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[bioontology-support] Ordering issues while making ontology submissions programmatically

Manuel Fiorelli manuel.fiorelli at gmail.com
Wed Nov 18 15:36:47 PST 2020


Hi Michael

thank you for the additional information that confirms John's answer,

Regards
Manuel

Il giorno mer 18 nov 2020 alle ore 00:04 Michael Dorf <mdorf at stanford.edu>
ha scritto:

> Hi Manuel,
>
> Just as John indicated, the Contact field ordering isn’t enforced in our
> system. The field “contact" is defined as a generic list, which is dumped
> into a triple store database.
>
>
> https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology_submission.rb#L42
>
> The ability to assign multiple contacts to a submission object does not
> necessarily imply a specific order of priority for those contacts. We have
> sample REST code examples below, but I don’t think they include a code for
> inserting a submission:
>
> https://github.com/ncbo/ncbo_rest_sample_code
>
> The best I can offer is our unit test code that uses POST to create a
> submission. Unfortunately, this is only in Ruby and may not be exactly what
> you’re looking for. The trial-and-error approach you’ve taken will probably
> take you much further than any of the sample code we can provide.
>
>
> https://github.com/ncbo/ontologies_api/blob/master/test/controllers/test_ontology_submissions_controller.rb#L58
>
> https://github.com/ncbo/ontologies_api/blob/master/controllers/ontology_submissions_controller.rb#L32
>
>
> https://github.com/ncbo/ontologies_api/blob/959eb70b72c3cf1e159c668ceb46e6deb25ba281/helpers/ontology_helper.rb#L8
>
>
> Michael
>
>
> On Nov 17, 2020, at 7:29 AM, Manuel Fiorelli <manuel.fiorelli at gmail.com>
> wrote:
>
> Hi john
>
> Thank you for the reply. Unfortunately, I've not found any example of
> making an ontology submission with file upload, so I tried by myself.
>
> As I said, I eventually used the formdata approach, and looking on the web
> it seems to me that the order should have been preserved.
>
> Since I don't no anything about Ruby and its conventions, can you
> reference some example code so I can be sure that I wrote the request
> correctly?
>
> Regards
> Manuel
>
> Il mar 17 nov 2020, 08:31 John Graybeal <jgraybeal at stanford.edu> ha
> scritto:
>
>> I'm not the final authority, but I do not recall that order can be
>> preserved.
>>
>> John
>>
>> On Nov 16, 2020, at 3:00 PM, Manuel Fiorelli <manuel.fiorelli at gmail.com>
>> wrote:
>>
>> Hi everybody
>>
>> I need to make ontology submissions programmatically, uploading the
>> ontology file as part of the submission (instead of providing a fetch URL).
>> I eventually figured out that it should be possible to encode the
>> submission using as form data: each property of the JSON object is put into
>> its own part, with a part for the uploaded file.
>> However, I had a problem with the property *contact*, which is supposed
>> to contain the list of the contacts for the ontology.
>> Using PostMan, I defined the following parts, given as name:value pairs:
>>
>> contact[][name]:Manuel Fiorelli
>> contact[][email]:manuel.fiorelli at gmail.com
>> contact[][name]:Mario Rossi
>> contact[][email]:mario.rossi at example.org
>> contact[][name]:Mario Bianchi
>> contact[][email]:mario.bianchi at example.org
>>
>> Contrary to my understanding of how the API should work, I noticed (by
>> fetching the newly created submission using the API) that the order of the
>> contacts is not preserved.
>>
>> Please, can you tell me whether the order is supposed to be preserved,
>> and if so, how to guarantee that it is preserved.
>>
>> Best regards,
>> Manuel Fiorelli
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  | ORCID  0000-0001-6875-5360
>>
>>
>>
>> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>

-- 
Manuel Fiorelli
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