[galaxy-dev] Help about zip upload (esd files)

26 Jul 2010

      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'"*

I tried somethings, but I don't have success.

Thank you,
--

[galaxy-dev] Help about zip upload (esd files)

Eric Aguiar