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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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Responses are all arrays unless id? #39

Closed edeutsch closed 4 years ago

edeutsch commented 5 years ago

In the current schema /datasets returns an array (except for the {identifier} form. But /spectra and /psms and all the rest are not returning arrays. Shouldn't they all return arrays?

ypriverol commented 5 years ago

@edeutsch this is actually a problem in all the other endpoints created by the ambiguity of the USI and the lack of identifiers for PSMs, Peptides, and Proteins. I will vote for not removing the dataset/{accession} endpoint because we would like to have a page in the future like this http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD010597 returning only one dataset.

edeutsch commented 5 years ago

sorry, I was too vague in my report. I fully agree that /datasets/{identifier} should be a singular Dataset returned But I note that plain /datasets returns an array of Dataset objects. This is also fine BUT, the issue is the /spectra does not return an array of spectra. but I think it should. and /psms does not return an array of psms. but I think it should. and /peptides does not .... etc. I believe we agreed in Tokyo that all endpoints performing queries (this excludes /xxx/{identifier}) should return an array of items. Did we not?

ypriverol commented 5 years ago

sorry, I was too vague in my report. I fully agree that /datasets/{identifier} should be a singular Dataset returned But I note that plain /datasets returns an array of Dataset objects. This is also fine BUT, the issue is the /spectra does not return an array of spectra. but I think it should. and /psms does not return an array of psms. but I think it should. and /peptides does not .... etc. I believe we agreed in Tokyo that all endpoints performing queries (this excludes /xxx/{identifier}) should return an array of items. Did we not?

@edeutsch I miss array definition, already included in the current PR https://github.com/HUPO-PSI/proxi-schemas/pull/42

edeutsch commented 4 years ago

I think this is resolved. All endpoints return and array of items except for /xxx/{identifier} is the policy.