Bewildered

Having been able to run the tutorial example I started to make my own 
baby annotators. Everything seems to be good until I tried to run 
document analyzer. A had to extend the UIMA_CLASSPATH as my pieces were 
not in exactly the same directories as the tutorial example, and that 
also worked well until this error: The error message says
org.apache.uima.resource.ResourceInitializationException: Annotator 
class "org.apache.uima.DDD.Sensor.java was not found. (Descriptor: 
file:/c:/apache-uima/examples/descriptors/DDD/Sensorannotator.xml)

I do have both of the named directories on the class path, and checked 
that the Sensor.java file indeed defines a Sensor class.  I'd appreciate 
a suggestion as to what to look for or do to make this error  go away.

Thanks

--

-- 
***********************************
Dennis Geller, Ph.D. Computer and Communication Science   
Senior Software Developer
Direct Dial: 781.496.2461   Main Number: 781.935.3966 ext. 261   
Fax Number:  781.496-2498
E-mail:  dgeller@...
Aptima, Inc.
12 Gill Street, Suite 1400
Woburn, MA 01801 USA
http://www.aptima.com
************************************

The information transmitted is intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. Any review, retransmission, dissemination or other

Re: Bewildered

Dennis Geller wrote:
> Having been able to run the tutorial example I started to make my own 
> baby annotators. Everything seems to be good until I tried to run 
> document analyzer. A had to extend the UIMA_CLASSPATH as my pieces were 
> not in exactly the same directories as the tutorial example, and that 
> also worked well until this error: The error message says
> org.apache.uima.resource.ResourceInitializationException: Annotator 
> class "org.apache.uima.DDD.Sensor.java was not found. (Descriptor: 
> file:/c:/apache-uima/examples/descriptors/DDD/Sensorannotator.xml)
> 
> I do have both of the named directories on the class path, and checked 
> that the Sensor.java file indeed defines a Sensor class.  I'd appreciate 
> a suggestion as to what to look for or do to make this error  go away.
> 
> Thanks
> 

Do you have the directory in the classpath where the org/apache/uima/DDD/Sensor.class
path *starts*, i.e., the directory that contains the "org" subdirectory.
If this was not the problem, please provide more details and we may be
able to help.

--Thilo

Re: Re: Bewildered

Re: Bewildered

Wow, that's a lot of info.  We'll get to the bottom
of this.

First of all, in the descriptor, you need to specify
just the class name, without the ".java" source file
extension.  The way you specified it, the system is
looking for a class called "java" in package
org.apache.uima.DDD.Sensor, which I'm pretty sure is
not what you want.

Secondly, you have added to the classpath the directory
that contains the source code.  Unless the compiled
.class files live in the same directory, that's not
going to help.

The UIMA examples class files are packaged into a jar
and get on the classpath via
%UIMA_HOME%\lib\uima-examples.jar.

So all we need to figure out is how you compile your
java source code.  Are you doing this inside Eclipse?
If in Eclipse, you can a) export the code to a jar
file and add that to the classpath, or b) add the
directory where eclipse puts the compiled code to
the classpath (probably c:\apache-uima\examples\bin,
but check on your disk, look for .class files).

If not eclipse, i.e., the command line, then a plain
invocation of javac should have placed the .class files
next to the .java files, and adding c:\apache-uima\examples\src
to the classpath will work.

