Mi diff --git a/docker-compose/docker-compose.probe.yaml b/docker-compose/docker-compose.probe.yaml index f76e5954..375386ec 100644 --- 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:8.1.1@sha256:5af13420d29b7aa7007419347519984ce44778aaf89c475c25edc9b48ca125b2 + image: docker.io/curlimages/curl:8.2.1@sha256:bb0843a1307b1aa73f65f24379d11dde881c16db62ba50810de0c64d48e740ed ipc: private security_opt: - "no-new-privileges:true" diff --git a/docker-compose/docker-compose.staging.yaml b/docker-compose/docker-compose.staging.yaml index c88bab2a..8a6a7094 100644 --- 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:v2.10.1@sha256:7347d4d189642064337fe4eb615d14de2d44f287cb7e1189752fb7399a5ad843 + image: docker.io/library/traefik:2.10.4@sha256:429f3398a3cd1aa7436aa4f59d809040d3903506a9d83bee61688bb1429c7693 restart: unless-stopped ipc: none security_opt: @@ -151,7 +151,7 @@ services: POSTGRES_DB: fhir maildev: - image: docker.io/maildev/maildev:2.0.5@sha256:082ec5ee92266c6e17493998ff1bf1c3eb70604b159fbeeaa435ee777f5cc953 + image: docker.io/maildev/maildev:2.1.0@sha256:f7429227b8f471b3fe761767d86a8794a2fc7488bccdcda46ea6d5ba5c2c7bf5 restart: unless-stopped ipc: none security_opt: diff --git a/docs/deployment/kubernetes.md b/docs/deployment/kubernetes.md index 21572805..53a6a2f7 100644 --- a/docs/deployment/kubernetes.md +++ b/docs/deployment/kubernetes.md @@ -30,16 +30,6 @@ helm install -n recruit \ recruit oci://ghcr.io/miracum/recruit/charts/recruit ``` -!!! warning "Auto generated default passwords for the included databases" - - The included HAPI FHIR server, OHDSI, and - if high-availability is enabled - recruIT chart itself depend on the - [Bitnami PostgreSQL chart](https://github.com/bitnami/charts/tree/master/bitnami/postgresql). By default, this chart - generates a random password for the `postgres` user unless either `auth.postgresPassword` or `auth.existingSecret` - are set. Upgrading the release (or simply re-running `helm upgrade --install`) will generate a new password which - will result in credential errors and the PostgreSQL pod will fail to start. You should therefore overwrite these - parameters or set them after the initial install. The `--render-subchart-notes` flag above will also print this - note. - As a quick check to make sure everything is running correctly, you can use the following to check the readiness of all services: ```sh diff --git a/fhir/.npmrc b/fhir/.npmrc deleted file mode 100644 index dfd82ce2..00000000 --- a/fhir/.npmrc +++ /dev/null @@ -1 +0,0 @@ -registry=https://packages.simplifier.net diff --git a/src/Dockerfile b/src/Dockerfile index 062bee46..8bdee6eb 100644 --- a/src/Dockerfile +++ b/src/Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/library/gradle:8.1.1-jdk17@sha256:e7a4bc8f4ee27feae2eac4de61ca64406b7137e6f6b107052accd24bf0806043 AS build +FROM docker.io/library/gradle:8.3.0-jdk17@sha256:5f4ab273b15961c5f22969136ea884ca0343f1d8b2df5c4c6fe0ca8939b401b1 AS build WORKDIR /home/gradle/src ENV GRADLE_USER_HOME="/gradle" @@ -24,7 +24,7 @@ ENV TZ="UTC" RUN gradle ":${MODULE_NAME}:test" && \ gradle jacocoTestReport -FROM gcr.io/distroless/java17-debian11:nonroot@sha256:61463fa9d1bb9994de4e50e71f3e487d0e61f1676e26306388a743ff96311777 +FROM gcr.io/distroless/java17-debian11:nonroot@sha256:41af86bc38476afb89e640959585e4fc81104bd9c56303c24b749cc3644b79a8 WORKDIR /app COPY --from=build /home/gradle/src/opentelemetry-javaagent.jar ./opentelemetry-javaagent.jar diff --git a/src/buildSrc/build.gradle b/src/buildSrc/build.gradle index 4d1180af..e5aacecd 100644 --- a/src/buildSrc/build.gradle +++ b/src/buildSrc/build.gradle @@ -15,10 +15,10 @@ repositories { } dependencies { - implementation 'org.springframework.boot:spring-boot-gradle-plugin:3.1.1' - implementation 'io.spring.gradle:dependency-management-plugin:1.1.0' + implementation 'org.springframework.boot:spring-boot-gradle-plugin:3.1.3' + implementation 'io.spring.gradle:dependency-management-plugin:1.1.3' implementation 'com.google.cloud.tools:jib-gradle-plugin:3.3.2' - implementation 'com.diffplug.spotless:spotless-plugin-gradle:6.19.0' + implementation 'com.diffplug.spotless:spotless-plugin-gradle:6.21.0' implementation 'io.freefair.gradle:lombok-plugin:6.6.3' - implementation 'de.undercouch:gradle-download-task:5.4.0' + implementation 'de.undercouch:gradle-download-task:5.5.0' } 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 index 214a29ad..5a822e37 100644 --- 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 @@ -37,10 +37,10 @@ dependencies { implementation 'org.springframework.boot:spring-boot-starter-jdbc' implementation 'org.springframework.boot:spring-boot-starter-data-jdbc' - implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:6.6.1' - implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:6.6.1' - implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.6.1' - implementation 