Thanks!
On Mar 23, 2010, at 6:20 PM, Nate Coraor wrote:
Hi Pieter,
As you've found, this is a ugly limitation. I've created a ticket for it here:
http://bitbucket.org/galaxy/galaxy-central/issue/304/make-binary-datatype-up...
--nate
Pieter Neerincx wrote:
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 # _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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