Hi,
Have you tried grep'ing the error message in the lib files to see where
Galaxy goes to during the upload of these files?
like: grep "/The uploaded binary file contains inappropriate content/"
`find *`
I had a similar problem when I modified Galaxy to manage .gz files
without uncompressing them automatically (I had to add a new file type
too), and diving into the code to see what is actually executed really
helped.
Good luck,
L-A
Le 24/05/2011 04:40, darren.culle...@csiro.au a écrit :
Hi All,
Sorry for the delay, I have had a couple of other projects on the go.
Still no good. I have made the data type unsniffable and added what I
thought was the correct information. I have also added the extension
(sfx) to the list of unsniffable binary formats in binary.py but it
does not make a difference.
Code is as follows:
./datatypes_conf.xml
<datatype extension="sfx" type="galaxy.datatypes.binary:Sfx"
display_in_upload="true"/>
./lib/galaxy/datatypes/binary.py
class Sfx( Binary ):
""" Kanga and uAssembler Suffix Array """
file_ext = "sfx"
def __init__( self, **kwd ):
Binary.__init__( self, **kwd )
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
dataset.peek = 'Suffix Array sfx'
dataset.blurb = 'binary data'
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
My gut feeling is that this is related to the fact that Galaxy wants
to look in the file, but as soon as its opened, it can't recognise the
characters and it reports "/The uploaded binary file contains
inappropriate content/". I thought the set_peekmethod I have above
would override the one described in the Class Binary. I have tried
adding a sniffer tag into datatypes_conf.xml, but I get the same
result whether the sniffer tag is there or not.
I am sure I have missed a step or piece of content but I have no idea
what I am missing...
Thanks again for your time,
Darren Cullerne
Computational Biology
CSIRO Plant Industry
x5042
+61 2 62465042
darren.culle...@csiro.au <mailto:darren.culle...@csiro.au>
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