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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> wrote:
Hi,
I will checkout the latest version. Thanks for the prompt
reply :)
On Fri, Jul 26, 2013 at 6:56 PM, Chen, Pei
<[email protected]
<mailto:[email protected]>> 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"
<[email protected] <mailto:[email protected]>>
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
