Graham, The SideAffect descriptor looks like it's out of date.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 <[email protected]> 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 >
