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
