DicionaryLookupAnnotatorCSV.xml is also a file I've not changed, and it does
reference LookupDesc_csv_sample.xml:
<externalResource>
<name>LookupDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/LookupDesc_csv_sample.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
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:[email protected]]
Sent: Thu, 16 Jan, 2014 11:09
To: [email protected]
Subject: RE: [External] RE: run-time error in processing LookupDesc_Db.xml
Richard,
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).
--Pei
From: Lee, Richard A. [USA] [mailto:[email protected]]
Sent: Wednesday, January 15, 2014 5:50 PM
To: [email protected]
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"/>
</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]
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.
