ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Jakob Rogstadius <Jakob.Rogstad...@who-umc.org>
Subject Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Date Thu, 09 Jul 2015 12:43:04 GMT
Hi cTakes devs,

I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer
fast one) through uimaFIT, and I am running into problems with resources that can't be found.
Please bear with me if my problem description omits any relevant details, as I don't have
much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.

cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline
running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified
the UMLS login details in the arguments of the Eclipse runtime configuration, which works.
However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail
to resolve their respective lookup descriptor files. I have included a stack trace for the
first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize()
(line 129), due to the fileResource variable being null.

I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription()
is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same
change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription()
is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven.
Have these files moved, so that I now need to include something else? Am I doing something
else wrong?

Also, I have downloaded the UMLS dictionary resources from http://ctakes.apache.org/downloads.cgi,
but where do I place them for cTakes to be able to find them?

Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():

java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
	at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
	at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
	at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
	at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
	at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
	at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
	at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
	at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
	at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
	... 1 more

Any pointers would be greatly appreciated.

Best regards,

Jakob Rogstadius
Research Engineer

Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring

Mime
View raw message