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 >
