Build Transmart from source: Unresolved dependencies

832 views
Skip to first unread message

Erwin Vast

unread,
Apr 3, 2014, 3:35:01 AM4/3/14
to transmar...@googlegroups.com
Hi all,

When building Transmart from source (with grails compile) I receive some errors that prevent a correct building. With grails run-app I get the same result. I tried with different Grails versions. I followed this tutorial: https://wiki.transmartfoundation.org/display/TSMTGPL/Installing+tranSMART+from+Source . But instead of the zip files I cloned the git repositories. I am using Ubuntu 12.04 (terminal only). 

With version 2.2.4 I get the question if I want to upgrade Hibernate. If I select no I get:

2.2.4 no

grails compile --stacktrace
| Environment set to development.....
> You currently already have a version of the plugin installed [hibernate-2.2.4]. Do you want to update to [hibernate-3.6.10.4]? [y,n] n
| Compiling 1 source files.
| Error Fatal error during compilation org.apache.tools.ant.BuildException: Compilation Failed (NOTE: Stack trace has been filtered. Use --verbose to see entire trace.)
org.springframework.beans.factory.BeanDefinitionStoreException: Failed to read candidate component class: URL [jar:file:/home/jenkins/.grails/ivy-cache/org.grails/grails-hibernate/jars/grails-hibernate-2.2.4.jar!/org/codehaus/groovy/grails/compiler/gorm/GormTransformer.class]; nested exception is java.lang.NoClassDefFoundError: org/springframework/core/type/classreading/AnnotationMetadataReadingVisitor
at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:290)
at org.springframework.context.annotation.ClassPathBeanDefinitionScanner.doScan(ClassPathBeanDefinitionScanner.java:242)
at org.springframework.context.annotation.ClassPathBeanDefinitionScanner.scan(ClassPathBeanDefinitionScanner.java:220)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.codehaus.gant.GantBuilder.invokeMethod(GantBuilder.java:99)
at _GrailsCompile_groovy$_run_closure3_closure8_closure9.doCall(_GrailsCompile_groovy:62)
at _GrailsCompile_groovy$_run_closure3_closure8_closure9.doCall(_GrailsCompile_groovy)
at _GrailsCompile_groovy.withCompilationErrorHandling(_GrailsCompile_groovy:69)
at _GrailsCompile_groovy.this$4$withCompilationErrorHandling(_GrailsCompile_groovy)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:133)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:168)
at _GrailsCompile_groovy$_run_closure3_closure8.doCall(_GrailsCompile_groovy:61)
at _GrailsCompile_groovy$_run_closure3_closure8.doCall(_GrailsCompile_groovy)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:133)
at _GrailsCompile_groovy$_run_closure3.doCall(_GrailsCompile_groovy:58)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:133)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16_closure18.doCall(GantBinding.groovy:185)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16_closure18.doCall(GantBinding.groovy)
at org.codehaus.gant.GantBinding.withTargetEvent(GantBinding.groovy:90)
at org.codehaus.gant.GantBinding.this$4$withTargetEvent(GantBinding.groovy)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16.doCall(GantBinding.groovy:185)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16.doCall(GantBinding.groovy)
at org.codehaus.gant.GantMetaClass.processClosure(GantMetaClass.java:81)
at org.codehaus.gant.GantMetaClass.processArgument(GantMetaClass.java:95)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:128)
at _GrailsCompile_groovy$_run_closure2.doCall(_GrailsCompile_groovy:45)
at org.codehaus.gant.GantMetaClass.invokeMethod(GantMetaClass.java:133)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16_closure18.doCall(GantBinding.groovy:185)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16_closure18.doCall(GantBinding.groovy)
at org.codehaus.gant.GantBinding.withTargetEvent(GantBinding.groovy:90)
at org.codehaus.gant.GantBinding.this$4$withTargetEvent(GantBinding.groovy)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16.doCall(GantBinding.groovy:185)
at org.codehaus.gant.GantBinding$_initializeGantBinding_closure5_closure16.doCall(GantBinding.groovy)
at gant.Gant$_dispatch_closure5.doCall(Gant.groovy:381)
at gant.Gant$_dispatch_closure7.doCall(Gant.groovy:415)
at gant.Gant$_dispatch_closure7.doCall(Gant.groovy)
at gant.Gant.withBuildListeners(Gant.groovy:427)
at gant.Gant.this$2$withBuildListeners(Gant.groovy)
at gant.Gant$this$2$withBuildListeners.callCurrent(Unknown Source)
at gant.Gant.dispatch(Gant.groovy:415)
at gant.Gant.this$2$dispatch(Gant.groovy)
at gant.Gant.invokeMethod(Gant.groovy)
at gant.Gant.executeTargets(Gant.groovy:591)If
at gant.Gant.executeTargets(Gant.groovy:590)
Caused by: java.lang.NoClassDefFoundError: org/springframework/core/type/classreading/AnnotationMetadataReadingVisitor
at org.springframework.core.type.classreading.SimpleMetadataReader.<init>(SimpleMetadataReader.java:63)
at org.springframework.core.type.classreading.SimpleMetadataReaderFactory.getMetadataReader(SimpleMetadataReaderFactory.java:80)
at org.springframework.core.type.classreading.CachingMetadataReaderFactory.getMetadataReader(CachingMetadataReaderFactory.java:102)
at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:266)
... 44 more
Caused by: java.lang.ClassNotFoundException: org.springframework.core.type.classreading.AnnotationMetadataReadingVisitor
... 48 more
| Error Fatal error during compilation org.apache.tools.ant.BuildException: Compilation Failed

