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Posted to dev@ctakes.apache.org by "Chen, Pei" <Pe...@childrens.harvard.edu> on 2013/11/12 22:20:49 UTC
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/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
RE: cTAKES installation problem
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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