Server Errors

Daniel_Bridges1 · 27 March 2013 06:41

Congrats to the team for releasing version 2.11 - it looks great.

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])

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.

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?

Thanks in advance,

Dan

Duttas · 27 March 2013 07:26

Hi all,

Congrats on the upgrade to 2.11!

I am just wondering if there is a way to filter by data element group when designing the data entry form? As it is now it has all of my data elements listed with the data set which can be a bit hard to manage sometimes. Thanks,

Nick

Lars · 27 March 2013 09:57

Hi Dan

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](http://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

···

On Wed, Mar 27, 2013 at 7:41 AM, Daniel Bridges dbridges@akrosresearch.com wrote:

Daniel_Bridges1 · 27 March 2013 11:17

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]

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@akrosresearch.com
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

bobj · 27 March 2013 11:52

Hi Dan

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

···

On 27 March 2013 11:17, Daniel Bridges <dbridges@akrosresearch.com> wrote:

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@akrosresearch.com> > 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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Lars · 29 March 2013 09:46

Hi Nick,

thanks for your feedback.

For quickly finding data elements we usually use the “filter” input field over the list of data elements. So far we have been deliberately avoiding having free-text filters and group filters for the same lists, as some find it confusing (does the filter apply within the selected group or for all elements?). So at the moment we don’t plan on including it… But if there is a huge need we will of course consider it.

regards,

Lars

···

On Wed, Mar 27, 2013 at 8:26 AM, duttas@wpro.who.int wrote:

Hi all,

Congrats on the upgrade to 2.11!

I am just wondering if there is a way to filter by data element group when designing the data entry form? As it is now it has all of my data elements listed with the data set which can be a bit hard to manage sometimes. Thanks,

Nick

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Daniel_Bridges1 · 3 April 2013 07:44

Thanks to Lars and Jason, found out that the problem was due to my
nginx set-up.

Am now getting into the database and noticed some things that I

can’t figure ut:

···

On 27/03/13 13:17, Daniel Bridges
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]
  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@akrosresearch.com
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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Lars · 3 April 2013 08:11

Hi Dan

···

I assume you are running the demo database.

      I can't seem to generate a user with either 'superuser' or 'system administrator' role when logged in as 'admin'. I also can't see the user 'admin' in the list of users. I can see that 3 users are assigned the role of system administrator and one to superuser, but none of the listed users have those roles. Am I missing something obvious?

In the demo db we have a user “system” which has the ALL authority through system administrator. The “admin” user has most authorities but not ALL through superuser. So this behavior is a consequence of the way authority is handled: When creating new users, you can assign the user roles for which your own account has all of the authorities. Also, you can view and edit other users for which your own account has all of the authorities. This is done so that authority can be deferred through a hierarchy - national users can create and manage province users, province users can create and manage district users and so on.

The pattern for the demo user’s username/password is:

keita

Keita123

      There are a number of charts / maps / pivot tables that can't be deleted by the user 'admin'. I presume this is related to the user role issue in question 1, or is it?

This happens because those charts are created by the system user, and set to public view access and private edit access through the sharing mechanism. This allows “super users” to create a set of charts / maps / pivots which should be view-able by all users, but only editable by themselves to avoid them being changed/messed up.

http://dhis2.org/doc/snapshot/en/user/html/ch07.html

      Creating a chart (or map / pivot table) as the user 'admin' seems to generate a system-wide chart by default i.e. all other users see that chart. If logged in as 'lower' user role the default is to save the favourite for just that user. Why isn't the default behaviour the same for different users?

This happens because admin has the “create public chart” authority through superuser role, while “lower” users do not have that authority in the demo db. Creating private charts / maps / pivots is now open to everyone and require no authority granted. The thinking behind this is that a set of “superusers” should be able to generate general-purpose charts which should be consumed by everyone, while allowing “lower” users to create their own charts while keeping the list of charts for the common users short and relevant to themselves (essentially people can create their own charts without messing up everyone else’s list of charts).

http://dhis2.org/doc/snapshot/en/user/html/ch07.html

      Running the data integrity check throws up a number of errors in 'Data elements without groups', Data elements in data set but not in forms or sections etc. Can these be ignored?

Yes these should be considered “best practices”. The second warning could be good to clean up in order to have a healthy database.

    Thanks for all the great work - am really enjoying version 2.11!

Thanks.

Lars

Daniel_Bridges1 · 3 April 2013 09:13

Lars,

Thanks for the clarifications - that all makes sense and I can now

get superuser access. One last question - what authority allows a
user to create a public user group - I can’t find one that confers
this ability? Sorry if I have missed the obvious.

One suggestion for you and the team - would it be possible to add a

link to the ‘User group’ screen (see section 6.1.4 in the user
manual) in the user module? Currently it seems like the only way to
access this screen is via the Dashboard? Perhaps there are good
reasons for not including this link, but it seems more logical to
me.