However, if I select yes I get:

grails compile --stacktrace
| Environment set to development.....
> You currently already have a version of the plugin installed [hibernate-2.2.4]. Do you want to update to [hibernate-3.6.10.4]? [y,n] y
| Installed plugin hibernate-3.6.10.4
| Error Plugin hibernate-3.6.10.4 requires version [2.3.2 > *] of Grails which your current Grails installation does not meet. Please try install a different version of the plugin or Grails.
| Installed plugin hibernate-3.6.10.4.

So I installed Grails 2.3.2 and selected it on my PATH instead of Grails 2.2.4. The command 'grails upgrade' completes successfully. If I then compile I get:

::::::::::::::::::::::::::::::::::::::::::::::
::          UNRESOLVED DEPENDENCIES         ::
::::::::::::::::::::::::::::::::::::::::::::::
:: org.grails.plugins#hibernate;2.3.2: not found
::::::::::::::::::::::::::::::::::::::::::::::

| Error Resolve error obtaining dependencies: Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

- org.grails.plugins:hibernate:2.3.2

 (Use --stacktrace to see the full trace)
| Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

- org.grails.plugins:tomcat:2.3.2

| Run 'grails dependency-report' for further information.
| Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

- org.grails.plugins:hibernate:2.3.2

| Run 'grails dependency-report' for further information.
| Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

- org.grails.plugins:hibernate:2.3.2

| Run 'grails dependency-report' for further information.
| Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

- org.grails.plugins:hibernate:2.3.2

| Run 'grails dependency-report' for further information.

grails dependency-report doesn't give me much more information than above, except that it tries different URL's which are not existing. 

Which version of Grails is required? I think 2.2.4 is the current default version for Transmart. I installed Grails by downloading and extracting the zip file from their website. On Ubuntu, Grails doesn't go further than 2.1.2 via the package manager. How can I solve the above errors?

Thanks so much in advance,
Erwin



Freek de Bruijn

unread,
Apr 3, 2014, 3:43:45 AM4/3/14
to transmar...@googlegroups.com
Hi Edwin,

When I tried to get tranSMART running from source a few weeks ago, I ran into similar issues (also on Ubuntu). In the end, I could not get it to work with the help of the tutorial you mentioned. However, I did get a working system using this repository (and the explanation in the README.md file):



Good luck!

Cheers, Freek



--
You received this message because you are subscribed to the Google Groups "transmart-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to transmart-disc...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Ruslan Forostianov

unread,
Apr 3, 2014, 3:50:18 AM4/3/14
to transmar...@googlegroups.com
Hi Erwin,

I guess you have hibernate plugin version depends on grails version in BuildConfig.groovy
Something like:
`
plugins {
        compile ':hibernate:${grailsVersion}'
}
`

But It looks like not the case for newer grails. I have grails 2.3.5 and hibernate plugin with version 3.6.10.7
I'd propose you to create new project with `grails create test` and see what hibernate version your grails refers to.



On Thu, Apr 3, 2014 at 9:35 AM, Erwin Vast <erwi...@gmail.com> wrote:

--
You received this message because you are subscribed to the Google Groups "transmart-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to transmart-disc...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.



