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From Graham Pitson <gpit...@alphalink.com.au>
Subject New user question on use of side effect component
Date Tue, 15 Dec 2015 00:03:37 GMT
Hi,

I've installed cTakes and am hoping for some help getting started.

I've downloaded and installed 3.2.2, including the umls dictionary. User 
name and password are setup and the user install demos are working for 
CVD and CPE.

I'm trying to look at the side effect component run against some plain 
text files as a next step and having problems with  file not found for 
"apache-ctakes-3.2.2\desc\ctakes-drug-ner\desc\analysis_engine\DrugCNP2LookupWindow.xml 
". Indeed, the file does not exist on my system

Loading and running SideEffectCPE.xml in the CPE gives the error 
messages below as per the CPE log (apologies for the length but I've 
posted more rather than less of the log). I get similar messages in the CVD.

So I'm wondering whether I'm actually missing the file or whether I 
haven't configured my system/request properly.

Any help would be appreciated.

Graham



-------------------------------------log file 
follows-----------------------------------

C:\Users\gpits\ctakes\apache-ctakes-3.2.2>cd 
C:\Users\gpits\ctakes\apache-ctakes-3.2.2

C:\Users\gpits\ctakes\apache-ctakes-3.2.2>java -cp 
"C:\Users\gpits\ctakes\apache-ctakes-3.2.2/desc/;C:\Users\gpits\ctakes\apache-ctakes-3.2.2/resources/;C:\Users\gpits\ctakes\apache-ctakes-3.2.2/lib/*"

-Dlog4j.configuration=file:/C:\Users\gpits\ctakes\apache-ctakes-3.2.2/config/log4j.xml 
-Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame
Dec 15, 2015 10:41:21 AM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs 
at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
org.apache.uima.resource.ResourceInitializationException: Initialization 
of CAS Processor with name "SideEffectSentenceAggregateTAE" failed.
     at 
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:83)
     at 
org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
     at 
org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:864)
     at 
org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
     at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
     at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
Caused by: org.apache.uima.resource.ResourceConfigurationException: 
Initialization of CAS Processor with name 
"SideEffectSentenceAggregateTAE" failed.
     at 
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1104)
     at 
org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:550)
     at 
org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
     at 
org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
     at 
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:75)
     ... 5 more
Caused by: org.apache.uima.resource.ResourceInitializationException: 
Import failed.  Could not read from URL 
file:/C:/Users/gpits/ctakes/apache-ctakes-3.2.2/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml.

(Descriptor: 
file:/C:/Users/gpits/ctakes/apache-ctakes-3.2.2/desc/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml)
     at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
     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:269)
     at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
     at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
     at 
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
     ... 9 more
Caused by: org.apache.uima.util.InvalidXMLException: Import failed. 
Could not read from URL 
file:/C:/Users/gpits/ctakes/apache-ctakes-3.2.2/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml.

(Descriptor: 
file:/C:/Users/gpits/ctakes/apache-ctakes-3.2.2/desc/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:812)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImports(AnalysisEngineDescription_impl.java:733)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
     at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
     ... 15 more
Caused by: java.io.FileNotFoundException: 
C:\Users\gpits\ctakes\apache-ctakes-3.2.2\desc\ctakes-drug-ner\desc\analysis_engine\DrugCNP2LookupWindow.xml

(The system cannot find the file specified)
     at java.io.FileInputStream.open(Native Method)
     at java.io.FileInputStream.<init>(Unknown Source)
     at java.io.FileInputStream.<init>(Unknown Source)
     at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
     at 
sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown Source)
     at org.apache.uima.util.XMLInputSource.<init>(XMLInputSource.java:120)
     at 
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:810)
     ... 20 more


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