[InterMine Dev] Error

Zacher, Stacy szacher at mcw.edu
Wed Sep 19 21:58:01 BST 2018


Hi:

We have attempted to copy our postgres environment for intermine to a new server.  Everything appears to have been copied over, and postgres starts etc. but when we run  

ant -Daction=create-search-index -v

it errors out after about 42 minutes with the errors below.  
Esp Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028


Does anyone have any idea what we might need to do to resolve this?  I'm not the person deploying it - I am the database administrator.
Thanks for any assistance.  

postprocess:
[postprocess] Found 9 post-processes
[postprocess] Performing postprocess: create-search-index
[postprocess] Creating lucene index for keyword search...


BUILD FAILED
/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:435)
        at org.apache.tools.ant.Target.performTasks(Target.java:456)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
        at org.apache.tools.ant.Main.runBuild(Main.java:851)
        at org.apache.tools.ant.Main.startAnt(Main.java:235)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
        ... 17 more
Caused by: Operation was:create-search-index
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)
        ... 22 more
Caused by: java.lang.RuntimeException: Index creation failed:
        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)
        at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)
        ... 22 more
Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
        at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)
        at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)
        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)
        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)
        at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)
        at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)
        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)
        ... 24 more

Total time: 42 minutes 59 seconds


-----Original Message-----
From: Zacher, Stacy 
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; dev at lists.intermine.org
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [mailto:julie at intermine.org]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; dev at lists.intermine.org
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
> Hello:
>
> Our developer is getting an error when trying to get intermine up and
> running on a server that we just rebuilt.   Originally these databases
> were built years ago and whoever built intermine chose the postgres 
> superuser to own all the databases. If possible, we would like to 
> appoint a different database owner instead of postgres.
>
> Is that possible or will intermine not cooperate?   Is it a matter of
> just altering the database and selecting a new owner or would other 
> permissions in postgres need to be changed as well.
>
>
> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for 
> relation intermine_metadata
>
> Any assistance would be appreciate.
>
>
> Thanks!
>
> *Stacy Zacher*
>
> Database Administrator | Information Services
>
> *Medical College of Wisconsin*
>
> szacher at mcw.edu <mailto:szacher at mcw.edu>
>
> 414-955-5654
>
>
>
> _______________________________________________
> dev mailing list
> dev at lists.intermine.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>


More information about the dev mailing list