Re: [galaxy-dev] Documentation of Galaxy API metadata objects

[Clare Sloggett]

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/hdas.py. Specifically I
suspect what might be relevant here are the lines

class HDASerializer( #
datasets._UnflattenedMetadataDatasetAssociationSerializer,
   def __init__( self, app ):

self.add_view( 'detailed', [

'file_name',

and

class HDASerializer( #
datasets._UnflattenedMetadataDatasetAssociationSerializer,
def add_serializers( self ):

self.serializers.update({
   
   '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 expect...in 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
> (https://chrome.google.com/webstore/detail/postman/fhbjgbiflinjbdggehcddcbncdddomop).
> 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
>> http://galaxy.readthedocs.org/en/master/api_doc.html . 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
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/



-- 

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of 

[galaxy-dev] Documentation of Galaxy API metadata objects

[Clare Sloggett]

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
http://galaxy.readthedocs.org/en/master/api_doc.html . 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
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Documentation of Galaxy API metadata objects

[Martin Čech]

Hi Clare,

I am sorry but you seem to have found the best resources already. Namely
'what dictionary keys to expect...in 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 (
https://chrome.google.com/webstore/detail/postman/fhbjgbiflinjbdggehcddcbncdddomop).
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
> http://galaxy.readthedocs.org/en/master/api_doc.html . 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
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/