wire nlp/annotate to scigraph service

nathandunn commented 5 years ago

nlp/annotate doesn't seem to connect properly to backend example:

gives 404:

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<title>404 Not Found</title>
<h1>Not Found</h1>
<p>The requested URL was not found on the server.  If you entered the URL manually please check your spelling and try again.</p>

nathandunn commented 5 years ago

Should probably be a POST instead of a GET.

monicacecilia commented 5 years ago

I am assuming that we no longer need to worry about this issue, given https://github.com/monarch-initiative/monarch-ui/pull/138 @kshefchek - requesting to close this ticket, please.

kshefchek commented 5 years ago

I still think we want this via biolink instead of directly from scigraph, and if not we need to remove the rest function that is currently 404ing.

monicacecilia commented 5 years ago

Agreed. Doing this via BioLink would be a good next step.

I cannot reproduce the error on the production site nor on the beta site. So I may be misunderstanding where I'm supposed to be looking.

What is https://api.monarchinitiative.org/api/nlp/annotate/ ? - This is where I'm getting a 404.
I don't understand what @nathandunn means by 'backend example' above in the description. Nathan, is this available somewhere else on our website? (Apologies, I know this ticket is about to turn 1 year old, so memory might be rusty).
Where did this error originate in the first place?
- I took the same abstract that is embedded in the search string in the URL from the description of this ticket, and used it in the new Text Annotator on the beta site; I am able to get results in https://beta.monarchinitiative.org/tools/text-annotate
- I also used the same abstract in the Text Annotator currently on the production site and also was able to retrieve results (see results here).

kshefchek commented 5 years ago

Theres a api/nlp/{text} route that is not functional, for example https://api-dev.monarchinitiative.org/api/nlp/annotate/test%20text

Both monarch legacy and beta use the scigraph annotator directly

monicacecilia commented 5 years ago

Looks like this will be an issue for @deepakunni3. 👀

deepakunni3 commented 5 years ago

Yes, this should be easy to implement. I just have to route SciGraph annotator calls via BioLink API.

deepakunni3 commented 4 years ago

This is done via #317

monarch-initiative / biolink-api

wire nlp/annotate to scigraph service #223