Binary datatypes - galaxy-dev

20 Mar 2010


      Hi Galaxy team,
Some time ago I added a binary data type to my Galaxy development machine. I simply defined the input for a tool as the standard binary data type. Recently I upgraded my Galaxy instance and afterwards I could no longer upload binary data successfully :(.
So, I looked at the docs to properly define a new binary data specific for that tool. I created a Python class, wrote a sniffer and listed the new stuff in the datatypes_conf.xml. To my surprise that did not work... After some digging I found that for a binary datatype I also had to hack the data upload tool in two places (see below). The word hack is maybe a bit too much for simply copying the lines for the already supported bam and Sff data types, but having to change code to support a new datatype sounds like a bad plan to me. Would it be possible to make sure support for a new binary data type is completely handled by config files and maybe a new python class, but without hacking code just like for non-binary data types?
Cheers,
Pi
-------------------
def check_bam( temp_name ):
    return Bam().sniff( temp_name )
def check_sff( temp_name ):
    return Sff().sniff( temp_name )
#
# Added mod for Thermo Finnigan RAW files START
#
def check_raw( temp_name ):
    return RAW().sniff( temp_name )
#
# Added mod for Thermo Finnigan RAW files END
#
.....
# Is dataset content supported sniffable binary?
    elif check_bam( dataset.path ):
        ext = 'bam'
        data_type = 'bam'
    elif check_sff( dataset.path ):
        ext = 'sff'
        data_type = 'sff'
#
# Added mod for Thermo Finnigan RAW files START
#
    elif check_raw( dataset.path ):
        ext = 'raw'
        data_type = 'raw'
#
# Added mod for Thermo Finnigan RAW files END
#