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From: "Chen, Pei" <Pei.Chen@childrens.harvard.edu>
To: "girinambari@gmail.com" <girinambari@gmail.com>
CC: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: UIMAFit and cTakes
Thread-Topic: UIMAFit and cTakes
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Date: Tue, 16 Apr 2013 18:40:34 +0000
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Hi Giri,
The NPE is due to the fact that the component can't find the model file (It=
 should probably give a more friendly error message though :).)
In eclipse/mvn, ensure that you have the ctakes-dependency-parser-res and a=
ny other resource project included in your dependencies.
Essentially, what it will need is everything in src/main/resources in the c=
lasspath.

--Pei


From: giri vara prasad nambari [mailto:girinambari@gmail.com]
Sent: Tuesday, April 16, 2013 2:36 PM
To: user
Cc: dev@ctakes.apache.org
Subject: Re: UIMAFit and cTakes

Hi Pei,

It was really tragic incident. My thoughts and prayers are with Boston.

Regarding the UIMAFit and analysis engine issues, I did some trail/error an=
d was able to successfully get Clinical-pipe-line --->Analysisi Engine--->D=
escriptors get loaded (after that Richard from UIMAFit chimed in suggested =
alternative code to get this run).

But when I use this alternative code (shown below), I am getting ctakes Nul=
lPointerException. Any input on this issue?

  AnalysisEngineDescription aaeDesc =3D AnalysisEngineFactory.createAggrega=
te(descPath) ;
  AnalysisEngine aee =3D AnalysisEngineFactory.createAggregate(aaeDesc);

Getting following Exception:

WARNING: The aggregate text analysis engine "AggregatePlaintextProcessor" h=
as declared the parameter , but has not declared any overrides.This usage i=
s deprecated.
org.apache.uima.resource.ResourceInitializationException: Initialization of=
 annotator class "org.apache.ctakes.dependency.parser.ae.ClearParserDepende=
ncyParserAE" failed.  (Descriptor: file:/C:/workspace/DataAnalyisEngine/res=
ources/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyP=
arserAE.xml)
          at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_i=
mpl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
          at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_i=
mpl.initialize(PrimitiveAnalysisEngine_impl.java:156)
          at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResourc=
e(AnalysisEngineFactory_impl.java:94)
          at org.apache.uima.impl.CompositeResourceFactory_impl.produceReso=
urce(CompositeResourceFactory_impl.java:62)
          at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.ja=
va:269)
          at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramew=
ork.java:387)
          at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_im=
pl.java:254)
          at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_i=
mpl.initASB(AggregateAnalysisEngine_impl.java:431)
          at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_i=
mpl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375=
)
          at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_i=
mpl.initialize(AggregateAnalysisEngine_impl.java:185)
          at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResourc=
e(AnalysisEngineFactory_impl.java:94)
          at org.apache.uima.impl.CompositeResourceFactory_impl.produceReso=
urce(CompositeResourceFactory_impl.java:62)
          at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.ja=
va:269)
          at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.ja=
va:314)
          at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramew=
ork.java:425)
          at org.uimafit.factory.AnalysisEngineFactory.createAggregate(Anal=
ysisEngineFactory.java:424)
          at com.dae.test.JcasParserTest.main(JcasParserTest.java:28)
Caused by: java.lang.NullPointerException
          at clear.morph.MorphEnAnalyzer.<init>(MorphEnAnalyzer.java:111)
          at org.apache.ctakes.dependency.parser.ae.ClearParserDependencyPa=
rserAE.initialize(ClearParserDependencyParserAE.java:136)
          at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_i=
mpl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
          ... 16 more

Here is the thread which lists the discussion I had with Richard from UIMAF=
it.

https://groups.google.com/forum/?fromgroups#!topic/uimafit-users/yI0NT2HynU=
0

I hope this will be last hurdle to overcome to get my code running as java =
client.

I am allowed to use Maven (and this is eclipse project), but I don't have f=
irst hand experience with it yet, so prefer to hold until one level of flow=
 is ready, which gives me comfort to work on improvements.

Thank you,
Giri
On Tue, Apr 16, 2013 at 12:46 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu=
<mailto:Pei.Chen@childrens.harvard.edu>> wrote:

[-user bcc, +dev as this is probably geared towards developers]

Hi Giri,

My apologies- a lot of us in the Boston area were out of the office yesterd=
ay for the holiday and also the tragic events that have transpired here.


1) Do I need to add ctakes resources some where in my eclipse project? If s=
o, how? Attached screenshot of the jars I have in build path.

Maven is excellent for handling and resolving dependencies.  If this is an =
eclipse project, I would suggest creating a mvn project or cloning one of t=
he existing pom.xml and add in any of the dependencies there.  If you inclu=
de any existing module as a dependency, it should automagically handle any =
resources/models without having to manually maintaining a lib directory.  P=
lease let us know if this works out for you or if you need more input in th=
is space.


2) What should be descPath in following code ( I figured that this should b=
e path for whatever the AE (like ctakes-clinical-pipeline) we would like to=
 use, but I am not clear on how could I get this desc into my project.

One way is to pass in any paths as configuration parameters so that it coul=
d be changed/reused if possible.

I'll let some of the uimaFIT experts here chime in as to best use it for yo=
ur use-case.  But the API is capable of creating pipelines programmatically=
, as well as reading in a xml descriptor (Either Aggregate or Primitive).


Some examples include that I could think of on the top of my head:

[1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dependency-parser/s=
rc/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalys=
isEngines.java

[2] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-temporal/src/main/j=
ava/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java


I hope that helps.

--Pei


From: giri vara prasad nambari [mailto:girinambari@gmail.com<mailto:girinam=
bari@gmail.com>]
Sent: Monday, April 15, 2013 10:45 AM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>; user
Subject: Re: UIMAFit and cTakes


Hi Team,


Good morning!


Any inputs on this issue?


Thank you,

Giri


On Sun, Apr 14, 2013 at 5:33 PM, giri vara prasad nambari <girinambari@gmai=
l.com<mailto:girinambari@gmail.com>> wrote:

Hi Community,


I am trying to write a simple java client program using UIMAFit and ctakes.


I have added all jars come with UIMAFit and ctakes specific jars from ctake=
s lib to my eclipse project --->Java build path--->libraries.


Sample code I have is (This is compiling fine, but runtime issue due to pat=
h is not valid for AnalysisEngineDescription):

TypeSystemDescription typeSystemDescription =3D TypeSystemDescriptionFactor=
y

.createTypeSystemDescription();

List<AnalysisEngineDescription> engines =3D new ArrayList<AnalysisEngineDes=
cription>();

List<String> componentNames =3D new ArrayList<String>();


AnalysisEngineDescription engine =3D AnalysisEngineFactory

.createAnalysisEngineDescription("com.resources.AggregatePlaintextProcessor=
", "", "");

engines.add(engine);

AnalysisEngine aggregateAE =3D AnalysisEngineFactory.createAggregate(

engines, componentNames, typeSystemDescription, null,

new SofaMapping[0]);


One thing I am little confused here is,


1) Do I need to add ctakes resources some where in my eclipse project? If s=
o, how? Attached screenshot of the jars I have in build path.


2) What should be descPath in following code ( I figured that this should b=
e path for whatever the AE (like ctakes-clinical-pipeline) we would like to=
 use, but I am not clear on how could I get this desc into my project.


AnalysisEngineDescription engine =3D AnalysisEngineFactory

.createAnalysisEngineDescription("descPath", "", "");


any inputs would be really appreciated.


Thanks for your time and help.


Thank you,

Giri


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