Fix NullPointerException in Mesquite headless initialization during NEXUS file upload

[Copilot]

NEXUS file uploads failed with NPE because Mesquite's HelpSearchManager.makeWindow() creates windows with null ownerModule in headless mode, and the Docker containers had an empty /usr/local/mesquite directory missing the required library files (including Apple API stubs).

Changes

Docker Configuration

• Dockerfile: Copy treebase-core/lib to /usr/local/mesquite in runtime image
• Dockerfile.dev: Updated to copy Mesquite library via entrypoint
• docker/entrypoint-dev.sh: Add Mesquite library copy step at container startup

MesquiteConverter.java

• Extract initialization into initializeMesquiteHeadless() to eliminate duplication
• Set both headless and suppressAllWindows flags before init
• Catch specific exceptions (NullPointerException, RuntimeException) instead of broad Exception
• Allow graceful continuation if mesquiteTrunk is available despite init exceptions

private static void initializeMesquiteHeadless(String[] args) {
    MesquiteWindow.headless = true;
    MesquiteWindow.suppressAllWindows = true;
    
    try {
        Mesquite.main(args);
        setInitMesquite(true);
    } catch (NullPointerException | RuntimeException e) {
        handleMesquiteInitException(e);
    }
}

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 {
        throw new RuntimeException("Failed to initialize Mesquite for NEXUS parsing", e);
    }
}

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• getahead.org
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index17026993226710648279.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java vent/FocusEvent.class p/bin/grep com/apple pperCase.class grep grep -l com/apple r.class cal/bin/grep com/apple axon.class rgo/bin/grep grep (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

I try to upload a nexus file, and:

treebase-web-dev | java.lang.NullPointerException: Cannot invoke "mesquite.lib.MesquiteModule.getProject()" because "ownerModule" is null
treebase-web-dev | at mesquite.lib.MesquiteWindow.(MesquiteWindow.java:128)
treebase-web-dev | at mesquite.lib.MesquiteHTMLWindow.(MesquiteHTMLWindow.java:39)
treebase-web-dev | at mesquite.lib.MesquiteHTMLWindow.(MesquiteHTMLWindow.java:36)
treebase-web-dev | at mesquite.lib.HSWindow.(HelpSearchManager.java:1068)
treebase-web-dev | at mesquite.lib.HelpSearchManager.makeWindow(HelpSearchManager.java:44)
treebase-web-dev | at mesquite.Mesquite.init(Mesquite.java:468)
treebase-web-dev | at mesquite.Mesquite.(Mesquite.java:2033)
treebase-web-dev | at mesquite.Mesquite.main(Mesquite.java:2088)
treebase-web-dev | at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:238)
treebase-web-dev | at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:179)
treebase-web-dev | at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:680)
treebase-web-dev | at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:604)
treebase-web-dev | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
treebase-web-dev | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
treebase-web-dev | at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
treebase-web-dev | at java.base/java.lang.reflect.Method.invoke(Method.java:569)
treebase-web-dev | at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
treebase-web-dev | at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
treebase-web-dev | at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
treebase-web-dev | at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
treebase-web-dev | at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388)
treebase-web-dev | at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
treebase-web-dev | at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
treebase-web-dev | at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:241)
treebase-web-dev | at jdk.proxy3/jdk.proxy3.$Proxy141.addNexusFilesJDBC(Unknown Source)
treebase-web-dev | at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:219)
treebase-web-dev | at org.cipres.treebase.web.compat.CancellableFormController.processFormSubmission(CancellableFormController.java:209)
treebase-web-dev | at org.cipres.treebase.web.compat.CancellableFormController.handleRequestInternal(CancellableFormController.java:112)
treebase-web-dev | at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:177)
treebase-web-dev | at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:51)
treebase-web-dev | at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1072)
treebase-web-dev | at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:965)
treebase-web-dev | at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
treebase-web-dev | at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)
treebase-web-dev | at javax.servlet.http.HttpServlet.service(HttpServlet.java:555)
treebase-web-dev | at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
treebase-web-dev | at javax.servlet.http.HttpServlet.service(HttpServlet.java:623)
treebase-web-dev | at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:197)
treebase-web-dev | at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142)
treebase-web-dev | at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
treebase-web-dev | at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:166)
treebase-web-dev | at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142)
treebase-web-de...

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