--
Ruslan Forostianov,
Software Developer
www.thehyve.nl
E rus...@thehyve.nl
M +31(0)6 83 51 30 81
Skype foro.ru

Erwin Vast

unread,
Apr 3, 2014, 4:00:27 AM4/3/14
to transmar...@googlegroups.com
Thanks Freek for sharing your experience! Are you sure you mean https://github.com/thehyve/transmart-data and not git checkout https://github.com/thehyve/transmartAppInstaller.git and git checkout https://github.com/transmart/transmartApp.git ? Or is transmart-data a super project of the other two?

@Rusian: I'm not exacte sure what you mean, but I run grails create test and selected createApp_. Then I see in the BuildConfig.groovy of that project:

runtime ":hibernate:3.6.10.3" // or ":hibernate4:4.1.11.2"

Is this something I can select during compilation? 

Freek de Bruijn

unread,
Apr 3, 2014, 4:12:53 AM4/3/14
to transmar...@googlegroups.com
Hi Erwin,


(I've tried the github.com/thehyve/transmartAppInstaller too, but couldn't get that to work either.)

Getting tranSMART to run from source is a bit of a challenge, but in the end it's very rewarding... :-)

Cheers, Freek

P.S. Sorry for misspelling your name, it' early ;-)
------
Freek de Bruijn
Scientific programmer | BioMedBridges & TraIT

Vivek Ratnaparkhi

unread,
Apr 3, 2014, 2:54:03 PM4/3/14
to transmar...@googlegroups.com
Hello Erwin,

I am facing the same issue while building the transmart v1.1 from source. I am using grails 2.2.5. I tried the solution what Freek has suggested but that didn't solved the issue. Are you able to solve the issue ?

Thanks,Vivek

Freek de Bruijn

unread,
Apr 3, 2014, 6:26:11 PM4/3/14
to transmar...@googlegroups.com
Hi Erwin and Vivek,

To clarify: you can use the github.com/thehyve/transmart-data repository to create the tranSMART database, import some example data, and other preparations before tranSMART can run on your system.

After the initialization work is done, you can use the github.com/thehyve/transmartApp repository to run tranSMART.

Just as Ruslan, I'm using Grails 2.3.5 and Hibernate 3.6.10.7 (as specified for the The Hyve branch of tranSMART, see the github.com/thehyve/transmartApp/blob/master/grails-app/conf/BuildConfig.groovy file). The transmart branch version of the BuildConfig.groovy file (see github.com/transmart/transmartApp/blob/master/grails-app/conf/BuildConfig.groovy) uses the Grails version for the Hibernate plugin version: 'compile ":hibernate:$grailsVersion"', which results in the error message.

For installing and managing (different versions of) Grails on Ubuntu, you can use gvm (the Groovy enVironment Manager, see gvmtool.net). I'm not sure which version of Grails is commonly used for tranSMART, but Grails 2.3.5 seems to work fine. (By the way, I'm using Ubuntu 13.10.)

Finally two changes I made to the BuildConfig.groovy file that could be useful:
  • On line 51 (after the "grails.project.dependency.resolver" line) I inserted port number 8090 (instead of the default 8080):
    grails.server.port.http = 8090

  • On line 63 (after the "either hyve or transmartfoundation repository" line) I inserted the configuration for the Maven repository of The Hyve:
        //Note: External configuration should contain
        //either hyve or transmartfoundation repository
        mavenRepo([
            name: 'repo.thehyve.nl-public',
        ])


Hope this helps to get things working.

Cheers, Freek


Erwin Vast

unread,
Apr 4, 2014, 3:06:11 AM4/4/14
to transmar...@googlegroups.com
Hi all,

Unfortunately I cannot test it before Monday, but I will definitely let you know if it works for me!

Thanks,
Erwin

Vivek Ratnaparkhi

unread,
Apr 4, 2014, 3:17:21 AM4/4/14
to transmar...@googlegroups.com
Hello Freek,

Thank you very much for your suggestions. I will try this and let you know.

