xnat 1.7 installation problem
Ibrahim A
Herrick, Rick
The xnat-conf.properties within the web app is only provided as a sample and isn’t used directly by the app (it should probably be renamed to indicate that). The only xnat-conf.properties that 1.7 looks at is the one in ${xnat.home}/config. Try putting it there and then restarting Tomcat.
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Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
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Ibrahim A
The xnat-conf.properties within the web app is only provided as a sample and isn’t used directly by the app (it should probably be renamed to indicate that). The only xnat-conf.properties that 1.7 looks at is the one in ${xnat.home}/config. Try putting it there and then restarting Tomcat.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Tuesday, December 6, 2016 at 4:18 PM
To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Subject: [XNAT Discussion] xnat 1.7 installation problem
Dear all,
I have installed Ubuntu server 16.04 and followed all the instructions here [1]. So far, tomcat7 works, Postgresql works. I have a user called xnatu who own tomcat7. I created a databse called xnatd . I extracted the war file to /var/lib/tomcat7/webapps/xnat. I also changed the xnat-conf.properties in /var/lib/tomcat7/webapps/xnat/WEB-INF/conf to be:
datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost/xnatd
datasource.username=xnatu
datasource.password=mypassword
I restart tomcat7 but nothing happens, I got "Unable to connect" in firefox. How the setup create the database contents? in xnat 1.6 we run a sql script but here I don't see this and I htink this step is missing as the database is empty.
Thanks for your input.
Ibraheem
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Herrick, Rick
Using the same name for the database and user is part of the standard PostgreSQL development pattern: if you type “psql” by itself on the command line, it takes your username and tries to open the database with that same name as the database role with that same name. If you have a Vagrant VM built using the XNAT Vagrant project and log in, you can access the database simply by typing “psql”, since the username is xnat as is the database name. We use that pattern to stay consistent with those PostgreSQL development patterns.
Also worth noting: you mention that you extracted the war file to the webapps folder. You can do that if you want, but you can also just copy the war file into the webapps folder and Tomcat will take care of exploding and managing the contents as it needs to.
As far as the permissions issue, you need to make sure all of the Tomcat folders are owned by the user specified in the TOMCAT_USER property. By default, this user is named the same as the service (tomcat7, tomcat, etc.) and all of the folders are owned appropriately. If you change the TOMCAT_USER setting, you need to change the owner accordingly. This is complicated by the fact that the packaged installations of Tomcat on Debian- and Fedora-based systems actually install parts of the Tomcat application in different folders, then “integrate” these parts through symlinks (located in /var/lib/tomcat7 on Debian-based systems and /usr/share/tomcat7 on Fedora-based systems). Changing ownership just through the integrated installation folder doesn’t usually suffice to change permissions on folders that are symlinked. That’s probably why you’re seeing that in the work folder, which is usually symlinked to /var/cache/tomcat7.
You can change ownership for all of the folders quickly with these two commands:
# chown -RH --dereference xnat.xnat /var/lib/tomcat7
# chown --no-dereference xnat.xnat /var/lib/tomcat7/*
Verify the results of these operations:
# ls -ld /var/lib/tomcat7 /var/lib/tomcat7/* /etc/tomcat7 /var/log/tomcat7 /var/cache/tomcat7
drwxr-xr-x 4 xnat xnat 4096 Dec 6 22:41 /etc/tomcat7
drwxr-x--- 3 xnat xnat 4096 Dec 6 22:42 /var/cache/tomcat7
drwxr-xr-x 6 xnat xnat 4096 May 28 2016 /var/lib/tomcat7
drwxr-xr-x 3 xnat xnat 4096 May 28 2016 /var/lib/tomcat7/common
lrwxrwxrwx 1 xnat xnat 12 Jun 19 2015 /var/lib/tomcat7/conf -> /etc/tomcat7
lrwxrwxrwx 1 xnat xnat 17 Jun 19 2015 /var/lib/tomcat7/logs -> ../../log/tomcat7
drwxr-xr-x 3 xnat xnat 4096 May 28 2016 /var/lib/tomcat7/server
drwxr-xr-x 3 xnat xnat 4096 May 28 2016 /var/lib/tomcat7/shared
drwxrwxr-x 3 xnat xnat 4096 Dec 6 22:42 /var/lib/tomcat7/webapps
lrwxrwxrwx 1 xnat xnat 19 Jun 19 2015 /var/lib/tomcat7/work -> ../../cache/tomcat7
drwxr-x--- 2 xnat xnat 4096 Dec 8 20:14 /var/log/tomcat7
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
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Date: Thursday, December 8, 2016 at 1:50 PM
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Ibrahim A
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Herrick, Rick
There are two log folders where you might find info on what’s going on: /var/log/tomcat7 (also linked to /var/lib/tomcat7/log) and ${xnat.home}/logs. Look in those folders and see which ones get updated when you try to start Tomcat. I usually set up a couple windows (I do this with tmux, but you can just open separate terminal windows or whatever works best for you) and run something like this:
$ watch -d ls -l /var/log/tomcat7
And:
$ watch -d ls -l /data/xnat/home/logs
Whenever a log file is updated, the watch command will highlight the changes, so if you keep your eye on those terminals as you’re starting Tomcat, you can see which specific log files are being updated when.
