ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: cTAKES installation problem
Date Tue, 12 Nov 2013 21:20:49 GMT
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/umls</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(JdbcConnectionResourceImpl.java:109)

... 51 more


Could someone help me with it?


Best,

Pan

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message