Upgrading Confluence 3.3.1?

[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.

Thanks!

[Andrew]

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?

[Edmund Woo]

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?

[Andrew]

Whath with database? Can you check it direct and found table with data? 

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

[Edmund Woo]

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.

[Andrew]

Hi @Edmund Woo!

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

[Andrew]

Old versions https://www.atlassian.com/software/confluence/download-archives

[Edmund Woo]

Awesome, thanks Andrew!