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[bioontology-support] Fwd: Proxy error when calling text mining service
Paul R Alexander
palexander at stanford.edu
Mon Oct 18 14:34:38 PDT 2010
Sorry for the delay in responding. I checked and it looks like there
isn't a hard limit on the text size, just however long your timeout is
set for. That being said, I was able to pass in chunks that were 8000
characters and get a response back in a reasonable time.
Essentially this means that you can determine the size, you'll just need
to determine how long you are willing to wait for a response and do some
testing against the service to make sure it works.
Let me know if you still have questions.
Paul R Alexander
Web / UI Developer
NCBO BioPortal <http://bioportal.bioontology.org>
Stanford Center for Biomedical Informatics Research
On 10/14/10 1:51 PM, Marco Ocana wrote:
> Hi Paul,
> Thanks for looking into this.
> I have in the past gotten results for this document, but not sure what
> were the circumstances.
> Do you guys have advice on on how big the chunks can be? If we need to
> split up the document, then we would like to keep the chunks as large
> as possible.
> *From:* Paul R Alexander <palexander at stanford.edu>
> *To:* Natasha F. Noy <noy at stanford.edu>
> *Cc:* support Support <support at bioontology.org>; Marco Ocana
> <marco.ocana at balboasystems.com>; Paolo Ciccarese
> <paolo.ciccarese at gmail.com>
> *Sent:* Wed, October 13, 2010 3:30:42 PM
> *Subject:* Re: [bioontology-support] Fwd: Proxy error when calling
> text mining service
> 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
> 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.
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
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