Tomcat hangs when setting up xnat 1.7.5.3

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Verdi Vanreusel

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May 20, 2019, 1:52:21 PM5/20/19
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Dear xnat experts,

I am trying to install xnat 1.7.5.3 on a CentOS 7.6. First I installed Tomcat7 using yum and I got the "NulPointerException".
I found here (https://groups.google.com/forum/#!msg/xnat_discussion/nw7g5tjhDTo/uUcdTuCrAQAJ) that this is because the version  of tomcat provided by CentOS, being 7.0.76, is not compatible with xnat 1.7.5.3, a tomcat version of at least 7.0.80 is required.
So I removed tomcat and reinstalled the latest version (tomcat 7.0.94) by downloading the source code.
I created the tomcat script in /etc/init.d/ that starts, stops and restarts tomcat and put the xnat-web-1.7.5.3.war file into the webapps folder.

At this point the xnat home folder is not yet set and tomcat runs fine. I can of course not start the xnat-web-1.7.5.3 application, but that seems normal to me.
Since I haven't installed tomcat with yum, there is no tomcat.conf file. I found that the "$CATALINA_OPTS" variable should in this case be defined in a setenv.sh file.
So, I got a setenv.sh file from the internet, which sets some stuff for java and added the following line:
CATALINA_OPTS="${CATALINA_OPTS} -Dxnat.home=/data/xnat/home"


If I then restart tomcat, some problems occur. If I go to \\localhost:8080, the page keeps on loading (even for multiple days).
When I try to stop tomcat again using the 'systemctl' command, I can see from the status that it stops a process with a different ID.
Restarting tomcat results in, if I understand this correctly, two tomcat instances running side by side...
This I make up from the outcome of 'systemctl -l status tomcat':

● tomcat.service - (null)
   Loaded: loaded (/etc/rc.d/init.d/tomcat; bad; vendor preset: disabled)
   Active: active (running) since ma 2019-05-20 12:34:18 CEST; 1s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 29320 ExecStop=/etc/rc.d/init.d/tomcat stop (code=exited, status=0/SUCCESS)
  Process: 29374 ExecStart=/etc/rc.d/init.d/tomcat start (code=exited, status=0/SUCCESS)
   CGroup: /system.slice/tomcat.service
           ├─29279 /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221-2.6.18.0.el7_6.x86_64//bin/java -Djava.util.logging.config.file=/usr/share/apache-tomcat-7.0.94/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xms64m -Xmx512m -XX:MaxPermSize=256m -Xss512k -XX:+UseParallelGC -XX:MaxGCPauseMillis=1500 -XX:GCTimeRatio=9 -server -XX:+DisableExplicitGC -Dxnat.home=/data/xnat/home -Dignore.endorsed.dirs= -classpath /usr/share/apache-tomcat-7.0.94/bin/bootstrap.jar:/usr/share/apache-tomcat-7.0.94/bin/tomcat-juli.jar -Dcatalina.base=/usr/share/apache-tomcat-7.0.94 -Dcatalina.home=/usr/share/apache-tomcat-7.0.94 -Djava.io.tmpdir=/usr/share/apache-tomcat-7.0.94/temp org.apache.catalina.startup.Bootstrap start
           └─29385 /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221-2.6.18.0.el7_6.x86_64//bin/java -Djava.util.logging.config.file=/usr/share/apache-tomcat-7.0.94/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xms64m -Xmx512m -XX:MaxPermSize=256m -Xss512k -XX:+UseParallelGC -XX:MaxGCPauseMillis=1500 -XX:GCTimeRatio=9 -server -XX:+DisableExplicitGC -Dxnat.home=/data/xnat/home -Dignore.endorsed.dirs= -classpath /usr/share/apache-tomcat-7.0.94/bin/bootstrap.jar:/usr/share/apache-tomcat-7.0.94/bin/tomcat-juli.jar -Dcatalina.base=/usr/share/apache-tomcat-7.0.94 -Dcatalina.home=/usr/share/apache-tomcat-7.0.94 -Djava.io.tmpdir=/usr/share/apache-tomcat-7.0.94/temp org.apache.catalina.startup.Bootstrap start


