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Posted to user@ctakes.apache.org by ravi garg <ra...@gmail.com> on 2013/07/26 14:07:55 UTC
Regarding Lucene upgradation
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
Re: Regarding Lucene upgradation
Posted by Tim Miller <ti...@childrens.harvard.edu>.
In that code it looks like you iterate over EventMention types. Have you
tried iterating over the Annotation superclass and see if any of the
earlier types are working? i.e. Segment, Sentence, and BaseToken? It
would be good to know if there is some point at which it's breaking down
or if nothing at all is working.
Tim
On 07/29/2013 08:59 AM, ravi garg wrote:
> 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
> <ma...@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
>> <ma...@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 <ma...@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
>> <ma...@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 <ma...@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
Re: Regarding Lucene upgradation
Posted by ravi garg <ra...@gmail.com>.
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 <ra...@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 <ra...@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" <ra...@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
Re: Regarding Lucene upgradation
Posted by Tim Miller <ti...@childrens.harvard.edu>.
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
> <ma...@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
> <ma...@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
> <ma...@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 <ma...@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
Re: Regarding Lucene upgradation
Posted by ravi garg <ra...@gmail.com>.
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 <ra...@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 <ra...@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" <ra...@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
Re: Regarding Lucene upgradation
Posted by ravi garg <ra...@gmail.com>.
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 <ra...@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" <ra...@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
Re: Regarding Lucene upgradation
Posted by ravi garg <ra...@gmail.com>.
Hi,
I will checkout the latest version. Thanks for the prompt reply :)
On Fri, Jul 26, 2013 at 6:56 PM, Chen, Pei
<Pe...@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" <ra...@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
Re: Regarding Lucene upgradation
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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" <ra...@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