HTH,
Thilo

Dennis Geller wrote:
> Thanks, Thilo.
> 
> Here's the classpath definition from the .bat file (line breaks added 
> for this email)
> @rem All this nonsense is necessary to remove quotes from the CLASSPATH 
> and also handle the case where there is no CLASSPATH
> @set _NOQUOTES=%CLASSPATH:"=%
> @set _REALLYNOQUOTES=%_NOQUOTES:"=%
> @if "%_REALLYNOQUOTES%"=="=" set _REALLYNOQUOTES=
> set UIMA_CLASSPATH=%UIMA_CLASSPATH%;
> %UIMA_HOME%\examples\resources;
> %UIMA_HOME%\lib\uima-core.jar;
> %UIMA_HOME%\lib\uima-document-annotation.jar;
> %UIMA_HOME%\lib\uima-cpe.jar;
> %UIMA_HOME%\lib\uima-tools.jar;
> %UIMA_HOME%\lib\uima-examples.jar;
> %UIMA_HOME%\lib\uima-adapter-soap.jar;
> %UIMA_HOME%\lib\uima-adapter-vinci.jar;
> CATALINA_HOME%\webapps\axis\WEB-INF\lib\activation.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\axis.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\commons-discovery.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\commons-discovery-0.2.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\commons-logging.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\commons-logging-1.0.4.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\jaxrpc.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\mail.jar;
> %CATALINA_HOME%\webapps\axis\WEB-INF\lib\saaj.jar;
> %UIMA_HOME%\lib\jVinci.jar;%_REALLYNOQUOTES%;
> %UIMA_HOME%\examples\descriptors\DDD;
> %UIMA_HOME%\examples\src\org\apache\uima\DDD;
> %UIMA_HOME%\examples\src\org\apache\uima\DDD\Senseattributes
> 
> And here's the echo of the actual definition in the bat file
> 
> C:\apache-uima\bin>set 
> UIMA_CLASSPATH=;c:\apache-uima\examples\resources;c:\apac
> he-uima\lib\uima-core.jar;c:\apache-uima\lib\uima-document-annotation.jar;c:\apa
> che-uima\lib\uima-cpe.jar;c:\apache-uima\lib\uima-tools.jar;c:\apache-uima\lib\u
> ima-examples.jar;c:\apache-uima\lib\uima-adapter-soap.jar;c:\apache-uima\lib\uim
> a-adapter-vinci.jar;C:\Program Files\Apache Software Foundation\Tomcat 
> 6.0\webap
> ps\axis\WEB-INF\lib\activation.jar;C:\Program Files\Apache Software 
> Foundation\T
> omcat 6.0\webapps\axis\WEB-INF\lib\axis.jar;C:\Program Files\Apache 
> Software Fou
> ndation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\commons-discovery.jar;C:\Program Fil
> es\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\commons-discov
> ery-0.2.jar;C:\Program Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\
> WEB-INF\lib\commons-logging.jar;C:\Program Files\Apache Software 
> Foundation\Tomc
> at 6.0\webapps\axis\WEB-INF\lib\commons-logging-1.0.4.jar;C:\Program 
> Files\Apach
> e Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\jaxrpc.jar;C:\Program
> Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\mail.jar;C:
> \Program Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\sa
> aj.jar;c:\apache-uima\lib\jVinci.jar;.;C:\openrdf-sesame-2.0\lib\slf4j-jdk14-1.3
> .0.jar;C:\apache-log4j-1.2.15\log4j-1.2.15.jar;C:\openrdf-sesame-2.0\lib\openrdf
> -sesame-2.0-onejar.jar;c:\jaxb-ri-20071219\lib\jaxb-api.jar;C:\Program 
> Files\Jav
> a\jre1.6.0_03\lib\ext\QTJava.zip;c:\apache-uima\examples\descriptors\DDD;c:\apac
> he-uima\examples\src\org\apache\uima\DDD;c:\apache-uima\examples\src\org\apache\
> uima\DDD\Senseattributes
> 
> These don't seem to have the directory containing org (same org as in 
> the example) so I added it
> ;c:\apache-uima\examples\src;
> but no difference. I also added the actual org directory, but that was 
> clearly a desperation move, and also didn't help.
> 
> The file being specified in DocumentAnalyzer as the source is: 
> C:\apache-uima\examples\descriptors\DDD\SensorAnnotator.xml
> 
> Here's the Directory structure
> C:
>   apache-uima
>     examples
>       src
>         org
>           apache
>             uima
>               DDD
>                  Senseattributes
>       descriptors
>         DDD
> 
> And here's the entire exception
> 
> C:\apache-uima\bin>"C:\Program Files\Java\jre1.6.0_03\bin\java" -cp 
> ";c:\apache-
> uima\examples\resources;c:\apache-uima\lib\uima-core.jar;c:\apache-uima\lib\uima
> -document-annotation.jar;c:\apache-uima\lib\uima-cpe.jar;c:\apache-uima\lib\uima
> -tools.jar;c:\apache-uima\lib\uima-examples.jar;c:\apache-uima\lib\uima-adapter-
> soap.jar;c:\apache-uima\lib\uima-adapter-vinci.jar;C:\Program 
> Files\Apache Softw
> are Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\activation.jar;C:\Program Fil
> es\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\axis.jar;C:\Pr
> ogram Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\commo
> ns-discovery.jar;C:\Program Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\
> axis\WEB-INF\lib\commons-discovery-0.2.jar;C:\Program Files\Apache 
> Software Foun
> dation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\commons-logging.jar;C:\Program Files\
> Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB-INF\lib\commons-logging-1
> .0.4.jar;C:\Program Files\Apache Software Foundation\Tomcat 
> 6.0\webapps\axis\WEB
> -INF\lib\jaxrpc.jar;C:\Program Files\Apache Software Foundation\Tomcat 
> 6.0\webap
> ps\axis\WEB-INF\lib\mail.jar;C:\Program Files\Apache Software 
> Foundation\Tomcat
> 6.0\webapps\axis\WEB-INF\lib\saaj.jar;c:\apache-uima\lib\jVinci.jar;.;C:\openrdf
> -sesame-2.0\lib\slf4j-jdk14-1.3.0.jar;C:\apache-log4j-1.2.15\log4j-1.2.15.jar;C:
> \openrdf-sesame-2.0\lib\openrdf-sesame-2.0-onejar.jar;c:\jaxb-ri-20071219\lib\ja
> xb-api.jar;C:\Program 
> Files\Java\jre1.6.0_03\lib\ext\QTJava.zip;c:\apache-uima\e
> xamples\descriptors\DDD;c:\apache-uima\examples\src\org\apache\uima\DDD;c:\apach
> e-uima\examples\src\org\apache\uima\DDD\Senseattributes;c:\apache-uima\examples\
> src;c:\apache-uima\examples\src\org;" "-Duima.home=c:\apache-uima" 
> "-Duima.datap
> ath=" -DVNS_HOST=localhost -DVNS_PORT=9000 
> "-Djava.util.logging.config.file=c:\a
> pache-uima\config\Logger.properties" -Xms128M -Xmx800M 
> org.apache.uima.tools.doc
> analyzer.DocumentAnalyzer
> org.apache.uima.resource.ResourceInitializationException: Annotator 
> class "org.a
> pache.uima.DDD.Sensor.java" was not found. (Descriptor: 
> file:/C:/apache-uima/exa
> mples/descriptors/DDD/SensorAnnotator.xml)
>         at 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:202)
>         at 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tialize(PrimitiveAnalysisEngine_impl.java:151)
>         at 
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
> sisEngineFactory_impl.java:94)
>         at 
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
> mpositeResourceFactory_impl.java:62)
>         at 
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:258)
> 
>         at 
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
> a:352)
>         at 
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java
> :243)
>         at 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tASB(AggregateAnalysisEngine_impl.java:413)
>         at 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:361)
>         at 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tialize(AggregateAnalysisEngine_impl.java:183)
>         at 
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
> sisEngineFactory_impl.java:94)
>         at 
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
> mpositeResourceFactory_impl.java:62)
>         at 
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:258)
> 
>         at 
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
> a:326)
>         at 
> org.apache.uima.tools.docanalyzer.DocumentAnalyzer.runProcessingThrea
> d(DocumentAnalyzer.java:1167)
>         at 
> org.apache.uima.tools.docanalyzer.DocumentAnalyzer$ProcessingThread.r
> un(DocumentAnalyzer.java:1267)
> Caused by: java.lang.ClassNotFoundException: org.apache.uima.DDD.Sensor.java
>         at java.net.URLClassLoader$1.run(Unknown Source)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(Unknown Source)
>         at java.lang.ClassLoader.loadClass(Unknown Source)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
>         at java.lang.ClassLoader.loadClass(Unknown Source)
>         at java.lang.ClassLoader.loadClassInternal(Unknown Source)
>         at java.lang.Class.forName0(Native Method)
>         at java.lang.Class.forName(Unknown Source)
>         at 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:199)
>         ... 15 more
> 
> 
> Here's the descriptor file
> <?xml version="1.0" encoding="UTF-8"?>
> <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
>   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
>   <primitive>true</primitive>
>   
> <annotatorImplementationName>org.apache.uima.DDD.Sensor.java</annotatorImplementationName>
>   <analysisEngineMetaData>
>     <name>Sensor Annotator</name>
>     <description>An example annotator that searches for sensor 
> definitions in a DDD script</description>
>     <version>1.0</version>
>     <vendor>The Apache Software Foundation</vendor>
>     <configurationParameters/>
>     <configurationParameterSettings/>
>     <typeSystemDescription>
>       <imports>
>         <import name="DDDTypeSystem"/>
>       </imports>
>     </typeSystemDescription>
>     <typePriorities/>
>     <fsIndexCollection/>
>     <capabilities>
>       <capability>
>         <inputs/>
>         <outputs>
>           <type>org.apache.uima.DDD.Sensor</type>
>           <feature>org.apache.uima.DDD.Sensor:name</feature>
>         </outputs>
>         <languagesSupported/>
>       </capability>
>     </capabilities>
>     <operationalProperties>
>       <modifiesCas>true</modifiesCas>
>       <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
>       <outputsNewCASes>false</outputsNewCASes>
>     </operationalProperties>
>   </analysisEngineMetaData>
>   <resourceManagerConfiguration/>
> </analysisEngineDescription>
> 
> Anything else I should provide?
> 
> Dennis
>              
> 
> ***********************************
> Dennis Geller, Ph.D. Computer and Communication Science
> Senior Software Developer
> Direct Dial: 781.496.2461 Main Number: 781.935.3966 ext. 261
> Fax Number: 781.496-2498
> E-mail: dgeller@...
> Aptima, Inc.
> 12 Gill Street, Suite 1400
> Woburn, MA 01801 USA
> http://www.aptima.com
> ************************************
> 
> The information transmitted is intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. Any review, retransmission, dissemination or other
use of, or taking of any action in reliance upon this information by persons or entities other than the
intended recipient is prohibited. If you received this in error, please contact the sender and delete the
material from any computer.