Also the log files from tomcat give no error as shown in the catalina.out:

mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.94
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Apr 10 2019 16:56:40 UTC
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.94.0
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            3.10.0-957.el7.x86_64
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221-2.6.18.0.el7_6.x86_64/jre
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_221-mockbuild_2019_04_22_15_03-b00
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /usr/share/apache-tomcat-7.0.94
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/apache-tomcat-7.0.94
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/share/apache-tomcat-7.0.94/conf/logging.properties
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms64m
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx512m
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xss512k
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseParallelGC
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxGCPauseMillis=1500
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:GCTimeRatio=9
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+DisableExplicitGC
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/share/apache-tomcat-7.0.94
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/apache-tomcat-7.0.94
mei 20, 2019 1:37:59 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/share/apache-tomcat-7.0.94/temp
mei 20, 2019 1:37:59 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
mei 20, 2019 1:38:00 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
mei 20, 2019 1:38:00 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
mei 20, 2019 1:38:00 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 985 ms
mei 20, 2019 1:38:00 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
mei 20, 2019 1:38:00 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
mei 20, 2019 1:38:00 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /usr/share/apache-tomcat-7.0.94/webapps/xnat-web-1.7.5.3.war

And log files in '/data/xnat/home/logs' are created, but remain empty...
Does anyone have an idea that I can try to make xnat work?

Thanks in avance,
Best regards
Verdi

Herrick, Rick

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May 20, 2019, 3:44:49 PM5/20/19
to xnat_di...@googlegroups.com

I’d suggest renaming the war file from xnat-web-1.7.5.3.war to either xnat.war or ROOT.war. You’ll also probably need to delete the exploded war folder, which would be in the webapps folder and named xnat-web-1.7.5.3. Tomcat takes the name of the war file and makes that the application context, i.e. the path used to access the application. If your war file is named xnat-web-1.7.5.3, then you’d access XNAT with the URL:

 

http://server/xnat-web-1.7.5.3

 

That’s a little cumbersome, so rename it to xnat.war:

 

$ mv /var/lib/tomcat/webapps/xnat-web-1.7.5.3.war /var/lib/tomcat/webapps/xnat.war

$ rm -rf  /var/lib/tomcat/webapps/xnat-web-1.7.5.3

 

That gives you:

 

http://server/xnat

 

Or rename it to ROOT.war, which is a special case:

 

$ mv /var/lib/tomcat/webapps/xnat-web-1.7.5.3.war /var/lib/tomcat/webapps/ROOT.war

$ rm -rf  /var/lib/tomcat/webapps/xnat-web-1.7.5.3

 

That gives you:

 

http://server

 

Another thing you need to check is that the same user owns all of the Tomcat folders, the various XNAT folders (/data/xnat/home, but also whatever you set for archive and other folders), AND that that user is the user that runs the Tomcat process. While I understand why you needed to configure the Tomcat service separate from the standard install under CentOS 7.6, once you do that it becomes much more difficult to figure out what’s going on because of issues like permissions, configuration, etc. Make sure you check the Tomcat logs in /var/log/tomcat as well: that’s where you’ll find info if something goes wrong at the Tomcat level, like configuration or permissions issues.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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Verdi Vanreusel

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May 23, 2019, 4:34:59 AM5/23/19
to xnat_discussion
Hi Rick,

Thanks a lot for your advise!

However, renaming the file to xnat didn't do the trick.
And as all tomcat and xnat folders are owned by the xnat user I created, that also didn't resolve the issue.
I started the tomcat process as the xnat user, but also no luck here. 

However, I found that when I kill the tomcat process, something gets written in the 'spring.log' file. 
When searching the internet, I found it had something to do with the version of java.
I then found on the tomcat website that tomcat7.0.94, which I use, runs on java 1.6 iso 1.7. 
When I installed java 1.6 and changed the JRE_HOME path, tomcat doesn't hang anymore and I can see in the web application manager that xnat is running.

When I try to browse to http://server/xnat however I get the '404-Not Found' error.
I have seen that this error has already been mentioned on this forum, so I will first look for a solution there.

