add jar build

.github/workflows/ci.yaml

@@ -4,9 +4,9 @@ name: CI
 # Run in master and dev branches and in all pull requests to those branches
 on:
   push:
-    branches: [ master ]
+    branches: [ master, webapi-3.0 ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, webapi-3.0 ]
 
 env:
   DOCKER_IMAGE: ohdsi/webapi
@@ -82,14 +82,14 @@ jobs:
         id: build_params
         run: |
           echo "::set-output name=sha8::${GITHUB_SHA::8}"
-          if [ ${{ github.event_name == 'pull_request' }} ]; then
-            echo "::set-output name=push::false"
-            echo "::set-output name=load::true"
-            echo "::set-output name=platforms::linux/amd64"
-          else
+          if [ "${{ 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"
+          else
+            echo "::set-output name=push::false"
+            echo "::set-output name=load::true"
+            echo "::set-output name=platforms::linux/amd64"
           fi
 
       - name: Login to DockerHub

.github/workflows/release.yaml

@@ -36,14 +36,17 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-maven-
 
-      - name: Build code
+      - name: Build JAR
         run: mvn -B -DskipTests=true -DskipUnitTests=true -P${{ env.MAVEN_PROFILE }} package
 
-      # Upload it to GitHub
+      - name: Build WAR
+        run: mvn -B -DskipTests=true -DskipUnitTests=true -P${{ env.MAVEN_PROFILE }},war package
+
+      # Upload both JAR and WAR to GitHub release
       - name: Upload to GitHub
         uses: AButler/upload-release-assets@v2.0
         with:
-          files: 'target/WebAPI.war'
+          files: 'target/WebAPI.jar;target/WebAPI.war'
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
   # Build and push tagged release docker image to

Dockerfile

@@ -12,6 +12,7 @@ RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentat
 COPY pom.xml /code/
 RUN mkdir .git \
     && mvn package \
+     -Dpackaging.type=jar \
      -P${MAVEN_PROFILE}
 
 ARG GIT_BRANCH=unknown
@@ -20,24 +21,18 @@ ARG GIT_COMMIT_ID_ABBREV=unknown
 # Compile code and repackage it
 COPY src /code/src
 RUN mvn package ${MAVEN_PARAMS} \
+    -Dpackaging.type=jar \
     -Dgit.branch=${GIT_BRANCH} \
     -Dgit.commit.id.abbrev=${GIT_COMMIT_ID_ABBREV} \
-    -P${MAVEN_PROFILE} \
-    && mkdir war \
-    && mv target/WebAPI.war war \
-    && cd war \
-    && jar -xf WebAPI.war \
-    && rm WebAPI.war
+    -P${MAVEN_PROFILE}
 
-# OHDSI WebAPI and ATLAS web application running as a Spring Boot application with Java 21
+# 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
 
 # Any Java options to pass along, e.g. memory, garbage collection, etc.
 ENV JAVA_OPTS=""
-# Additional classpath parameters to pass along. If provided, start with colon ":"
-ENV CLASSPATH=""
 # Default Java options. The first entry is a fix for when java reads secure random numbers:
 # in a containerized system using /dev/random may reduce entropy too much, causing slowdowns.
 # https://ruleoftech.com/2016/avoiding-jvm-delays-caused-by-random-number-generation
@@ -47,21 +42,13 @@ ENV DEFAULT_JAVA_OPTS="-Djava.security.egd=file:///dev/./urandom"
 WORKDIR /var/lib/ohdsi/webapi
 
 COPY --from=builder /code/opentelemetry-javaagent.jar .
-
-# deploy the just built OHDSI WebAPI war file
-# copy resources in order of fewest changes to most changes.
-# This way, the libraries step is not duplicated if the dependencies
-# do not change.
-COPY --from=builder /code/war/WEB-INF/lib*/* WEB-INF/lib/
-COPY --from=builder /code/war/org org
-COPY --from=builder /code/war/WEB-INF/classes WEB-INF/classes
-COPY --from=builder /code/war/META-INF META-INF
+COPY --from=builder /code/target/WebAPI.jar .
 
 EXPOSE 8080
 
 USER 101
 
-# Directly run the code as a WAR.
+# Run the executable JAR
 CMD exec java ${DEFAULT_JAVA_OPTS} ${JAVA_OPTS} \
-    -cp ".:WebAPI.jar:WEB-INF/lib/*.jar${CLASSPATH}" \
-    org.springframework.boot.loader.WarLauncher
+    --add-opens java.naming/com.sun.jndi.ldap=ALL-UNNAMED \
+    -jar WebAPI.jar

README.md

@@ -24,6 +24,18 @@ The API Documentation is found at [http://webapidoc.ohdsi.org/](http://webapidoc
 
 Documentation can be found a the [Web API Installation Guide](https://github.com/OHDSI/WebAPI/wiki) which covers the system requirements and installation instructions.
 
