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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: cTAKES installation problem
Date Tue, 12 Nov 2013 21:28:27 GMT
Pan 
Also one more thing, per download instructions, ensure you have the resources downloaded:
Resources
Resources are required to run most of cTAKES. They are available for download from: ctakes-resources-3.1.0.zip.

http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
Please download, unzip and add/merge the contents to the existing resources directory. Follow
the User or Developer Install Guide to direct you through the installation process.

--Pei

> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Tuesday, November 12, 2013 4:22 PM
> To: Pan Teng
> Cc: dev@ctakes.apache.org
> Subject: RE: cTAKES installation problem
> 
> Pan,
> That error seems to be caused by something else (it looks like it can't use the
> local hsqldb) not invalid umls license validated by their web service).
> 
> Try removing any logins to the local database in the xml config:
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-
> lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
> In particular:
>             <configurationParameterSettings>
>               <nameValuePair>
>                 <name>DriverClassName</name>
>                 <value>
>                   <string>org.hsqldb.jdbcDriver</string>
>                 </value>
>               </nameValuePair>
>               <nameValuePair>
>                 <name>URL</name>
>                 <value>
> 
> <string>jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/u
> mls</string>
>                 </value>
>               </nameValuePair>
>               <nameValuePair>
>                 <name>Username</name>
>                 <value>
>                   <string>SA</string>
>                 </value>
>               </nameValuePair>
>               <nameValuePair>
>                 <name>Password</name>
>                 <value>
>                   <string/>
>                 </value>
>               </nameValuePair>
>             </configurationParameterSettings>
> 
> 
> From: Pan Teng [mailto:tengpan@udel.edu]
> Sent: Tuesday, November 12, 2013 4:12 PM
> To: user-owner@ctakes.apache.org
> Subject: cTAKES installation problem
> 
> Hi there,
> 
> I was trying to run the user version cTAKES. I couldn't load the
> AggregatePlaintextUMLSprocesso r.xml or the
> DictionaryLookupAnnotatorUMLS.xml these analysis engines. I added the
> UMLS access rights to the <cTAKES_HOME>/bin/runctakesCVD.sh
> <cTAKES_HOME>/bin/runctakesCPE.sh
> 
> Here is how the script look like in the runctakesCPE.sh:
> 
> java -Dctakes.umlsuser=[REMOVED] -Dctakes.umlspw=[REMOVED] -cp
> $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -
> Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -
> Xmx1024M org.apache.uima.tools.cpm.CpmFrame
> 
> 
> There used to be a "*" in my password, I thought there might be some issue
> when the script is reading this, so I changed my password to end with "_"
> which still doesn't work.
> 
> 
> Here is how the error message look in the log file:
> 
> 
> Caused by: java.sql.SQLException: File input/output error:
> java.io.IOException: Stream closed
> 
> at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
> 
> at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
> 
> at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
> 
> at org.hsqldb.jdbcDriver.connect(Unknown Source)
> 
> at java.sql.DriverManager.getConnection(DriverManager.java:582)
> 
> at java.sql.DriverManager.getConnection(DriverManager.java:185)
> 
> at
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcCo
> nnectionResourceImpl.java:109)
> 
> ... 51 more
> 
> 
> Could someone help me with it?
> 
> 
> Best,
> 
> Pan

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