Hi Bruce, Would you mind opening up a Jira item with the details for this; sounds like a bug. Also, there seems to be a related one in the drug-ner that going into a loop and also causes a StackOverflow- you may also want to check out: https://issues.apache.org/jira/browse/CTAKES-246
--Pei > -----Original Message----- > From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com] > Sent: Tuesday, October 22, 2013 3:29 PM > To: dev@ctakes.apache.org > Subject: Infinite recursion in DrugMentionAnnotator.java > > I've been debugging the processing of a document using the pipeline defined > by DrugAggregatePlaintextUMLSProcessor.xml that results in a > StackOverflowError. > > I have traced it down to what I think is the cause and have a code > modification that appears to solve the problem but there is probably a more > appropriate solution. > > Is there someone who is more experienced with the code that can evaluate > the bug? > > > Bug Detail: > > Test document text (minimal text necessary to trigger the bug): > aspirin decreased from 2:00 PM. > > > Call path: > generageDrugMentionsAndAnnotations > statusChangePhraseGenerator > > (infinite recursion starts here) > generateAdditionalNER > generateDrugMentionsAndAnnotations > statusChangePhraseGenerator > generateAdditionalNER > ... > > > I believe the problem occurs in generateAdditionalNER() at ~line 2213 with > getAdjustedWindowSpan() returning -1. > This causes the call to generateDrugMentionsAndAnnotations() to process > the whole document again rather than the remaining portion of the text. > > Source code snippet: > > } else if (drugChangeStatus.getChangeStatus().compareTo( > DrugChangeStatusToken.DECREASEFROM) == 0) > { > if (noPriorMention) {//Look for lowest value on right side > beginChunk = getAdjustedWindowSpan(jcas, beginChunk, endSpan, > true)[0]; > } > String [] changeStatusArray = new String [] > {DrugChangeStatusToken.DECREASE, new Integer > (drugChangeStatus.getBegin()).toString(), new > Integer(drugChangeStatus.getEnd()).toString()}; > generateDrugMentionsAndAnnotations(jcas, > buildNewNER, beginChunk, endSpan, > tokenDrugNER, changeStatusArray, count, globalNER); > > > A simple fix might be to add the two lines: > > if (noPriorMention) {//Look for lowest value on right side > beginChunk = getAdjustedWindowSpan(jcas, beginChunk, endSpan, > true)[0]; > --> if (beginChunk == -1) > --> beginChunk = drugChangeStatus.getEnd(); > } > > Changing the logic inside getAdjustedWindowSpan() might be a more correct > and complete fix, but requires a much more detailed knowledge of the code. > > > Your evaluation of the correctness of this code modification would be > appreciated. > > Bruce Tietjen > Perfect Search Corp.