'ca.uhn.hapi.fhir:hapi-fhir-client-okhttp:6.6.1' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:6.8.2' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:6.8.2' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.8.2' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-client-okhttp:6.8.2' implementation 'com.squareup.okhttp3:okhttp:4.11.0' @@ -48,8 +48,8 @@ dependencies { implementation 'org.postgresql:postgresql:42.6.0' - implementation 'io.micrometer:micrometer-registry-prometheus:1.11.1' - implementation 'io.micrometer:micrometer-core:1.11.1' + implementation 'io.micrometer:micrometer-registry-prometheus:1.11.3' + implementation 'io.micrometer:micrometer-core:1.11.3' constraints { implementation('org.apache.commons:commons-text:1.10.0') @@ -105,7 +105,7 @@ spotless { } checkstyle { - toolVersion '10.12.0' + toolVersion '10.12.3' configFile = file('../config/checkstyle/checkstyle.xml') } diff --git a/src/gradle/wrapper/gradle-wrapper.jar b/src/gradle/wrapper/gradle-wrapper.jar index 943f0cbf..7f93135c 100644 Binary files a/src/gradle/wrapper/gradle-wrapper.jar and b/src/gradle/wrapper/gradle-wrapper.jar differ diff --git a/src/gradle/wrapper/gradle-wrapper.properties b/src/gradle/wrapper/gradle-wrapper.properties index 37aef8d3..ac72c34e 100644 --- a/src/gradle/wrapper/gradle-wrapper.properties +++ b/src/gradle/wrapper/gradle-wrapper.properties @@ -1,6 +1,7 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip networkTimeout=10000 +validateDistributionUrl=true zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/src/gradlew b/src/gradlew index 79a61d42..0adc8e1a 100755 --- a/src/gradlew +++ b/src/gradlew @@ -83,10 +83,8 @@ done # This is normally unused # shellcheck disable=SC2034 APP_BASE_NAME=${0##*/} -APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit - -# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. -DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit # Use the maximum available, or set MAX_FD != -1 to use that value. MAX_FD=maximum @@ -133,10 +131,13 @@ location of your Java installation." fi else JAVACMD=java - which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the location of your Java installation." + fi fi # Increase the maximum file descriptors if we can. @@ -197,6 +198,10 @@ if "$cygwin" || "$msys" ; then done fi + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + # Collect all arguments for the java command; # * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of # shell script including quotes and variable substitutions, so put them in diff --git a/src/hack/docker-compose.yaml b/src/hack/docker-compose.yaml index 57bac5dc..d731dc96 100644 --- a/src/hack/docker-compose.yaml +++ b/src/hack/docker-compose.yaml @@ -1,6 +1,6 @@ services: traefik: - image: docker.io/library/traefik:v2.10.1@sha256:7347d4d189642064337fe4eb615d14de2d44f287cb7e1189752fb7399a5ad843 + image: docker.io/library/traefik:2.10.4@sha256:429f3398a3cd1aa7436aa4f59d809040d3903506a9d83bee61688bb1429c7693 restart: unless-stopped ipc: none security_opt: @@ -78,7 +78,7 @@ services: POSTGRES_DB: fhir broadsea-atlasdb: - image: docker.io/ohdsi/broadsea-atlasdb:2.0.0@sha256:da28ed2179efe4f74f5d30da14b348b20acd792e90518e452f37748e89aec179 + image: docker.io/ohdsi/broadsea-atlasdb:2.1.0@sha256:99b4bd5515b3d82adb5bac9b14558b434df55fced6c194c965e3fb1371cb36c5 ports: - "127.0.0.1:25432:5432" @@ -269,7 +269,7 @@ services: OTEL_EXPORTER_JAEGER_ENDPOINT: "http://jaeger:14250" jaeger: - image: docker.io/jaegertracing/all-in-one:1.45.0@sha256:5d5c9d2d8c8cbb42f1db4aac1f1f8487bac63da6802004d0da8580fc0c7311a1 + image: docker.io/jaegertracing/all-in-one:1.49.0@sha256:0edcea978eb4a631a0d9078f435908852f20013cf5d66908521c5ac2815aeb28 ports: - "127.0.0.1:16686:16686" - "127.0.0.1:6831:6831/udp" @@ -282,7 +282,7 @@ services: - "traefik.http.routers.jaeger.entrypoints=web" maildev: - image: docker.io/maildev/maildev:2.0.5@sha256:082ec5ee92266c6e17493998ff1bf1c3eb70604b159fbeeaa435ee777f5cc953 + image: docker.io/maildev/maildev:2.1.0@sha256:f7429227b8f471b3fe761767d86a8794a2fc7488bccdcda46ea6d5ba5c2c7bf5 restart: unless-stopped ipc: none security_opt: @@ -324,7 +324,7 @@ services: - "127.0.0.1:6432:5432" keycloak: - image: quay.io/keycloak/keycloak:21.1.1@sha256:8ebb3930c41e8a066c4246eaf351ac09cdc984e11b1f607d6ff4ce10d69dc808 + image: quay.io/keycloak/keycloak:21.1.2@sha256:3408c186dde4a95c2b99ef1290721bf1d253d64ba3a1de0a46c667b8288051f0 restart: unless-stopped ipc: none security_opt: diff --git a/src/list/Dockerfile b/src/list/Dockerfile index faba0871..2dfbc614 100644 --- a/src/list/Dockerfile +++ b/src/list/Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/library/node:18.16.0@sha256:8cdf7234449f35e579f7491137807ddb3a089f028862f7ab69af437cc9f47ff1 AS base +FROM docker.io/library/node:18.17.1@sha256:933bcfad91e9052a02bc29eb5aa29033e542afac4174f9524b79066d97b23c24 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 index e0b1668b..ad9759c7 100644 --- a/src/list/frontend/deploy/docker-compose.dev.yml +++ b/src/list/frontend/deploy/docker-compose.dev.yml @@ -14,7 +14,7 @@ services: - 8082:8080 loader: - image: docker.io/curlimages/curl:8.1.1@sha256:5af13420d29b7aa7007419347519984ce44778aaf89c475c25edc9b48ca125b2 + image: docker.io/curlimages/curl:8.2.1@sha256:bb0843a1307b1aa73f65f24379d11dde881c16db62ba50810de0c64d48e740ed command: > sh -c "curl -X POST -H 'Content-Type:application/fhir+json' --retry-connrefuse --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-connrefuse --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:1.45@sha256:5d5c9d2d8c8cbb42f1db4aac1f1f8487bac63da6802004d0da8580fc0c7311a1 + image: docker.io/jaegertracing/all-in-one:1.49@sha256:0edcea978eb4a631a0d9078f435908852f20013cf5d66908521c5ac2815aeb28 environment: COLLECTOR_OTLP_ENABLED: "true" ports: @@ -50,7 +50,7 @@ services: - 8083:8080 fhir-pseudonymizer: - image: ghcr.io/miracum/fhir-pseudonymizer:v2.17.0@sha256:431a7f4516c1f641966c507941b87a997441665656572a1c00c44376ef08fe24 + image: ghcr.io/miracum/fhir-pseudonymizer:v2.20.0@sha256:8128ddc10f3abfcd59a32e2f90ddfa622b58ac6bda95182d056aa0c98411efa2 environment: APIKEY: "fhir-pseudonymizer-api-key" TRACING__ENABLED: "true" diff --git a/src/list/frontend/package.json b/src/list/frontend/package.json index 7bf89e07..d734fba3 100644 --- a/src/list/frontend/package.json +++ b/src/list/frontend/package.json @@ -10,38 +10,38 @@ "test:unit": "vue-cli-service test:unit --coverage" }, "dependencies": { - "@dsb-norge/vue-keycloak-js": "2.2.0", + "@dsb-norge/vue-keycloak-js": "2.4.0", "@fortawesome/fontawesome-svg-core": "1.2.36", "@fortawesome/free-solid-svg-icons": "5.15.4", "@fortawesome/vue-fontawesome": "2.0.10", - "axios": "1.3.5", + "axios": "1.5.0", "buefy": "0.9.23", - "core-js": "3.30.0", - "csv-stringify": "6.3.0", + "core-js": "3.32.2", + "csv-stringify": "6.4.2", "fhirclient": "2.5.2", - "fhirpath": "3.3.1", + "fhirpath": "3.6.1", "vue": "2.7.14", "vue-router": "3.6.5", "vuejs-logger": "1.5.5" }, "devDependencies": { - "@babel/eslint-parser": "7.21.3", + "@babel/eslint-parser": "7.22.15", "@vue/cli-plugin-babel": "5.0.8", "@vue/cli-plugin-eslint": "5.0.8", "@vue/cli-plugin-router": "5.0.8", "@vue/cli-plugin-unit-jest": "5.0.8", "@vue/cli-service": "5.0.8", "@vue/eslint-config-airbnb": "6.0.0", - "@vue/test-utils": "1.3.0", + "@vue/test-utils": "1.3.6", "@vue/vue2-jest": "29.2.2", - "cypress-keycloak": "2.0.0", - "eslint": "8.37.0", - "eslint-config-prettier": "8.8.0", - "eslint-plugin-vue": "9.10.0", + "cypress-keycloak": "2.0.1", + "eslint": "8.48.0", + "eslint-config-prettier": "8.10.0", + "eslint-plugin-vue": "9.17.0", "jest": "29.3.1", - "pino": "8.11.0", - "sass": "1.60.0", - "sass-loader": "13.2.2", + "pino": "8.15.0", + "sass": "1.66.1", + "sass-loader": "13.3.2", "vue-template-compiler": "2.7.14" }, "optionalDependencies": { diff --git a/src/list/frontend/tests/e2e/cypress.Dockerfile b/src/list/frontend/tests/e2e/cypress.Dockerfile index b56621bb..4ec5ffb8 100644 --- a/src/list/frontend/tests/e2e/cypress.Dockerfile +++ b/src/list/frontend/tests/e2e/cypress.Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/cypress/included:12.13.0@sha256:bb18d50ddaad4c846c432ee5e6b83bbf239cfe8454d52b546dc2ceb57d4b60af +FROM docker.io/cypress/included:12.17.4@sha256:102b34b9e4cb9895c44a74293c6931e7282535775045dd8b1c7608667a34c4b6 WORKDIR /root ENV CI=1 diff --git a/src/list/frontend/tests/e2e/docker-compose.yaml b/src/list/frontend/tests/e2e/docker-compose.yaml index 2f455cdc..2e91536e 100644 --- a/src/list/frontend/tests/e2e/docker-compose.yaml +++ b/src/list/frontend/tests/e2e/docker-compose.yaml @@ -42,7 +42,7 @@ services: HAPI_FHIR_CORS_ALLOWED_ORIGIN: "http://list:8080" loader: - image: docker.io/curlimages/curl:8.1.1@sha256:5af13420d29b7aa7007419347519984ce44778aaf89c475c25edc9b48ca125b2 + image: docker.io/curlimages/curl:8.2.1@sha256:bb0843a1307b1aa73f65f24379d11dde881c16db62ba50810de0c64d48e740ed command: > sh -c "curl -X POST -H 'Content-Type: application/fhir+json' --retry-connrefuse --connect-timeout 30 --max-time 60 --retry 10 --retry-delay 15 --data '@/data/sample-record-1.json' http://fhir:8080/fhir && curl -X POST -H 'Content-Type: application/fhir+json' --retry-connrefuse --connect-timeout 30 --max-time 60 --retry 10 --retry-delay 15 --data '@/data/sample-record-2.json' http://fhir:8080/fhir && @@ -69,4 +69,4 @@ services: - ${PWD}/frontend/deploy/data/aio-export.json:/tmp/realm.json:ro