+## JAR Build (Executable)
+
+WebAPI can also be built as a self-contained executable JAR with embedded Tomcat:
+
+```bash
+# Build as JAR
+mvn clean package -DskipTests -Dpackaging.type=jar
+
+# Run
+java -jar target/WebAPI.jar --spring.profiles.active=webapi-postgresql
+```
+
 ## SAML Auth support
 
 The following parameters are used:
@@ -82,20 +94,20 @@ It was chosen to use embedded PG instead of H2 for unit tests since H2 doesn't s
 
 To start the application locally, the following quick steps (all commands are executed from repository root directory)
 
-1. Ensure that you have the following tools installed: Java 1.8, maven (check via `mvn -v`), docker-ce (check via `docker -v`), psql command line client 
+1. Ensure that you have the following tools installed: Java 1.8, maven (check via `mvn -v`), docker-ce (check via `docker -v`), psql command line client
 (check via psql --version) or other tool that allows to connect to postgres DB.
 2. Run `mvn clean install` and make sure it completes successfully, resolve dependency issues if any.
 3. Create a new database in docker: `docker create --name postgres-webapi -p 8432:5432 -e POSTGRES_PASSWORD=ohdsi postgres:15.0-alpine`.
 4. Start DB container: `docker start postgres-webapi`.
 	 Verify that you can connect via psql console (`PGPASSWORD='ohdsi' psql -d postgresql://localhost:8432/?user=postgres`).
-5. If your default java version is too high (e.g. 17), set JAVA_HOME to point to 1.8 installaction, for example `export JAVA_HOME=/usr/lib/jvm/zulu8-ca-amd64` 
+5. If your default java version is too high (e.g. 17), set JAVA_HOME to point to 1.8 installaction, for example `export JAVA_HOME=/usr/lib/jvm/zulu8-ca-amd64`
 6. Start WebAPI `mvn clean install spring-boot:run -Dmaven.test.skip=true -P webapi-postgresql -s src/dev/settings.xml -f pom.xml`
 7. Log in with the username of your liking
 8. Grant this newly created user admin privileges by running the following sql `INSERT INTO sec_user_role (user_id, role_id, origin) VALUES (1000, 2, 'SYSTEM');`
    and log in again.
 
-At this point you have the application running and admin account operational. To actually use it, additional steps are required to set up privileges 
-and at least one CDM database. They are covered in the respective documentation sections. 
-	 
+At this point you have the application running and admin account operational. To actually use it, additional steps are required to set up privileges
+and at least one CDM database. They are covered in the respective documentation sections.
+
 ## License
-OHDSI WebAPI is licensed under Apache License 2.0
+OHDSI WebAPI is licensed under Apache License 2.0

pom.xml

@@ -5,10 +5,11 @@
 
   <groupId>org.ohdsi</groupId>
   <artifactId>WebAPI</artifactId>
-  <packaging>war</packaging>
+  <packaging>${packaging.type}</packaging>
   <version>3.0.0-SNAPSHOT</version>
   <name>WebAPI</name>
   <properties>
+    <packaging.type>war</packaging.type>
     <build.number>${BUILD_NUMBER}</build.number>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <!-- Spring Boot manages spring.version as well -->
@@ -416,7 +417,6 @@
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-maven-plugin</artifactId>
         <version>${spring.boot.version}</version>
-        <!-- executable-war via 'java -jar WebAPI-exec.war' currently fails with Jersey FileNotFound exception. TODO -->
         <configuration>
           <!-- Since we filter properties files via Maven, do not add resources. -->
           <addResources>false</addResources>
@@ -476,15 +476,6 @@
           </compilerArgs>
         </configuration>
       </plugin>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-war-plugin</artifactId>
-        <version>3.4.0</version>
-        <configuration>
-          <failOnMissingWebXml>false</failOnMissingWebXml>
-          <attachClasses>true</attachClasses>
-        </configuration>
-      </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-failsafe-plugin</artifactId>
@@ -689,16 +680,14 @@
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-tomcat</artifactId>
-      <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-batch</artifactId>
     </dependency>
 
