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/proteomics.py
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 <mjohn...@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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