Thanks,Vivek

Erwin Vast

unread,
Apr 8, 2014, 9:23:47 AM4/8/14
to transmar...@googlegroups.com
Hi Freek,

Thanks a lot! Got much further know. But it's not working yet ;)

When starting Tomcat I get the following error:

2014-04-08 15:14:08,647 [pool-2-thread-1] ERROR resource.ResourceMeta  - While processing /bundle-bundle_main_mod_head.css, /css/main.css, a resource was required but not found: /images/feedback.png
2014-04-08 15:14:08,697 [pool-2-thread-1] ERROR resource.ResourceMeta  - While processing /bundle-bundle_main_mod_head.css, /css/main.css, a resource was required but not found: /images/feedback.png
2014-04-08 15:14:14,288 [pool-2-thread-1] ERROR BootStrap  - Something wrong happened parsing the externalized Config.groovy, because we could not find the configuration setting 'org.transmart.configFine set to true.
Tip: on ~/.grails/transmartConfig, run
groovy -e 'new ConfigSlurper().parse(new File("Config.groovy").toURL())'
to detect compile errors. Other errors can be detected with a breakpoing on the catch block in ConfigurationHelper::mergeInLocations().
Alternatively, you can change the console logging settings by editing $GRAILS_HOME/scripts/log4j.properties, adding a proper appender and log org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper at level WARN
2014-04-08 15:14:14,312 [pool-2-thread-1] ERROR context.GrailsContextLoader  - Error initializing the application: Configuration magic setting not found
org.codehaus.groovy.grails.exceptions.GrailsConfigurationException: Configuration magic setting not found
at BootStrap$_closure1.doCall(BootStrap.groovy:59)
at grails.util.Environment.evaluateEnvironmentSpecificBlock(Environment.java:308)
at grails.util.Environment.executeForEnvironment(Environment.java:301)
at grails.util.Environment.executeForCurrentEnvironment(Environment.java:277)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
2014-04-08 15:14:14,315 [pool-2-thread-1] ERROR context.GrailsContextLoader  - Error initializing Grails: Configuration magic setting not found
org.codehaus.groovy.grails.exceptions.GrailsConfigurationException: Configuration magic setting not found
at BootStrap$_closure1.doCall(BootStrap.groovy:59)
at grails.util.Environment.evaluateEnvironmentSpecificBlock(Environment.java:308)
at grails.util.Environment.executeForEnvironment(Environment.java:301)
at grails.util.Environment.executeForCurrentEnvironment(Environment.java:277)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
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:722)

When running groovy -e 'new ConfigSlurper().parse(new File("Config.groovy").toURL())' I get an empty response. 

Did you also received this error and/or know a solution to solve it? Perhaps it has to do with that it has to use a configuration of transmart-data?

Thanks,
Erwin

Freek de Bruijn

unread,
Apr 8, 2014, 10:02:06 AM4/8/14
to transmar...@googlegroups.com
Hi Erwin,

Yes, I've encountered the "Configuration magic setting not found" message too. This is something of a safety measure: the Config.groovy file in the ~/.grails/transmartConfig directory should have the "org.transmart.configFine = true" setting (at the end of the file).

You could check whether you have a Config.groovy file in the ~/.grails/transmartConfig directory and make sure it has the configFine line. The file is indeed generated by the makefiles of the transmart-data repository (check the transmart-data/config directory); I'm not sure whether the file has to be copied to the ~/.grails/transmartConfig directory manually.

By the way, when you wrote "starting Tomcat", did you mean by running the "grails run-app" command?

When I run groovy -e 'new ConfigSlurper().parse(new File("Config.groovy").toURL())' in the ~/.grails/transmartConfig directory, I don't get any output either. I assume this is good news; it should detect compile errors, so no output = no errors.

Cheers, Freek


Erwin Vast

unread,
Apr 8, 2014, 10:31:28 AM4/8/14
to transmar...@googlegroups.com
Hi Freek,

Yes, all the Config.groovy files are there. In fact, the transmart-data/config/Config.groovy is exactly the same as the ~/.grails/transmartConfig/Config.groovy. I did not copied it. The configFine line is also set. 

