[Psidev-ms-dev] mzML base64binary data type question

[Florian R. <fl...@eb...>]

Hi,

due to requests for jmzml, the Java API for mzML we developed in the PRIDE team, we had to deal with 
the 'binary' data elements in the BinaryDataArray.

The default JAXB mapping of the xsd:base64Binary type to Java results in a byte[], which seems to 
cause troubles when trying to convert with standard base64 algorithms as it does not produce the 
expected result.

I had to add an extension to the mzML schema defining the binary type to be of type "text/plain" 
(see below), so the Java mapping would result in a String representation of the binary data instead 
of a byte[]. The byte[] obtained from that String can then be converted to/from base64binary without 
problem.

The change in the schema is as follows:

original:
<xs:element name="binary" type="xs:base64Binary"/>

modified:
<xs:element name="binary" type="xs:base64Binary" xmime:expectedContentTypes="text/plain" 
xmlns:xmime="http://www.w3.org/2005/05/xmlmime"/>


Now, I was wondering if someone else has experienced similar issues or if someone can see issues 
with this modification of the schema (is there a potential issue with the schema specs? or should it 
be defined in more detail in case there might be issues with other tools as well?).

Also, I am not a expert in XML/Java mapping, so if there is an alternative/preferred way to handle 
this type of data, I would be happy to know about it.

Thanks,
Florian