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From "Milinovich, Alex" <mili...@ccf.org>
Subject RE: DB DictionaryLookupAnnotator sqlserver exception
Date Wed, 15 Apr 2015 19:44:54 GMT
Ah, that led me in the right direction.  I was accidentally combining Lucene for the rxnorm
& orange book with jdbc for the lookup.

Swapped rxnorm & orange book to the jdbc version and it works.  Thanks!

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Wednesday, April 15, 2015 2:59 PM
To: dev@ctakes.apache.org
Subject: RE: DB DictionaryLookupAnnotator sqlserver exception

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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 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World
Report (2014).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our services,
staff and locations.


Confidentiality Note:  This message is intended for use only by the individual or entity to
which it is addressed and may contain information that is privileged, confidential, and exempt
from disclosure under applicable law.  If the reader of this message is not the intended recipient
or the employee or agent responsible for delivering the message to the intended recipient,
you are hereby notified that any dissemination, distribution or copying of this communication
is strictly prohibited.  If you have received this communication in error,  please contact
the sender immediately and destroy the material in its entirety, whether electronic or hard
copy.  

Thank you.

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