Best regards,
Verdi

Op maandag 20 mei 2019 21:44:49 UTC+2 schreef Herrick, Rick:

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Herrick, Rick

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May 23, 2019, 4:55:06 PM5/23/19
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Tomcat 7 definitely does not require Java 6. In fact, in our lab we actually run almost exclusively now on Java 8. And XNAT itself uses a number of language features that aren’t in Java 6, so there’s no way that that will work. Rather than rolling back to Java 6, trying upgrading to Java 8 and giving that a try.

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Verdi Vanreusel

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May 24, 2019, 4:39:19 AM5/24/19
to xnat_discussion
Hi Rick,

I indeed wasn't able yet to get the xnat running using java 6. 
However, after the upgrade to java 8, I get the same problem as with java 7 that when I browse to http://server:8080 or http://server:8080/xnat the webpage keeps on loading and nothing happens. 

I checked some more differences between the use of java 6 and java 7/8, maybe this can give you an idea of what is going wrong.

If I use java 8 and try to stop a running tomcat session using 'service tomcat stop', I get:

Using CATALINA_OPTS:
>>  -Xms64m
>>  -Xmx512m
>>  -XX:MaxPermSize=256m
>>  -Xss512k
>>  -XX:+UseParallelGC
>>  -XX:MaxGCPauseMillis=1500
>>  -XX:GCTimeRatio=9
>>  -server
>>  -XX:+DisableExplicitGC
>>  -Dxnat.home=/data/xnat/home

Using JAVA_OPTS:
_______________________________________________

Using CATALINA_BASE:   /usr/share/apache-tomcat-7.0.94
Using CATALINA_HOME:   /usr/share/apache-tomcat-7.0.94
Using CATALINA_TMPDIR: /usr/share/apache-tomcat-7.0.94/temp
Using JRE_HOME:        /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.el7_6.x86_64/jre/
Using CLASSPATH:       /usr/share/apache-tomcat-7.0.94/bin/bootstrap.jar:/usr/share/apache-tomcat-7.0.94/bin/tomcat-juli.jar
May 24, 2019 9:39:31 AM org.apache.catalina.startup.Catalina stopServer
SEVERE: Could not contact localhost:8005. Tomcat may not be running.
May 24, 2019 9:39:31 AM org.apache.catalina.startup.Catalina stopServer
SEVERE: Catalina.stop: 
java.net.ConnectException: Connection refused (Connection refused)
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.net.Socket.connect(Socket.java:589)
        at java.net.Socket.connect(Socket.java:538)
        at java.net.Socket.<init>(Socket.java:434)
        at java.net.Socket.<init>(Socket.java:211)
        at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:511)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:343)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)



If I however use java 6, there is no exception:

Using CATALINA_OPTS:
>>  -Xms64m
>>  -Xmx512m
>>  -XX:MaxPermSize=256m
>>  -Xss512k
>>  -XX:+UseParallelGC
>>  -XX:MaxGCPauseMillis=1500
>>  -XX:GCTimeRatio=9
>>  -server
>>  -XX:+DisableExplicitGC
>>  -Dxnat.home=/data/xnat/home

Using JAVA_OPTS:
_______________________________________________

Using CATALINA_BASE:   /usr/share/apache-tomcat-7.0.94
Using CATALINA_HOME:   /usr/share/apache-tomcat-7.0.94
Using CATALINA_TMPDIR: /usr/share/apache-tomcat-7.0.94/temp
Using JRE_HOME:        /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre
Using CLASSPATH:       /usr/share/apache-tomcat-7.0.94/bin/bootstrap.jar:/usr/share/apache-tomcat-7.0.94/bin/tomcat-juli.jar


A start and stop of tomcat using java 8 results in this catalina,2019-05-24,log:

May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Apr 10 2019 16:56:40 UTC
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.94.0
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            3.10.0-957.el7.x86_64
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221-2.6.18.0.el7_6.x86_64/jre
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_221-mockbuild_2019_04_22_15_03-b00
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /usr/share/apache-tomcat-7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/apache-tomcat-7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/share/apache-tomcat-7.0.94/conf/logging.properties
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms64m
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx512m
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xss512k
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseParallelGC
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxGCPauseMillis=1500
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:GCTimeRatio=9
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+DisableExplicitGC
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/share/apache-tomcat-7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/apache-tomcat-7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/share/apache-tomcat-7.0.94/temp
May 24, 2019 10:35:36 AM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
May 24, 2019 10:35:36 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:35:36 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
May 24, 2019 10:35:36 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 985 ms
May 24, 2019 10:35:36 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
May 24, 2019 10:35:36 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
May 24, 2019 10:35:36 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /usr/share/apache-tomcat-7.0.94/webapps/xnat.war



