[InterMine Dev] bioseg lower limit of range greater than upper

Richard Smith richard at flymine.org
Wed Feb 29 10:34:20 GMT 2012


Hi Initikhab,
If the script doesn't show any errors that seems strange.  You could run
a query in the database after data has been loaded in but before the
post-processing runs just to make sure:

select * from location where intermine_start > intermine_end;

In FlyMine we don't have any locations with the start as 0, it's
possible that if 0 isn't valid in bioseg and the error message is
just misleading.

Cheers,
Richard.



On 28/02/2012 14:01, Dr. Intikhab Alam wrote:
> Hi,
>
> I am loading my objects from an xml source, all goes fine but the
> postprocess create-bioseg-location-index fails with the following error:
>
> BUILD FAILED
> /home/intikhab/biosoft/intermine_0_98/imbuild/postprocess.xml:31: error
> running PostProcessTask (action: create-bioseg-location-index)
>> ... 17 more
> Caused by: Operation was:create-bioseg-location-index
> at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
> ... 22 more
> Caused by: org.postgresql.util.PSQLException: ERROR: bad bioseg
> representation
> Detail: lower limit of range greater than upper
>
>
> I explicitly check in my script, that produces the objects in xml, to
> throw an error and die if and start value is > end value before I fill
> any of the 'Location'. My script does not show any errors.
>
>
> Any ideas to locate what could be the problem?
>
> Regards,
>
> Intikhab
>
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




More information about the dev mailing list