Unable to convert mzXML files

The conversion to pride.xml files worked with most of my files, but some are 
reproducibly producing an error.

What steps will reproduce the problem?
1. java -jar pride-converter-2.0-SNAPSHOT.jar -converter -engine mzXML -mode 
CONVERT -sourcefile /Users/../20080624_21_HL60_2.mzXML
2.
3.

What is the expected output? What do you see instead?
I see:
Exception in thread "main" java.util.EmptyStackException
    at java.util.Stack.peek(Stack.java:85)
    at java.util.Stack.pop(Stack.java:67)
    at psidev.psi.tools.xxindex.index.XmlXpathIndexer.buildIndex(XmlXpathIndexer.java:222)
    at psidev.psi.tools.xxindex.index.XmlXpathIndexer.buildIndex(XmlXpathIndexer.java:94)
    at psidev.psi.tools.xxindex.StandardXpathAccess.<init>(StandardXpathAccess.java:87)
    at psidev.psi.tools.xxindex.StandardXpathAccess.<init>(StandardXpathAccess.java:54)
    at uk.ac.ebi.pride.tools.mzxml_parser.MzXMLFile.indexFile(MzXMLFile.java:280)
    at uk.ac.ebi.pride.tools.mzxml_parser.MzXMLFile.<init>(MzXMLFile.java:111)
    at uk.ac.ebi.pride.tools.converter.dao.impl.MzXmlDAO.<init>(MzXmlDAO.java:82)
    at uk.ac.ebi.pride.tools.converter.dao.DAOFactory.getDAO(DAOFactory.java:160)
    at uk.ac.ebi.pride.tools.converter.dao.DAOFactory.getDAO(DAOFactory.java:128)
    at uk.ac.ebi.pride.tools.converter.conversion.PrideConverter.main(PrideConverter.java:164)
    at uk.ac.ebi.pride.tools.converter.gui.ConverterApplicationSelector.main(ConverterApplicationSelector.java:120)

What version of the product are you using? On what operating system?
Product: pride-converter-2.0-SNAPSHOT.jar
Environment:
Name of the OS: Mac OS X
Version of the OS: 10.7.5
Architecture of The OS: x86_64
Java Home: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java Version: 1.6.0_65 (Apple Inc.)
Number of processors: 4
Memory Usage: 61MB used, 54MB free, 1015MB Max

Original issue reported on code.google.com by bau...@imsb.biol.ethz.ch on 19 Nov 2013 at 6:53

Dear Damaris,

Sorry that you've encountered this problem with the Converter 2 tool. First I 
would like to let you know that for valid PRIDE XML generation, both 
identifiers and spectra need to be present. If you're just trying to run the 
tool with mzXML alone, then the output files won't be of any use, since mzXML 
just has spectra.

Apparently there are many tools out there that do not conform to the mzXML 
schema, and the converter tool definitely needs up-to-date and correct mzXML, 
otherwise the tool won't work properly.

So it might be best for you to make a Partial submission instead of a Complete 
submission for your dataset (i.e. without PRIDE XML). To read more about what 
this means, please see our FAQ:
http://www.ebi.ac.uk/pride/help/archive/faq#partial-PX

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 19 Nov 2013 at 11:56

PRIDE-Toolsuite / pride-converter-2

Unable to convert mzXML files #11