Thanks Martin!

I could have the details wrong for the API change example I gave (in
fact, checking this was part of my motivation for asking about
documentation, I wasn't sure whether our local setup was normal, and I
would like our scripts to be reusable on other systems). But I'm
fairly certain I have successfully (and exclusively) used file_path vs
file_name on different servers set up at different times.

It's not a big deal, as I can make the code handle both cases. But
just in the interests of knowing how to look into this stuff I thought
I'd see if it's feasible to examine the Galaxy source code itself to
spot these changes. I was thinking it might be relatively simple to do
(at least if I'm looking for a specific attribute and just need to
look for diffs in a specific file). Anyway after looking - I don't
think it's relatively simple, but I think I have traced the relevant
code :)

Following code from lib/galaxy/webapps/galaxy/api , I think the code
I'm interested in may actually be handled by various classes under
galaxy.managers; in the case of histories and datasets, the
HDASerialiser class in lib/galaxy/managers/ Specifically I
suspect what might be relevant here are the lines

class HDASerializer( #
   def __init__( self, app ):
        self.add_view( 'detailed', [


class HDASerializer( #
    def add_serializers( self ):
           'file_path' : self._remap_from( 'file_name' ),

But I'm not sure what the purpose of this remapping is - possibly a
deliberate API update?

On 30 September 2015 at 23:23, Martin Čech <> wrote:
> Hi Clare,
> I am sorry but you seem to have found the best resources already. Namely
> 'what dictionary keys to a particular Galaxy version' is a hard
> problem with the current docs. :/
> We could definitely do a better job providing example calls and responses in
> the docs with the code, so they are versioned together.
> I believe we are trying pretty hard not to break backward compatibility on
> both Galaxy side and BioBlend side so the change of file_name to file_path
> attribute you described sounds alarming. I will look into it.
> What I usualy do when I need to have a sample response is to actually call
> the endpoint using Postman Chrome extension
> (
> However if you need this for multiple Galaxy versions it might be tedious to
> set them up.
> Sorry I couldn't be of more help.
> Thank you for using Galaxy!
> Martin
> On Wed, Sep 30, 2015 at 6:58 AM Clare Sloggett <> wrote:
>> Hi all,
>> I'm wondering if there is any documentation of the JSON structures
>> returned by particular Galaxy REST API calls.
>> Some aspects of the Galaxy API are effectively documented via
>> bioblend's structure, and others are documented at
>> . However I don't
>> know where to look to find out the actual JSON structure that should
>> be returned by an API call. Does this exist?
>> For instance, if I call (using bioblend)
>>    gi.histories.show_history(..., contents=True, details="all"),
>> I will get back a list of dicts where each dict contains dataset metadata,
>> e.g.:
>> { u'api_type': u'file',
>>   u'create_time': u'2015-09-28T06:00:19.850421',
>>   u'data_type': u'galaxy.datatypes.sequence.FastqSanger',
>>   u'file_name': u'/mnt/galaxy/files/000/dataset_2.dat',
>>   ....
>> I'd like to know how to find out what dictionary keys to expect for a
>> particular API call in a particular Galaxy version. In this example,
>> IIRC at some point the key 'file_name' changed to 'file_path', but I
>> don't know how to determine which version of Galaxy uses which
>> convention. I don't think this change would necessarily be reflected
>> in bioblend, because bioblend just returns the entire JSON structure
>> as a Python object without caring much about its contents.
>> I also don't know how to derive this information from the Galaxy
>> source code itself (even though I know where the API code is under
>> webapp), so alternatively any guidance on that would be helpful!
>> Thanks,
>> Clare
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Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
LAB-14, 700 Swanston St, Carlton VIC 3053, Australia
Ph: 03 903 53357          M: 0414 854 759
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