jaeger: - image: docker.io/jaegertracing/all-in-one:1.45@sha256:5d5c9d2d8c8cbb42f1db4aac1f1f8487bac63da6802004d0da8580fc0c7311a1 + image: docker.io/jaegertracing/all-in-one:1.49@sha256:0edcea978eb4a631a0d9078f435908852f20013cf5d66908521c5ac2815aeb28 diff --git a/src/list/package-lock.json b/src/list/package-lock.json index 9e4e6026..3bf051eb 100644 --- a/src/list/package-lock.json +++ b/src/list/package-lock.json @@ -16,38 +16,38 @@ "name": "list", "version": "0.0.0", "dependencies": { - "@dsb-norge/vue-keycloak-js": "2.2.0", + "@dsb-norge/vue-keycloak-js": "2.4.0", "@fortawesome/fontawesome-svg-core": "1.2.36", "@fortawesome/free-solid-svg-icons": "5.15.4", "@fortawesome/vue-fontawesome": "2.0.10", - "axios": "1.3.5", + "axios": "1.5.0", "buefy": "0.9.23", - "core-js": "3.30.0", - "csv-stringify": "6.3.0", + "core-js": "3.32.2", + "csv-stringify": "6.4.2", "fhirclient": "2.5.2", - "fhirpath": "3.3.1", + "fhirpath": "3.6.1", "vue": "2.7.14", "vue-router": "3.6.5", "vuejs-logger": "1.5.5" }, "devDependencies": { - "@babel/eslint-parser": "7.21.3", + "@babel/eslint-parser": "7.22.15", "@vue/cli-plugin-babel": "5.0.8", "@vue/cli-plugin-eslint": "5.0.8", "@vue/cli-plugin-router": "5.0.8", "@vue/cli-plugin-unit-jest": "5.0.8", "@vue/cli-service": "5.0.8", "@vue/eslint-config-airbnb": "6.0.0", - "@vue/test-utils": "1.3.0", + "@vue/test-utils": "1.3.6", "@vue/vue2-jest": "29.2.2", - "cypress-keycloak": "2.0.0", - "eslint": "8.37.0", - "eslint-config-prettier": "8.8.0", - "eslint-plugin-vue": "9.10.0", + "cypress-keycloak": "2.0.1", + "eslint": "8.48.0", + "eslint-config-prettier": "8.10.0", + "eslint-plugin-vue": "9.17.0", "jest": "29.3.1", - "pino": "8.11.0", - "sass": "1.60.0", - "sass-loader": "13.2.2", + "pino": "8.15.0", + "sass": "1.66.1", + "sass-loader": "13.3.2", "vue-template-compiler": "2.7.14" }, "optionalDependencies": { @@ -55,12 +55,6 @@ "cypress": "12.9.0" } }, - "frontend/node_modules/@types/node": { - "version": "14.18.42", - "resolved": "https://registry.npmjs.org/@types/node/-/node-14.18.42.tgz", - "integrity": "sha512-xefu+RBie4xWlK8hwAzGh3npDz/4VhF6icY/shU+zv/1fNn+ZVG7T7CRwe9LId9sAYRPxI+59QBPuKL3WpyGRg==", - "optional": true - }, "frontend/node_modules/@vue/vue2-jest": { "version": "29.2.2", "resolved": "https://registry.npmjs.org/@vue/vue2-jest/-/vue2-jest-29.2.2.tgz", @@ -95,7 +89,8 @@ "version": "4.3.0", "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==", - "devOptional": true, + "dev": true, + "peer": true, "dependencies": { "color-convert": "^2.0.1" }, @@ -162,7 +157,8 @@ "version": "2.0.1", "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz", "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==", - "devOptional": true, + "dev": true, + "peer": true, "dependencies": { "color-name": "~1.1.4" }, @@ -174,115 +170,8 @@ "version": "1.1.4", "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz", "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==", - "devOptional": true - }, - "frontend/node_modules/cypress": { - "version": "12.9.0", - "resolved": "https://registry.npmjs.org/cypress/-/cypress-12.9.0.tgz", - "integrity": "sha512-Ofe09LbHKgSqX89Iy1xen2WvpgbvNxDzsWx3mgU1mfILouELeXYGwIib3ItCwoRrRifoQwcBFmY54Vs0zw7QCg==", - "hasInstallScript": true, - "optional": true, - "dependencies": { - "@cypress/request": "^2.88.10", - "@cypress/xvfb": "^1.2.4", - "@types/node": "^14.14.31", - "@types/sinonjs__fake-timers": "8.1.1", - "@types/sizzle": "^2.3.2", - "arch": "^2.2.0", - "blob-util": "^2.0.2", - "bluebird": "^3.7.2", - "buffer": "^5.6.0", - "cachedir": "^2.3.0", - "chalk": "^4.1.0", - "check-more-types": "^2.24.0", - "cli-cursor": "^3.1.0", - "cli-table3": "~0.6.1", - "commander": "^5.1.0", - "common-tags": "^1.8.0", - "dayjs": "^1.10.4", - "debug": "^4.3.4", - "enquirer": "^2.3.6", - "eventemitter2": "6.4.7", - "execa": "4.1.0", - "executable": "^4.1.1", - "extract-zip": "2.0.1", - "figures": "^3.2.0", - "fs-extra": "^9.1.0", - "getos": "^3.2.1", - "is-ci": "^3.0.0", - "is-installed-globally": "~0.4.0", - "lazy-ass": "^1.6.0", - "listr2": "^3.8.3", - "lodash": "^4.17.21", - "log-symbols": "^4.0.0", - "minimist": "^1.2.6", - "ospath": "^1.2.2", - "pretty-bytes": "^5.6.0", - "proxy-from-env": "1.0.0", - "request-progress": "^3.0.0", - "semver": "^7.3.2", - "supports-color": "^8.1.1", - "tmp": "~0.2.1", - "untildify": "^4.0.0", - "yauzl": "^2.10.0" - }, - "bin": { - "cypress": "bin/cypress" - }, - "engines": { - "node": "^14.0.0 || ^16.0.0 || >=18.0.0" - } - }, - "frontend/node_modules/cypress/node_modules/chalk": { - "version": "4.1.2", - "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz", - "integrity": "sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==", - "optional": true, - "dependencies": { - "ansi-styles": "^4.1.0", - "supports-color": "^7.1.0" - }, - "engines": { - "node": ">=10" - }, - "funding": { - "url": "https://github.com/chalk/chalk?sponsor=1" - } - }, - "frontend/node_modules/cypress/node_modules/chalk/node_modules/supports-color": { - "version": "7.2.0", - "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz", - "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==", - "optional": true, - "dependencies": { - "has-flag": "^4.0.0" - }, - "engines": { - "node": ">=8" - } - }, - "frontend/node_modules/execa": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/execa/-/execa-4.1.0.tgz", - "integrity": "sha512-j5W0//W7f8UxAn8hXVnwG8tLwdiUy4FJLcSupCg6maBYZDpyBvTApK7KyuI4bKj8KOh1r2YH+6ucuYtJv1bTZA==", - "optional": true, - "dependencies": { - "cross-spawn": "^7.0.0", - "get-stream": "^5.0.0", - "human-signals": "^1.1.1", - "is-stream": "^2.0.0", - "merge-stream": "^2.0.0", - "npm-run-path": "^4.0.0", - "onetime": "^5.1.0", - "signal-exit": "^3.0.2", - "strip-final-newline": "^2.0.0" - }, - "engines": { - "node": ">=10" - }, - "funding": { - "url": "https://github.com/sindresorhus/execa?sponsor=1" - } + "dev": true, + "peer": true }, 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"https://registry.npmjs.org/semver/-/semver-7.3.8.tgz", - "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==", + "version": "7.5.4", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", + "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", "dev": true, "dependencies": { "lru-cache": "^6.0.0" @@ -31845,10 +31924,10 @@ "peer": true }, "node_modules/word-wrap": { - "version": "1.2.3", - "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz", - "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==", - "devOptional": true, + "version": "1.2.5", + "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz", + "integrity": "sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==", + "dev": true, "engines": { "node": ">=0.10.0" } @@ -31962,9 +32041,9 @@ } }, "node_modules/xml2js": { - "version": "0.4.23", - "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.23.tgz", - "integrity": "sha512-ySPiMjM0+pLDftHgXY4By0uswI3SPKLDw/i3UXbnO8M/p28zqexCUoPmQFrYD+/1BzhGJSs2i1ERWKJAtiLrug==", + "version": "0.6.0", + "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.0.tgz", + "integrity": "sha512-eLTh0kA8uHceqesPqSE+VvO1CDDJWMwlQfB6LuN6T8w6MaDJ8Txm8P7s5cHD0miF0V+GGTZrDQfxPZQVsur33w==", "optional": true, "peer": true, "dependencies": { @@ -32260,17 +32339,17 @@ "version": "0.0.0", "dependencies": { "@opentelemetry/api": "1.4.1", - "@opentelemetry/exporter-jaeger": "1.11.0", - "@opentelemetry/exporter-trace-otlp-grpc": "0.37.0", - "@opentelemetry/instrumentation": "0.37.0", - "@opentelemetry/instrumentation-express": "0.32.1", - "@opentelemetry/instrumentation-http": "0.37.0", - "@opentelemetry/instrumentation-pino": "0.33.1", - "@opentelemetry/resources": "1.11.0", - "@opentelemetry/sdk-trace-base": "1.11.0", - "@opentelemetry/sdk-trace-node": "1.11.0", - "@opentelemetry/semantic-conventions": "1.11.0", - "axios": "1.3.5", + "@opentelemetry/exporter-jaeger": "1.15.2", + "@opentelemetry/exporter-trace-otlp-grpc": "0.41.2", + "@opentelemetry/instrumentation": "0.41.2", + "@opentelemetry/instrumentation-express": "0.33.1", + "@opentelemetry/instrumentation-http": "0.41.2", + "@opentelemetry/instrumentation-pino": "0.34.1", + "@opentelemetry/resources": "1.15.2", + "@opentelemetry/sdk-trace-base": "1.15.2", + "@opentelemetry/sdk-trace-node": "1.15.2", + "@opentelemetry/semantic-conventions": "1.15.2", + "axios": "1.5.0", "connect-history-api-fallback": "2.0.0", "cors": "2.8.5", "debug": "4.3.4", @@ -32278,14 +32357,14 @@ "express-bearer-token": "2.4.0", "express-jwt": "8.4.1", "express-prom-bundle": "6.6.0", - "helmet": "6.0.1", + "helmet": "6.2.0", "http-proxy-middleware": "2.0.6", "js-yaml": "4.1.0", "jwks-rsa": "2.1.5", "node-http-proxy-json": "0.1.9", "path": "0.12.7", - "pino": "8.11.0", - "pino-http": "8.3.3", + "pino": "8.15.0", + "pino-http": "8.5.0", "prom-client": "14.2.0", "retry-axios": "2.6.0" } diff --git a/src/list/server/package.json b/src/list/server/package.json index bf072b82..d8604367 100644 --- a/src/list/server/package.json +++ b/src/list/server/package.json @@ -9,17 +9,17 @@ }, "dependencies": { "@opentelemetry/api": "1.4.1", - "@opentelemetry/exporter-jaeger": "1.11.0", - "@opentelemetry/exporter-trace-otlp-grpc": "0.37.0", - "@opentelemetry/instrumentation": "0.37.0", - "@opentelemetry/instrumentation-express": "0.32.1", - "@opentelemetry/instrumentation-http": "0.37.0", - "@opentelemetry/instrumentation-pino": "0.33.1", - "@opentelemetry/resources": "1.11.0", - "@opentelemetry/sdk-trace-base": "1.11.0", - "@opentelemetry/sdk-trace-node": "1.11.0", - "@opentelemetry/semantic-conventions": "1.11.0", - "axios": "1.3.5", + "@opentelemetry/exporter-jaeger": "1.15.2", + "@opentelemetry/exporter-trace-otlp-grpc": "0.41.2", + "@opentelemetry/instrumentation": "0.41.2", + "@opentelemetry/instrumentation-express": "0.33.1", + "@opentelemetry/instrumentation-http": "0.41.2", + "@opentelemetry/instrumentation-pino": "0.34.1", + "@opentelemetry/resources": "1.15.2", + "@opentelemetry/sdk-trace-base": "1.15.2", + "@opentelemetry/sdk-trace-node": "1.15.2", + "@opentelemetry/semantic-conventions": "1.15.2", + "axios": "1.5.0", "connect-history-api-fallback": "2.0.0", "cors": "2.8.5", "debug": "4.3.4", @@ -27,14 +27,14 @@ "express-bearer-token": "2.4.0", "express-jwt": "8.4.1", "express-prom-bundle": "6.6.0", - "helmet": "6.0.1", + "helmet": "6.2.0", "http-proxy-middleware": "2.0.6", "js-yaml": "4.1.0", "jwks-rsa": "2.1.5", "node-http-proxy-json": "0.1.9", "path": "0.12.7", - "pino": "8.11.0", - "pino-http": "8.3.3", + "pino": "8.15.0", + "pino-http": "8.5.0", "prom-client": "14.2.0", "retry-axios": "2.6.0" } diff --git a/src/notify/tests/e2e/docker-compose.yaml b/src/notify/tests/e2e/docker-compose.yaml index c4b8f471..781c4e34 100644 --- a/src/notify/tests/e2e/docker-compose.yaml +++ b/src/notify/tests/e2e/docker-compose.yaml @@ -28,7 +28,7 @@ services: POSTGRES_DB: recruit_notify_jobs tester: - image: docker.io/curlimages/curl:8.1.1@sha256:5af13420d29b7aa7007419347519984ce44778aaf89c475c25edc9b48ca125b2 + image: docker.io/curlimages/curl:8.2.1@sha256:bb0843a1307b1aa73f65f24379d11dde881c16db62ba50810de0c64d48e740ed command: > -X GET --fail @@ -51,4 +51,4 @@ services: HAPI_FHIR_CORS_ALLOWED_ORIGIN: "*" maildev: - image: docker.io/maildev/maildev:2.0.5@sha256:082ec5ee92266c6e17493998ff1bf1c3eb70604b159fbeeaa435ee777f5cc953 + image: docker.io/maildev/maildev:2.1.0@sha256:f7429227b8f471b3fe761767d86a8794a2fc7488bccdcda46ea6d5ba5c2c7bf5 diff --git a/src/query/build.gradle b/src/query/build.gradle index e2f09fd3..279dca6b 100644 --- a/src/query/build.gradle +++ b/src/query/build.gradle @@ -12,24 +12,24 @@ plugins { dependencies { implementation 'org.springframework.boot:spring-boot-starter-webflux' - implementation 'org.apache.camel:camel-sql:4.0.0-M3' - implementation 'org.apache.camel:camel-jackson:4.0.0-M3' - implementation 'org.apache.camel:camel-jsonpath:4.0.0-M3' - implementation 'org.apache.camel:camel-fhir:4.0.0-M3' - implementation 'org.apache.camel:camel-http:4.0.0-M3' - implementation 'org.apache.camel:camel-cron:4.0.0-M3' - - implementation 'org.apache.camel.springboot:camel-rest-starter:4.0.0-M3' - implementation 'org.apache.camel.springboot:camel-servlet-starter:4.0.0-M3' - implementation 'org.apache.camel.springboot:camel-spring-boot-starter:4.0.0-M3' - implementation 'org.apache.camel.springboot:camel-micrometer-starter:4.0.0-M3' + implementation 'org.apache.camel:camel-sql:4.0.0' + implementation 'org.apache.camel:camel-jackson:4.0.0' + implementation 'org.apache.camel:camel-jsonpath:4.0.0' + implementation 'org.apache.camel:camel-fhir:4.0.0' + implementation 'org.apache.camel:camel-http:4.0.0' + implementation 'org.apache.camel:camel-cron:4.0.0' + + implementation 'org.apache.camel.springboot:camel-rest-starter:4.0.0' + implementation 'org.apache.camel.springboot:camel-servlet-starter:4.0.0' + implementation 'org.apache.camel.springboot:camel-spring-boot-starter:4.0.0' + implementation 'org.apache.camel.springboot:camel-micrometer-starter:4.0.0' implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.2' - implementation 'net.minidev:json-smart:2.4.11' + implementation 'net.minidev:json-smart:2.5.0' implementation 'com.github.slugify:slugify:3.0.5' - testImplementation 'com.approvaltests:approvaltests:18.6.0' + testImplementation 'com.approvaltests:approvaltests:18.7.1' testImplementation 'com.google.code.gson:gson:2.10.1' } diff --git a/src/query/tests/e2e/Dockerfile b/src/query/tests/e2e/Dockerfile index 9c8bad01..72c85dc0 100644 --- a/src/query/tests/e2e/Dockerfile +++ b/src/query/tests/e2e/Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/library/python:3.11.3-alpine@sha256:4e8e9a59bf1b3ca8e030244bc5f801f23e41e37971907371da21191312087a07 +FROM docker.io/library/python:3.11.5-alpine@sha256:5d769f990397afbb2aca24b0655e404c0f2806d268f454b052e81e39d87abf42 WORKDIR /opt/tests COPY requirements.txt . diff --git a/src/query/tests/e2e/docker-compose.yaml b/src/query/tests/e2e/docker-compose.yaml index cf12cc99..676722dc 100644 --- a/src/query/tests/e2e/docker-compose.yaml +++ b/src/query/tests/e2e/docker-compose.yaml @@ -41,7 +41,7 @@ services: HAPI_FHIR_NARRATIVE_ENABLED: "false" broadsea-atlasdb: - image: docker.io/ohdsi/broadsea-atlasdb:2.0.0@sha256:da28ed2179efe4f74f5d30da14b348b20acd792e90518e452f37748e89aec179 + image: docker.io/ohdsi/broadsea-atlasdb:2.1.0@sha256:99b4bd5515b3d82adb5bac9b14558b434df55fced6c194c965e3fb1371cb36c5 ohdsi-webapi: image: docker.io/ohdsi/webapi:2.13.0@sha256:04313754fc79a6e362a8116ef462360e3891581a045924f4ec5ed404fbb9b837 diff --git a/src/query/tests/e2e/requirements.in b/src/query/tests/e2e/requirements.in index 05004078..4a129a2e 100644 --- a/src/query/tests/e2e/requirements.in +++ b/src/query/tests/e2e/requirements.in @@ -1,3 +1,3 @@ fhirclient==4.1.0 -pytest==7.4.0 +pytest==7.4.2 retrying==1.3.4 diff --git a/src/query/tests/e2e/requirements.txt b/src/query/tests/e2e/requirements.txt index 54c3fb47..e4278937 100644 --- a/src/query/tests/e2e/requirements.txt +++ b/src/query/tests/e2e/requirements.txt @@ -4,35 +4,49 @@ # # pip-compile --generate-hashes requirements.in # -certifi==2023.5.7 \ - --hash=sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7 \ - --hash=sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716 +certifi==2023.7.22 \ + --hash=sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082 \ + --hash=sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9 # via requests charset-normalizer==3.2.0 \ --hash=sha256:04e57ab9fbf9607b77f7d057974694b4f6b142da9ed4a199859d9d4d5c63fe96 \ --hash=sha256:09393e1b2a9461950b1c9a45d5fd251dc7c6f228acab64da1c9c0165d9c7765c \ --hash=sha256:0b87549028f680ca955556e3bd57013ab47474c3124dc069faa0b6545b6c9710 \ + --hash=sha256:1000fba1057b92a65daec275aec30586c3de2401ccdcd41f8a5c1e2c87078706 \ + --hash=sha256:1249cbbf3d3b04902ff081ffbb33ce3377fa6e4c7356f759f3cd076cc138d020 \ + --hash=sha256:1920d4ff15ce893210c1f0c0e9d19bfbecb7983c76b33f046c13a8ffbd570252 \ --hash=sha256:193cbc708ea3aca45e7221ae58f0fd63f933753a9bfb498a3b474878f12caaad \ --hash=sha256:1a100c6d595a7f316f1b6f01d20815d916e75ff98c27a01ae817439ea7726329 \ --hash=sha256:1f30b48dd7fa1474554b0b0f3fdfdd4c13b5c737a3c6284d3cdc424ec0ffff3a \ + --hash=sha256:203f0c8871d5a7987be20c72442488a0b8cfd0f43b7973771640fc593f56321f \ --hash=sha256:246de67b99b6851627d945db38147d1b209a899311b1305dd84916f2b88526c6 \ + --hash=sha256:2dee8e57f052ef5353cf608e0b4c871aee320dd1b87d351c28764fc0ca55f9f4 \ --hash=sha256:2efb1bd13885392adfda4614c33d3b68dee4921fd0ac1d3988f8cbb7d589e72a \ --hash=sha256:2f4ac36d8e2b4cc1aa71df3dd84ff8efbe3bfb97ac41242fbcfc053c67434f46 \ --hash=sha256:3170c9399da12c9dc66366e9d14da8bf7147e1e9d9ea566067bbce7bb74bd9c2 \ --hash=sha256:3b1613dd5aee995ec6d4c69f00378bbd07614702a315a2cf6c1d21461fe17c23 \ + --hash=sha256:3bb3d25a8e6c0aedd251753a79ae98a093c7e7b471faa3aa9a93a81431987ace \ --hash=sha256:3bb7fda7260735efe66d5107fb7e6af6a7c04c7fce9b2514e04b7a74b06bf5dd \ --hash=sha256:41b25eaa7d15909cf3ac4c96088c1f266a9a93ec44f87f1d13d4a0e86c81b982 \ + --hash=sha256:45de3f87179c1823e6d9e32156fb14c1927fcc9aba21433f088fdfb555b77c10 \ --hash=sha256:46fb8c61d794b78ec7134a715a3e564aafc8f6b5e338417cb19fe9f57a5a9bf2 \ --hash=sha256:48021783bdf96e3d6de03a6e39a1171ed5bd7e8bb93fc84cc649d11490f87cea \ --hash=sha256:4957669ef390f0e6719db3613ab3a7631e68424604a7b448f079bee145da6e09 \ + --hash=sha256:5e86d77b090dbddbe78867a0275cb4df08ea195e660f1f7f13435a4649e954e5 \ --hash=sha256:6339d047dab2780cc6220f46306628e04d9750f02f983ddb37439ca47ced7149 \ --hash=sha256:681eb3d7e02e3c3655d1b16059fbfb605ac464c834a0c629048a30fad2b27489 \ + --hash=sha256:6c409c0deba34f147f77efaa67b8e4bb83d2f11c8806405f76397ae5b8c0d1c9 \ + --hash=sha256:7095f6fbfaa55defb6b733cfeb14efaae7a29f0b59d8cf213be4e7ca0b857b80 \ --hash=sha256:70c610f6cbe4b9fce272c407dd9d07e33e6bf7b4aa1b7ffb6f6ded8e634e3592 \ --hash=sha256:72814c01533f51d68702802d74f77ea026b5ec52793c791e2da806a3844a46c3 \ --hash=sha256:7a4826ad2bd6b07ca615c74ab91f32f6c96d08f6fcc3902ceeedaec8cdc3bcd6 \ --hash=sha256:7c70087bfee18a42b4040bb9ec1ca15a08242cf5867c58726530bdf3945672ed \ + --hash=sha256:855eafa5d5a2034b4621c74925d89c5efef61418570e5ef9b37717d9c796419c \ + --hash=sha256:8700f06d0ce6f128de3ccdbc1acaea1ee264d2caa9ca05daaf492fde7c2a7200 \ --hash=sha256:89f1b185a01fe560bc8ae5f619e924407efca2191b56ce749ec84982fc59a32a \ + --hash=sha256:8b2c760cfc7042b27ebdb4a43a4453bd829a5742503599144d54a032c5dc7e9e \ --hash=sha256:8c2f5e83493748286002f9369f3e6607c565a6a90425a3a1fef5ae32a36d749d \ + --hash=sha256:8e098148dd37b4ce3baca71fb394c81dc5d9c7728c95df695d2dca218edf40e6 \ --hash=sha256:94aea8eff76ee6d1cdacb07dd2123a68283cb5569e0250feab1240058f53b623 \ --hash=sha256:95eb302ff792e12aba9a8b8f8474ab229a83c103d74a750ec0bd1c1eea32e669 \ --hash=sha256:9bd9b3b31adcb054116447ea22caa61a285d92e94d710aa5ec97992ff5eb7cf3 \ @@ -48,18 +62,26 @@ charset-normalizer==3.2.0 \ --hash=sha256:bf420121d4c8dce6b889f0e8e4ec0ca34b7f40186203f06a946fa0276ba54029 \ --hash=sha256:c04a46716adde8d927adb9457bbe39cf473e1e2c2f5d0a16ceb837e5d841ad4f \ --hash=sha256:c0b21078a4b56965e2b12f247467b234734491897e99c1d51cee628da9786959 \ + --hash=sha256:c1c76a1743432b4b60ab3358c937a3fe1341c828ae6194108a94c69028247f22 \ --hash=sha256:c4983bf937209c57240cff65906b18bb35e64ae872da6a0db937d7b4af845dd7 \ + --hash=sha256:c4fb39a81950ec280984b3a44f5bd12819953dc5fa3a7e6fa7a80db5ee853952 \ --hash=sha256:c57921cda3a80d0f2b8aec7e25c8aa14479ea92b5b51b6876d975d925a2ea346 \ + --hash=sha256:c8063cf17b19661471ecbdb3df1c84f24ad2e389e326ccaf89e3fb2484d8dd7e \ + --hash=sha256:ccd16eb18a849fd8dcb23e23380e2f0a354e8daa0c984b8a732d9cfaba3a776d \ + --hash=sha256:cd6dbe0238f7743d0efe563ab46294f54f9bc8f4b9bcf57c3c666cc5bc9d1299 \ --hash=sha256:d62e51710986674142526ab9f78663ca2b0726066ae26b78b22e0f5e571238dd \ --hash=sha256:db901e2ac34c931d73054d9797383d0f8009991e723dab15109740a63e7f902a \ --hash=sha256:e03b8895a6990c9ab2cdcd0f2fe44088ca1c65ae592b8f795c3294af00a461c3 \ --hash=sha256:e1c8a2f4c69e08e89632defbfabec2feb8a8d99edc9f89ce33c4b9e36ab63037 \ --hash=sha256:e4b749b9cc6ee664a3300bb3a273c1ca8068c46be705b6c31cf5d276f8628a94 \ + --hash=sha256:e6a5bf2cba5ae1bb80b154ed68a3cfa2fa00fde979a7f50d6598d3e17d9ac20c \ + --hash=sha256:e857a2232ba53ae940d3456f7533ce6ca98b81917d47adc3c7fd55dad8fab858 \ --hash=sha256:ee4006268ed33370957f55bf2e6f4d263eaf4dc3cfc473d1d90baff6ed36ce4a \ --hash=sha256:eef9df1eefada2c09a5e7a40991b9fc6ac6ef20b1372abd48d2794a316dc0449 \ --hash=sha256:f058f6963fd82eb143c692cecdc89e075fa0828db2e5b291070485390b2f1c9c \ --hash=sha256:f25c229a6ba38a35ae6e25ca1264621cc25d4d38dca2942a7fce0b67a4efe918 \ --hash=sha256:f2a1d0fd4242bd8643ce6f98927cf9c04540af6efa92323e9d3124f57727bfc1 \ + --hash=sha256:f7560358a6811e52e9c4d142d497f1a6e10103d3a6881f18d04dbce3729c0e2c \ --hash=sha256:f779d3ad205f108d14e99bb3859aa7dd8e9c68874617c72354d7ecaec2a054ac \ --hash=sha256:f87f746ee241d30d6ed93969de31e5ffd09a2961a051e60ae6bddde9ec3583aa # via requests @@ -83,13 +105,13 @@ packaging==23.1 \ --hash=sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61 \ --hash=sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f # via pytest -pluggy==1.2.0 \ - --hash=sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849 \ - --hash=sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3 +pluggy==1.3.0 \ + --hash=sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12 \ + --hash=sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7 # via pytest -pytest==7.4.0 \ - --hash=sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32 \ - --hash=sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a +pytest==7.4.2 \ + --hash=sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002 \ + --hash=sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069 # via -r requirements.in requests==2.31.0 \ --hash=sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f \ @@ -105,7 +127,7 @@ six==1.16.0 \ # via # isodate # retrying -urllib3==2.0.3 \ - --hash=sha256:48e7fafa40319d358848e1bc6809b208340fafe2096f1725d05d67443d0483d1 \ - --hash=sha256:bee28b5e56addb8226c96f7f13ac28cb4c301dd5ea8a6ca179c0b9835e032825 +urllib3==2.0.4 \ + --hash=sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11 \ + --hash=sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4 # via requests diff --git a/tests/chaos/tester/Dockerfile b/tests/chaos/tester/Dockerfile index eee8aea0..9a665392 100644 --- a/tests/chaos/tester/Dockerfile +++ b/tests/chaos/tester/Dockerfile @@ -1,5 +1,5 @@ # syntax=docker/dockerfile:1.4 -FROM mcr.microsoft.com/dotnet/sdk:7.0-jammy@sha256:d2a0f255365a16fab863424a74ebbbcb0e033142268ceda8083eb37b2f02a3a1 AS build +FROM mcr.microsoft.com/dotnet/sdk:7.0-jammy@sha256:fff616cce9131105bd3a09bd7033e8604ac761490a703c5ece071751c155b218 AS build WORKDIR /build ENV DOTNET_CLI_TELEMETRY_OPTOUT=1 @@ -21,13 +21,13 @@ dotnet publish tester.csproj \ -o /build/publish EOF -FROM mcr.microsoft.com/dotnet/nightly/runtime:7.0-jammy-chiseled@sha256:a3455b37de54bdd46f60984c06f34883fdc3a8add5584eb0da83aaa729a97920 AS runtime +FROM mcr.microsoft.com/dotnet/nightly/runtime:7.0-jammy-chiseled@sha256:a91b1132db1cb6310e8e68e7ba513be5ac96234446461eb4de2439856dd84fa5 AS runtime WORKDIR /opt/chaos-tester USER 65532:65532 ENV DOTNET_ENVIRONMENT="Production" \ DOTNET_CLI_TELEMETRY_OPTOUT=1 -COPY --from=docker.io/bitnami/kubectl:1.27.2@sha256:f84620143febefe8823d52554b32fd76b4e34d4f9a0f9d2df7648bc752a3d602 /opt/bitnami/kubectl/bin/kubectl /usr/bin/kubectl +COPY --from=docker.io/bitnami/kubectl:1.27.5@sha256:de14320baddeead24f572b10b18df7dd66315ebc9b88f015d392f1c466b46211 /opt/bitnami/kubectl/bin/kubectl /usr/bin/kubectl COPY ./sample-list-bundle.json /tmp/ COPY ./chaos.yaml /tmp/ diff --git a/tests/chaos/tester/tester.csproj b/tests/chaos/tester/tester.csproj index 9eeee54b..5d9f4e0b 100644 --- a/tests/chaos/tester/tester.csproj +++ b/tests/chaos/tester/tester.csproj @@ -8,7 +8,7 @@ - +