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From Tim Miller <timothy.mil...@childrens.harvard.edu>
Subject Re: Regarding Lucene upgradation
Date Mon, 29 Jul 2013 12:51:16 GMT
Ravi,
My email reader doesn't seem to know what format the attachment is. If 
it's short enough you may be able to just paste your source into the 
body of the email, otherwise could you resend the file with an 
appropriate file extension?
Thanks
Tim

On 07/28/2013 08:58 AM, ravi garg wrote:
> Hi,
> I skipped the tests for now and was able to build it successfully. But 
> I am facing another problem here. I get a NoSuchElementFound Exception 
> when I run the pipeline. I have attached the code for reference. 
> Please do have a look. The AnalysisEngine get initialised fine but for 
> some reasons I am not getting any Annotation. The exact error is,
>
> |Caused by: java.util.NoSuchElementException
> ||	at org.apache.uima.cas.impl.FSIndexRepositoryImpl$PointerIterator.ll_get(FSIndexRepositoryImpl.java||:542)
> ||	at org.apache.uima.cas.impl.FSIndexRepositoryImpl$PointerIterator.get(FSIndexRepositoryImpl.java:537||)
> ||	at org.apache.uima.cas.impl.FSIteratorWrapper.get(FSIteratorWrapper.java:48)
> ||	at org.apache.uima.cas.impl.FSIteratorImplBase.next(FSIteratorImplBase.java:67)
> ||	at org.apache.uima.cas.impl.FSIteratorImplBase.next(FSIteratorImplBase.java:33)
> ||	at org.phenotips.ctakes.CTAKESScriptService.extract(CTAKESScriptService.java:400)
> ||	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> ||	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> ||	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> ||	at java.lang.reflect.Method.invoke(Method.java:616)
> ||	at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:395||)
> ||	at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:384||)
> ||	at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:173)
> ||	... 116 more
>
> |
> |
>
> |
>
>
>
> On Sat, Jul 27, 2013 at 5:13 PM, ravi garg <ravigarg27@gmail.com 
> <mailto:ravigarg27@gmail.com>> wrote:
>
>     Hi,
>
>     I downloaded the 3.1 version
>     (https://svn.apache.org/repos/asf/ctakes/branches/ctakes-3.1.0/).
>     But while running mvn clean install I get a build error. The error is
>
>     Results :
>
>     Tests in error:
>     testTokenizerAnnotatorPTB(org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests):
>     Initialization of annotator class
>     "org.apache.ctakes.core.ae.SentenceDetector" failed. (Descriptor:
>     file:/home/ravi/cTAKES3.1/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml)
>
>     Tests run: 3, Failures: 0, Errors: 1, Skipped: 0
>
>     [INFO]
>     ------------------------------------------------------------------------
>     [INFO] Reactor Summary:
>     [INFO]
>     [INFO] Apache cTAKES ..................................... SUCCESS
>     [4.215s]
>     [INFO] Apache cTAKES common type system .................. SUCCESS
>     [7.806s]
>     [INFO] Apache cTAKES utils ............................... SUCCESS
>     [2.361s]
>     [INFO] Apache cTAKES Resources core ...................... SUCCESS
>     [0.979s]
>     [INFO] Apache cTAKES core ................................ FAILURE
>     [6.078s]
>     [INFO] Apache cTAKES Resources pos-tagger ................ SKIPPED
>     [INFO] Apache cTAKES part-of-speech tagger ............... SKIPPED
>     [INFO] Apache cTAKES Resources ctakes-chunker-res ........ SKIPPED
>     [INFO] Apache cTAKES chunker ............................. SKIPPED
>     [INFO] Apache cTAKES document preprocessor ............... SKIPPED
>     [INFO] Apache cTAKES Resources dictionary-lookup ......... SKIPPED
>     [INFO] Apache cTAKES dictionary lookup ................... SKIPPED
>     [INFO] Apache cTAKES context dependent tokenizer ......... SKIPPED
>     [INFO] Apache cTAKES Resources lvg ....................... SKIPPED
>     [INFO] Apache cTAKES LVG lexical tools ................... SKIPPED
>     [INFO] Apache cTAKES Resources ne-contexts ............... SKIPPED
>     [INFO] Apache cTAKES named entity contexts ............... SKIPPED
>     [INFO] Apache cTAKES Resources constituency-parser ....... SKIPPED
>     [INFO] Apache cTAKES Constituency Parser ................. SKIPPED
>     [INFO] Apache cTAKES Resources coreference ............... SKIPPED
>     [INFO] Apache cTAKES Resources relation-extractor ........ SKIPPED
>     [INFO] Apache cTAKES Resources dependency-parser ......... SKIPPED
