在 tomcat 9 中设置 xnat webapp 时出错

Question

我已按照xnat网站上的在线文档（https://wiki.xnat.org/documentation/getting-started-with-xnat/xnat-i ​​nstallation-guide）并安装了apache tomcat 9（版本9.0.75，JVM版本） ：1.8.0_372_b07，JVM 供应商：Temurin）。但是当我在 xnat web 应用程序上单击“开始”时，出现错误：

FAIL - Application at context path [/xnat-web-1.8.8] could not be started
FAIL - Encountered exception [org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@35a50a4c]]

日志文件显示以下内容（被截断以允许在此处发布）：

... org.apache.catalina.core.ApplicationContext.log HTMLManager: Error starting [/xnat-web-1.8.8]
        org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@6dde5c8c]
                at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:440)
              
...
...
...
                at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
                at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
                at java.lang.Thread.run(Thread.java:750)
        Caused by: java.lang.NullPointerException
                at java.lang.String.startsWith(String.java:1405)
                at java.lang.String.startsWith(String.java:1434)
                at org.apache.catalina.webresources.AbstractFileResourceSet.file(AbstractFileResourceSet.java:98)
                at org.apache.catalina.webresources.DirResourceSet.getResource(DirResourceSet.java:94)
                at org.apache.catalina.webresources.StandardRoot.getResourceInternal(StandardRoot.java:272)
                at org.apache.catalina.webresources.Cache.getResource(Cache.java:64)
                at org.apache.catalina.webresources.StandardRoot.getResource(StandardRoot.java:211)
                at org.apache.catalina.webresources.StandardRoot.listResources(StandardRoot.java:347)
                at org.apache.catalina.webresources.StandardRoot.processWebInfLib(StandardRoot.java:585)
                at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:722)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

根据 ChatGPT 的说法：

Based on the provided log file, it appears that there is an error during the deployment of the web application '/xnat-web-1.8.8' in Tomcat. The error message indicates a NullPointerException and a LifecycleException related to the StandardRoot component.

The root cause of the issue seems to be the NullPointerException occurring within the AbstractFileResourceSet class. It specifically fails when attempting to access a file resource, likely due to a missing or invalid file path.

我想知道问题是否出在单元文件中或 postgresql 配置（TCP/IP 连接）设置中。我只在本地主机上使用 tomcat。在我的 pg_hba.conf 文件中，我刚刚添加了这一行listen_addresses = '*' 如果您查看下面的单元文件，我已为其提供了多个文件夹以供读写。Tomcat 默认使用 /opt/tomcat。但 xnat 文档设置表明我使用 /var/lib/tomcat、/var/log/tomcat 和 /etc/tomcat/Catalina 作为 ReadWritePaths。我刚刚在我的单元文件中添加了所有这些以及我的安装默认路径。我想知道这是否是错误所在。我的 tomcat 单元文件是：

[Unit]
Description=Apache Tomcat Web Application Container
After=network.target
[Service]
Type=forking
User=xnat
Group=xnat
PrivateTmp=yes
Environment="JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-amd64"
Environment="JAVA_OPTS=-Djava.security.egd=file:///dev/urandom -Djava.awt.headless=true"
Environment="CATALINA_BASE=/opt/tomcat"
Environment="CATALINA_HOME=/opt/tomcat"
Environment="CATALINA_PID=/opt/tomcat/temp/tomcat.pid"
Environment="CATALINA_OPTS="-Xms512M -Xmx1024M -server -XX:+UseParallelGC -Dxnat.home=/data/xnat/home"
ExecStart=/opt/tomcat/bin/startup.sh
ExecStop=/opt/tomcat/bin/shutdown.sh
#AmbientCapabilities=CAP_NET_BIND_SERVICE
NoNewPrivileges=true
CacheDirectory=tomcat
CacheDirectoryMode=750
#ProtectSystem=strict
ReadWritePaths=/etc/tomcat/Catalina/
ReadWritePaths=/opt/tomcat/webapps/
ReadWritePaths=/var/lib/tomcat/webapps/
ReadWritePaths=/opt/log/tomcat/
ReadWritePaths=/var/log/tomcat/
ReadWritePaths=/data/xnat/home
ReadWritePaths=/home/xnat/
[Install]
WantedBy=multi-user.target

/opt/tomcat/webapps/xnat-1.8.8/META-INF 下的 context.xml 文件为：

xml version="1.0" encoding="utf-8"?>
<!--
  ~ web: context.xml
  ~ XNAT http://www.xnat.org
  ~ Copyright (c) 2005-2021, Washington University School of Medicine and Howard Hughes Medical Institute
  ~ All Rights Reserved
  ~
  ~ Released under the Simplified BSD.
  -->

<Context>
    <!--
    For Tomcat 7 compatibility, uncomment the <Loader> element and comment out the <Resources>
    and <CookieProcessor> elements under that.
    -->
    <!-- Loader className="org.apache.catalina.loader.VirtualWebappLoader" searchVirtualFirst="true" virtualClasspath="${xnat.home}/plugins/*.jar"/ -->

    <!--
    For Tomcat 8 compatibility, uncomment the <Resources> and <CookieProcessor> elements below and
    comment out the <Loader> element below that.
    -->
    <Resources>
        <PreResources className="org.apache.catalina.webresources.DirResourceSet" base="${xnat.home}/plugins" webAppMount="/WEB-INF/lib" />
    </Resources>
    <CookieProcessor className="org.apache.tomcat.util.http.LegacyCookieProcessor" />
    <JarScanner scanAllDirectories="true" />
    <Parameter name="xnatHome" value="${xnat.home}"/>
    <Manager pathname="" />
</Context>

此后我也尝试通过 vagrant 和 docker 部署 xnat，但没有成功。我将非常感谢您能给我的任何帮助。

Answer 1

在我看来，问题与 Tomcat 无法正确处理文件中定义的应用程序资源有关context.xml：

<Resources>
  <PreResources className="org.apache.catalina.webresources.DirResourceSet" base="${xnat.home}/plugins" webAppMount="/WEB-INF/lib" />
</Resources>

其原因很可能是${xnat.home}占位符未成功解析，可能是因为未正确定义同名的系统属性。

您在定义环境变量时尝试在单元文件中定义该系统属性CATALINA_OPTS：

Environment="CATALINA_OPTS="-Xms512M -Xmx1024M -server -XX:+UseParallelGC -Dxnat.home=/data/xnat/home"

请注意，它的定义不正确，请注意"后面的CATALINA_OPTS=。

它应该是：

Environment="CATALINA_OPTS=-Xms512M -Xmx1024M -server -XX:+UseParallelGC -Dxnat.home=/data/xnat/home"

这可能是一个错字，但也可以解释问题。