Extract trexsql

.gitignore

@@ -20,6 +20,7 @@ specs/
 docs
 .claude
 *.bak
+**/test-results/
 logs
 
 ### Developer's personal properties ###

Dockerfile

@@ -2,7 +2,6 @@ FROM maven:3.9-eclipse-temurin-21 AS builder
 
 WORKDIR /code
 
-ARG MAVEN_PROFILE=trexsql
 ARG MAVEN_PARAMS="" # can use maven options, e.g. -DskipTests=true -DskipUnitTests=true
 
 ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0
@@ -17,8 +16,7 @@ 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}
+    -Dgit.commit.id.abbrev=${GIT_COMMIT_ID_ABBREV}
 
 # OHDSI WebAPI running as a Spring Boot executable JAR with Java 21
 FROM index.docker.io/library/eclipse-temurin:21-jre
@@ -40,11 +38,23 @@ 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 2>/dev/null && \
-    unzip -j /tmp/trexsql-ext-*.jar 'libtrexsql_java.so_linux_amd64' -d /tmp/trexsql 2>/dev/null && \
-    mv /tmp/trexsql/libtrexsql_java.so_linux_amd64 /tmp/trexsql/libtrexsql_java.so 2>/dev/null && \
-    rm -f /tmp/trexsql-ext-*.jar || true)
+# Plugin setup: download trexsql plugin JAR
+ARG TREXSQL_VERSION=0.2.0
+RUN mkdir -p /opt/webapi/plugins && \
+    if curl -fL -o /opt/webapi/plugins/trexsql.jar \
+      "https://github.com/OHDSI/trex/releases/download/v${TREXSQL_VERSION}/trexsql-${TREXSQL_VERSION}.jar"; then \
+      echo "Downloaded trexsql plugin v${TREXSQL_VERSION}"; \
+    else \
+      echo "WARNING: Failed to download trexsql plugin v${TREXSQL_VERSION}, trexsql will be unavailable"; \
+    fi
+
+# Download native libtrexsql.so (JNA resolves it from linux-x86-64/ on the plugin classpath)
+ARG LIBTREXSQL_VERSION=v1.4.4-trex
+RUN mkdir -p /opt/webapi/plugins/linux-x86-64 && \
+    curl -fL -o /tmp/libtrexsql.zip \
+      "https://github.com/p-hoffmann/trexsql-rs/releases/download/${LIBTREXSQL_VERSION}/libtrexsql-linux-amd64.zip" && \
+    unzip -j /tmp/libtrexsql.zip 'libtrexsql.so' -d /opt/webapi/plugins/linux-x86-64/ && \
+    rm /tmp/libtrexsql.zip
 
 # Create logs directory for logback before switching to non-root user
 RUN mkdir -p logs && chown 101:101 logs
@@ -53,5 +63,4 @@ EXPOSE 8080
 
 USER 101
 
-# 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"]
+CMD ["sh", "-c", "exec java ${DEFAULT_JAVA_OPTS} ${JAVA_OPTS} -Dloader.path=/opt/webapi/plugins --add-opens java.naming/com.sun.jndi.ldap=ALL-UNNAMED -jar WebAPI.jar"]

docker/auth-test/run-tests.sh

@@ -60,7 +60,7 @@ fi
 if [ "$BUILD_WEBAPI" = true ]; then
     log_info "Building WebAPI..."
     cd ../..
-    mvn clean package -DskipTests -Dpackaging.type=jar -P webapi-postgresql,trexsql -B
+    mvn clean package -DskipTests -Dpackaging.type=jar -P webapi-postgresql -B
     cd "$SCRIPT_DIR"
 fi
 

docker/integration-test/run-tests.sh

@@ -45,7 +45,7 @@ fi
 if [ "$BUILD_WEBAPI" = true ]; then
     log_info "Building WebAPI..."
     cd ../..
-    mvn clean package -DskipTests -Dpackaging.type=jar -P webapi-postgresql,trexsql -B
+    mvn clean package -DskipTests -Dpackaging.type=jar -P webapi-postgresql -B
     cd "$SCRIPT_DIR"
 fi
 

pom.xml

@@ -126,6 +126,7 @@
         <artifactId>spring-boot-maven-plugin</artifactId>
         <version>${spring.boot.version}</version>
         <configuration>
+          <layout>ZIP</layout>
           <addResources>false</addResources>
           <includeSystemScope>false</includeSystemScope>
           <mainClass>org.ohdsi.webapi.WebApi</mainClass>
@@ -180,10 +181,6 @@
             <!-- Preserve parameter names for reflection (required for AspectJ parameter resolution) -->
             <arg>-parameters</arg>
           </compilerArgs>
-          <!-- Exclude TrexSQL sources by default (included when -Ptcache is active) -->
-          <excludes>
-            <exclude>**/trexsql/**</exclude>
-          </excludes>
         </configuration>
       </plugin>
       <plugin>
@@ -775,38 +772,6 @@
   </dependencies>
 
   <profiles>
-    <profile>
-      <id>trexsql</id>
-      <properties>
-        <trexsql.enabled>true</trexsql.enabled>
-      </properties>
-      <dependencies>
-        <dependency>
-          <groupId>com.github.p-hoffmann</groupId>
-          <artifactId>trexsql-ext</artifactId>
-          <version>v0.1.23</version>
-        </dependency>
-      </dependencies>
-      <build>
-        <plugins>
-          <plugin>
-            <groupId>org.apache.maven.plugins</groupId>
-            <artifactId>maven-compiler-plugin</artifactId>
-            <configuration>
-              <!-- Include TrexSQL sources when tcache profile is active -->
-              <excludes combine.self="override"/>
-            </configuration>
-          </plugin>
-          <plugin>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-maven-plugin</artifactId>
-            <configuration>
-              <includeSystemScope>true</includeSystemScope>
-            </configuration>
-          </plugin>
-        </plugins>
-      </build>
-    </profile>
     <profile>
       <id>webapi-oracle</id>
       <dependencies>

src/main/java/org/ohdsi/webapi/plugins/PluginsConfigurationInfo.java

@@ -4,11 +4,24 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Collections;
+import java.util.List;
+
 @Component
 public class PluginsConfigurationInfo extends ConfigurationInfo {
     private static final String KEY = "plugins";
 
-    public PluginsConfigurationInfo(@Value("${atlasgis.enabled}") Boolean atlasgisEnabled) {
+    public PluginsConfigurationInfo(
+            @Autowired(required = false) List<WebApiPlugin> plugins,
+            @Value("${atlasgis.enabled}") Boolean atlasgisEnabled) {
+        if (plugins == null) {
+            plugins = Collections.emptyList();
+        }
+        for (WebApiPlugin plugin : plugins) {
+            properties.put(plugin.getId() + "Enabled", plugin.isActive());
+        }
         properties.put("atlasgisEnabled", atlasgisEnabled);
     }
 

src/main/java/org/ohdsi/webapi/plugins/WebApiPlugin.java

@@ -0,0 +1,8 @@
+package org.ohdsi.webapi.plugins;
+
+public interface WebApiPlugin {
+    String getId();
+    String getName();
+    String getVersion();
+    boolean isActive();
+}