-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I noticed that you are referring to biomart-web:
/cvsroot/CVSmaster/biomart-web/cgi-bin/martservice.PLS Since 0.5, biomart-web and biomart-plib are longer used. You need to be using biomart-perl instead which is an amalgamation of these. cheers, Richard. Arek Kasprzyk wrote: > > 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(MartServiceUtils.java:269) >> >> at >> org.biomart.martservice.MartService.getDatasetConfigFromCache(MartService.java:350) >> >> at >> org.biomart.martservice.MartService.getDatasetConfig(MartService.java:305) >> >> at >> org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory05.getDatasetConfig(MartServiceQueryConfigUIFactory05.java:177) >> >> at >> org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory05$1.run(MartServiceQueryConfigUIFactory05.java:228) >> >> Caused by: org.ensembl.mart.lib.config.ConfigurationException: >> org.jdom.input.JDOMParseException: Error on line 2: The processing >> instruction target matching "[xX][mM][lL]" is not allowed. >> at >> org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getDocumentForXMLStream(DatasetConfigXMLUtils.java:162) >> >> at >> org.biomart.martservice.MartServiceUtils.getDatasetConfig(MartServiceUtils.java:260) >> >> ... 4 more >> Caused by: org.jdom.input.JDOMParseException: Error on line 2: The >> processing instruction target matching "[xX][mM][lL]" is not allowed. >> at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468) >> at >> org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getDocumentForXMLStream(DatasetConfigXMLUtils.java:158) >> >> ... 5 more >> Caused by: org.xml.sax.SAXParseException: The processing instruction >> target matching "[xX][mM][lL]" is not allowed. >> at >> org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown >> Source) >> at >> org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) >> at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown >> Source) >> at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown >> Source) >> at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown >> Source) >> at org.apache.xerces.impl.XMLScanner.scanPIData(Unknown Source) >> at >> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanPIData(Unknown >> Source) >> at org.apache.xerces.impl.XMLScanner.scanPI(Unknown Source) >> at >> org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown >> Source) >> at >> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown >> 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 >> > > > ------------------------------------------------------------------------------- > > 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 > ------------------------------------------------------------------------------- > > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFsNkG4C5LeMEKA/QRAotGAJ9aupqOdB8hojoRQGnm2fbBFQ9FuACgp8XH TCDsxh1iNS8EfWp2bmoK2bU= =lYhB -----END PGP SIGNATURE-----
