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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: DB DictionaryLookupAnnotator sqlserver exception
Date Wed, 15 Apr 2015 18:59:27 GMT
Hi Alex,

This is some pretty odd behavior.  Obviously, it is indicating that the resource type loaded
or specified is not the correct class.  Specification is (for the standard UMLS pipeline)
in ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml lines #226
and #289.  Both should be
        <implementationName>org.apache.ctakes.core.resource.JdbcConnectionResourceImpl</implementationName>

There is an identical specification on line #352, but that is for Orangebook which (I'm pretty
sure) is no longer used and I think that this is one of a couple sections that was missed
during refactoring, so you can ignore it.

If you are running from source then you could try editing org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.java
lines #140, #141 and add to the exception message something like
+ " instead of " + (extResrc == null ? "NULL" : extResrc.getClass().getName() )
To find out what it thinks that it has underfoot.

Sean


From: Milinovich, Alex [mailto:milinoa@ccf.org]
Sent: Wednesday, April 15, 2015 12:50 PM
To: dev@ctakes.apache.org
Subject: DB DictionaryLookupAnnotator sqlserver exception

Attempting to use the sqlserver jdbc connection for the DictionaryLookupAnnotator.  When loading
the aggregate engine, the connection is established fine, but then it gives the error -

java.lang.Exception: Expected external resource to be:interface org.apache.ctakes.core.resource.JdbcConnectionResource
        at org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.parseDictionaryXml(LookupParseUtilities.java:140)
        at org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.parseDictionaries(LookupParseUtilities.java:94)
        at org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.parseDescriptor(LookupParseUtilities.java:80)
        at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.configInit(DictionaryLookupAnnotator.java:88)
        ... 26 more


Any ideas as to why this isn't working?


[cid:image001.jpg@01D0777A.A2C77340]

Alex Milinovich  |  System Analyst III  |  Quantitative Health Sciences
9500 Euclid Ave. - JJN3 | Cleveland, OH 44195 | p: (216) 444-9931 | m: (216) 245-7655




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