Hey Mark, A few things, instead of printing stuff out you could use the global variable log in the binary.py file. Maybe something like log.warn("SNIFFING csra"). I think your logging statements will be more likely to show up then. I don't know why what you are doing won't work (it looks like it should), but a recent dist update included some changes that I submitted that allow for the addition of binary datatypes without needing to modify upload.py which I think is a big improvement. I would recommend updating galaxy and transitioning to this new mechanism. I have been working with Ira Cooke to gather a lot of generally useful proteomics datatypes into one place, this includes Pieter Neerincx RAW file datatype from the original dev list e-mail you linked to so it is a good example of how this has changed. Here is said file: https://bitbucket.org/iracooke/protk-toolshed/src/tip/lib/galaxy/datatypes/p... Basically, after you define your binary type all you need to do is register it as a sniffable binary format, in your case this would be adding this line: Binary.register_sniffable_binary_format('crsa', 'crsa', Crsa) after the last line of this example: http://pastie.org/5030960. Note there is no indenting this should be at the top level of the python code. As a side note (since this isn't documented anywhere else), in the proteomics.py example I went a step further to allow for backward compatibility with Galaxy versions predating the inclusion of these binary datatype rewrites by using the following construct: if hasattr(Binary, 'register_sniffable_binary_format'): Binary.register_sniffable_binary_format('RAW', 'RAW', RAW) I hope this helps, but I imagine my rambling e-mails only ever serve to confuse issues. -John ------------------------------------------------ John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http://jmchilton.net On Wed, Oct 10, 2012 at 1:21 PM, Mark Johnson <mjohnson@ncbi.nlm.nih.gov> wrote:

I'm trying to add CSRA (NCBI Compressed Sequence Read Archive) as a new datatype for Galaxy.

I've followed the instructions on the wiki, and the module seems to load OK. csra shows up as a datatype in the upload view.

But the upload fails, and the uploaded file size is always 0. The actual file I upload is 156k.

Here are my changes:

In binary.py: http://pastie.org/5030960

In upload.py (following the example at http://dev.list.galaxyproject.org/Binary-datatypes-td4135969.html): http://pastie.org/5030967

datatypes_conf.xml: http://pastie.org/5030970

I also have a very hard time debugging Galaxy. Where can I look for an error stream that explains what it's doing? paster.log only tells me the HTTP traffic. I need to know where it is failing to know where to look. And my code needs to be able to, at the very least, print debug messages. How do people generally do that in Galaxy?

Thanks

--Mark Johnson

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