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 <[email protected]>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:[email protected]] > *Sent:* Tuesday, April 16, 2013 2:36 PM > *To:* user > *Cc:* [email protected] > > *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 < > [email protected]> 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:[email protected]] > *Sent:* Monday, April 15, 2013 10:45 AM > *To:* [email protected]; 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 < > [email protected]> 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**** > > **** > > **** > > **** > > ** ** >
