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[bioontology-support] bioontology-support Digest, Vol 70, Issue 14

Paul R Alexander palexander at stanford.edu
Thu Feb 13 18:30:28 PST 2014


Mona,

I cannot reproduce the problem. I am running the AnnotateText.java file exactly as it appears in the git repository.

I would wait until tomorrow and try again. If you are still having problems, please send me a copy of your file with your API Key removed.

Thanks,
Paul


On Feb 13, 2014, at 12:35 PM, Mona Salem <monasalem123 at gmail.com> wrote:

> I just tried it again.  Same error:  java.net.SocketException: Connection reset
> 
> Mona
> 
> 
> On Thu, Feb 13, 2014 at 12:07 PM, <bioontology-support-request at lists.stanford.edu> wrote:
> Send bioontology-support mailing list submissions to
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> Today's Topics:
> 
>    1. Re: Has the AnnotateText.java code changed? (Ray Fergerson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 13 Feb 2014 12:03:31 -0800 (PST)
> From: Ray Fergerson <ray.fergerson at stanford.edu>
> To: "Mona Salem" <monasalem123 at gmail.com>,
>         <bioontology-support at lists.stanford.edu>
> Subject: Re: [bioontology-support] Has the AnnotateText.java code
>         changed?
> Message-ID: <2faa3923.00002390.00000015 at BMIR-WIN8L-RF1.stanford.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Mona,
> 
> 
> 
> Please try it again and let us know if you are still having problems.
> Annotation seems to work for us. We have been notified by Stanford IT that
> there are intermittent networking issues related to outside access to
> Stanford machines this morning. Our outside monitoring is not reporting
> any problem though.
> 
> 
> 
> Ray
> 
> 
> 
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Mona
> Salem
> Sent: Thursday, February 13, 2014 11:44 AM
> To: bioontology-support at lists.stanford.edu
> Subject: [bioontology-support] Has the AnnotateText.java code changed?
> 
> 
> 
> Hi again
> 
> I am  calling AnnotateText.java from my Java code.  I have not altered my
> code from last weeks run.  I am using the same test file that I used last
> week.  The test file includes 20 articles to annotate.
> 
> 
> 
> I am getting the following errors today:
> 
> 
> 
>         prefLabel: Base
> 
>             prefLabel: Quality
> 
>             prefLabel: Reporting
> 
> com.fasterxml.jackson.databind.JsonMappingException: No content to map due
> to end-of-input
> 
>  at [Source: java.io.StringReader at 4316d76a; line: 1, column: 1]
> 
>             at
> com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingExcept
> ion.java:164)
> 
>             at
> com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.j
> ava:2931)
> 
>             at
> com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.
> java:2873)
> 
>             at
> com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:175
> 0)
> 
>             at AnnotateText.jsonToNode(AnnotateText.java:80)
> 
>             at AnnotateText.stringToAnnotate(AnnotateText.java:51)
> 
>             at siteParser.getTitle(siteParser.java:292)
> 
>             at siteParser.getAllUrlNames(siteParser.java:118)
> 
>             at siteParser.main(siteParser.java:720)
> 
> java.lang.NullPointerException
> 
> 
> 
> Thanks for any help on this.
> 
> Mona Nafoosi
> 
> 
> 
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