[InterMine Dev] build-db-userprofile fails

Julie Sullivan julie at flymine.org
Fri Oct 26 13:01:57 BST 2012


Hi Intikhab

I took a look but the line numbers in the code in the error message you supplied 
don't match with my line numbers.

Can you verify that you are on the "master" branch?

$ git branch
* master
   release-intermine-1.1

And you have the latest code:

$ git pull
remote: Counting objects: 21, done.
remote: Compressing objects: 100% (1/1), done.
remote: Total 11 (delta 8), reused 11 (delta 8)
Unpacking objects: 100% (11/11), done.
 From github.com:intermine/intermine
    b43c708..5f20ab1  dev        -> origin/dev
Already up-to-date.

Thanks!

On 26/10/12 12:58, Dr Intikhab Alam wrote:
> Dear intermine help, we could not resolve the unable to construct query error c/o my email below, can u help?
>
> Intikhab
> -----Original Message-----
> From: Dr Intikhab Alam
> Sent:  24/10/2012, 16:12
> To: dev at intermine.org
> Subject: [InterMine Dev] build-db-userprofile fails
>
> Dear Intermine,
>
> I am seeing the following error when running ant build-db-userprofile in my webapp dir. This is a test on the latest intermien release.
>
> -init-build-db:
>
> -do-build-db-userprofile:
>   [build-db] Our new url ->  jdbc:postgresql://localhost/userprofile-cbrcredseamine
>   [build-db] Our new url ->  jdbc:postgresql://localhost/userprofile-cbrcredseamine
>
> -load-default-templates:
> [load-default-templates] Loading default templates and tags into profile intikhab.alam at kaust.edu.sa
> [load-default-templates] java.lang.RuntimeException: Error retrieving the bag with bagId : null
> [load-default-templates]        at org.intermine.api.bag.SharedBagManager.getSharedBags(SharedBagManager.java:161)
> [load-default-templates]        at org.intermine.api.profile.Profile.getSharedBags(Profile.java:735)
> [load-default-templates]        at org.intermine.api.search.UserRepository.populateSearchItems(UserRepository.java:67)
> [load-default-templates]        at org.intermine.api.search.SearchRepository.<init>(SearchRepository.java:66)
> [load-default-templates]        at org.intermine.api.search.UserRepository.<init>(UserRepository.java:28)
> [load-default-templates]        at org.intermine.api.profile.Profile.<init>(Profile.java:108)
> [load-default-templates]        at org.intermine.api.profile.Profile.<init>(Profile.java:141)
> [load-default-templates]        at org.intermine.web.ProfileHandler.getProfile(ProfileHandler.java:110)
> [load-default-templates]        at org.intermine.web.ProfileBinding.unmarshal(ProfileBinding.java:176)
> [load-default-templates]        at org.intermine.web.task.LoadDefaultTemplatesTask.execute(LoadDefaultTemplatesTask.java:150)
> [load-default-templates]        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> [load-default-templates]        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> [load-default-templates]        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> [load-default-templates]        at java.lang.reflect.Method.invoke(Method.java:616)
> [load-default-templates]        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> [load-default-templates]        at org.apache.tools.ant.Task.perform(Task.java:348)
> [load-default-templates]        at org.apache.tools.ant.Target.execute(Target.java:392)
> [load-default-templates]        at org.apache.tools.ant.Target.performTasks(Target.java:413)
> [load-default-templates]        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> [load-default-templates]        at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> [load-default-templates]        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> [load-default-templates]        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> [load-default-templates]        at org.apache.tools.ant.Main.runBuild(Main.java:811)
> [load-default-templates]        at org.apache.tools.ant.Main.startAnt(Main.java:217)
> [load-default-templates]        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> [load-default-templates]        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> [load-default-templates] Caused by: java.lang.NullPointerException
> [load-default-templates]        at org.intermine.api.bag.SharedBagManager.getSharedBags(SharedBagManager.java:150)
> [load-default-templates]        ... 25 more
>
> BUILD FAILED
> /home/cbrcmine/biosoft/intermine.20121024.1316hrs/intermine/imbuild/application.xml:88: java.lang.RuntimeException: java.lang.RuntimeException: Error retrieving the bag with bagId : null
>
>
>
> What does this "Error retrieving the bag with bagId : null" mean and how can I resolve this, please.
>
>
> Thanks,
>
> Intikhab
>
> This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
>
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