difficulty creating composite data type

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difficulty creating composite data type

Brian Haas
I'm having some trouble creating a composite data type in galaxy.  The composite type is created but is always empty.  I've tried to put together a very simple test for the system.  Attached are my input files as well as a screenshot of what I'm experiencing.  

I've registered my new data type in 'config/datatypes_conf.xml'

 <datatype extension="compositeDatatypeTest" type="galaxy.datatypes.composite_datatype_test:CompositeDataTest" display_in_upload="True" />

and I've added the attached module 'composite_datatype_test.py' to the 'lib/galaxy/datatypes/' area.

The module is being parsed properly on start-up (log from the galaxy/run.sh)

galaxy.datatypes.registry DEBUG 2015-05-16 11:13:51,869 Loading datatypes from ./config/datatypes_conf.xml

galaxy.datatypes.registry DEBUG 2015-05-16 11:13:51,872 Retrieved datatype module galaxy.datatypes.composite_datatype_test from the datatype registry.

galaxy.datatypes.composite_datatype_test DEBUG 2015-05-16 11:13:51,872 ######### Composite Data Test ############

I've tried running the system with my composite type set to 'basic' as well as 'auto_primary_file' and neither work.  Under 'auto_primary_file', the html file isn't generated.

Thanks in advance for any help!


Brian J. Haas
The Broad Institute


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Screen Shot 2015-05-16 at 11.22.37 AM.png (402K) Download Attachment
composite_datatype_test.py (3K) Download Attachment
composite_datatype_test.runner.pl (294 bytes) Download Attachment
composite_datatype_test.xml (1K) Download Attachment