I created a (grails) war from the transmartApp and then copied it to the webapps directory in tomcat, then started tomcat. For some reason this apparently doesn't work. I just tested grails run-app and then it "works". It now prints info messages that is loads the transmart groovy files :) I think I'm going to use this setup: it is only for development, not production. I now get the error:

  | Error 2014-04-08 16:24:05,455 [localhost-startStop-1] ERROR pool.ConnectionPool  - Unable to create initial connections of pool.
  Message: Driver:org.postgresql.Driver@35d58c95 returned null for URL:jdbc:postgresql://localhost:/

Did you get this error too? I think the database is setup correctly, all other steps (primarily transmart-data) completed succesfully. This is my vars-ubuntu:

PGHOST=
PGPORT=5432
PGDATABASE=transmart
PGUSER=postgres
PGPASSWORD=

Thanks,
Erwin

Erwin Vast

unread,
Apr 8, 2014, 10:33:46 AM4/8/14
to transmar...@googlegroups.com
In my previous post I only pasted a part of vars-ubuntu. This is the remaining part:

PGSQL_BIN="sudo -E -u postgres /usr/bin/"
TABLESPACES=/var/lib/postgresql/tablespaces/
KETTLE_JOBS_PSQL=/home/jenkins/transmart-data/env/tranSMART-ETL/Postgres/GPL-1.0/Kettle/Kettle-ETL/
KITCHEN=/home/jenkins/transmart-data/env/data-integration/kitchen.sh

PATH=/home/jenkins/transmart-data/env:$PATH

export PGHOST PGPORT PGDATABASE PGUSER PGPASSWORD TABLESPACES PGSQL_BIN \
        KETTLE_JOBS_PSQL KITCHEN PATH

Erwin

Erwin Vast

unread,
Apr 8, 2014, 10:41:22 AM4/8/14
to transmar...@googlegroups.com
Are sudo rights perhaps required? This is not preferred I think, but is requires the postgres user (also in PGSQL_BIN), which in turn required sudoers rights.

Terry Weymouth

unread,
Apr 8, 2014, 5:16:13 PM4/8/14
to transmar...@googlegroups.com
The missing image file is here: https://github.com/transmart/transmartApp/tree/master/web-app/images (as you can see from the commet, which is from the latest commit, someone else found that file to be missing). What branch, or tag, are you building from?

Terry Weymouth

unread,
Apr 8, 2014, 5:29:06 PM4/8/14
to transmar...@googlegroups.com
Regarding the requirement for 'org.transmart.configFine' to appear in the configuration file: This requirement first appeared in the ImperialBranch branch of transmartApp, about 8 months ago. Are you using the ImperialBranch branch of transmartApp for your build? 

The configuration files are loaded from this archive: https://github.com/transmart/transmartApp-Config and it is probably a good idea to check for a tag or branch that seems to correspond to the tag or branch that you are using for the build, and use the Config.groovy file from that tag or branch, e.g. https://github.com/transmart/transmartApp-Config/blob/ImperialBranch/Config.groovy. Or, at least check that file against the one you are using and fix the differences.

Gustavo André dos Santos Lopes

unread,
Apr 8, 2014, 7:30:34 PM4/8/14
to transmar...@googlegroups.com
On 8 April 2014 16:33, Erwin Vast <erwi...@gmail.com> wrote:
> In my previous post I only pasted a part of vars-ubuntu. This is the
> remaining part:
>
> PGSQL_BIN="sudo -E -u postgres /usr/bin/"
> TABLESPACES=/var/lib/postgresql/tablespaces/
> KETTLE_JOBS_PSQL=/home/jenkins/transmart-data/env/tranSMART-ETL/Postgres/GPL-1.0/Kettle/Kettle-ETL/
> KITCHEN=/home/jenkins/transmart-data/env/data-integration/kitchen.sh
>
> PATH=/home/jenkins/transmart-data/env:$PATH
>
> export PGHOST PGPORT PGDATABASE PGUSER PGPASSWORD TABLESPACES PGSQL_BIN \
> KETTLE_JOBS_PSQL KITCHEN PATH
>

The relevant setting here would be TSUSER_HOME. This is not set in
vars-ubuntu, in which case it defaults to $HOME. This is OK for
development (which is what transmart-data's defaults are oriented
towards) because then you typically run transmart under your own user,
but it won't work if you're running transmart as another user. In that
case, the config files should be in that user's home directory
instead. Try

TSUSER_HOME=~tomcat7 sudo -E make -C config install

Replace tomcat7 with whatever user you're running transmart under.

