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

[Matt C. <mat...@va...>]

Hi Florian,

You might do better to customize the interface for binaryDataHandler in 
order to provide the array data as an Object that may be a Float[], 
Double[], Int32[], Int64[], and now String[]. Relying on your users to 
convert byte[] to the desired array type is a bit harsh, especially if 
it's compressed. But just having them check the type of the array before 
doing anything with it is easy and convenient. :)

-Matt


Florian Reisinger wrote:
> 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
>