I meant to add to this earlier. You asked what happened to the requirement to run the SQL script between 1.6 and 1.7. In 1.7, the code that created the SQL script is now integrated into the XNAT start-up process. Instead of parsing the data-type schemas in folders then writing out an SQL script that has to be run manually, 1.7 finds all XSDs available on the classpath, parses them there, and generates the SQL required to create or update the database schema on the fly. Basically, on an XNAT 1.7 installation, there’s no need to do anything before starting Tomcat other than creating the XNAT home folder, configuring Tomcat to know where that’s at, creating an empty database, and setting up your xnat-conf.properties file in XNAT’s config folder so that XNAT can access the database. Everything else is handled on application start-up.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From:
"xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Thursday, December 8, 2016 at 2:52 PM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
Hi Rick,
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Ibrahim A
There are two log folders where you might find info on what’s going on: /var/log/tomcat7 (also linked to /var/lib/tomcat7/log) and ${xnat.home}/logs. Look in those folders and see which ones get updated when you try to start Tomcat. I usually set up a couple windows (I do this with tmux, but you can just open separate terminal windows or whatever works best for you) and run something like this:
$ watch -d ls -l /var/log/tomcat7
And:
$ watch -d ls -l /data/xnat/home/logs
Whenever a log file is updated, the watch command will highlight the changes, so if you keep your eye on those terminals as you’re starting Tomcat, you can see which specific log files are being updated when.
I meant to add to this earlier. You asked what happened to the requirement to run the SQL script between 1.6 and 1.7. In 1.7, the code that created the SQL script is now integrated into the XNAT start-up process. Instead of parsing the data-type schemas in folders then writing out an SQL script that has to be run manually, 1.7 finds all XSDs available on the classpath, parses them there, and generates the SQL required to create or update the database schema on the fly. Basically, on an XNAT 1.7 installation, there’s no need to do anything before starting Tomcat other than creating the XNAT home folder, configuring Tomcat to know where that’s at, creating an empty database, and setting up your xnat-conf.properties file in XNAT’s config folder so that XNAT can access the database. Everything else is handled on application start-up.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
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Date: Thursday, December 8, 2016 at 2:52 PM
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Moore, Charlie
Some googling took me here: http://stackoverflow.com/questions/38583495/getting-error-while-running-webservices-on-tomcat7-server-ubuntu-16-04-lts.
If this is the same error (and it sure looks like it is), you might have to use Ubuntu 14.04 instead of 16.04 or use Java 8 instead of Java 7 (although we haven’t really tested Java 8 with XNAT much…).