--
Gustavo Lopes

Erwin Vast

unread,
Apr 9, 2014, 6:51:34 AM4/9/14
to transmar...@googlegroups.com
Hi all, 

Thanks for your responses. I'm using the Transmart versions of https://github.com/transmart/transmart-data and https://github.com/transmart/transmartApp, as Freek suggested. I found out that the database configuration in /home/jenkins/.grails/transmartConfig/DataSource.groovy was incorrect, I don't know why. After I changed the URL and password, I didn't receive any errors anymore with grails run-app. However, I get the following error when loading the webpage:

Error 500: Internal Server Error
URI:/transmart/login/auth
Class:org.postgresql.util.PSQLException
Message: ERROR: relation "search_auth_user" does not exist Position: 689

Followed by a stacktrace. I also recreated the database with the manual on https://github.com/transmart/transmart-data, but with no success. Perhaps there is a version incompatibility between the two repositories, as Terry suggested. Any ideas?

Thanks,
Erwin

Erwin Vast

unread,
Apr 9, 2014, 7:19:04 AM4/9/14
to transmar...@googlegroups.com
An update to my previous post. I added the incorrect URL's. It should be github.com/thehyve/transmart-data and github.com/thehyve/transmartApp

Thehyve transmartApp does not have a setup.sh file as the normal transmartApp has. The manual describes the required steps, but I'm not sure if something is missing, because my postgresql transmart database is quite empty (3 or 4 tables). 

Kees van Bochove

unread,
Apr 9, 2014, 9:07:21 AM4/9/14
to transmar...@googlegroups.com
Hello Erwin,

3 or 4 tables definitely isn't right. Something most have run amiss when you recreated the database using transmart-data. Check the logs?


Met vriendelijke groet / Kind regards,

Kees van Bochove

www.thehyve.nl
E
ke...@thehyve.nl
T +31(0)30 700 9713
M +31(0)6 10 83 53 64
Skype
keesboston



--

Erwin Vast

unread,
Apr 10, 2014, 2:59:03 AM4/10/14
to transmar...@googlegroups.com
Hi Kees,

Found out I only saw the public tables with /dt in psql. Should have used /dt .* to see all tables (51). 

Perhaps something is going wrong with the queries themself. The error message via the postgres log is:

    2014-04-09 08:53:15 CEST ERROR:  relation "search_auth_user" does not exist at character 678
    2014-04-10 08:53:15 CEST STATEMENT:  select this_.ID as ID69_1_, this_1_.DATE_CREATED as DATE2_69_1_, this_1_.DESCRIPTION as DESCRIPT3_69_1_, this_1_.ENABLED as ENABLED69_1_, this_1_.LAST_UPDATED as LAST5_69_1_, this_1_.NAME as NAME69_1_,   this_1_.PRINCIPAL_TYPE as PRINCIPAL7_69_1_, this_1_.UNIQUE_ID as UNIQUE8_69_1_, this_.EMAIL as EMAIL70_1_, this_.EMAIL_SHOW as EMAIL3_70_1_, this_.federated_id as federated4_70_1_, this_.PASSWD as PASSWD70_1_, this_.USER_REAL_NAME as USER6_70_1_, this_.USERNAME as USERNAME70_1_, authoritie3_.AUTHORITIES_ID as AUTHORIT1_69_3_, a1_.id as PEOPLE2_3_, a1_.id as id127_0_, a1_.version as version127_0_, a1_.authority as authority127_0_, a1_.description as descript4_127_0_ from SEARCH_AUTH_USER this_ inner join SEARCH_AUTH_PRINCIPAL this_1_ on this_.ID=this_1_.ID left outer join SEARCH_ROLE_AUTH_USER authoritie3_ on this_.ID=authoritie3_.AUTHORITIES_ID left outer join SEARCH_ROLE a1_ on authoritie3_.PEOPLE_ID=a1_.id where this_.USERNAME=$1

If I execute the query 'SELECT * FROM search_auth_user' in the console via psql (after connecting with database 'transmart') I receive a similar error. But if I execute the following query:

    SELECT * FROM searchapp.search_auth_user;

It works (in the console) by prepending the searchapp schema. There are also other schema's, such as biomart, deapp, tm_cs. 
Is this correct? Why does the transmart webapp not add the searchapp schema? I'm using postgresql version 9.1.13.

