Hi Bhagwat,

Thanks for the heads up on the "file:" issue.  I will check to see if the usage 
has changed and fix the piper.

Sean

-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] 
Sent: Thursday, November 23, 2017 9:17 AM
To: dev@ctakes.apache.org
Subject: Re: Interpret context out of clinical note [EXTERNAL]

Thanks James, It worked using cast to Map. !

Sean,
In AssertionDefaults.piper you set the file like:

set
assertionModelResource=file:org/apache/ctakes/assertion/models/i2b2.model

As I run this piper file it throws file not found exception, it resolved for me 
by removing "file:" from command, I suppose this needs to be fixed.


On 22 November 2017 at 23:21, Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:

> Wow, that is really strange.
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org_d
> _uimafit-2Dcurrent_api_org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1A9asf1ga
> bEGz-5fQfVfXbp2BcZEJaZIiJ4zSk09P1M&s=jo0yN7BJTt98IHerLXLK4aQvmSOAn90pU
> lzHg00ynFI&e=
> apache/uima/fit/util/JCasUtil.html
>
>
>
> -----Original Message-----
> From: James Masanz [mailto:masanz.ja...@gmail.com]
> Sent: Wednesday, November 22, 2017 12:50 PM
> To: dev@ctakes.apache.org
> Subject: Re: Interpret context out of clinical note [EXTERNAL]
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org
> > _& 
> > d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZst
> > Tp 
> > yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=rVKcbkbznwk6V-PLUy56sA4hGgN0F4qrLN5
> > Ik 6FIDnM&s=ebIFQbW0D4VLpTWv9a4YQqy_G30S_hDeDEbhCTesFuk&e=
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org
> > _d 
> > _&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZ
> > st
> > TpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=rVKcbkbznwk6V-PLUy56sA4hGgN0F4qrL
> > N5 Ik6FIDnM&s=I_7BH2bDGR48vI03bE1dirKGCgq33PKB9vXN2VDrMA8&e=
> > 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
> >
>



--
Thanks,
Bhagwat Posane

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