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 Attached are diffs against changeset 058a5d7a4f84 (bit outdated - can provide newer if desired..).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 <g...@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 > notdatatypes_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 > > > >
datatypes_conf.xml.diff
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images.py.diff
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upload.py.diff
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