Error while processing few Medical records using CPE

[Ramprasad Reddy <ra...@gmail.com>]

Hi,

I have been trying to run CPE using AggregatePlainTextUMLSProcessor.xml
engine against few medical records. I am getting the following error
"*org.apache.uima.analysis_**engine.*
*AnalysisEngineProcessException *
* CausedBy: org.apache.uima.resource.*
*ResourceProcessException*

* CausedBy: org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0*
*character: ,0xb*"

I am running the engine using the default settings only. Few medical
records are able to run successfully, but after it is stopping giving the
above error.

Has anyone also faced this issue and identified a solution?

Thank you,
Ramprasad(RP).

RE: Error while processing few Medical records using CPE

[Ramprasad Reddy <ra...@gmail.com>]

Hi Pei Chen,

I am using plain text files as source. But I noticed, it has some special
characters. I will try removing them and retry the process.

Thank you for your quick response.

RP
On May 13, 2014 1:46 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:

> RP,
> From the exception, could you check to see if there were some special/non
> xml chars in the source documents?
> I assume you were using the default XML/XMI Writer to write the output as
> XML…
>
> 1) Can change the specials chars.  This of course would depend on your
> application needs.
> 2) Save the output in some char sequence or other alternative
> serialization method.
>
> There might be some useful utils from the UIMA package itself:
> org.apache.uima.internal.util.XMLUtils
>
> From: Ramprasad Reddy [mailto:ramprasadreddy.a@gmail.com]
> Sent: Tuesday, May 13, 2014 11:55 AM
> To: user@ctakes.apache.org
> Subject: Error while processing few Medical records using CPE
>
> Hi,
> I have been trying to run CPE using AggregatePlainTextUMLSProcessor.xml
> engine against few medical records. I am getting the following error
> "org.apache.uima.analysis_engine.AnalysisEngineProcessException
>  CausedBy: org.apache.uima.resource.ResourceProcessException
>  CausedBy: org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
> character: ,0xb"
>
> I am running the engine using the default settings only. Few medical
> records are able to run successfully, but after it is stopping giving the
> above error.
> Has anyone also faced this issue and identified a solution?
> Thank you,
> Ramprasad(RP).
>

RE: Error while processing few Medical records using CPE

["Chen, Pei" <Pe...@childrens.harvard.edu>]

RP,
From the exception, could you check to see if there were some special/non xml chars in the source documents?  
I assume you were using the default XML/XMI Writer to write the output as XML…

1) Can change the specials chars.  This of course would depend on your application needs.
2) Save the output in some char sequence or other alternative serialization method.

There might be some useful utils from the UIMA package itself:
org.apache.uima.internal.util.XMLUtils

From: Ramprasad Reddy [mailto:ramprasadreddy.a@gmail.com] 
Sent: Tuesday, May 13, 2014 11:55 AM
To: user@ctakes.apache.org
Subject: Error while processing few Medical records using CPE

Hi,
I have been trying to run CPE using AggregatePlainTextUMLSProcessor.xml engine against few medical records. I am getting the following error
"org.apache.uima.analysis_engine.AnalysisEngineProcessException
 CausedBy: org.apache.uima.resource.ResourceProcessException
 CausedBy: org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
character: ,0xb"

I am running the engine using the default settings only. Few medical records are able to run successfully, but after it is stopping giving the above error.
Has anyone also faced this issue and identified a solution?
Thank you,
Ramprasad(RP).