Hi Sean, Issue with 4.0.1 is not custom changes, I just don't have the environment to do this.
Any chance of getting the entire build? Thanks! Greg-- On Wed, Feb 10, 2021 at 10:10 AM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Greg, > > It looks like the offending class might be > org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter, which seems to be > the only NumberTokenAdapter without a try/catch around the parse(..). > > I made a fix that runs on my tests. Since you say that you cannot build > trunk/4.0.1 locally (custom changes?) I can do one of two things: > > 1. Send you a copy of the compiled DecimalTokenAdapter class, or > 2. Send you a copy of the complete ctakes-core jar. > > The advantage to #1 is that any local custom changes that you have for the > ctakes-core module shouldn't be overwritten. If you haven't updated trunk > in a while then there are most likely some changes. > The disadvantage to #1 is minor. You will need to manually insert the > DecimalTokenAdapter.class file into your local ctakes-core.jar file. As > the jar file is just a zip file with a different name this is actually > pretty easy to do - you can find loads of "how to" on the web. > The advantage to #2 is that you just replace the jar file in your bin/ > directory with the new copy. However, there are the disadvantages as > listed above. > > I recommend #1. > > Sean > > ________________________________________ > From: Greg Silverman <g...@umn.edu.INVALID> > Sent: Wednesday, February 10, 2021 10:25 AM > To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo > Subject: error: CRITICAL [EXTERNAL] > > * External Email - Caution * > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-u760Da1zvrINW3S87TjC6FqWdNhNselgSQIfTTg4-c&s=oKao5Bz-_QkhcdgBtI7kF7CYmF1jl3v-7oaijC0jwZ4&e= > > > 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