Thanks

Dan

···

On 03/04/13 10:11, Lars Helge Øverland
wrote:

Hi Dan

      I assume you are running the demo

database.

                  I can't seem to generate a user with either
‘superuser’ or ‘system administrator’ role when
logged in as ‘admin’. I also can’t see the user
‘admin’ in the list of users. I can see that 3
users are assigned the role of system
administrator and one to superuser, but none of
the listed users have those roles. Am I missing
something obvious?

          In the demo db we have a user "system" which
has the ALL authority through system administrator. The
“admin” user has most authorities but not ALL through
superuser. So this behavior is a consequence of the way
authority is handled: When creating new users, you can
assign the user roles for which your own account has all
of the authorities. Also, you can view and edit other
users for which your own account has all of the
authorities. This is done so that authority can be
deferred through a hierarchy - national users can create
and manage province users, province users can create and
manage district users and so on.

          The pattern for the demo user's

username/password is:

keita

Keita123

                  There are a number of charts / maps / pivot
tables that can’t be deleted by the user ‘admin’.
I presume this is related to the user role issue
in question 1, or is it?

          This happens because those charts are created
by the system user, and set to public view access and
private edit access through the sharing mechanism. This
allows “super users” to create a set of charts / maps /
pivots which should be view-able by all users, but only
editable by themselves to avoid them being changed/messed
up.

http://dhis2.org/doc/snapshot/en/user/html/ch07.html

                  Creating a chart (or map / pivot table) as the
user ‘admin’ seems to generate a system-wide chart
by default i.e. all other users see that chart. If
logged in as ‘lower’ user role the default is to
save the favourite for just that user. Why isn’t
the default behaviour the same for different
users?

          This happens because admin has the "create
public chart" authority through superuser role, while
“lower” users do not have that authority in the demo db.
Creating private charts / maps / pivots is now open to
everyone and require no authority granted. The thinking
behind this is that a set of “superusers” should be able
to generate general-purpose charts which should be
consumed by everyone, while allowing “lower” users to
create their own charts while keeping the list of charts
for the common users short and relevant to themselves
(essentially people can create their own charts without
messing up everyone else’s list of charts).

http://dhis2.org/doc/snapshot/en/user/html/ch07.html

                  Running the data integrity check throws up a
number of errors in ‘Data elements without
groups’, Data elements in data set but not in
forms or sections etc. Can these be ignored?

          Yes these should be considered "best
practices". The second warning could be good to clean up
in order to have a healthy database.

                Thanks for all the great work - am really enjoying

version 2.11!

Thanks.

          Lars

Lars · 3 April 2013 09:29

Thanks for the clarifications - that all makes sense and I can now get
superuser access. One last question - what authority allows a user to
create a public user group - I can't find one that confers this ability?
Sorry if I have missed the obvious.

Seems you have found a glitch - will get back on this shortly.

One suggestion for you and the team - would it be possible to add a link
to the 'User group' screen (see section 6.1.4 in the user manual) in the
user module? Currently it seems like the only way to access this screen is
via the Dashboard? Perhaps there are good reasons for not including this
link, but it seems more logical to me.

Yes - we decided to move user groups to dashboard since user groups are an
essential part of the new sharing feature. We want all users to be able to
create groups and share reports within those groups to foster
collaboration.

Reason for not linking from user module is that currently we allow links
from the dashboard module to other modules only - this to maintain a degree
of modularity where it should be possible to leave out/plug in modules
without worrying about breaking interlinks.. Agree that it is a little bit
confusing though.

Lars · 3 April 2013 16:46

This has now been fixed, backported to 2.11, you can get the update war on
dhis2.org/downloads.

Lars

···

On Wed, Apr 3, 2013 at 11:29 AM, Lars Helge Øverland <larshelge@gmail.com>wrote:

Thanks for the clarifications - that all makes sense and I can now get

superuser access. One last question - what authority allows a user to
create a public user group - I can't find one that confers this ability?
Sorry if I have missed the obvious.

Seems you have found a glitch - will get back on this shortly.

Daniel_Bridges1 · 4 April 2013 05:27

Thanks Lars - downloading now…

···

On 03/04/13 18:46, Lars Helge Øverland
wrote:

        On Wed, Apr 3, 2013 at 11:29 AM, Lars
Helge Øverland larshelge@gmail.com
wrote:
                      Thanks
for the clarifications - that all makes sense
and I can now get superuser access. One last
question - what authority allows a user to
create a public user group - I can’t find one
that confers this ability? Sorry if I have
missed the obvious.

                  Seems you have found a glitch - will get back

on this shortly.

          This has now been fixed, backported to 2.11, you can get

the update war on dhis2.org/downloads.

Lars