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
