Hi Mark, The & sign issue is not related to version. Some special characters are XML sensitive, and needs to be escaped to be able to be exported in XML. BASE do not check for this for every text string today, you need to track it down in your outputted XML files, and from the context find out where in BASE you have some annotation using this special character and alter it.
For the identifier issue, I thought this was fixed by Vegard in an earlier release, before or equal to 1.2.15. Otherwise any export would fail validating on the very first element, so that's quite strange. Anyways, to get the full export you'll need the soon to come 1.2.18 release, so I wouldn't spend to much effort on debugging these things in old code. Cheers, Kjell mark alston (IFR) wrote: >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] > > _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
