Add webapi-3.0 ci (#2477)

* cleanup

* add ci to publish docker image

* fix

* fix

* fix

* fix

* fix

* fix

* update trexsql

* readd migrations for broadsea

* update

Author: p-hoffmann

.github/workflows/ci.yaml

@@ -8,9 +8,6 @@ on:
   pull_request:
     branches: [ master, webapi-3.0 ]
 
-env:
-  DOCKER_IMAGE: ohdsi/webapi
-
 jobs:
   # Build and test the code
   build:
@@ -23,7 +20,7 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-java@v4
         with:
@@ -47,15 +44,24 @@ jobs:
         run: mvn -B -P${{ env.MAVEN_PROFILE }} test
 
   # Check that the docker image builds correctly
-  # Push to ohdsi/atlas:master for commits on master.
+  # Push to ghcr.io for commits on master or webapi-3.0.
   docker:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - name: Set Docker image name
+        run: |
+          REPO="${GITHUB_REPOSITORY:-ohdsi/webapi}"
+          DOCKER_IMAGE="ghcr.io/$(echo "${REPO}" | tr '[:upper:]' '[:lower:]')"
+          echo "DOCKER_IMAGE=${DOCKER_IMAGE}" >> $GITHUB_ENV
+
+      - name: Debug Docker image name
+        run: echo "DOCKER_IMAGE=${DOCKER_IMAGE}"
 
       - name: Cache Docker layers
         uses: actions/cache@v4
@@ -68,40 +74,54 @@ jobs:
       # Add Docker labels and tags
       - name: Docker meta
         id: docker_meta
-        uses: crazy-max/ghaction-docker-meta@v1
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.DOCKER_IMAGE }}
+          tags: |
+            type=raw,value=dev,enable=${{ github.ref == 'refs/heads/master' }}
+            type=raw,value=3.0-dev,enable=${{ github.ref == 'refs/heads/webapi-3.0' }}
+            type=sha,prefix=pr-,enable=${{ github.event_name == 'pull_request' }}
+            type=ref,event=branch,prefix=branch-,enable=${{ github.ref != 'refs/heads/master' && github.ref != 'refs/heads/webapi-3.0' }}
+
+      - name: Debug Docker metadata
+        run: |
+          echo "Docker metadata outputs:"
+          echo "version: ${{ steps.docker_meta.outputs.version }}"
+          echo "tags: ${{ steps.docker_meta.outputs.tags }}"
+          echo "labels: ${{ steps.docker_meta.outputs.labels }}"
+          echo "json: ${{ steps.docker_meta.outputs.json }}"
 
       # Setup docker build environment
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Set build parameters
         id: build_params
         run: |
-          echo "::set-output name=sha8::${GITHUB_SHA::8}"
-          if [ "${{ github.event_name }}" != "pull_request" ] && [ "${{ github.ref }}" == "refs/heads/master" ]; then
-            echo "::set-output name=push::true"
-            echo "::set-output name=load::false"
-            echo "::set-output name=platforms::linux/amd64,linux/arm64"
+          echo "sha8=${GITHUB_SHA::8}" >> $GITHUB_OUTPUT
+          if [ "${{ github.event_name }}" != "pull_request" ] && ( [ "${{ github.ref }}" == "refs/heads/master" ] || [ "${{ github.ref }}" == "refs/heads/webapi-3.0" ] ); then
+            echo "push=true" >> $GITHUB_OUTPUT
+            echo "load=false" >> $GITHUB_OUTPUT
+            echo "platforms=linux/amd64,linux/arm64" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=push::false"
-            echo "::set-output name=load::true"
-            echo "::set-output name=platforms::linux/amd64"
+            echo "push=false" >> $GITHUB_OUTPUT
+            echo "load=true" >> $GITHUB_OUTPUT
+            echo "platforms=linux/amd64" >> $GITHUB_OUTPUT
           fi
 
-      - name: Login to DockerHub
-        uses: docker/login-action@v1
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
         if: steps.build_params.outputs.push == 'true'
         with:
-          username: ${{ secrets.DOCKER_HUB_USERNAME }}
-          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: ./
           file: ./Dockerfile
@@ -113,6 +133,7 @@ jobs:
           build-args: |
             GIT_BRANCH=${{ steps.docker_meta.outputs.version }}
             GIT_COMMIT_ID_ABBREV=${{ steps.build_params.outputs.sha8 }}
+            MAVEN_PROFILE=webapi-docker,tcache
           tags: ${{ steps.docker_meta.outputs.tags }}
           # Use runtime labels from docker_meta as well as fixed labels
           labels: |

