If I use Eclipse, at build time I also get the error

method putAll(Map<? extends Annotation,? extends
List<IdentifiedAnnotation>>) in the type
Map<Annotation,List<IdentifiedAnnotation>>
is not applicable for the arguments (Map)

I haven't looked into why.

A quick workaround is to add a cast to Map

allCovering.putAll( (Map)JCasUtil.indexCovering( jCas, covered, covering )
);




On Wed, Nov 22, 2017 at 8:40 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> 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.Finan@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
>

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