While using java 6 we get:

May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Apr 10 2019 16:56:40 UTC
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.94.0
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            3.10.0-957.el7.x86_64
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.6.0_41-b41
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Sun Microsystems Inc.
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /usr/share/apache-tomcat-7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/apache-tomcat-7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/share/apache-tomcat-7.0.94/conf/logging.properties
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms64m
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx512m
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xss512k
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseParallelGC
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxGCPauseMillis=1500
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:GCTimeRatio=9
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+DisableExplicitGC
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/share/apache-tomcat-7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/apache-tomcat-7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/share/apache-tomcat-7.0.94/temp
May 24, 2019 10:26:44 AM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
May 24, 2019 10:26:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:26:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
May 24, 2019 10:26:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 860 ms
May 24, 2019 10:26:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
May 24, 2019 10:26:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
May 24, 2019 10:26:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /usr/share/apache-tomcat-7.0.94/webapps/xnat.war
May 24, 2019 10:26:57 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
May 24, 2019 10:26:57 AM org.apache.tomcat.websocket.server.WsSci onStartup
INFO: JSR 356 WebSocket (Java WebSocket 1.1) support is not available when running on Java 6. To suppress this message, run Tomcat on Java 7, remove the WebSocket JARs from $CATALINA_HOME/lib or add the WebSocket JARs to the tomcat.util.scan.DefaultJarScanner.jarsToSkip property in $CATALINA_BASE/conf/catalina.properties. Note that the deprecated Tomcat 7 WebSocket API will be available. 
May 24, 2019 10:26:57 AM org.apache.jasper.EmbeddedServletOptions <init>
SEVERE: The scratchDir you specified: /usr/share/apache-tomcat-7.0.94/work/Catalina/localhost/xnat is unusable.
May 24, 2019 10:26:57 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/share/apache-tomcat-7.0.94/webapps/xnat.war has finished in 13,118 ms
May 24, 2019 10:26:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/share/apache-tomcat-7.0.94/webapps/ROOT
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/share/apache-tomcat-7.0.94/webapps/ROOT has finished in 135 ms
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/share/apache-tomcat-7.0.94/webapps/docs
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/share/apache-tomcat-7.0.94/webapps/docs has finished in 51 ms
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/share/apache-tomcat-7.0.94/webapps/examples
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/share/apache-tomcat-7.0.94/webapps/examples has finished in 234 ms
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/share/apache-tomcat-7.0.94/webapps/host-manager
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/share/apache-tomcat-7.0.94/webapps/host-manager has finished in 65 ms
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/share/apache-tomcat-7.0.94/webapps/manager
May 24, 2019 10:26:58 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/share/apache-tomcat-7.0.94/webapps/manager has finished in 68 ms
May 24, 2019 10:26:58 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:26:58 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
May 24, 2019 10:26:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 13778 ms
May 24, 2019 10:27:49 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
May 24, 2019 10:27:49 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:27:49 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
May 24, 2019 10:27:49 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:49 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/xnat] appears to have started a thread named [DefaultQuartzScheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak.
May 24, 2019 10:27:50 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:27:50 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
May 24, 2019 10:27:50 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
May 24, 2019 10:27:50 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]


As I am running out of ideas, I hope you spot something that could solve the issue.
Thank you for all the fast answers and finding the solution with me.

