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Posted to user@ctakes.apache.org by Tiffany Buu <ti...@yahoo.com> on 2018/06/18 13:04:10 UTC
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 moreCaused 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
Re: Apache JCAS Term Annotator Error
Posted by Tiffany Buu <ti...@yahoo.com>.
Thanks so much for clarifying!
-Tiffany Buu
On Tuesday, June 19, 2018, 9:13:57 AM GMT+2, Ewan Mellor <ct...@ewanmellor.org.uk> wrote:
The important thing is that the folder structure, rooted at the org/ folder,
needs to be on your classpath. If you're using the standard install
instructions[1] then <cTAKES_HOME>/resources is put on your classpath for
you, so that means you should end up with
<cTAKES_HOME>/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
HTH,
Ewan.
[1] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
On Mon, Jun 18, 2018 at 07:45:14PM +0000, Tiffany Buu wrote:
> 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
> <Gu...@ucsf.edu> wrote:
>
> 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 <ti...@yahoo.com>
> Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Date: Monday, June 18, 2018 at 06:09
> To: "user@ctakes.apache.org" <us...@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
>
>
Re: Apache JCAS Term Annotator Error
Posted by Ewan Mellor <ct...@ewanmellor.org.uk>.
The important thing is that the folder structure, rooted at the org/ folder,
needs to be on your classpath. If you're using the standard install
instructions[1] then <cTAKES_HOME>/resources is put on your classpath for
you, so that means you should end up with
<cTAKES_HOME>/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
HTH,
Ewan.
[1] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
On Mon, Jun 18, 2018 at 07:45:14PM +0000, Tiffany Buu wrote:
> 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
> <Gu...@ucsf.edu> wrote:
>
> 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 <ti...@yahoo.com>
> Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Date: Monday, June 18, 2018 at 06:09
> To: "user@ctakes.apache.org" <us...@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
>
>
Re: Apache JCAS Term Annotator Error
Posted by Tiffany Buu <ti...@yahoo.com>.
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 <Gu...@ucsf.edu> wrote:
#yiv8766304717 #yiv8766304717 -- _filtered #yiv8766304717 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8766304717 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv8766304717 {panose-1:2 0 5 3 0 0 0 2 0 4;}#yiv8766304717 #yiv8766304717 p.yiv8766304717MsoNormal, #yiv8766304717 li.yiv8766304717MsoNormal, #yiv8766304717 div.yiv8766304717MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv8766304717 a:link, #yiv8766304717 span.yiv8766304717MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv8766304717 a:visited, #yiv8766304717 span.yiv8766304717MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv8766304717 p.yiv8766304717msonormal0, #yiv8766304717 li.yiv8766304717msonormal0, #yiv8766304717 div.yiv8766304717msonormal0 {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv8766304717 span.yiv8766304717EmailStyle18 {font-family:sans-serif;color:windowtext;}#yiv8766304717 .yiv8766304717MsoChpDefault {font-size:10.0pt;} _filtered #yiv8766304717 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv8766304717 div.yiv8766304717WordSection1 {}#yiv8766304717
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 <ti...@yahoo.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, June 18, 2018 at 06:09
To: "user@ctakes.apache.org" <us...@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
Re: Apache JCAS Term Annotator Error
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
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 <ti...@yahoo.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Monday, June 18, 2018 at 06:09
To: "user@ctakes.apache.org" <us...@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