Thanks,
Erwin

Gustavo André dos Santos Lopes

unread,
Apr 10, 2014, 4:22:16 AM4/10/14
to transmar...@googlegroups.com
On 10 April 2014 08:59, Erwin Vast <erwi...@gmail.com> wrote:
> If I execute the query 'SELECT * FROM search_auth_user' in the console via
> psql (after connecting with database 'transmart') I receive a similar error.
> But if I execute the following query:
>
> SELECT * FROM searchapp.search_auth_user;
>
> It works (in the console) by prepending the searchapp schema. There are also
> other schema's, such as biomart, deapp, tm_cs.
> Is this correct? Why does the transmart webapp not add the searchapp schema?
> I'm using postgresql version 9.1.13.
>

See http://www.postgresql.org/docs/9.1/static/ddl-schemas.html#DDL-SCHEMAS-PATH

If you login as biomart_user (default password is biomart_user), the
search path should be correctly set. See here:
https://github.com/thehyve/transmart-data/blob/master/ddl/postgres/GLOBAL/roles.sql

--
Gustavo Lopes

Erwin Vast

unread,
Apr 10, 2014, 5:37:08 AM4/10/14
to transmar...@googlegroups.com
Thanks all! Now it works :)

Vivek Ratnaparkhi

unread,
Apr 10, 2014, 10:51:12 AM4/10/14
to transmar...@googlegroups.com
Hello Freek,

I have followed the steps you have mentioned. After upgrading and running 'grails run-app' I am getting below exception.

Any idea, what can be the isssue ?

Thanks,Vivek

2014-04-10 20:00:25,489 [localhost-startStop-1] ERROR context.GrailsContextLoader  - Error initializing the application: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    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:744)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
Caused by: org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
2014-04-10 20:00:25,493 [localhost-startStop-1] ERROR context.GrailsContextLoader  - Error initializing Grails: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    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:744)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
Caused by: org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
    ... 5 more
Apr 10, 2014 8:00:25 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Apr 10, 2014 8:00:25 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/transmart] startup failed due to previous errors
Apr 10, 2014 8:00:25 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/transmart] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Apr 10, 2014 8:00:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /home/viv/Desktop/transMART/apache-tomcat-7.0.52/webapps/ROOT
Apr 10, 2014 8:00:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /home/viv/Desktop/transMART/apache-tomcat-7.0.52/webapps/docs
Apr 10, 2014 8:00:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /home/viv/Desktop/transMART/apache-tomcat-7.0.52/webapps/examples
Apr 10, 2014 8:00:26 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /home/viv/Desktop/transMART/apache-tomcat-7.0.52/webapps/host-manager
Apr 10, 2014 8:00:26 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /home/viv/Desktop/transMART/apache-tomcat-7.0.52/webapps/manager
Apr 10, 2014 8:00:26 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Apr 10, 2014 8:00:26 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Apr 10, 2014 8:00:26 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 37178 ms

Michael Tommie McDuffie

unread,
Apr 10, 2014, 10:56:59 AM4/10/14
to transmar...@googlegroups.com
Sometimes when I've gotten "Second-level cache is not enabled for usage" it is because grails can't find my external DataSource.groovy configuration file. 

The path to that config should be "${userHome}/.grails/${appName}Config/DataSource.groovy". You can try debugging or printing from the internal Config.groovy to verify the correct path is being used.

Vivek Ratnaparkhi

unread,
Apr 15, 2014, 4:51:07 AM4/15/14
to transmar...@googlegroups.com
Thanks Michael. It was the same issue, now it's working.

Thanks,Vivek


--
You received this message because you are subscribed to a topic in the Google Groups "transmart-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/transmart-discuss/KUT6ctvn5wM/unsubscribe.
To unsubscribe from this group and all its topics, send an email to transmart-disc...@googlegroups.com.

kpr...@uic.edu

unread,
Jun 18, 2015, 3:57:22 PM6/18/15
to transmar...@googlegroups.com
Hi Vivek,

I am very new to transmart installation and I am currently facing the same issue that you faced: 
"2015-06-16 16:19:51,602 [localhost-startStop-1] ERROR context.GrailsContextLoader  - Error initializing Grails: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]"

I read your and Michael's comments on the same, however I did not follow how it was resolved. Can you please share your resolution steps for this error.

Regards
Kartikey

Vivek Ratnaparkhi

unread,
Jun 19, 2015, 6:15:52 AM6/19/15
to transmar...@googlegroups.com
Hello Kartikey,

I was getting that error when transmart was not able to connect to the database server. To connect to the database server transmart looks for the file "DataSource.groovy" at location "$HOME/.grails/transmartConfig/DataSource.groovy" (I assume you are using Linux). Please check if the same file is present at specified location with correct database parameters.

