Upgrading Confluence 3.3.1?
Asked by Edmund Woo:

Hi All,  

First time to the Community, been using Confluence 3.3.1 ever since release and never had the need to upgrade. And maybe that was a big mistake.  

I'm not a sysadmin, I use Confluence as a wiki for personal use. I honestly don't even remember how the Apache/Tomcat6 service was set up, it was so long ago. But yesterday I started getting exceptions and errors I don't understand, and I haven't done any system changes to Windows 7 at all nor installed any new software or drivers.  

I am running this off my desktop, running the service every time I ever need to use Confluence. Been doing this and never had any problems.  

I had considered upgrading Confluence to see if it will fix it, but figured I should try to get the system working again and back up the dbase before I attempt to upgrade.

Here's the log for when the startup.bat file is executed.

The following are the usual logging entries when it starts.  

Oct 21, 2018 10:50:59 PM org.apache.tomcat.util.digester.SetPropertiesRule begin  

WARNING: \[SetPropertiesRule\]{Server} Setting property 'debug' to '0' did not fin  
d a matching property.  
Oct 21, 2018 10:50:59 PM org.apache.tomcat.util.digester.SetPropertiesRule begin  

WARNING: \[SetPropertiesRule\]{Server/Service/Engine} Setting property 'debug' to  
'0' did not find a matching property.  
Oct 21, 2018 10:50:59 PM org.apache.tomcat.util.digester.SetPropertiesRule begin  

WARNING: \[SetPropertiesRule\]{Server/Service/Engine/Host} Setting property 'debug  
' to '0' did not find a matching property.  
Oct 21, 2018 10:50:59 PM org.apache.tomcat.util.digester.SetPropertiesRule begin  

WARNING: \[SetPropertiesRule\]{Server/Service/Engine/Host/Context} Setting propert  
y 'debug' to '0' did not find a matching property.  
Oct 21, 2018 10:50:59 PM org.apache.coyote.http11.Http11Protocol init  
INFO: Initializing Coyote HTTP/1.1 on http-8080  
Oct 21, 2018 10:50:59 PM org.apache.catalina.startup.Catalina load  
INFO: Initialization processed in 288 ms  
Oct 21, 2018 10:50:59 PM org.apache.catalina.core.StandardService start  
INFO: Starting service Tomcat-Standalone  
Oct 21, 2018 10:50:59 PM org.apache.catalina.core.StandardEngine start  
INFO: Starting Servlet Engine: Apache Tomcat/6.0.26  
2018-10-21 22:51:03,081 INFO \[main\] \[com.atlassian.confluence.lifecycle\] context  
Initialized Starting Confluence 3.3.1 (build #1923)  
2018-10-21 22:51:06,176 INFO \[main\] \[atlassian.plugin.manager.DefaultPluginManag  
er\] init Initialising the plugin system  
2018-10-21 22:51:06,377 INFO \[main\] \[atlassian.plugin.manager.DefaultPluginManag  
er\] init Plugin system started in 0:00:00.199  
2018-10-21 22:51:07,331 WARN \[main\] \[atlassian.config.xml.AbstractDom4jXmlConfig  
urationPersister\] saveDocumentAtomically Unable to move D:\\confluence\\data\\confl  
uence.cfg.xml4598269542301959598tmp to D:\\confluence\\data\\confluence.cfg.xml. Fa  
lling back to non-atomic overwrite.  

Then the following was all new:  