Re: Bewildered

Bug with POS tagger in Sandbox

Hi guys,

I don't think there is a separate list for the sandbox so I am sending to
the main one. I've found a problem with the HMM Tagger which generates :

java.lang.ArrayIndexOutOfBoundsException: -2
    at java.util.ArrayList.get(ArrayList.java:323)
    at org.apache.uima.examples.tagger.Viterbi.process(Viterbi.java:328)

when I analyze the following sentence "pH The test." (tokenized as
[pH][The][test][.])

Who usually looks after that part of the code?

Thanks

Julien

--

-- 
DigitalPebble Ltd
http://www.digitalpebble.com

Simone Daum is out of the office.

I will be out of the office starting  03/05/2008 and will not return until
03/10/2008.

I am out of office. In urgent cases contact my manager Andreas Zekl.

Re: Bug with POS tagger in Sandbox

Julien Nioche wrote:
> Hi guys,
> 
> I don't think there is a separate list for the sandbox so I am sending to
> the main one. I've found a problem with the HMM Tagger which generates :
> 
> java.lang.ArrayIndexOutOfBoundsException: -2
>     at java.util.ArrayList.get(ArrayList.java:323)
>     at org.apache.uima.examples.tagger.Viterbi.process(Viterbi.java:328)
> 
> when I analyze the following sentence "pH The test." (tokenized as
> [pH][The][test][.])
> 
> Who usually looks after that part of the code?
> 
> Thanks
> 
> Julien
> 

Julien, is this with the latest version of the tagger (as of
last Friday, I think)?  If so, please open a Jira issue.
Thanks.

--Thilo

Re: Bewildered

Dennis Geller wrote:
> Thanks. Very helpful.  However, having cleared that (and lots more 
> that derived from it) up, I think I'm good for now (with one more 
> question, below)
> First, in case it helps anyone else, after following your suggestions 
> I found  that art of my problem/confusion was that I had managed to 
> not have parallel directory hierarchies under descriptors and src -- 
> that made attempting to replicate the tutorial example unlikely to 
> succeed. When I straightened that out I was unable to run until I 
> added the directory that contains the TypeSystem.xml file to the class 
> path.  I don't believe the example needed that, but I sure did.
UIMA Descriptors have an "<import>" capability, to include other 
descriptors within them.  Many of the examples use this, for instance, 
to include a common type system specification.  There are 2 ways to 
refer to what you are importing - by "location" or by "name".  If you do 
things by "name", then UIMA uses Java's ability to locate resources by 
name in the Classpath (or UIMA Datapath).  If your descriptors import 
the type system "by name", then it is best to include it in your class path.
>
> I just almost had a successful run. However, it coughed because a file 
> had a "non-XML character, 0x0." 
Where was this character?  If it was in your XML descriptors, then that 
needs to be corrected.  It is possible to analyze arbitrary data, 
including "byte" data containing any characters, in UIMA; see 
http://incubator.apache.org/uima/downloads/releaseDocs/2.2.1-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.aas.sofa_data_formats
> This also happened when i was running the unmodified tutorial example.
Can you say where this character occurred in the unmodified tutorial example

-Marshall

Re: Bewildered

Sorry that I was unclear. The bad characters appeared when I took the 
compiled tutorial and pointed it at a directory of mine, rather than the 
one that came with the tutorial (no data problems in there!).

Could be that there was a jpeg in the directory, or an embedded image in 
a word document.  I'll follow up on that tutorial reference . Thanks.
>>
>> I just almost had a successful run. However, it coughed because a 
>> file had a "non-XML character, 0x0." 
> Where was this character?  If it was in your XML descriptors, then 
> that needs to be corrected.  It is possible to analyze arbitrary data, 
> including "byte" data containing any characters, in UIMA; see 
>
http://incubator.apache.org/uima/downloads/releaseDocs/2.2.1-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.aas.sofa_data_formats 
>
>> This also happened when i was running the unmodified tutorial example.
> Can you say where this character occurred in the unmodified tutorial 
> example
>
> -Marshall

-- 
***********************************
Dennis Geller, Ph.D. Computer and Communication Science   
Senior Software Developer
Direct Dial: 781.496.2461   Main Number: 781.935.3966 ext. 261   
Fax Number:  781.496-2498
E-mail:  dgeller <at> aptima.com
Aptima, Inc.
12 Gill Street, Suite 1400
Woburn, MA 01801 USA
http://www.aptima.com

************************************


The information transmitted is intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. Any review, retransmission, dissemination or other
use of, or taking of any action in reliance upon this information by persons or entities other than the
intended recipient is prohibited. If you received this in error, please contact the sender and delete the
material from any computer.