Let me know if that helps.

Thanks,
Vivek

kpr...@uic.edu

unread,
Jun 22, 2015, 11:16:40 AM6/22/15
to transmar...@googlegroups.com
HI Vivek,

I checked for "DataSource.groovy" file in my system and i found it in 2 places:
./usr/share/tomcat7.grails/transmartConfig/DataSource.groovy
./home/kartikey/tranSMARTV1.2/transmart-data/config/DataSource.groovy

Also, there does not exist any .grails directory in my system. I followed the steps mentioned in the "TranSMART Installation (The Hyve)" --> https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205

Can you please let me know if there should be any other location as well that there should exist "DataSource.groovy" file. 

Regards
Kartikey

Vivek Ratnaparkhi

unread,
Jun 22, 2015, 2:31:25 PM6/22/15
to transmar...@googlegroups.com
Hi Karikey,

Please try moving the ".grails" directory located in "/usr/share/tomcat7" directory into your users home directory. For example if you are running Tomcat with root user then please move ".grails" directory to "/root" directory.

The ".grails" directory should be present in users home directory.

Thanks,
Vivek

Kartikey Pradhan

unread,
Jun 22, 2015, 2:43:55 PM6/22/15
to transmar...@googlegroups.com
Thanks a lot Vivek,

I tried your suggestion just few minutes back and still I am facing the same problem. Here are the results from catalina.out:

INFO: Server startup in 31246 ms
Jun 22, 2015 1:50:44 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Jun 22, 2015 1:50:44 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Jun 22, 2015 1:50:44 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Jun 22, 2015 1:50:44 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Jun 22, 2015 1:50:49 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 22, 2015 1:50:49 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 22, 2015 1:50:49 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Jun 22, 2015 1:50:49 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 22, 2015 1:50:49 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Jun 22, 2015 1:50:50 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Jun 22, 2015 1:50:50 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 677 ms
Jun 22, 2015 1:50:50 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jun 22, 2015 1:50:50 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Jun 22, 2015 1:50:50 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/examples.xml
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/manager.xml
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/docs.xml
Jun 22, 2015 1:50:51 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/transmart.war
Jun 22, 2015 1:51:01 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
[INFO] Configuration file /usr/share/tomcat7/.grails/transmartConfig/Config.groovy does not exist.
[INFO] Configuration file /usr/share/tomcat7/.grails/transmartConfig/DataSource.groovy does not exist.
[INFO] Configuration file /usr/share/tomcat7/.grails/transmartConfig/Config.groovy does not exist.
[INFO] Configuration file /usr/share/tomcat7/.grails/transmartConfig/DataSource.groovy does not exist.

Configuring Spring Security Core ...
... finished configuring Spring Security Core

2015-06-22 13:51:20,082 [localhost-startStop-1] ERROR context.GrailsContextLoader  - Error initializing the application: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        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)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
Caused by: org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
2015-06-22 13:51:20,084 [localhost-startStop-1] ERROR context.GrailsContextLoader  - Error initializing Grails: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        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)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
Caused by: org.hibernate.cache.NoCachingEnabledException: Second-level cache is not enabled for usage [hibernate.cache.use_second_level_cache | hibernate.cache.use_query_cache]
        ... 5 more
Jun 22, 2015 1:51:20 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Jun 22, 2015 1:51:20 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/transmart] startup failed due to previous errors
Jun 22, 2015 1:51:20 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/transmart] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Jun 22, 2015 1:51:20 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Jun 22, 2015 1:51:20 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/test
Jun 22, 2015 1:51:20 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jun 22, 2015 1:51:20 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 30077 ms

Please be advised that I am trying to install transmart V1.2 so I am not sure how grails dependency are associated in installation.
Please advise if you think of any other step that I can follow to resolve this problem.
Thanks a lot.

Regards
Kartikey

Kartikey Pradhan

unread,
Jun 22, 2015, 3:17:43 PM6/22/15
to transmar...@googlegroups.com
Hi Vivek,

Now my application is running. 
I followed you suggestion of moving the .grails file, however not to /root, but to /usr/share/tomcat7/ directory.
Thanks a lot for your suggestions.

Regards
Kartikey
Reply all
Reply to author
Forward
0 new messages