Thanks,
Charlie
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of Ibrahim A
Sent: Monday, December 12, 2016 12:11 PM
To: xnat_di...@googlegroups.com
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
Many thanks for your response. In tomcat7 I have this log:
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Ibrahim A
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Herrick, Rick
This issue is caused when compiling 1.7-compatible code (which XNAT is) with a Java 1.8 compiler without providing the Java 1.7 run-time library. There are a few changes in the core Java libraries between 1.7 and 1.8. If the code references something that changed between those versions, you end up with errors like the one you’re seeing. The problem is that this doesn’t appear to be in the XNAT code but in the Tomcat code, since you’ll notice that the line where the error occurs is in the Catalina code base:
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
I think what you need to do is use Java 8, but I’m guessing you changed *your* JAVA_HOME. What you actually need to change is the JAVA_HOME for your Tomcat installation. Check the file /etc/default/tomcat7 (on Fedora/RH dists like CentOS and, well, Fedora, this is in /etc/tomcat7/tomcat7.conf, I think). There’s a line there that will probably be like this:
#JAVA_HOME=/usr/lib/jvm/openjdk-6-jdk
Change this so that it’s like this:
JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
Restart Tomcat and your NoSuchMethodError should go away.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Voice: (314) 273-1645
Web: http://www.xnat.org
Twitter: @NrgXnat
From:
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Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Monday, December 12, 2016 at 2:05 PM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
Thanks Charlie for your input,
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Ibrahim A
This issue is caused when compiling 1.7-compatible code (which XNAT is) with a Java 1.8 compiler without providing the Java 1.7 run-time library. There are a few changes in the core Java libraries between 1.7 and 1.8. If the code references something that changed between those versions, you end up with errors like the one you’re seeing. The problem is that this doesn’t appear to be in the XNAT code but in the Tomcat code, since you’ll notice that the line where the error occurs is in the Catalina code base:
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
I think what you need to do is use Java 8, but I’m guessing you changed *your* JAVA_HOME. What you actually need to change is the JAVA_HOME for your Tomcat installation. Check the file /etc/default/tomcat7 (on Fedora/RH dists like CentOS and, well, Fedora, this is in /etc/tomcat7/tomcat7.conf, I think). There’s a line there that will probably be like this:
#JAVA_HOME=/usr/lib/jvm/openjdk-6-jdk
Change this so that it’s like this:
JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
Restart Tomcat and your NoSuchMethodError should go away.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Voice: (314) 273-1645
Web: http://www.xnat.org
Twitter: @NrgXnat
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Monday, December 12, 2016 at 2:05 PM
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Ibrahim A
Herrick, Rick
Try downloading XNAT 1.7.1 (http://xnat.org/download) and see if that fixes the problem. There are a couple possible causes for this issue. One is a strange timing issue with loading graphics that basically hijacks and replaces your authenticated session with an anonymous session. 1.7.1 fixes that issue.
The other is caused by the configuration of the front-end proxy server. Basically the request URL doesn’t match what XNAT thinks should be set. Technically, the appropriate way to fix this is to fix the header rewrites configured in the front-end proxy, but practically speaking it was best for XNAT to figure out that that was happening and expand its security checks to take that configuration into account. In a lot of cases (e.g. the Amazon elastic load balancer), the person administering XNAT may not even be able to change the front-end proxy configuration. So this is also a fix in 1.7.1.
Grab that and let me know if that solves your issue.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From:
"xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Tuesday, December 13, 2016 at 6:18 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
I tried login using admin/admin but I keep getting:
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Ibrahim A
Try downloading XNAT 1.7.1 (http://xnat.org/download) and see if that fixes the problem. There are a couple possible causes for this issue. One is a strange timing issue with loading graphics that basically hijacks and replaces your authenticated session with an anonymous session. 1.7.1 fixes that issue.
The other is caused by the configuration of the front-end proxy server. Basically the request URL doesn’t match what XNAT thinks should be set. Technically, the appropriate way to fix this is to fix the header rewrites configured in the front-end proxy, but practically speaking it was best for XNAT to figure out that that was happening and expand its security checks to take that configuration into account. In a lot of cases (e.g. the Amazon elastic load balancer), the person administering XNAT may not even be able to change the front-end proxy configuration. So this is also a fix in 1.7.1.
Grab that and let me know if that solves your issue.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Tuesday, December 13, 2016 at 6:18 AM
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Herrick, Rick
Do you have a front-end proxy? If so, what are you using? Can you send the configuration proxying to your Tomcat?
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From:
"xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Tuesday, December 13, 2016 at 11:37 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
thanks for the info, actually the resulted logs are from 1.7.1 version which I downloaded today. To be sure, I will redownload and reinstall xnat again.
On Tue, Dec 13, 2016 at 6:26 PM, Herrick, Rick <jrhe...@wustl.edu> wrote:
Try downloading XNAT 1.7.1 (http://xnat.org/download) and see if that fixes the problem. There are a couple possible causes for this issue. One is a strange timing issue with loading graphics that basically hijacks and replaces your authenticated session with an anonymous session. 1.7.1 fixes that issue.
The other is caused by the configuration of the front-end proxy server. Basically the request URL doesn’t match what XNAT thinks should be set. Technically, the appropriate way to fix this is to fix the header rewrites configured in the front-end proxy, but practically speaking it was best for XNAT to figure out that that was happening and expand its security checks to take that configuration into account. In a lot of cases (e.g. the Amazon elastic load balancer), the person administering XNAT may not even be able to change the front-end proxy configuration. So this is also a fix in 1.7.1.
Grab that and let me know if that solves your issue.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Tuesday, December 13, 2016 at 6:18 AM
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Ibrahim A
Do you have a front-end proxy? If so, what are you using? Can you send the configuration proxying to your Tomcat?
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Tuesday, December 13, 2016 at 11:37 AM
Subject: Re: [XNAT Discussion] xnat 1.7 installation problem
thanks for the info, actually the resulted logs are from 1.7.1 version which I downloaded today. To be sure, I will redownload and reinstall xnat again.
