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From Pei Chen <chen...@apache.org>
Subject Re: New user question on use of side effect component
Date Tue, 15 Dec 2015 02:04:53 GMT
Graham,
The SideAffect descriptor looks like it's out of date.
What I would do if I were you is use the default CPE and default
aggregate from the clinical pipeline project and just add the
SideAffectAnnotator into your pipeline. (instead of using the
SideAffectAggregateTAE.xml)

<delegateAnalysisEngine key="SideEffectAnnotator">
<import location="SideEffectAnnotator.xml"/>
</delegateAnalysisEngine>
....
<node>SideEffectAnnotator</node>

I think it's better to actually remove these example aggregate.xml's
from individual projects as it is confusing and a pain to maintain.
If anything, just have uimaFIT dynamically generate these at build
time..  Just my 2 cents.

On Mon, Dec 14, 2015 at 7:03 PM, Graham Pitson <gpitson@alphalink.com.au> wrote:
> 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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