dhis2-users team mailing list archive

[Bob Jolliffe <bobjolliffe@xxxxxxxxx>]

Hi Dan

On 27 March 2013 11:17, Daniel Bridges <dbridges@xxxxxxxxxxxxxxxxx> wrote:
> Thanks for the explanations Lars. Will check data integrity when I get the
> server up and running. If the 404 error isn't related then guess my tomcat
> server isn't running properly?
>
> Guess I am doing something stupid, but can't see what it is. When I run the
> startup script and look at the logs in catalina.out I get the following:
>
> Mar 27, 2013 1:12:23 PM org.apache.catalina.startup.Catalina load
> INFO: Initialization processed in 601 ms
> Mar 27, 2013 1:12:23 PM org.apache.catalina.core.StandardService
> startInternal
> INFO: Starting service Catalina
> Mar 27, 2013 1:12:23 PM org.apache.catalina.core.StandardEngine
> startInternal
> INFO: Starting Servlet Engine: Apache Tomcat/7.0.26
> Mar 27, 2013 1:12:23 PM org.apache.catalina.startup.HostConfig deployWAR
> INFO: Deploying web application archive /home/dhis/tomcat/webapps/ROOT.war
> Mar 27, 2013 1:12:24 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO:
> validateJarFile(/home/dhis/tomcat/webapps/ROOT/WEB-INF/lib/geronimo-servlet_2.5_spec-1.1.2.jar)
> - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
> javax/servlet/Servlet.class
> * INFO  2013-03-27 13:12:30,869 System property dhis2.home not set
> (DefaultLocationManager.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:30,873 Environment variable DHIS2_HOME points to
> /home/dhis/dhis_home (DefaultLocationManager.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:49,219 Found the following message senders:
> [org.hisp.dhis.message.EmailMessageSender@cccda4]
> (DefaultMessageService.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:54,797 Scheduled task with key: 0 0 0 ? * 1-6 and
> cron: 0 0 0 ? * 1-6 (SpringScheduler.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:54,801 Scheduled task with key: 0 0 0 ? * 0 and
> cron: 0 0 0 ? * 0 (SpringScheduler.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:57,979 Camel context started
> (DHIS2LifecycleStrategy.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:57,980 Searching for routes in directory:
> /home/dhis/dhis_home/routes (DHIS2LifecycleStrategy.java [pool-2-thread-1])
> * INFO  2013-03-27 13:12:58,499 Executing startup routine [1 of 10, runlevel
> 1]: TableAlteror (DefaultStartupRoutineExecutor.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:00,944 Tables updated (TableAlteror.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:00,945 Executing startup routine [2 of 10, runlevel
> 1]: MapViewUpgrader (DefaultStartupRoutineExecutor.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,038 Executing startup routine [3 of 10, runlevel
> 2]: IdentityPopulator (DefaultStartupRoutineExecutor.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,297 Executing startup routine [4 of 10, runlevel
> 2]: PeriodTypePopulator (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,306 Executing startup routine [5 of 10, runlevel
> 3]: TableCreator (DefaultStartupRoutineExecutor.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,392 Executing startup routine [6 of 10, runlevel
> 3]: DataElementDefaultDimensionPopulator (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,557 Linked default category with default concept
> (DataElementDefaultDimensionPopulator.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:01,965 Executing startup routine [7 of 10, runlevel
> 4]: PatientTableAlteror (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:02,352 Executing startup routine [8 of 10, runlevel
> 5]: OrganisationUnitGroupSetPopulator (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:02,361 Executing startup routine [9 of 10, runlevel
> 5]: DataEntryFormUpgrader (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * INFO  2013-03-27 13:13:02,408 Upgraded custom case entry form identifiers:
> 6 (DataEntryFormUpgrader.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:02,420 Executing startup routine [10 of 10,
> runlevel 6]: ExpressionUpgrader (DefaultStartupRoutineExecutor.java
> [pool-2-thread-1])
> * ERROR 2013-03-27 13:13:02,510 Failed to upgrade expression: ([66.4] * 1.0)
> + ([191.4] * 1.0) (ExpressionUpgrader.java [pool-2-thread-1])
> * ERROR 2013-03-27 13:13:02,510 java.lang.NullPointerException
> (ExpressionUpgrader.java [pool-2-thread-1])
> * INFO  2013-03-27 13:13:02,514 All startup routines done
> (DefaultStartupRoutineExecutor.java [pool-2-thread-1])
> Mar 27, 2013 1:13:09 PM org.apache.coyote.AbstractProtocol start
> INFO: Starting ProtocolHandler ["http-bio-8080"]
> Mar 27, 2013 1:13:09 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 45441 ms
>
> When I run the shutdown script I get:
> Using CATALINA_BASE:   /home/dhis/tomcat
> Using CATALINA_HOME:   /usr/share/tomcat7
> Using CATALINA_TMPDIR: /home/dhis/tomcat/temp
> Using JRE_HOME:        /usr
> Using CLASSPATH:
> /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar
> Using CATALINA_PID:    /home/dhis/tomcat/work/test-tomcat.pid
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/common/classes], exists:
> [false], isDirectory: [false], canRead: [false]
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/common], exists: [false],
> isDirectory: [false], canRead: [false]
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/server/classes], exists:
> [false], isDirectory: [false], canRead: [false]
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/server], exists: [false],
> isDirectory: [false], canRead: [false]
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/shared/classes], exists:
> [false], isDirectory: [false], canRead: [false]
> Mar 27, 2013 1:14:39 PM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/var/lib/tomcat7/shared], exists: [false],
> isDirectory: [false], canRead: [false]

