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Posted to dev@ctakes.apache.org by "Milinovich, Alex" <mi...@ccf.org> on 2015/04/15 18:49:41 UTC
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
===================================
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.
RE: DB DictionaryLookupAnnotator sqlserver exception
Posted by "Milinovich, Alex" <mi...@ccf.org>.
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
===================================
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.
===================================
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.
RE: DB DictionaryLookupAnnotator sqlserver exception
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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
===================================
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.