[MOBY-dev] Problems with biomoby plugins in taverna

[Stian Soiland-Reyes]

On Thu, Oct 2, 2008 at 14:26, Stian Soiland-Reyes
<soiland-reyes at cs.manchester.ac.uk> wrote:

> this needs further investigation.
>

A BioMoby exception happens as it's calling runDecypherBlastp with:

<?xml version="1.0" encoding="UTF-8"?>
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
  <moby:mobyContent>
    <moby:mobyData moby:queryID="a1">
      <moby:Simple moby:articleName="sequence">
        <moby:AminoAcidSequence namespace="" id="aaaa">
          <Integer xmlns="http://www.biomoby.org/moby" namespace=""
id="" articleName="Length">20</Integer>
          <String xmlns="http://www.biomoby.org/moby" namespace=""
id="" articleName="SequenceString">YKSLTNDWEDHLAVKHFSVE</String>
        </moby:AminoAcidSequence>
      </moby:Simple>
      <moby:Parameter moby:articleName="database">
        <moby:Value>Swissprot</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="evalue">
        <moby:Value>10</moby:Value>
      </moby:Parameter>
    </moby:mobyData>
  </moby:mobyContent>
</moby:MOBY>


If you want a silly workaround I would try to avoid getting that exception! :-)

Then when this happens, he needs to initialise the MobyException
class, which tries to access org.apache.commons.logging.Log - but
somehow this fails.


-- 
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester