Re: [galaxy-dev] Binary datatypes

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... --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(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev