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

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,

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