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'
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