On 18 Jan 2007, at 15:19, sneumann wrote:
Hi,
Biomart as of CVS-today (and already in nov 2006)
is causing taverna-1.5 to throw an exception when accessing my
own local installation of biomart,
even though the "production" www.biomart.org works fine.
org.biomart.martservice.MartServiceException: Error getting
configuration from
http://lathan.ipb-sub.ipb-halle.de/biomart/martservice
at
org.biomart.martservice.MartServiceUtils.getDatasetConfig(MartServiceUt
ils.java:269)
at
org.biomart.martservice.MartService.getDatasetConfigFromCache(MartServi
ce.java:350)
at
org.biomart.martservice.MartService.getDatasetConfig(MartService.java:
305)
at
org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory05.get
DatasetConfig(MartServiceQueryConfigUIFactory05.java:177)
at
org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory05$1.r
un(MartServiceQueryConfigUIFactory05.java:228)
Caused by: org.ensembl.mart.lib.config.ConfigurationException:
org.jdom.input.JDOMParseException: Error on line 2: The processing
instruction target matching "[xX][mM][lL]" is not allowed.
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getDocumentForXMLStre
am(DatasetConfigXMLUtils.java:162)
at
org.biomart.martservice.MartServiceUtils.getDatasetConfig(MartServiceUt
ils.java:260)
... 4 more
Caused by: org.jdom.input.JDOMParseException: Error on line 2: The
processing instruction target matching "[xX][mM][lL]" is not allowed.
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getDocumentForXMLStre
am(DatasetConfigXMLUtils.java:158)
... 5 more
Caused by: org.xml.sax.SAXParseException: The processing instruction
target matching "[xX][mM][lL]" is not allowed.
at
org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unkn
own Source)
at
org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown
Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown
Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown
Source)
at org.apache.xerces.impl.XMLScanner.scanPIData(Unknown Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanPIData(Unknow
n Source)
at org.apache.xerces.impl.XMLScanner.scanPI(Unknown Source)
at
org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch
(Unknown Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unkn
own Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
Source)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453)
... 6 more
It turns out that the returned XML had an empty first line, cuasing
the error:
___________________--
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE DatasetConfig>
<DatasetConfig dataset="xcms" datasetID="2"
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
--
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle New phone number !
Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
------------------------------------------------------------------------
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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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