I did not change LookupDesc_Db.xml; I’ve been wondering if there’s something I should have added there. The intended CSV dictionary – which I haven’t changed yet – is just the provided dictionary1.csv referenced in …\apache-ctakes-3.1.1\desc\ctakes-dictionary-lookup\desc\analysis_engine\DictionaryLookupAnnotatorCSV.xml.
Here’s all I’ve changed, as per my understanding of the recommendation: You would add the following to the delegateAnalysisEngine list of [a copy of] AggregatePlainTextUMLSProcessor.xml <delegateAnalysisEngine key="DictionaryLookupAnnotator"> <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml"/> </delegateAnalysisEngine> And then add <node>DictionaryLookupAnnotator</node> Just before or just after <node>DictionaryLookupAnnotatorDB</node> -- Richard From: Chen, Pei [mailto:[email protected]] Sent: Wed, 15 Jan, 2014 17:17 To: [email protected] Subject: [External] RE: run-time error in processing LookupDesc_Db.xml Richard, Would it be possible to attach the customized LookupDesc_Db.xml? In particular, did you just add your CSV dictionary file (in addition to the existing DbConnection resources?) If so, then I believe you’ll still need to include them in your descriptor: Take a look at ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml as an example. HTH. --Pei From: Lee, Richard A. [USA] [mailto:[email protected]] Sent: Wednesday, January 15, 2014 5:02 PM To: [email protected]<mailto:[email protected]> Subject: run-time error in processing LookupDesc_Db.xml I received advice on this list from James Masanz to add a couple things to AggregatePlainTextUMLSProcessor.xml, in order to add a CSV dictionary lookup to my cTAKES processing. I chose to instead make a copy of AggregatePlainTextUMLSProcessor.xml with the additions, and pointed Run > Load AE at that new file. This resulted in a quite uninformative run-time error which I reported but no-one has offered any suggestions on. I’ve now set up Eclipse with all the needed plugins and cTAKES files – a challenge in itself – in order to try to isolate the problem somewhat. The error seems to occur in the 2nd invocation of DictionaryLookupAnnotator.configInit(), with the complaint while processing …\workspace\ctakes\ctakes-dictionary-lookup-res\target\classes\org\apache\ctakes\dictionary\lookup\LookupDesc_Db.xml that it is “Unable to find external resource with key:DbConnection”. Digging a bit further, it looks like the 1st time it constructs a QualifiedName it constructs “/DictionaryLookupAnnotatorDB/DbConnection” which it is able to find, but the 2nd time it constructs “/DictionaryLookupAnnotator/DbConnection” which it is not. This second time is due to the recommended addition of <delegateAnalysisEngine key="DictionaryLookupAnnotator"> <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml"/> </delegateAnalysisEngine> in the AE file. Please advise.
