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[bioontology-support] Fwd: Proxy error when calling text mining service
Paul R Alexander
palexander at stanford.edu
Wed Oct 13 12:30:42 PDT 2010
I'm not an Annotator expert, but I did look into the problem and it
appears that the file is just too big to be processed in one call (it
timed out for me). I had no problem processing the entire thing so long
as I split it up into chunks that were generally 6000-8000 characters long.
Is this test case something that you are normally able to process
without difficulty? There's a possibility that if you set your timeout
long enough it would eventually come back with a result. As far as I
know, the Annotator isn't built to handle text from an entire article,
which it appears this is (someone please correct me on this if I am wrong).
Let me know if this workaround is suitable for you.
Paul R Alexander
Web / UI Developer
NCBO BioPortal <http://bioportal.bioontology.org>
Stanford Center for Biomedical Informatics Research
On 10/13/10 10:29 AM, Natasha F. Noy wrote:
> Forwarding this to support so that we can get more eyeballs on this. I
> myself don't know what is going on.
> Begin forwarded message:
>> *From: *Marco Ocana <marco.ocana at balboasystems.com
>> <mailto:marco.ocana at balboasystems.com>>
>> *Date: *October 13, 2010 8:22:46 AM PDT
>> *To: *"Natasha F. Noy" <noy at stanford.edu <mailto:noy at stanford.edu>>,
>> Trish Whetzel <whetzel at stanford.edu <mailto:whetzel at stanford.edu>>
>> *Cc: *Paolo Ciccarese <paolo.ciccarese at gmail.com
>> <mailto:paolo.ciccarese at gmail.com>>
>> *Subject: **Proxy error when calling text mining service*
>> Hi Natasha and Trish,
>> On one of my test cases I am consistently getting an error from the
>> text mining service. I was able to reproduce it using the html form
>> at http://rest.bioontology.org/test_oba.html. Below is the text from
>> the returned web page:
>> Proxy Error
>> The proxy server received an invalid response from an upstream server.
>> The proxy server could not handle the request /POST /obs/annotator
>> Reason: *Error reading from remote server*
>> To reproduce from the online form, below are the steps:
>> 1. For ontologiesToKeepInResult:
>> 2. For textToAnnotate, I copied and pasted the text in attached file.
>> Note: need to open in an editor that can read UTF-8 . The test for
>> this is that you can find: Aβ in the document.
>> 3. For format, xml.
>> If this is something you can fix at your end and/or have a
>> workaround, it would be greatly appreciated.
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