Hello, I have located the sno_rx_16ab.xml file in that folder. However, I might
be able to sense the problem here. When I downloaded the additional resources
folder (ctakes-resources-4.0-bin), I copied the contents of that folder
(license, notice, readme, and resources folder) into the CTAKES_HOME resources
folder. The downloaded resources folder contains a folder called org. In that
CTAKES_HOME resources folder, there is a separate ORG folder along with a
META_INF folder. Am i supposed to add the downloaded resources folder into the
org folder of the CTAKES_HOME resources folder? Or am I supposed to put the
downloaded resources folder's org folder into the CTAKES_HOME resources folder,
thus overwriting the original CTAKES_HOME org folder?
Thank You,Tiffany Buu On Monday, June 18, 2018, 8:14:08 PM GMT+2, Schenk,
Gundolf <gundolf.sch...@ucsf.edu> wrote:
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Hi Tiffany,
It seems like your installation cannot find file sno_rx_16ab.xml in
resources/org/apache/ctakes/dictionary/lookup/fast/. This file is part of the
additional resources. Please double-check that you have installed them properly.
Cheers,
Gundolf.
From: Tiffany Buu <tiffany...@yahoo.com>
Reply-To: "user@ctakes.apache.org" <user@ctakes.apache.org>
Date: Monday, June 18, 2018 at 06:09
To: "user@ctakes.apache.org" <user@ctakes.apache.org>
Subject: Apache JCAS Term Annotator Error
Hello,
I am trying to use ctakes with UMLS, but I am getting an error. I have included
the log file below.
01:23:31.191 - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526):
SEVERE: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/tiffanybuu/Desktop/CTAKES_HOME/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/tiffanybuu/Desktop/CTAKES_HOME/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.CVD.main(CVD.java:164)
Caused by: org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 16 more
Caused by: java.io.FileNotFoundException: No File exists at
org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:193)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:99)
at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:73)
at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:53)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128)
... 17 more
I have downloaded the resources and put its contents in the existing resource
folder, and also have added my UMLS user and password in the two sh files. I
was following the cTakes user installation guide step by step, but I do not
know my error. Can someone help me?
Thank You,
Tiffany Buu