Oct 21, 2018 10:52:08 PM org.apache.catalina.core.StandardContext start  
SEVERE: Error listenerStart  
Oct 21, 2018 10:52:08 PM org.apache.catalina.core.StandardContext start  
SEVERE: Context \[\] startup failed due to previous errors  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearRefer  
encesJdbc  
SEVERE: A web application registered the JBDC driver \[com.mysql.jdbc.Driver\] but  
failed to unregister it when the web application was stopped. To prevent a memo  
ry leak, the JDBC Driver has been forcibly unregistered.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearRefer  
encesJdbc  
SEVERE: A web application registered the JBDC driver \[org.postgresql.Driver\] but  
failed to unregister it when the web application was stopped. To prevent a memo  
ry leak, the JDBC Driver has been forcibly unregistered.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearRefer  
encesJdbc  
SEVERE: A web application registered the JBDC driver \[org.hsqldb.jdbcDriver\] but  
failed to unregister it when the web application was stopped. To prevent a memo  
ry leak, the JDBC Driver has been forcibly unregistered.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearRefer  
encesThreads  
SEVERE: A web application appears to have started a thread named \[HSQLDB Timer @  
6aea88\] but has failed to stop it. This is very likely to create a memory leak.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@7a9af7\]) and a value of type \[org.apache.  
lucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@15  
3f975\]) but failed to remove it when the web application was stopped. To prevent  
a memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@1e8fc7\]) and a value of type \[org.apache.  
lucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@71  
7cf6\]) but failed to remove it when the web application was stopped. To prevent  
a memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@c30c24\]) and a value of type \[org.apache.  
lucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@15  
234cd\]) but failed to remove it when the web application was stopped. To prevent  
a memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@8bf02\]) and a value of type \[org.apache.l  
ucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@342  
cbc\]) but failed to remove it when the web application was stopped. To prevent a  
memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[null\] (value \[  
com.atlassian.core.logging.ThreadLocalErrorCollection$2@17eb44a\]) and a value of  
type \[java.lang.Boolean\] (value \[false\]) but failed to remove it when the web a  
pplication was stopped. To prevent a memory leak, the ThreadLocal has been forci  
bly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@16e83c3\]) and a value of type \[org.apache  
.lucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@8  
c8e82\]) but failed to remove it when the web application was stopped. To prevent  
a memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@1e012bb\]) and a value of type \[org.apache  
.lucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@1  
edc877\]) but failed to remove it when the web application was stopped. To preven  
t a memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@4184a\]) and a value of type \[org.apache.l  
ucene.index.SegmentTermEnum\] (value \[org.apache.lucene.index.SegmentTermEnum@d6a  
976\]) but failed to remove it when the web application was stopped. To prevent a  
memory leak, the ThreadLocal has been forcibly removed.  
Oct 21, 2018 10:52:08 PM org.apache.catalina.loader.WebappClassLoader clearThrea  
dLocalMap  
SEVERE: A web application created a ThreadLocal with key of type \[java.lang.Thre  
adLocal\] (value \[java.lang.ThreadLocal@10f9a00\]) and a value of type \[org.dom4j.  
DocumentFactory\] (value \[org.dom4j.DocumentFactory@1477db9\]) but failed to remov  
e it when the web application was stopped. To prevent a memory leak, the ThreadL  
ocal has been forcibly removed.  
log4j:ERROR LogMananger.repositorySelector was null likely due to error in class  
reloading, using NOPLoggerRepository.  
Oct 21, 2018 10:52:09 PM org.apache.coyote.http11.Http11Protocol start  
INFO: Starting Coyote HTTP/1.1 on http-8080  
Oct 21, 2018 10:52:09 PM org.apache.catalina.startup.Catalina start  
INFO: Server startup in 69845 ms  
Exception in thread "HSQLDB Timer @6aea88" java.lang.NullPointerException  
at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)  
at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)  
at java.lang.Thread.run(Thread.java:722)  

And then attempting to load the wiki page in my browser, I would get a 404 error.  

HTTP Status 404 -  
type Status report  
message  
description The requested resource () is not available.  
Apache Tomcat/6.0.26  

Any help is very much appreciated.  

Is there another way to access the information in the wiki pages other than using Confluence? I need access to some of the data as it does house critical information my family needs.  

I've looked at the upgrade path from 3.3.1 to 3.5.17 first, then to 5.0.3, then to Confluence 6. Where can I get 3.5.17 and 5.0.3? I can't find it on the website for Windows 7 32bit.

<br />

Thanks!


Answers:
author: Andrew
body: > ```
> 2018-10-21 22:51:07,331 WARN [main] [atlassian.config.xml.AbstractDom4jXmlConfig
> urationPersister] saveDocumentAtomically Unable to move D:\confluence\data\confl
> uence.cfg.xml4598269542301959598tmp to D:\confluence\data\confluence.cfg.xml. Fa
> lling back to non-atomic overwrite.
> ```

Check your space and permission on drive. Maybe changed some politics for tomcat user or update antivirus soft?

comments: author: Edmund Woo
body: Hi Andrew, thanks for your answer. Yeah, I checked the permissions for that folder and it's read write. So I actually moved the confluence.cfg.xml file and started the service, it started right up but it was as if I was setting it up for the first time when I accessed it via the browser. It wanted the key and to set up the administrator user.

So I looked in the xml file and saw that it included my license key and a bunch of other information. So is it safe to assume that something is wrong with my confluence.cfg.xml file? Some parameter isn't set correctly? I don't remember ever editing this file at the initial set up, but then again, it was like 7 years ago.

Something may have changed with AVGFree I've been using, but the software itself wasn't changed at the time. Maybe some type of permission it's preventing from occurring?


author: Andrew
body: Whath with database? Can you check it direct and found table with data?

In confluence.cfg.xml must be DB connection settings.


author: Edmund Woo
body: Sorry for the delay, I've been out of town.

I restored an older version of the config xml file, no joy. Still the same problem.

I also compared the two files and they both looked the same. So, it's got to be something else going on.

Now I'm wondering whether or not I need to restore the confluence data folder from an older date. That always makes me nervous.


author: Andrew
body: Hi [@Edmund Woo](/t5/user/viewprofilepage/user-id/2162663)!

Did You check database?

What type of DB is in Your confluence.cfg.xml?

You have Apache Tomcat/6.0.26 and some error with
> SEVERE: A web application registered the JBDC driver \[org.hsqldb.jdbcDriver\]

Here <https://stackoverflow.com/questions/3320400/to-prevent-a-memory-leak-the-jdbc-driver-has-been-forcibly-unregistered>

said than function for tomcat since version 6.0.24. Maybe You update tomcat?

Try direct connect to DB and check data <https://stackoverflow.com/questions/4990864/best-sql-browser-for-hsqldb>


author: Andrew
body: Old versions <https://www.atlassian.com/software/confluence/download-archives>

comments: author: Edmund Woo
body: Awesome, thanks Andrew!


Tags: confluence-server

server