-------- Original Message --------
Eric Aguiar wrote:
> Dear,
>
> I followed all steps in the galaxy tutorial, but I didn't have success.
> I'm trying to create a datatype for megabase chromatograms (.esd) very
> similar to the Ab1 ones.
>
> Here is my configurations.
>
>
> *1 - Creating datatypes in datatypes_conf.xml*
>
> <datatype extension="zip" type="galaxy.datatypes.binary:Esd"
> mimetype="application/zip" display_in_upload="true"/>
> <datatype extension="esd" type="galaxy.datatypes.binary:Esd"
> mimetype="application/octet-stream" display_in_upload="true"/>
>
> *2 - Defining types in lib/galaxy/datatypes/binary.py*
>
> class Esd( Binary ):
> """Class describing an ab1 binary sequence file"""
> file_ext = "esd"
>
> def set_peek( self, dataset, is_multi_byte=False ):
> if not dataset.dataset.purged:
> dataset.peek = "Binary chromatograms sequence file"
> dataset.blurb = data.nice_size( dataset.get_size() )
> else:
> dataset.peek = 'file does not exist'
> dataset.blurb = 'file purged from disk'
> def display_peek( self, dataset ):
> try:
> return dataset.peek
> except:
> return "Binary esd sequence file (%s)" % ( data.nice_size(
> dataset.get_size() ) )
>
>
> class Zip( Binary ):
> """Class describing a zip archive of binary sequence files"""
> file_ext = "zip"
>
> def set_peek( self, dataset, is_multi_byte=False ):
> if not dataset.dataset.purged:
> zip_file = zipfile.ZipFile( dataset.file_name, "r" )
> num_files = len( zip_file.namelist() )
> dataset.peek = "Archive of %s binary sequence files" % (
> str( num_files ) )
> dataset.blurb = data.nice_size( dataset.get_size() )
> else:
> dataset.peek = 'file does not exist'
> dataset.blurb = 'file purged from disk'
> def display_peek( self, dataset ):
> try:
> return dataset.peek
> except:
> return "Binary sequence file archive (%s)" % (
> data.nice_size( dataset.get_size() ) )
> def get_mime( self ):
> """Returns the mime type of the datatype"""
> return 'application/zip'
>
>
> When I'm going to send the file in zip format (.esd files compressed),it
> shows me the following error:
> *"An error occurred running this job: Invalid 'File Format' for archive
> consisting of binary files - use 'Binseq.zip'"*
Hi Eric,
Have you updated to a recent revision of Galaxy? Binseq.zip and the
code that prevents uploading zip files has been removed. Currently,
though, a zip file can only contain one member.
--nate
>
> I tried somethings, but I don't have success.
>
> Thank you,
> --
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev