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From giri vara prasad nambari <girinamb...@gmail.com>
Subject Re: UIMAFit and cTakes
Date Wed, 17 Apr 2013 14:16:48 GMT
Hi Pei and Team,

Here is the news!!!!!!! after few days of struggle, I got my client program
to work late last night.

Now I am able to run Analysis Engine and parse the same text as CVD does. I
have observed few things

1) *This is documentation related.* It seems we need to give 1GB RAM to
eclipse to make this work, otherwise getting heap space error. May be we
need to update Wiki with this requirement.

2) When I run my sample program against test text we have in ctkaes User
Guide link, some how it is ignoring *Hyperlipidemia *as concept, whereas in
CVD we will get this as concept.

So far these are the two issues I have observed. Tonight I will do more
cases and see how it behaves.

May be I will compile small notes on client program setup, which we can use
as Wiki page for users like me.

Thank you everyone for your time and help so far.

Thank you,
Giri


On Wed, Apr 17, 2013 at 9:58 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

>  I see, It looks like you are using the 3.0.0 released binaries And not
> developing out of trunk.  Sorry for the confusion.****
>
> If so, ensure ****
>
> **1)      **you’ve downloaded and unpacked the separate resources file:***
> *
>
>
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip
> ****
>
> **2)      **Your C:\apache-ctakes-3.0.0\resources is in your classpath.***
> *
>
> I hope that works for you.****
>
> --Pei****
>
> ** **
>
> *From:* giri vara prasad nambari [mailto:girinambari@gmail.com]
> *Sent:* Tuesday, April 16, 2013 11:12 PM
> *To:* Chen, Pei
>
> *Cc:* dev@ctakes.apache.org
> *Subject:* Re: UIMAFit and cTakes****
>
>  ** **
>
> Hi Pei,****
>
> ** **
>
> I couldn't get this working by adding resources to path. I think I need to
> move to Maven to make my life easy here. Could you provide any reference
> for this approach?****
>
> ** **
>
> Another question I have is, in resource folder I am seeing following
> structure, not *ctakes-dependency-parser-res, * am I missing something.***
> *
>
> ** **
>
> C:\apache-ctakes-3.0.0\resources\org\apache\ctakes\dependency\parser****
>
> ** **
>
> Thanks for your time and help.****
>
> ** **
>
> Thank you,****
>
> Giri****
>
> ** **
>
> On Tue, Apr 16, 2013 at 2:40 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
> wrote:****
>
> 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 J.)****
>
> In eclipse/mvn, ensure that you have the ctakes-dependency-parser-res and
> any other resource project included in your dependencies.****
>
> Essentially, what it will need is everything in src/main/resources in the
> classpath.****
>
>  ****
>
> --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
> and was able to successfully get Clinical-pipe-line --->Analysisi
> Engine--->Descriptors 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
> NullPointerException. Any input on this issue?****
>
>  ****
>
>   AnalysisEngineDescription aaeDesc =
> AnalysisEngineFactory.createAggregate(descPath) ;
>   AnalysisEngine aee = AnalysisEngineFactory.createAggregate(aaeDesc); ***
> *
>
>  ****
>
> *Getting following Exception:*****
>
>  ****
>
> WARNING: The aggregate text analysis engine "AggregatePlaintextProcessor"
> has declared the parameter , but has not declared any overrides.This usage
> is deprecated.****
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class
> "org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE"
> failed.  (Descriptor:
> file:/C:/workspace/DataAnalyisEngine/resources/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> ****
>
>           at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> ****
>
>           at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> ****
>
>           at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)****
>
>           at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> ****
>
>           at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> ****
>
>           at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> ****
>
>           at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> ****
>
>           at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)****
>
>           at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)****
>
>           at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> ****
>
>           at
> org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.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.ClearParserDependencyParserAE.initialize(ClearParserDependencyParserAE.java:136)
> ****
>
>           at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ****
>
>           ... 16 more****
>
>  ****
>
> Here is the thread which lists the discussion I had with Richard from
> UIMAFit.****
>
>  ****
>
>
> https://groups.google.com/forum/?fromgroups#!topic/uimafit-users/yI0NT2HynU0
> ****
>
>  ****
>
> 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
> first 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> 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
> yesterday 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
> so, 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
> the existing pom.xml and add in any of the dependencies there.  If you
> include any existing module as a dependency, it should automagically handle
> any resources/models without having to manually maintaining a lib
> directory.  Please let us know if this works out for you or if you need
> more input in this space.****
>
>  ****
>
> 2) What should be descPath in following code ( I figured that this should
> be 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
> could be changed/reused if possible.****
>
> I’ll let some of the uimaFIT experts here chime in as to best use it for
> your 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/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java
> ****
>
> [2]
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
> ****
>
>  ****
>
> I hope that helps.****
>
> --Pei****
>
>  ****
>
> *From:* giri vara prasad nambari [mailto:girinambari@gmail.com]
> *Sent:* Monday, April 15, 2013 10:45 AM
> *To:* 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@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
> ctakes lib to my eclipse project --->Java build path--->libraries.****
>
>  ****
>
> Sample code I have is *(This is compiling fine, but runtime issue due to
> path is not valid for AnalysisEngineDescription):*****
>
> TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory
> ****
>
> .createTypeSystemDescription();****
>
> List<AnalysisEngineDescription> engines = new
> ArrayList<AnalysisEngineDescription>();****
>
> List<String> componentNames = new ArrayList<String>();****
>
>  ****
>
> AnalysisEngineDescription engine = AnalysisEngineFactory****
>
> .createAnalysisEngineDescription("com.resources.AggregatePlaintextProcessor",
> "", "");****
>
> engines.add(engine);****
>
> AnalysisEngine aggregateAE = 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
> so, how? Attached screenshot of the jars I have in build path. ****
>
>  ****
>
> 2) What should be descPath in following code ( I figured that this should
> be 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 = AnalysisEngineFactory****
>
> .createAnalysisEngineDescription("descPath", "", "");****
>
>  ****
>
> any inputs would be really appreciated. ****
>
>  ****
>
> Thanks for your time and help.****
>
>  ****
>
> Thank you,****
>
> Giri****
>
>  ****
>
>  ****
>
>  ****
>
>  ****
>
> ** **
>

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