Hi Greg,

this was indeed causing the problem. I added some code which now allows to sniff image files. It is practically untested (it does work for me on bmp, jpg, png, tiff) - didn't try with PIL although the code is there.

Attached are diffs against changeset 058a5d7a4f84 (bit outdated - can provide newer if desired..).

Sniffed formats:

http://infohost.nmt.edu/tcc/help/pubs/pil/formats.html or http://docs.python.org/library/imghdr.html depending if PIL is available or not.

Cheers,
Jelle

On Fri, Jul 22, 2011 at 6:46 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:

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" <greg@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
>> ___________________________________________________________
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>
> Greg Von Kuster
> Galaxy Development Team
> greg@bx.psu.edu
>
>
>

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu

<datatypes_conf.xml.diff><images.py.diff><upload.py.diff>