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From ravi garg <ravigar...@gmail.com>
Subject Re: Regarding Lucene upgradation
Date Sun, 28 Jul 2013 12:58:07 GMT
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> 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> 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> 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> 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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