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[bioontology-support] Has the AnnotateText.java code changed?

Ray Fergerson ray.fergerson at stanford.edu
Thu Feb 13 12:03:31 PST 2014


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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