[InterMine Dev] Adding XML properties to GFF3 sources

JD Wong jdmswong at gmail.com
Thu Nov 29 21:11:43 GMT 2012


Thanks Julie,

I'm trying to set up my own values to pass.  I've created a property in the
project XML and a complementary setter in GFF3ConverterTask to handle this
new property, but this function never gets called.  Do you know if there
are any more steps I need to take?

I can access these properties for the converter on a custom-file source,
but it looks as if GFF3ConverterTask properties are handled differently.

Cheers,
-JD

On Thu, Nov 29, 2012 at 4:55 AM, Julie Sullivan <julie at flymine.org> wrote:

> The values from the project XML file are passed to org.intermine.bio.task.
> **GFF3ConverterTask which then calls the converter to parse the files.
>
>
> On 28/11/12 19:18, JD Wong wrote:
>
>> Hi friends,
>>
>> I'm trying to modify the packaged GFF3converter to only store data types
>> specified in the project XML.  In a mailing list
>> post<http://mail.intermine.**org/pipermail/dev/2011-July/**000920.html<http://mail.intermine.org/pipermail/dev/2011-July/000920.html>
>> >it
>>
>> was mentioned that converters have access to xml properties through
>> setters.  GFF3 sources have many
>> properties<http://intermine.**readthedocs.org/en/latest/**
>> database/data-sources/library/**gff/#project-xml<http://intermine.readthedocs.org/en/latest/database/data-sources/library/gff/#project-xml>
>> >,
>>
>> yet org.intermine.bio.**dataconversion.GFF3Converter.**java has none of
>> these
>> setters.  Does anyone mind describing how properties are passed into
>> source-handling code and what classes are involved?
>>
>> Thanks!
>> -JD
>>
>>
>>
>>
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>
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