Hi Darren,

when you hit the count button, please see what goes in the error_log. you would need to switch on the logging to INFO from FATAL in conf/log4perl.conf and reconfigure/restart.

Cheers
Syed


Darren Oakley wrote:
Hi All,

Sorry to disturb, but I'm getting an error which I just can't figure out when doing a count on one of our Marts...

Here's the URL for the search:

http://www.sanger.ac.uk/htgt/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=kermits.default.attributes.sponsor|kermits.default.attributes.marker_symbol|kermits.default.attributes.status&FILTERS=kermits.default.filters.status_code."GC"|kermits.default.filters.centre."WTSI"&VISIBLEPANEL=resultspanel

The search works fine and returns results, but when I try to get a count from this search (I'd like to know the number of genes with this criteria), the mart throws the following error (both in MartView and through the APIs):

Query ERROR: caught BioMart::Exception: non-BioMart die(): Can't use an undefined value as an ARRAY reference at /software/team87/biomart/biomart-0_7-prod/lib/BioMart/Dataset/TableSet.pm line 911.

To get the count, I'm hitting it via the rest api with the following xml:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="1" count="1" datasetConfigVersion="0.6">
  <Dataset name="kermits" interface="default">
    <Filter name="status_code" value="GC"/>
    <Filter name="centre" value="WTSI"/>
  </Dataset>
</Query>

Any idea what could be the issue here?

Thanks,

Daz

P.S. Forgot to let you all know - our new (preview) Mouse portal at the Sanger is now running off Biomart: http://www.sanger.ac.uk/mouseportal/ (well, several biomarts really...) It's still in development, and things can be flaky every now and then, so be gentle! ;)


Reply via email to