Cheers 
Verdi


Op donderdag 23 mei 2019 22:55:06 UTC+2 schreef Herrick, Rick:

Verdi Vanreusel

unread,
May 24, 2019, 4:55:46 AM5/24/19
to xnat_discussion
I almost forgot to send you also the content of the spring.log file which is in /data/xnat/home/logs:

2019-05-24 10:01:07,996 [localhost-startStop-1] WARN  org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.b
eans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/usr/share/apache-tomcat-7.0.94/webapps/xnat/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecur
ityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.nrg.xnat.configurat
ion.ApplicationConfig': Unsatisfied dependency expressed through method 'setAsyncOperationsPreferences' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'asyncOperati
onsPreferences': Invocation of init method failed; nested exception is org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.Generi
cJDBCException: Could not open connection
2019-05-24 10:01:08,016 [localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/usr/share/apache-tomcat-7.0.94/webapps/xnat/WEB-INF/classes/org/nrg/xnat/event/listener
s/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'or
g.nrg.xnat.configuration.ApplicationConfig': Unsatisfied dependency expressed through method 'setAsyncOperationsPreferences' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean wi
th name 'asyncOperationsPreferences': Invocation of init method failed; nested exception is org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hiber
nate.exception.GenericJDBCException: Could not open connection
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1201)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1103)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237)
        at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:528)
        at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
        at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
        at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5195)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5720)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1018)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:994)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2020)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.nrg.xnat.configuration.ApplicationConfig': Unsatisfied dependency expressed through method 'setAsyncOperationsPreferences' pa
rameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'asyncOperationsPreferences': Invocation of init method failed; nested exception is org.springframework.transaction.Can
notCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.GenericJDBCException: Could not open connection
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredMethodElement.inject(AutowiredAnnotationBeanPostProcessor.java:667)
        at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1272)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1181)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1075)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
        ... 28 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'asyncOperationsPreferences': Invocation of init method failed; nested exception is org.springframework.transaction.CannotCreateTransaction
Exception: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.GenericJDBCException: Could not open connection
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1626)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredMethodElement.inject(AutowiredAnnotationBeanPostProcessor.java:659)
        ... 51 more
Caused by: org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.GenericJDBCException: Could not open connection
        at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:544)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:377)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:461)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
        at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
        at org.nrg.prefs.services.impl.hibernate.HibernateToolService$$EnhancerBySpringCGLIB$$8bd8ba71.getToolIds(<generated>)
        at org.nrg.prefs.services.impl.DefaultNrgPreferenceService.getToolIds(DefaultNrgPreferenceService.java:226)
        at org.nrg.prefs.beans.AbstractPreferenceBean.processDefaultPreferences(AbstractPreferenceBean.java:1039)
        at org.nrg.prefs.beans.AbstractPreferenceBean.initialize(AbstractPreferenceBean.java:130)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
        ... 63 more
Caused by: org.hibernate.exception.GenericJDBCException: Could not open connection
        at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:54)
        at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
        at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
        at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.obtainConnection(LogicalConnectionImpl.java:235)
        at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.getConnection(LogicalConnectionImpl.java:171)
        at org.hibernate.internal.SessionImpl.connection(SessionImpl.java:450)
        at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:450)
        ... 80 more
Caused by: java.sql.SQLException: Cannot create PoolableConnectionFactory (Connection to localhost:8080 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.)
        at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2294)
        at org.apache.commons.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2039)
        at org.apache.commons.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1533)
        at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:139)
        at org.hibernate.internal.AbstractSessionImpl$NonContextualJdbcConnectionAccess.obtainConnection(AbstractSessionImpl.java:380)
        at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.obtainConnection(LogicalConnectionImpl.java:228)
        ... 83 more
Caused by: org.postgresql.util.PSQLException: Connection to localhost:8080 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
        at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:270)
        at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
        at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:211)
        at org.postgresql.Driver.makeConnection(Driver.java:407)
        at org.postgresql.Driver.connect(Driver.java:275)
        at org.apache.commons.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:39)
        at org.apache.commons.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:256)
        at org.apache.commons.dbcp2.BasicDataSource.validateConnectionFactory(BasicDataSource.java:2304)
        at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2290)
        ... 88 more
Caused by: java.net.ConnectException: Verbinding is geweigerd (Connection refused)
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.net.Socket.connect(Socket.java:589)
        at org.postgresql.core.PGStream.<init>(PGStream.java:64)
        at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:150)
        ... 96 more

I don't really know anything about beans, but to me it seems like xnat cannot connect to something... maybe postgresql-9.4? 
However, my xnat-conf.properties file is quite general:

