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[bioontology-support] API access to NCBITAXON

John Graybeal jbgmeta1 at stanford.edu
Tue Dec 29 22:09:12 PST 2015


Erik,

I have created a task for this, NCBO-1606.

On reflection and comparison with other issues, I suspect we are seeing a combination of a real timeout, and a cached response causing the timeout message to be retiurned immediately when you retry it.

An actual timeout may be especially likely if you are making requests for later pages, since the system has to walk the internal query response to paginate it, and it’s a quite large ontology. Then once you have the timeout for a particular query, that same query will receive the cached error response.

I doubt there is an elegant strategy to avoid this. One technique would be to just save any failed queries and skip past them, then come back later (at low-volume times) when the caches may have expired (I think 2 or 3 hours may be typical). Also, be sure not to overlap these queries, so they don’t compete for resources. At some point, given a resource-limited system and a big ontology like this, timeouts seem inevitable, if our pagination strategy is as I understand it.

(I do see this problem has occurred for this ontology in another query request. We pre-warmed those queries; the same strategy might work here, though I’m not sure if we’ll have time to implement it. We’ll see.)

John

On Dec 29, 2015, at 6:45 AM, Erik Fäßler <erik.faessler at uni-jena.de<mailto:erik.faessler at uni-jena.de>> wrote:

John,

holidays distractions actually sounds good, sorry to bother you at this time.

I did try again and it worked - for a few hours. I got my job nearly completed but than the very same error appeared again. I am getting in right now. It seems the system is up for some time and then down again. You described it yourself, first you get the error, then it is gone - and then it comes back.

I will continue to try. Thanks for your efforts!

Best,

Erik

On 28 Dec 2015, at 07:36, John Graybeal <jbgmeta1 at stanford.edu<mailto:jbgmeta1 at stanford.edu>> wrote:

Erik,

Sorry, not sure why I did not see this earlier. (Perhaps too much holiday distraction.)

Please try this request again. Just a little while I was getting the error you describe, but now I am no longer getting that error.

I could not duplicate your issue with visiting the BIoPortal page at all — it worked consistently for me.

Happy holidays to you!

John

On Dec 24, 2015, at 12:43 AM, Erik Fäßler <erik.faessler at uni-jena.de<mailto:erik.faessler at uni-jena.de>> wrote:

Dear BioOntologies team,

I try to access the classes of NCBITAXON via the BioPortal API for a few day now with always the same error.

Request: http://data.bioontology.org/ontologies/NCBITAXON/classes?include=prefLabel,synonym,definition,parents,obsolete,notation,semanticType,cui,xref&pagesize=100&no_context=true&no_links=true
Error:
<html>
<head><title>504 Gateway Time-out</title></head>
<body bgcolor="white">
<center><h1>504 Gateway Time-out</h1></center>
<hr><center>nginx/1.6.2</center>
</body>
</html>

Other ontologies could be accessed exactly like this. I also cannot visit the BioPortal page for the NCBITAXON, it says "We're sorry but something has gone wrong. We have been notified of this error.

I wish happy holidays despite my report ;-) Best, Erik

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski




========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


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