Based on the error message you gave, I assume the following code in
~/lib/galaxy/datatypes/sniff.py is presenting the problem.
if check_binary( filename ):
if ext not in unsniffable_binary_formats and not
datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):
raise InappropriateDatasetContentError, 'The binary uploaded file
contains inappropriate content.'
Have you tried adding your 'jpg' extension to the following in
~/lib/galaxy/datatypes/binary.py?
# Currently these supported binary data types must be manually set on upload
unsniffable_binary_formats = [ 'ab1', 'scf' ]
On Jul 22, 2011, at 11:52 AM, Jelle Scholtalbers wrote:
> Hi Greg,
>
> I used that link when trying to create the support. The jpg datatype was
> already present in the datatypes_conf.xml (
>
> <datatype extension="jpg" type="galaxy.datatypes.images:Image"
> mimetype="image/jpeg"/> )
> , so I first made it available at upload -> display_in_upload=True. As far as
> I understood, if galaxy doesn't have to guess what the format is, this would
> be sufficient? From step2:
>
> "Galaxy tools are configured to automatically set the data type of an output
> dataset. However, in some scenarios, Galaxy will attempt to determine the
> data type of a file using a sniffer"
>
> However manually setting the format on upload still gave the mentioned error.
> Therefore I followed the rest of the guide (adding a sniffer) but still seem
> to fail here..
>
> Cheers,
> Jelle
>
>
>
> On Jul 22, 2011 3:26 PM, "Greg Von Kuster" <g...@bx.psu.edu> wrote:
> > Hello Jelle,
> >
> > There are a few things you need to do to add support for a new data type.
> > The steps are described here:
> >
> > http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes
> >
> > Greg Von Kuster
> >
> > On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote:
> >
> >> Hi all,
> >>
> >> I would like to be able to upload images to my Galaxy instance - in
> >> particular jpg/png to data libraries. I can't however find out how to
> >> overcome the problem of inappropriate content in binary file.
> >> How to go about?
> >>
> >> When I create a sniffer class in the galaxy.datatypes.images.py that
> >> always returns true (for testing purposes) I still don't get the jpg
> >> uploaded without an error (sniffer is incl. in the datatypes_conf.xml ).
> >> class Jpg( Image ):
> >> file_ext = "jpg"
> >> def sniff(self, filename):
> >> """Determine if the file is in jpg format.
> >> """
> >> return True
> >>
> >> It seems I'm missing something obvious and could use some help.
> >>
> >> Cheers,
> >> Jelle
> >> ___________________________________________________________
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client. To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >> http://lists.bx.psu.edu/
> >
> > Greg Von Kuster
> > Galaxy Development Team
> > g...@bx.psu.edu
> >
> >
> >
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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