[galaxy-dev] Outputting zip files from galaxy

9 Nov 2011

      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?

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 }

[galaxy-dev] Outputting zip files from galaxy

wfmartin