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From Tim Miller <timothy.mil...@childrens.harvard.edu>
Subject Re: UIMAFit and cTakes
Date Wed, 17 Apr 2013 14:19:01 GMT
Thank you for sticking with it, I'm sure your documentation of your 
experience and feedback will be helpful to future users.
Tim

On 04/17/2013 10:16 AM, giri vara prasad nambari wrote:
> 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 
> <mailto: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
>     <mailto:girinambari@gmail.com>]
>     *Sent:* Tuesday, April 16, 2013 11:12 PM
>     *To:* Chen, Pei
>
>
>     *Cc:* dev@ctakes.apache.org <mailto: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
>     <mailto: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
>     <mailto:girinambari@gmail.com>]
>     *Sent:* Tuesday, April 16, 2013 2:36 PM
>     *To:* user
>     *Cc:* dev@ctakes.apache.org <mailto: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
>     <https://groups.google.com/forum/?fromgroups#%21topic/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
>     <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 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
>     <mailto:girinambari@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@gmail.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 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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