These warnings are not serious.  Have you used tomcat7-instance-create
to set up the CATALINA_BASE?  I think the catalina.properties has an
excessive list of potential directories it might find things in, some
of which don't actually exist.  I suspect its a hangover from tomcat6.

Bob

> Hope this is something obvious....
>
> Cheers
> Dan
>
>
> On 27/03/13 11:57, Lars Helge Øverland wrote:
>
> Hi Dan
>
> On Wed, Mar 27, 2013 at 7:41 AM, Daniel Bridges <dbridges@xxxxxxxxxxxxxxxxx>
> wrote:
>>
>> Congrats to the team for releasing version 2.11 - it looks great.
>
>
> Thanks..
>
>>
>>
>> I am trying to upgrade my local server (Ubuntu 12.04 LTS) to 2.11, but am
>> struggling to get it working. First I upgraded the server to postgres 9.2. I
>> then created a new database and restored the 2.11 demo data into the new
>> database. Everything seemed to run fine, although when I start up tomcat I
>> get these two errors in catalina.out:
>>
>> * ERROR 2013-03-27 08:24:39,596 Failed to upgrade expression: ([66.4] *
>> 1.0) + ([191.4] * 1.0) (ExpressionUpgrader.java [pool-2-thread-1])
>> * ERROR 2013-03-27 08:24:39,597 java.lang.NullPointerException
>> (ExpressionUpgrader.java [pool-2-thread-1])
>
>
> In 2.11 we are using UIDs for indicator and validation rules expressions.
> This means that the upgrade routine failed for one of the expressions
> because the formula was invalid. This is mostly often caused by an
> identifier in the formula pointing to a non-existing data element or
> category option combination. You can identify this by running "Data
> integrity checks" in data admin module and look for invalid indicator /
> validation rule formulas.
>
> I can see we could have given a more descriptive error message her. But the
> system will ignore it and continue starting up.
>
>>
>> When I try to login to the server I get a 404 error from nginx. Happy to
>> give more info, but does anyone know what these errors could relate to and
>> how to solve them.
>>
>
> Would be good with some more info. The above issue should not be related.
>
>>
>> I also noticed that the dhis2-demo.zip file is listed on the dhis2.org
>> download page as 74Mb, but the file I downloaded is actually 103Mb in size.
>> Which should it be? Are there any md5 / SHA1 checksums that I can check my
>> download against?
>
>
> I have corrected it now, the size should be 103 Mb. Will add checksums
> later.
>
> Thanks for reporting.
>
>
> Lars
>
>
>
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