Hi Peter,
Unfortunately, the notes are full of phi, so I can't send it out.

Thanks!

Greg--



On Wed, Feb 10, 2021 at 10:27 AM Peter Abramowitsch <pabramowit...@gmail.com>
wrote:

> Hi Greg
>
> I would help you, but unfortunately I'm in italy at the back end of an
> abysmally slow internet, especially in upload.   But still it would be
> interesting if I could see an example anonymized note that has this FP
> error problem as I could try it on my version of 4.0.0.     The fact that
> 4.0.1 is no longer working makes me wonder whether you have some kind of
> deployment context error rather than the core cTakes code itself.
>
> Peter
>
> On Wed, Feb 10, 2021 at 4:25 PM Greg Silverman <g...@umn.edu.invalid>
> wrote:
>
> > We're running version 4.0.0.1 on ~12K notes. The first time we ran it I
> got
> > a heap space error at ~10.5k notes processed (at about ~38 hours).
> >
> > I increased the heap space params and then reran. This time it died at
> the
> > same place, but with a different error (see below):
> >
> > SEVERE: Exception occurred
> > org.apache.uima.analysis_engine.AnalysisEngineProcessException
> >         at
> > org.apache.ctakes.contexttokenizer.ae
> >
> .ContextDependentTokenizerAnnotator.process(ContextDependentTokenizerAnnotator.java:105)
> >         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)
> >         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)
> > ...
> > Caused by: java.lang.NumberFormatException: For input string: "f"
> >         at
> > sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
> >         at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
> >         at java.lang.Double.parseDouble(Double.java:538)
> > --------
> >
> > Thus, it looks like a string is being detected as a float. This had
> worked
> > in version 4.0.1, so it must have been fixed at some point. Even after I
> > made changes for the new NLM authentication for UMLS and tested it in
> 4.0.1
> > based on Peter's authentication solution, it stopped working after
> January
> > 15th.  Unfortunately, we're not set up to compile 4.0.1.
> >
> > That being said, does someone have a working version of 4.0.1 built from
> > the trunk? If so, could you please send me a copy?
> >
> > If not, how can I find the offending file?
> >
> > This is kind of critical, since we're in the middle of an experiment and
> > another side effect of reverting to 4.0.0.1 is it is a LOT slower than
> > 4.0.1.
> >
> > Thanks very much in advance!
> >
> > Greg--
> >
> > --
> > Greg M. Silverman
> > Senior Systems Developer
> > NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> > Department of Surgery
> > University of Minnesota
> > g...@umn.edu
> >
>


-- 
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
g...@umn.edu

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