Hi Lance, Thank you for the reply. I noticed the problem with the current instructions for copying resources. However, I do not think that's the problem. I used cp -R for copying the resources and as I mentioned ctakesCVD works fine.
Best, Saeed On Wed, Apr 8, 2015 at 10:04 AM, Lance Eason <[email protected]> wrote: > The instructions should read: > > ditto /tmp/resources /usr/local/apache-ctakes-3.2.1/resources > > On Wed, Apr 8, 2015 at 11:47 AM, Lance Eason <[email protected]> > wrote: >> >> Saeed, >> >> The install instructions for Mac tell you to merge in the resources using: >> >> ditto /tmp/resources/* /usr/local/apache-ctakes-3.2.1/resources >> >> This places the files at the wrong location and leads to the error above. >> I ended up copying the resources into the appropriate location by hand. >> >> - Lance >> >> On Wed, Apr 8, 2015 at 11:24 AM, Saeed Hassanpour <[email protected]> >> wrote: >>> >>> Hi, >>> >>> I am running ctakes 3.2.1 on my mac and I went through user install >>> guide step by step >>> >>> (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide). >>> I successfully ran ctakesCVD with UMLS and >>> AggregatePlaintextFastUMLSProcessor.xml. However, when I tested >>> bin/runctakesCPE.sh with test1.xml as it is described in the tutorial, >>> I am getting the following error in the terminal: >>> >>> org.apache.uima.resource.ResourceInitializationException: >>> Initialization of CAS Processor with name "AggregateCdaProcessor" >>> 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 "AggregateCdaProcessor" >>> 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: java.lang.IllegalArgumentException: URI is not hierarchical >>> at java.io.File.<init>(File.java:418) >>> at >>> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44) >>> at >>> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) >>> at >>> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) >>> at >>> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) >>> at >>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) >>> at >>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) >>> 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.produceAnalysisEngine(UIMAFramework.java:387) >>> at >>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) >>> at >>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) >>> at >>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) >>> at >>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) >>> 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 >>> >>> Could you please help me to resolve this error? >>> >>> Best, >>> Saeed >> >> >> >> >> -- >> ......................................................... >> Lance Eason >> Iodine Software >> Vice President of Engineering >> [email protected] >> 512.785.5195 office | 801.203.8987 fax >> ......................................................... >> > > > > -- > ......................................................... > Lance Eason > Iodine Software > Vice President of Engineering > [email protected] > 512.785.5195 office | 801.203.8987 fax > ......................................................... >