-    <!-- We are intentionally overriding the Tomcat version from Spring Boot 1.5.22.RELEASE -->
-    <!-- and assuming tomcat-jdbc.jar will be in the Tomcat installation folder (\apache-tomcat-8.5.xxx\lib). -->
-    <!-- WebAPI.war.original should not contain overridden libraries -->
+    <!-- Embedded Tomcat dependencies for executable JAR -->
+    <!-- Note: WAR packaging is available via 'mvn package -Pwar' profile -->
     <dependency>
       <groupId>org.apache.tomcat.embed</groupId>
       <artifactId>tomcat-embed-el</artifactId>
@@ -711,7 +700,6 @@
     <dependency>
       <groupId>org.apache.tomcat</groupId>
       <artifactId>tomcat-jdbc</artifactId>
-      <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.apache.tomcat</groupId>
@@ -779,12 +767,15 @@
         </exclusion>
       </exclusions>
     </dependency> -->
+    <!-- javax.servlet-api is now provided by spring-boot-starter-tomcat (Jakarta Servlet API) -->
+    <!-- This old javax.servlet dependency can be removed for JAR packaging -->
+    <!--
     <dependency>
       <groupId>javax.servlet</groupId>
       <artifactId>javax.servlet-api</artifactId>
       <version>3.1.0</version>
-      <scope>provided</scope>
     </dependency>
+    -->
     <dependency>
       <groupId>javax.cache</groupId>
       <artifactId>cache-api</artifactId>
@@ -1902,5 +1893,49 @@
         </dependency>
       </dependencies>
     </profile>
+
+    <!-- WAR packaging profile - use with: mvn package -Pwar -->
+    <profile>
+      <id>war</id>
+      <properties>
+        <packaging.type>war</packaging.type>
+      </properties>
+      <dependencies>
+        <!-- Mark embedded Tomcat as provided for external servlet container deployment -->
+        <dependency>
+          <groupId>org.springframework.boot</groupId>
+          <artifactId>spring-boot-starter-tomcat</artifactId>
+          <scope>provided</scope>
+        </dependency>
+        <dependency>
+          <groupId>org.apache.tomcat</groupId>
+          <artifactId>tomcat-jdbc</artifactId>
+          <scope>provided</scope>
+        </dependency>
+      </dependencies>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-war-plugin</artifactId>
+            <version>3.4.0</version>
+            <executions>
+              <execution>
+                <id>build-war</id>
+                <phase>package</phase>
+                <goals>
+                  <goal>war</goal>
+                </goals>
+                <configuration>
+                  <failOnMissingWebXml>false</failOnMissingWebXml>
+                  <attachClasses>true</attachClasses>
+                  <warName>WebAPI</warName>
+                </configuration>
+              </execution>
+            </executions>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
   </profiles>
 </project>

src/main/java/org/ohdsi/webapi/WebApi.java

@@ -1,12 +1,12 @@
 package org.ohdsi.webapi;
 
 import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
+import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration;
-import org.springframework.boot.autoconfigure.web.servlet.error.ErrorMvcAutoConfiguration;
 import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
-import org.springframework.context.annotation.ComponentScan;
+import org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration;
+import org.springframework.boot.autoconfigure.web.servlet.error.ErrorMvcAutoConfiguration;
 import org.springframework.context.annotation.EnableAspectJAutoProxy;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
@@ -15,25 +15,26 @@
 
 
 /**
- * Launch as java application or deploy as WAR (@link {@link WebApplication}
- * will source this file).
+ * OHDSI WebAPI Spring Boot Application
+ *
+ * Supports both JAR and WAR deployment:
+ * - JAR: java -jar WebAPI.jar (embedded Tomcat)
+ * - WAR: Deploy to external servlet container (mvn package -Pwar)
  */
 @EnableScheduling
 @SpringBootApplication(exclude={HibernateJpaAutoConfiguration.class, ErrorMvcAutoConfiguration.class})
 @EnableAspectJAutoProxy(proxyTargetClass = true)
 public class WebApi extends SpringBootServletInitializer {
 
-
-
     @Override
-    protected SpringApplicationBuilder configure(final SpringApplicationBuilder application) {
-        return application.sources(WebApi.class);
+    protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
+        return builder.sources(WebApi.class);
     }
 
     public static void main(final String[] args) throws Exception
     {
         TomcatURLStreamHandlerFactory.disable();
-        new SpringApplicationBuilder(WebApi.class).run(args);
+        SpringApplication.run(WebApi.class, args);
     }
 
     @PostConstruct