On Tue, Dec 13, 2016 at 6:26 PM, Herrick, Rick <jrhe...@wustl.edu> wrote:
Try downloading XNAT 1.7.1 (http://xnat.org/download) and see if that fixes the problem. There are a couple possible causes for this issue. One is a strange timing issue with loading graphics that basically hijacks and replaces your authenticated session with an anonymous session. 1.7.1 fixes that issue.
The other is caused by the configuration of the front-end proxy server. Basically the request URL doesn’t match what XNAT thinks should be set. Technically, the appropriate way to fix this is to fix the header rewrites configured in the front-end proxy, but practically speaking it was best for XNAT to figure out that that was happening and expand its security checks to take that configuration into account. In a lot of cases (e.g. the Amazon elastic load balancer), the person administering XNAT may not even be able to change the front-end proxy configuration. So this is also a fix in 1.7.1.
Grab that and let me know if that solves your issue.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Ibrahim A <ibr...@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Tuesday, December 13, 2016 at 6:18 AM
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Ibrahim A
Ibrahim A
Ibrahim A
Mohammad Mahdavi Doust
James Hawkins
INFO: Deploying web application directory /usr/local/tomcat/webapps/xnatJan 18, 2017 6:17:45 PM 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.
Jan 18, 2017 6:18:12 PM org.apache.catalina.session.StandardManager startInternalSEVERE: Exception loading sessions from persistent storagejava.lang.NullPointerExceptionat org.nrg.xft.ItemWrapper.getItem(ItemWrapper.java:212)at org.nrg.xdat.base.BaseElement.readExternal(BaseElement.java:454)at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1837)at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1796)at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)at org.apache.catalina.session.StandardSession.readObject(StandardSession.java:1609)at org.apache.catalina.session.StandardSession.readObjectData(StandardSession.java:1075)at org.apache.catalina.session.StandardManager.doLoad(StandardManager.java:259)at org.apache.catalina.session.StandardManager.load(StandardManager.java:176)at org.apache.catalina.session.StandardManager.startInternal(StandardManager.java:465)at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5624)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)at java.util.concurrent.FutureTask.run(FutureTask.java:262)at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)at java.lang.Thread.run(Thread.java:745)
Right now, after downgrading and then upgrading back, the site seems functional, but there is this error in the catalina logs on start-up:
SEVERE: Error waiting for multi-thread deployment of directories to completejava.lang.InterruptedExceptionat java.util.concurrent.FutureTask.awaitDone(FutureTask.java:400)at java.util.concurrent.FutureTask.get(FutureTask.java:187)at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1163)at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:497)at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1757)at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:333)at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1370)at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1542)at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1552)at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1520)at java.lang.Thread.run(Thread.java:745)
Herrick, Rick
Try editing the context.xml file for your Tomcat installation. That’s probably in /usr/local/tomcat/conf/context.xml.
There’s a line in there that should look something like this:
<!--
<Manager pathname="" />
-->
The <!-- and --> delimiters comment that out. Remove those delimiters and restart Tomcat.
The error loading sessions is pretty typical, but the NPE when that happens is not. I can add a check for that there, but that won’t help you with running the current code base. But when you add that manager element, Tomcat will no longer try to load sessions on start-up, so hopefully that will get you around the error.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Sarah K
When this happens I'm seeing the following error repeated in my xnat.home/logs/turbine.log:
2017-02-06 22:08:58,826 [http-bio-8080-exec-4] ERROR org.nrg.xnat.turbine.utils.ArcSpecManager -
org.nrg.framework.exceptions.NrgServiceRuntimeException: Error [Unknown]: Error [Unknown]: Couldn't create the base prearchive folder in /data/xnat/prearchive
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.getPrearchiveFolderTimestamps(PrearcDatabase.java:848)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.pruneDatabase(PrearcDatabase.java:836)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.initDatabase(PrearcDatabase.java:159)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.initDatabase(PrearcDatabase.java:100)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:86)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:55)
at org.nrg.xnat.security.XnatExpiredPasswordFilter.doFilter(XnatExpiredPasswordFilter.java:70)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:152)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:218)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:958)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:452)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1087)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
I have my xnat.home variable set in a setenv.sh file (I'm using Mac OS X 10.11.6), set to /Users/[username]/xnat/home. I've also created a prearchive folder already, stored in /Users/[username]/xnat.
When I try the context.xml fix, all pages (including the Tomcat manager page) show up blank in Firefox.
I'd appreciate anything you can come up with!
Thanks so much,
Sarah