Fix NullPointerException in Mesquite headless initialization during NEXUS file upload

Dockerfile

@@ -16,6 +16,7 @@ RUN mvn dependency:go-offline -B || true
 
 # Copy source code
 COPY treebase-core/src treebase-core/src
+COPY treebase-core/lib treebase-core/lib
 COPY treebase-web/src treebase-web/src
 COPY treebase-web/lib treebase-web/lib
 COPY oai-pmh_data_provider oai-pmh_data_provider
@@ -45,8 +46,13 @@ COPY --from=builder /build/treebase-web/target/treebase-web.war /usr/local/tomca
 RUN curl -o /usr/local/tomcat/lib/postgresql.jar \
     https://jdbc.postgresql.org/download/postgresql-42.7.7.jar
 
-# Create a directory for Mesquite (placeholder)
-RUN mkdir -p /usr/local/mesquite
+# Create a directory for Mesquite and copy the headless Mesquite library
+# The treebase-core/lib folder contains the headless Mesquite distribution with:
+# - mesquite/ - Mesquite core classes
+# - headless/ - Headless AWT implementation
+# - com/apple/ - Apple API stubs (required by Mesquite even on non-Mac platforms)
+# - Other supporting libraries
+COPY --from=builder /build/treebase-core/lib /usr/local/mesquite
 
 # Set environment variables for Tomcat
 # Java 17 compatibility flags based on GitHub Actions workflow

Dockerfile.dev

@@ -19,6 +19,8 @@ RUN curl -o /usr/local/tomcat/lib/postgresql.jar \
     https://jdbc.postgresql.org/download/postgresql-42.7.7.jar
 
 # Create Mesquite directory placeholder
+# Note: In development mode, the entrypoint script will copy
+# the Mesquite library from the mounted /app/treebase-core/lib
 RUN mkdir -p /usr/local/mesquite
 
 # Set up environment variables

docker/entrypoint-dev.sh

@@ -81,6 +81,21 @@ if [ -d "WEB-INF/dtd" ]; then
   ls -la /tmp/dtd/
 fi
 
+# Copy Mesquite library files from the mounted source directory
+# The treebase-core/lib folder contains the headless Mesquite distribution with:
+# - mesquite/ - Mesquite core classes
+# - headless/ - Headless AWT implementation  
+# - com/apple/ - Apple API stubs (required by Mesquite even on non-Mac platforms)
+# - Other supporting libraries
+if [ -d "/app/treebase-core/lib" ]; then
+  echo "Copying Mesquite library to /usr/local/mesquite..."
+  cp -r /app/treebase-core/lib/* /usr/local/mesquite/
+  echo "Mesquite library installed."
+else
+  echo "WARNING: Mesquite library not found at /app/treebase-core/lib"
+  echo "Nexus file parsing may not work correctly."
+fi
+
 echo "Setup complete! Starting Tomcat..."
 echo "========================================"
 echo "JSP files are mounted from: ./treebase-web/src/main/webapp"

treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java

@@ -185,6 +185,48 @@ private void setCurrentTreeTaxa(Taxa pNewCurrentTreeTaxa) {
 		mCurrentTreeTaxa = pNewCurrentTreeTaxa;
 	}
 
+	/**
+	 * Initialize Mesquite in headless mode. This method sets the necessary flags
+	 * and handles exceptions that may occur during initialization.
+	 * 
+	 * @param args Command line arguments to pass to Mesquite.main()
+	 * @throws RuntimeException if Mesquite fails to initialize and mesquiteTrunk is null
+	 */
+	private static void initializeMesquiteHeadless(String[] args) {
+		// Set headless mode before initializing Mesquite to prevent GUI window creation
+		// Also set suppressAllWindows to skip all window operations
+		MesquiteWindow.headless = true;
+		MesquiteWindow.suppressAllWindows = true;
+
+		try {
+			Mesquite.main(args);
+			setInitMesquite(true);
+			LOGGER.info("Mesquite initialization completed successfully");
+		} catch (NullPointerException e) {
+			// NPE may occur during headless initialization when window creation fails
+			// Check if mesquiteTrunk was still initialized despite the exception
+			handleMesquiteInitException(e);
+		} catch (RuntimeException e) {
+			// RuntimeException (including HeadlessException) may occur during initialization
+			handleMesquiteInitException(e);
+		}
+	}
+
+	/**
+	 * Handle exceptions during Mesquite initialization.
+	 * If mesquiteTrunk is available, log warning and continue.
+	 * If mesquiteTrunk is null, throw RuntimeException.
+	 */
+	private static void handleMesquiteInitException(Exception e) {
+		if (MesquiteTrunk.mesquiteTrunk != null) {
+			LOGGER.warn("Mesquite initialization threw exception but trunk is available: " + e.getMessage());
+			setInitMesquite(true);
+		} else {
+			LOGGER.error("Mesquite initialization failed: " + e.getMessage(), e);
+			throw new RuntimeException("Failed to initialize Mesquite for NEXUS parsing", e);
+		}
+	}
+
 	/**
 	 * 
 	 * @see org.cipres.treebase.domain.nexus.NexusParserConverter#processLoadFile(java.util.Collection,
@@ -200,10 +242,7 @@ public void processLoadFile(
 
 		synchronized (MesquiteConverter.class) {
 			if (!isInitMesquite()) {
-				// Set headless mode before initializing Mesquite to prevent GUI window creation
-				MesquiteWindow.headless = true;
-				Mesquite.main(new String[] {"-w"});
-				setInitMesquite(true);
+				initializeMesquiteHeadless(new String[] {"-w"});
 			}
 		}
 
@@ -233,10 +272,7 @@ public void parseOneFile(File pFile, Study pStudy, NexusDataSet pDataSet) {
 		// make sure no two calls can fight each other:
 		synchronized (MesquiteConverter.class) {
 			if (!isInitMesquite()) {
-				// Set headless mode before initializing Mesquite to prevent GUI window creation
-				MesquiteWindow.headless = true;
-				Mesquite.main(new String[] {"-w", "-b"});
-				setInitMesquite(true);
+				initializeMesquiteHeadless(new String[] {"-w", "-b"});
 			}
 		}