Dockerfile

@@ -1,8 +1,8 @@
-FROM maven:3.9-eclipse-temurin-21 as builder
+FROM maven:3.9-eclipse-temurin-21 AS builder
 
 WORKDIR /code
 
-ARG MAVEN_PROFILE=webapi-docker
+ARG MAVEN_PROFILE=webapi-docker,tcache
 ARG MAVEN_PARAMS="" # can use maven options, e.g. -DskipTests=true -DskipUnitTests=true
 
 ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0
@@ -29,7 +29,7 @@ RUN mvn package ${MAVEN_PARAMS} \
 # OHDSI WebAPI running as a Spring Boot executable JAR with Java 21
 FROM index.docker.io/library/eclipse-temurin:21-jre
 
-MAINTAINER Lee Evans - www.ltscomputingllc.com
+LABEL maintainer="Lee Evans - www.ltscomputingllc.com"
 
 # Any Java options to pass along, e.g. memory, garbage collection, etc.
 ENV JAVA_OPTS=""
@@ -41,14 +41,20 @@ ENV DEFAULT_JAVA_OPTS="-Djava.security.egd=file:///dev/./urandom"
 # set working directory to a fixed WebAPI directory
 WORKDIR /var/lib/ohdsi/webapi
 
+RUN apt-get update && apt-get install -y unzip && rm -rf /var/lib/apt/lists/*
+
 COPY --from=builder /code/opentelemetry-javaagent.jar .
 COPY --from=builder /code/target/WebAPI.jar .
 
+RUN mkdir -p /tmp/trexsql && \
+    unzip -j WebAPI.jar 'BOOT-INF/lib/trexsql-ext-*.jar' -d /tmp && \
+    unzip -j /tmp/trexsql-ext-*.jar 'libtrexsql_java.so_linux_amd64' -d /tmp/trexsql 2>/dev/null || true && \
+    mv /tmp/trexsql/libtrexsql_java.so_linux_amd64 /tmp/trexsql/libtrexsql_java.so 2>/dev/null || true && \
+    rm -f /tmp/trexsql-ext-*.jar
+
 EXPOSE 8080
 
 USER 101
 
-# Run the executable JAR
-CMD exec java ${DEFAULT_JAVA_OPTS} ${JAVA_OPTS} \
-    --add-opens java.naming/com.sun.jndi.ldap=ALL-UNNAMED \
-    -jar WebAPI.jar
+# Run the executable JAR with TrexSQL native library path
+CMD ["sh", "-c", "exec java ${DEFAULT_JAVA_OPTS} ${JAVA_OPTS} -Dorg.duckdb.lib_path=/tmp/trexsql/libtrexsql_java.so --add-opens java.naming/com.sun.jndi.ldap=ALL-UNNAMED -jar WebAPI.jar"]

README.md

@@ -36,6 +36,26 @@ mvn clean package -DskipTests -Dpackaging.type=jar
 java -jar target/WebAPI.jar --spring.profiles.active=webapi-postgresql
 ```
 
+## Database configuration (single source of truth)
+
+Set your datasource and schema once; the packaged properties reuse the shared schema key.
+
+Minimal local run example (PostgreSQL):
+
+```bash
+export WEBAPI_SCHEMA=webapi   # optional; defaults to webapi
+export SPRING_DATASOURCE_URL=jdbc:postgresql://localhost:5432/postgres
+export SPRING_DATASOURCE_USERNAME=postgres
+export SPRING_DATASOURCE_PASSWORD=your_password
+
+java -jar target/WebAPI.jar \
+	--spring.profiles.active=webapi-postgresql \
+	--datasource.ohdsi.schema=${WEBAPI_SCHEMA:-webapi}
+```
+
+Notes:
+- Batch uses a table prefix and the security datasource can be overridden if you choose a separate connection, but both are optional when you keep everything on the main datasource/schema.
+
 ## SAML Auth support
 
 The following parameters are used: