ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
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:

      <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: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

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: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"/>
</delegateAnalysisEngine>

And then add
<node>DictionaryLookupAnnotator</node>
Just before or just after
<node>DictionaryLookupAnnotatorDB</node>

-- 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

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: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
…\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.
Mime
View raw message