Hi Kjell, I should have said that I'm using BASE 1.2.15 - is that the problem?
Regards, Mark -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kjell Petersen Sent: 21 June 2006 11:57 To: BASE ML Subject: Re: [base] mage-ml export gives org.xml.sax.SAXParseException Hi Mark, You probably have a & sign somewhere in your text that is exported. That is confusing the XML parser, since the & means something special in XML... The missing identifier of MAGE-ML is something that I thought was fixed some time ago, and definitely is fixed in the CVS, which version are you using ? Cheers, Kjell mark alston (IFR) wrote: > Hi everyone, > > The base-users forum seems to be down so I'll have to put my question > here - sorry if it has already been dealt with. > > I'm trying to get mage-ml export working. I updated my mysql-connector > to 3.1.13-bin.jar, put it into pathToBase/include/java and renamed it > with the old jar file name (as per previous posting), but I now see > the following: > > *MAGE-ML document** */ not created yet/ [_Create_ > <http://ifrnl04.ifrn.bbsrc.ac.uk/base/experiment_makemageml.phtml?i_e=19 &oldlocation=data_main.phtml>] > > *MAGE-ML log file** */ Last changed 2006-06-21 11:29:21/ > > dirname= /applications/base/data/mageml/0/19/experiment19 > > stage= all > > dtdpath= /applications/base/misc/MAGE-ML.dtd > > created mageobjects > > writeMAGEML > > [Fatal Error] experiment19.xml:1:3104: The entity name must > immediately follow the '&' in the entity reference. > > org.xml.sax.SAXParseException: The entity name must immediately follow > the '&' in the entity reference. > > at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) > > at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) > > at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:151) > > at BASEutils.repairMAGEML(BASEutils.java:961) > > at exportMAGEML.main(exportMAGEML.java:78) > > validate > > error: Attribute "identifier" is required and must be specified for > element type "MAGE-ML". > > org.xml.sax.SAXParseException: Attribute "identifier" is required and > must be specified for element type "MAGE-ML". > > at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) > > at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) > > at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:151) > > at BASEutils.validate(BASEutils.java:1137) > > at exportMAGEML.main(exportMAGEML.java:79) > > So, what's all this about then?! > > Best regards, > > Mark > > ****************************************** > > Dr Mark Alston, > > Computational Biologist, > > Institute of Food Research, > > Norwich Research Park, Colney, > > Norwich NR4 7UA, UK. > > Tel +44 (0)1603 251432 > > e-mail [EMAIL PROTECTED] > > e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ > > _www.ifr.ac.uk_ <http://www.ifr.ac.uk> > > _www.foodandhealthnetwork.com_ <http://www.foodandhealthnetwork.com> > > ****************************************** > >----------------------------------------------------------------------- - > >_______________________________________________ >The BASE general discussion mailing list >basedb-users@lists.sourceforge.net >unsubscribe: send a mail with subject "unsubscribe" to >[EMAIL PROTECTED] > > _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED] _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
