ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From giri vara prasad nambari <girinamb...@gmail.com>
Subject Re: UIMAFit and cTakes
Date Wed, 17 Apr 2013 03:11:13 GMT
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****
>
>  ****
>
>  ****
>
>  ****
>
> ** **
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message