Re: [galaxy-dev] Outputting zip files from galaxy

[wfmartin]

Hi Nate:

Thanks for your response.  The zip command always creates files with the 
extension.  Utilities that validate, examine, or extract from zip files 
expect the file to have a ".zip" extension.
I can understand why it was easier to architect Galaxy with a simple, 
uniform file naming scheme.

Thanks again,
Bill

On 11/10/2011 08:11 AM, Nate Coraor wrote:
On Nov 9, 2011, at 5:21 PM, wfmartin wrote:

I have an application that needs to return a zip file.

I attempted to follow the instructions to add a "zip" datatype, with no success.
It appears to me that Galaxy insists on generating the output file name and I can't get 
it to generate one with a ".zip" extension.
The documentation on the wiki is missing a lot of details.

Can you please point me to a working example of some code returning a zip file?
Bill,

I don't believe there are any tools in the distribution outputting zip files, 
although there might be other third party tools which do.

Is there a reason that the disk filename must end with the .zip extension?  
Galaxy names all of its datasets uniformly, and in the cases where certain 
tools need inputs to have a certain extension, we've worked around this with 
symbolic links.  The goal is to keep data access as abstract as possible.

--nate

Below are snippets of my code.

Thanks,
Bill Martin




==================
tool_conf.xml:

<toolbox>
<section name="test" id="test_section_1">
<tool file="test/my_test.xml"/>
</section>



=================
tools/test/my_test.pl:


#!/usr/bin/perl
use strict;

my ($output_1) = @ARGV;

system("zip ${output_1} /home/bill/.* in.csv");


=====================
tools/test/my_test.xml:

<tool id="my_test_1" name="my_test">
<description>  the descr</description>
<command interpreter="perl">
my_test.pl $output_1
</command>
<inputs>
<param format="tabular" name="input" type="data" label="inp"
    help="Dataset missing? See TIP below."/>
</inputs>

<outputs>
<data format="zip" name="output_1"/>
</outputs>

</tool>


===================
datatypes_conf.xml:

<datatypes>
<registration converters_path="lib/galaxy/datatypes/converters" 
display_path="display_applications">
{ some lines omitted here }
<datatype extension="zip" type="galaxy.datatypes.binary:Zip" mimetype="application/zip" 
display_in_upload="true"/>
{ ... }
</registration>


======================
lib/galaxy/datatypes/binary.py:

{ many lines omitted here }

class Binary( data.Data ):
    """Binary data"""
    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = 'binary data'
            dataset.blurb = 'data'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def get_mime( self ):
        """Returns the mime type of the datatype"""
        return 'application/octet-stream'

class Zip( Binary ):
    """Zip File"""
    file_ext = "zip"
    def get_mime( self ):
        """Returns the mime type of the datatype"""
        return 'application/zip'

{ many lines omitted here }
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