[InterMine Dev] build-db-userprofile fails

Dr Intikhab Alam intikhab.alam at kaust.edu.sa
Fri Oct 26 13:48:47 BST 2012

Dear Julie, this error i reported was from intermine release we downloaded from git last month. My collegue observed the same error from the latest release we got this week.

-----Original Message-----
From: Julie Sullivan
Sent:  26/10/2012, 15:02
To: Dr Intikhab Alam
Cc: dev at intermine.org
Subject: Re: [InterMine Dev] build-db-userprofile fails

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

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.


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
> /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
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