#
# xnat-conf.properties
# Copyright (c) 2016, Washington University School of Medicine
# All Rights Reserved
#
# Released under the Simplified BSD.
#
datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost:8080/xnat
datasource.username=xnat
datasource.password=xnatxnat

hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
hibernate.hbm2ddl.auto=update
hibernate.show_sql=false
hibernate.cache.use_second_level_cache=true
hibernate.cache.use_query_cache=true


Best regards,
Verdi

Op vrijdag 24 mei 2019 10:39:19 UTC+2 schreef Verdi Vanreusel:

Verdi Vanreusel

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May 24, 2019, 8:40:51 AM5/24/19
to xnat_discussion
For completeness, I only get the spring.log and application.log files after starting AND restarting tomcat and then killing the process running on the 8080 port. 
It is thus likely that the connection error occurs because the running process wants to disconnect with postgresql (and maybe other programs), but these are already on the 'new process' so the disconnection is imposible.
Does this make any sense?

Best,
Verdi

Op vrijdag 24 mei 2019 10:55:46 UTC+2 schreef Verdi Vanreusel:
...

McKay, Mike

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May 24, 2019, 9:13:19 AM5/24/19
to xnat_discussion

Does it work if you remove the ":8080" from your xnat-conf.properties file and restart Tomcat? The datasource url is not the same as your XNAT site URL (see https://wiki.xnat.org/documentation/xnat-administration/xnat-setup-first-time-configuration/xnat-setup-options-custom-configuration-settings for more information).


-Mike

XNAT is an open source project produced by NRG at the Washington University School of Medicine | NRG Home Contributions to the XNAT Documentation site are licensed under a Creative Commons Attribution 3.0 Unported License.

Sent: Monday, May 20, 2019 6:46:27 AM
To: xnat_discussion

Subject: [XNAT Discussion] Tomcat hangs when setting up xnat 1.7.5.3
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Verdi Vanreusel

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May 24, 2019, 10:34:11 AM5/24/19
to xnat_discussion
Hi Mike,

Thank you for the idea, but saddly it didn't do the trick. 

The main thing that I find strange is that I am able to reach the tomcat welcome page if I don't set the xnat home variable, but I am not anymore once I set it.
I would think that the tomcat welcome page is independent of the xnat page.

Best regards,
Verdi

Op vrijdag 24 mei 2019 15:13:19 UTC+2 schreef Mike McKay:
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Moore, Charlie

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May 24, 2019, 10:38:17 AM5/24/19
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Verdi,

 

Do you have the default tomcat webapp installed in your webapps folder? Can you try removing that (both ROOT/ and ROOT.war if they exist in the webapps folder), and then renaming XNAT to ROOT.war?

 

Thanks,

Charlie

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McKay, Mike

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May 24, 2019, 10:40:21 AM5/24/19
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Could you try what Charlie suggested, while keeping the ":8080" removed from your xnat-conf.properties file, and let us know what errors you get after making those changes?


-Mike

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Moore, Charlie <moo...@wustl.edu>
Sent: Friday, May 24, 2019 9:38:12 AM
To: xnat_di...@googlegroups.com
Subject: RE: [XNAT Discussion] Tomcat hangs when setting up xnat 1.7.5.3
 

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Verdi Vanreusel

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May 24, 2019, 10:58:33 AM5/24/19
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Hi Charlie and Mike,

Wonderful!!!
Thank you so much, it works now. 

As I am curious, does any one of you have an idea why it didn't work when I still had both xnat and the default tomcat webapp there? 

Thanks again.
Cheers,
Verdi

Op vrijdag 24 mei 2019 16:40:21 UTC+2 schreef Mike McKay:

 

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Moore, Charlie

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May 24, 2019, 4:14:43 PM5/24/19
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If you have a webapp installed with a name that isn't just ROOT.war or ROOT/, the URL for accessing it is going to depend on the file name. It looks like from previous messages that the war was kept with the original name of xnat-web-1.7.5.3.war, but attempts to reach it were at localhost:8080. It's possible that it was actually working previously at localhost:8080/xnat-web-1.7.5.3, or maybe tomcat doesn't handle dashes/periods in the webapp name.

 

- Charlie

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