>     [INFO] Apache cTAKES Dependency Parser ................... SKIPPED
>     [INFO] Apache cTAKES Relation Extractor .................. SKIPPED
>     [INFO] Apache cTAKES CoReference Resolver ................ SKIPPED
>     [INFO] Apache cTAKES Resources drug-ner .................. SKIPPED
>     [INFO] Apache cTAKES Drug NER ............................ SKIPPED
>     [INFO] Apache cTAKES Resources side-effect ............... SKIPPED
>     [INFO] Apache cTAKES Side Effects ........................ SKIPPED
>     [INFO] Apache cTAKES Resources smoking-status ............ SKIPPED
>     [INFO] Apache cTAKES Smoking Status ...................... SKIPPED
>     [INFO] Apache cTAKES Resources pad-term-spotter-res ...... SKIPPED
>     [INFO] Apache cTAKES Pad Term Spotter .................... SKIPPED
>     [INFO] Apache cTAKES Resources assertion ................. SKIPPED
>     [INFO] Apache cTAKES Resources assertion-zoner ........... SKIPPED
>     [INFO] Apache cTAKES Assertion's zoner ................... SKIPPED
>     [INFO] Apache cTAKES Assertion ........................... SKIPPED
>     [INFO] Apache cTAKES Resources temporal .................. SKIPPED
>     [INFO] Apache cTAKES Temporal Information Extraction ..... SKIPPED
>     [INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
>     [INFO] Apache cTAKES Distribution ........................ SKIPPED
>     [INFO] Apache cTAKES Regression-test ..................... SKIPPED
>     [INFO] Apache cTAKES template filler ..................... SKIPPED
>     [INFO]
>     ------------------------------------------------------------------------
>     [INFO] BUILD FAILURE
>     [INFO]
>     ------------------------------------------------------------------------
>     [INFO] Total time: 23.783s
>     [INFO] Finished at: Sat Jul 27 17:07:40 IST 2013
>     [INFO] Final Memory: 30M/198M
>     [INFO]
>     ------------------------------------------------------------------------
>     [ERROR] Failed to execute goal
>     org.apache.maven.plugins:maven-surefire-plugin:2.12:test
>     (default-test) on project ctakes-core: There are test failures.
>
>
>     Any ideas what I am doing wrong or what am I missing something. I
>     checked and confirmed to have updated version of 3.1
>
>
>     On Fri, Jul 26, 2013 at 9:52 PM, ravi garg <ravigarg27@gmail.com
>     <mailto:ravigarg27@gmail.com>> wrote:
>
>         Hi,
>
>         I will checkout the latest version. Thanks for the prompt
>         reply :)
>
>
>         On Fri, Jul 26, 2013 at 6:56 PM, Chen, Pei
>         <Pei.Chen@childrens.harvard.edu
>         <mailto:Pei.Chen@childrens.harvard.edu>> wrote:
>
>             Ravi,
>             trunk an the upcoming release (3.1) - have been upgraded
>             to Lucene 4.x. There should be an RC very soon... I would
>             strongly recommend using that as there were some code
>             changes as well new updating the resources/indexes.
>
>             Sent from my iPhone
>
>             On Jul 26, 2013, at 8:08 AM, "ravi garg"
>             <ravigarg27@gmail.com <mailto:ravigarg27@gmail.com>> wrote:
>
>             > Hi,
>             >
>             > I am working on a project which uses upgraded Lucene
>             version (4.0). I have to integrate cTAKES with it but
>             unfortunately cTAKES still uses older version of Lucene
>             (3.0 I believe). So is there a workaround you could please
>             suggest. Also is the newer version of Apache cTAKES
>             scheduled to arrive soon with the updated Lucene version.
>             Could you please provide any info on that.
>             >
>             > Thanks,
>             > Ravi Garg
>             >
>             > --
>             > Ravi Garg
>             > 3rd Year
>             > MSc (hons) Biological Sciences
>             > B.E (hons) Computer Science and Engineering
>             > BITS Pilani KK Birla Goa Campus
>
>
>
>
>         -- 
>         Ravi Garg
>         3rd Year
>         MSc (hons) Biological Sciences
>         B.E (hons) Computer Science and Engineering
>         BITS Pilani KK Birla Goa Campus
>
>
>
>
>     -- 
>     Ravi Garg
>     3rd Year
>     MSc (hons) Biological Sciences
>     B.E (hons) Computer Science and Engineering
>     BITS Pilani KK Birla Goa Campus
>
>
>
>
> -- 
> Ravi Garg
> 3rd Year
> MSc (hons) Biological Sciences
> B.E (hons) Computer Science and Engineering
> BITS Pilani KK Birla Goa Campus


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