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From "Lee, Richard A. [USA]" <lee_rich...@bah.com>
Subject RE: [External] RE: run-time error in processing LookupDesc_Db.xml
Date Fri, 17 Jan 2014 17:29:15 GMT
DicionaryLookupAnnotatorCSV.xml is also a file I've not changed, and it does reference LookupDesc_csv_sample.xml:


The only files that contain "LookupDesc_Db.xml" are DictionaryLookupAnnotatorDB.xml and DictionaryLookupAnnotatorUMLS.xml,
as the corresponding fileResourceSpecifier for their LookupDescriptorFile configuration.

Perhaps I should reiterate that I am not "just using DicionaryLookupAnnotatorCSV.xml", I am
trying to use it to supplement UMLS, and perhaps that's getting things confused. Or perhaps
I'm just misunderstanding you?

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Thu, 16 Jan, 2014 11:09
To: user@ctakes.apache.org
Subject: RE: [External] RE: run-time error in processing LookupDesc_Db.xml

If I’m not mistaken, if you’re just using DicionaryLookupAnnotatorCSV.xml, then it should
reference Something like: file:org/apache/ctakes/dictionary/lookup/LookupDesc_csv_sample.xml
for the lookup descriptor Where there is something like externalResourceKey="DictionaryFile"
defined in DicionaryLookupAnnotatorCSV.xml Rather than something like LookupDesc_Db.xml (DbConnection).


From: Lee, Richard A. [USA] [mailto:lee_richard@bah.com]
Sent: Wednesday, January 15, 2014 5:50 PM
To: user@ctakes.apache.org
Subject: RE: [External] RE: run-time error in processing LookupDesc_Db.xml

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"/>

And then add
Just before or just after

-- Richard

From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Wed, 15 Jan, 2014 17:17
To: user@ctakes.apache.org
Subject: [External] RE: run-time error in processing LookupDesc_Db.xml

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.


From: Lee, Richard A. [USA] [mailto:lee_richard@bah.com]
Sent: Wednesday, January 15, 2014 5:02 PM
To: user@ctakes.apache.org
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
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"/>

in the AE file. 

Please advise.
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