On 19 Jan 2007, at 15:35, David Withers wrote:
The following patch fixes that. It might be worthwile
to do something like grep 'print "\n.*xml'
to find other instances of this problem lurking in the code.
Yours,
Steffen
Index: martservice.PLS
===================================================================
RCS file: /cvsroot/CVSmaster/biomart-web/cgi-bin/martservice.PLS,v
retrieving revision 1.18
diff -r1.18 martservice.PLS
389c389
< print "\n$xmlTree\n";
---
print "$xmlTree\n";
Hi Steffen,
as I suspected I had already fixed this problem a while back. I just
double checked
with the latest branch and the head code:
bigmac: ~/temp[arek] grep "\$xmlTree"
biomart-perl/cgi-bin/martservice.PLS
my $xmlTree;
$xmlTree = $dset->getConfigurationTree($interface)->toXML() if
($dset);
if ($xmlTree){
print "$xmlTree\n";
bigmac: ~/temp[arek] grep "\$xmlTree"
biomart-perl-branch/cgi-bin/martservice.PLS
my $xmlTree;
$xmlTree = $dset->getConfigurationTree($interface)->toXML() if
($dset);
if ($xmlTree){
print "$xmlTree\n";
so the only explanation for your problem is that your biomart-plib is
not up to date
a.
PS. Cc'ing this mail to mart-dev so David Withers can confirm that
this
should no longer
cause any problems with taverna 1.5
The dataset configuration stream returned by the martservice is handled
by the MartJ method DatasetConfigXMLUtils.getDocumentForXMLStream().
Blank lines at the begining of the stream will cause the
JDOMParseException seen above.
yes I agree but the point is that they are no longer there :)
please check www.biomart.org which is running the latest code.
While we're on the subject of blank lines, I noticed today that when I
send a query that has count="1" the result starts with a blank line.
apart from the one above that is, which I have just removed :)
thanks for reporting this David,
a.
David.
--
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
Tel: +44(0)161 275 0145
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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