Merge pull request #32 from elimuinformatics/update-fork

Update fork

.dockerignore

@@ -1,3 +1,12 @@
-target
+target/classes/
+target/failsafe-reports/
+target/generated-*
+target/maven-*
+target/ROOT
+target/test-classes/
+target/war
+target/duplicate-finder-result.xml
+target/jacoco.exec
+target/*.original
 .idea
 .git

.editorconfig

@@ -1,5 +1,5 @@
 [*.java]
 charset = utf-8
-indent_style = space
-indent_size = 2
+indent_style = tab
+indent_size = 3
 

.github/ct/chart-schema.yaml

@@ -0,0 +1,23 @@
+name: str()
+home: str()
+version: str()
+apiVersion: str()
+appVersion: any(str(), num(), required=False)
+type: str()
+dependencies: any(required=False)
+description: str()
+keywords: list(str(), required=False)
+sources: list(str(), required=False)
+maintainers: list(include('maintainer'), required=False)
+icon: str(required=False)
+engine: str(required=False)
+condition: str(required=False)
+tags: str(required=False)
+deprecated: bool(required=False)
+kubeVersion: str(required=False)
+annotations: map(str(), str(), required=False)
+---
+maintainer:
+  name: str()
+  email: str(required=False)
+  url: str(required=False)

.github/ct/config.yaml

@@ -0,0 +1,16 @@
+debug: true
+remote: origin
+chart-yaml-schema: .github/ct/chart-schema.yaml
+validate-maintainers: false
+validate-chart-schema: true
+validate-yaml: true
+check-version-increment: true
+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-name-template: "helm-v{{ .Version }}"

.github/workflows/build-images.yaml

@@ -0,0 +1,84 @@
+name: Build Container Images
+
+on:
+  push:
+    tags:
+      - "image/v*"
+    paths-ignore:
+      - "charts/**"
+  pull_request:
+    branches: [master]
+    paths-ignore:
+      - "charts/**"
+env:
+  IMAGES: docker.io/hapiproject/hapi
+  PLATFORMS: linux/amd64,linux/arm64/v8
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Docker meta
+        id: docker_meta
+        uses: docker/metadata-action@v3
+        with:
+          images: ${{ env.IMAGES }}
+          tags: |
+            type=match,pattern=image-(.*),group=1,enable=${{github.event_name != 'pull_request'}}
+            type=sha
+
+      - name: Docker distroless meta
+        id: docker_distroless_meta
+        uses: docker/metadata-action@v3
+        with:
+          images: ${{ env.IMAGES }}
+          tags: |
+            type=match,pattern=image-(.*),group=1,enable=${{github.event_name != 'pull_request'}}
+            type=sha
+          flavor: |
+            suffix=-distroless,onlatest=true
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        if: github.event_name != 'pull_request'
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          labels: ${{ steps.docker_meta.outputs.labels }}
+          platforms: ${{ env.PLATFORMS }}
+
+      - name: Build and push distroless
+        id: docker_build_distroless
+        uses: docker/build-push-action@v2
+        with:
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.docker_distroless_meta.outputs.tags }}
+          labels: ${{ steps.docker_distroless_meta.outputs.labels }}
+          platforms: ${{ env.PLATFORMS }}
+          target: release-distroless

.github/workflows/chart-release.yaml

@@ -0,0 +1,40 @@
+name: Release Charts
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - "charts/**"
+
+jobs:
+  release:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Configure Git
+        run: |
+          git config user.name "$GITHUB_ACTOR"
+          git config user.email "[email protected]"
+
+      - name: Install Helm
+        uses: azure/setup-helm@v1
+        with:
+          version: v3.7.0
+
+      - name: Add bitnami repo
+        run: helm repo add bitnami https://charts.bitnami.com/bitnami
+
+      - name: Update dependencies
+        run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \;
+
+      - name: Run chart-releaser
+        uses: helm/[email protected]
+        with:
+          config: .github/ct/config.yaml
+        env:
+          CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/chart-test.yaml

@@ -0,0 +1,68 @@
+name: Lint and Test Charts
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "charts/**"
+
+jobs:
+  lint:
+    runs-on: ubuntu-20.04
+    container: quay.io/helmpack/chart-testing:v3.4.0
+    steps:
+      - name: Install helm-docs
+        working-directory: /tmp
+        env:
+          HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.5.0/helm-docs_1.5.0_Linux_x86_64.tar.gz
+        run: |
+          curl -LSs $HELM_DOCS_URL | tar xz && \
+          mv ./helm-docs /usr/local/bin/helm-docs && \
+          chmod +x /usr/local/bin/helm-docs && \
+          helm-docs --version
+
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Check if documentation is up-to-date
+        run: helm-docs && git diff --exit-code HEAD
+
+      - name: Run chart-testing (lint)
+        run: ct lint --config .github/ct/config.yaml
+
+  test:
+    runs-on: ubuntu-20.04
+    needs:
+      - lint
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Helm
+        uses: azure/setup-helm@v1
+        with:
+          version: v3.7.0
+
+      - name: Set up chart-testing
+        uses: helm/[email protected]
+
+      - name: Run chart-testing (list-changed)
+        id: list-changed
+        run: |
+          changed=$(ct list-changed --config .github/ct/config.yaml)
+          if [[ -n "$changed" ]]; then
+            echo "::set-output name=changed::true"
+          fi
+
+      - name: Create k8s Kind Cluster
+        uses: helm/[email protected]
+        if: steps.list-changed.outputs.changed == 'true'
+
+      - name: Run chart-testing (install)
+        run: ct install --config .github/ct/config.yaml
+        if: steps.list-changed.outputs.changed == 'true'

.github/workflows/maven.yml

@@ -5,7 +5,8 @@ name: Java CI with Maven
 
 on:
   push:
-    branches: [ master ]
+    branches: 
+      - '**' 
   pull_request:
     branches: [ master ]
 

.gitignore

@@ -119,6 +119,13 @@ local.properties
 
 # STS (Spring Tool Suite)
 .springBeans
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
 
 # Code Recommenders
 .recommenders/
@@ -157,4 +164,7 @@ Icon
 .AppleDesktop
 Network Trash Folder
 Temporary Items
-.apdisk
+.apdisk
+
+# Helm Chart dependencies
+**/charts/*.tgz

Dockerfile

@@ -1,17 +1,33 @@
-FROM maven:3.6.3-jdk-11-slim as build-hapi
+FROM maven:3.8.2-jdk-11-slim as build-hapi
 WORKDIR /tmp/hapi-fhir-jpaserver-starter
 
 COPY pom.xml .
+COPY server.xml .
 RUN mvn -ntp dependency:go-offline
 
 COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
 RUN mvn clean install -DskipTests
 
-FROM tomcat:9.0.38-jdk11-openjdk-slim-buster
+FROM build-hapi AS build-distroless
+RUN mvn package spring-boot:repackage -Pboot
+RUN mkdir /app && \
+    cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
 
-RUN mkdir -p /data/hapi/lucenefiles && chmod 775 /data/hapi/lucenefiles && rm -rf /usr/local/tomcat/webapps/ROOT
-COPY --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/target/*.war /usr/local/tomcat/webapps/ROOT.war
+FROM gcr.io/distroless/java-debian11:11 AS release-distroless
+COPY --chown=nonroot:nonroot --from=build-distroless /app /app
+# 65532 is the nonroot user's uid
+# used here instead of the name to allow Kubernetes to easily detect that the container
+# is running as a non-root (uid != 0) user.
+USER 65532:65532
+WORKDIR /app
+CMD ["/app/main.war"]
 
-EXPOSE 8080
+FROM tomcat:9.0.53-jdk11-openjdk-slim-bullseye
+
+RUN mkdir -p /data/hapi/lucenefiles && chmod 775 /data/hapi/lucenefiles
+COPY --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/target/*.war /usr/local/tomcat/webapps/
+
+COPY catalina.properties /usr/local/tomcat/conf/catalina.properties
+COPY server.xml /usr/local/tomcat/conf/server.xml
 
 CMD ["catalina.sh", "run"]