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From ravi garg <ravigar...@gmail.com>
Subject Re: Regarding Lucene upgradation
Date Mon, 29 Jul 2013 12:59:58 GMT
Hi,
I have attached a txt version. Sorry for wrong format. Do have a look.

Thanks,
Ravi



On Mon, Jul 29, 2013 at 6:21 PM, Tim Miller <
timothy.miller@childrens.harvard.edu> wrote:

>  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> 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
>
>
>


-- 
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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