Hi Bhagwat, I have no idea what is going on with your system.
> The method putAll(Map<? extends Annotation,? extends > List<IdentifiedAnnotation>>) in the type > Map<Annotation,List<IdentifiedAnnotation>> is not applicable for the > arguments (Map) That doesn't make any sense to me. That is exactly what putAll is for ... Unless your uimafit does not return a typed map? In which case it is an old version? I am not sure how that would happen. > When I run AssertionSubPipe.piper I am getting below error: The .piper files should all have line comments in them. The *SubPipe pipers should all have something like "This is not a complete pipeline" at the top. This means that it cannot be run alone. The annotators in the Assertion piper require several other annotators to run first. In addition to the default clinical piper I think that there are some piper files in ctakes-example-res that you can look at to start. >, I don't find any variables value in understandable format like (JCas jcas) >object. How would I understand JCas object values? ctakes is built upon the Apache UIMA framework. https://uima.apache.org/ This should probably be on our wiki ... Anyway, the best way to learn about how ctakes pipelines are put together and how data is passed is to read some of the intro documentation for uima. The Javadoc for jcas is here: https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/jcas/JCas.html Sean -----Original Message----- From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] Sent: Wednesday, November 22, 2017 3:38 AM To: dev@ctakes.apache.org Subject: Re: Interpret context out of clinical note [EXTERNAL] Hello Sean, Thank you for the inputs. I have gone through both the piper files which you have mentioned. When I run AssertionSubPipe.piper I am getting below error: //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////// 22 Nov 2017 12:55:31 WARN SingleDocumentProcessor - This class cannot be used until CTAKES-76 is implemented. 22 Nov 2017 12:55:31 WARN SingleDocumentProcessor - This class cannot be used until CTAKES-76 is implemented. Nov 22, 2017 12:55:31 PM org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(430) SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed. at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:412) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator. processUntilNextOutputCas(ASB_impl.java:570) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$ AggregateCasIterator.<init>(ASB_impl.java:412) at org.apache.uima.analysis_engine.asb.impl.ASB_impl. process(ASB_impl.java:344) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator. processUntilNextOutputCas(ASB_impl.java:570) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$ AggregateCasIterator.<init>(ASB_impl.java:412) at org.apache.uima.analysis_engine.asb.impl.ASB_impl. process(ASB_impl.java:344) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process( AnalysisEngineImplBase.java:269) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline( SimplePipeline.java:150) at org.apache.ctakes.core.pipeline.PipelineBuilder.run( PipelineBuilder.java:348) at org.apache.ctakes.core.pipeline.PiperFileRunner.run( PiperFileRunner.java:72) at org.apache.ctakes.core.pipeline.PiperFileRunner.main( PiperFileRunner.java:30) Caused by: java.lang.NullPointerException at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngineFit.process( AssertionAnalysisEngineFit.java:145) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process( JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396) ... 14 more //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// /////////////////////// The error is causing due to the command : add AssertionAnalysisEngineFit I have comment out this command and ran it, the html output doesn't have any difference with previous output. Could you please help me to resolve this error. On 21 November 2017 at 18:43, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Bhagwat, > > You can visit the ctakes-assertion-res module for some clues. > > Navigate to ctakes-assertion-res src/main/resources/ > org/apache/ctakes/assertion/pipeline/ > > There are two .piper files there. Each one covers a different way to > get the information that Tim mentioned. In those files each "add" > statement is followed by an annotator class name. In IntelliJ you can > press CTRL-N and enter the class name to view the code. There are > also a few comments in the piper files that may help. > > Sean > > -----Original Message----- > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > Sent: Tuesday, November 21, 2017 6:21 AM > To: dev@ctakes.apache.org > Subject: Interpret context out of clinical note [EXTERNAL] > > Hello Sean,Tim, et al, > > I would like to Interpret context out of clinical note, e.g. > interpretation of the procedure, lab tests for a patient. For this, I > suppose TLINK statements would be of much help. > > Ex. for the note- "Cystoscopy is planned on 3 / 26 / 2018." > I get TLINK as > Cystoscopy contains 3 / 26 / 2018, > 3 / 26 / 2018 contains Cystoscopy > 3 / 26 / 2018 contains planned > we can make out that Cystoscopy is not yet done looking at > "planned"(in this case), > > Could you please let me know if I am on right path and also help me > understand if any other approach to do this. > > > @Tim, > Couple of days back you mentioned about the context understanding : > > "if any procedure is happened or not." > > I think you need a formal definition of this to understand what > > you're trying to do. > > As a guess, you want it to be in the past, related to the patient > > (not a family member), and not negated or hypothetical or uncertain, etc.? > > This would require multiple components, but most of them should run > > in the temporal pipeline. > > > > Tim > > > Could you please provide some insight on this, as what are the > multiple components are required and how to use them to achieve this goal. > > -- > Thanks, > Bhagwat Posane > -- Thanks, Bhagwat Posane
