You may be getting the same “URI is not hierarchical error” I was experiencing last month. This is a known problem. While it’s getting fixed, there’s a temporary fix. Please take a look at the message archive and look for the messages with title: “URI is not hierarchical”. Here’s the gist of what you need to do:
"I checked out lvg from svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/ and put it in target/classes/org/apache/ctakes/." Dima > On May 18, 2017, at 13:55, Mullane, Sean *HS <[email protected]> > wrote: > > I have so far been unable to build and install ctakes 4.0.0 or > 4.0.1-snapshot. With both versions, the mvn clean install fails on the > ctakes-temporal module test. Environment info and test results below. Has > anyone else encountered this? This seems similar to the "URI is not > hierarchical" thread from last month but it's not clear to me whether that > thread applies here. > > Environment: > Windows 7 Pro > Eclipse 4.5 Mars > jdk1.8.0_131 > > I followed the step by step install instructions here exactly: > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide > Then in Eclipse I right-clicked the top-level package -> Run As -> Maven > Build... -> mvn clean install > > The results are below: > > > ------------------------------------------------------- > T E S T S > ------------------------------------------------------- > Running org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest > log4j: reset attribute= "false". > log4j: Threshold ="null". > log4j: Retreiving an instance of org.apache.log4j.Logger. > log4j: Setting [ProgressAppender] additivity to [false]. > log4j: Level value for ProgressAppender is [INFO]. > log4j: ProgressAppender level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%m]. > log4j: Adding appender named [noEolAppender] to category [ProgressAppender]. > log4j: Retreiving an instance of org.apache.log4j.Logger. > log4j: Setting [ProgressDone] additivity to [false]. > log4j: Level value for ProgressDone is [INFO]. > log4j: ProgressDone level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%m%n]. > log4j: Adding appender named [eolAppender] to category [ProgressDone]. > log4j: Level value for root is [INFO]. > log4j: root level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p > %c{1} - %m%n]. > log4j: Adding appender named [consoleAppender] to category [root]. > 18 May 2017 14:09:40 INFO LvgAnnotator - URL for lvg.properties > =file:/C:/Users/*****/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > 18 May 2017 14:09:41 INFO SentenceDetector - Sentence detector model file: > org/apache/ctakes/core/sentdetect/sd-med-model.zip > 18 May 2017 14:09:42 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.311 sec <<< > FAILURE! > Running org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest > 18 May 2017 14:09:42 INFO LvgAnnotator - URL for lvg.properties > =file:/C:/Users/*****/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > 18 May 2017 14:09:44 INFO SentenceDetector - Sentence detector model file: > org/apache/ctakes/core/sentdetect/sd-med-model.zip > 18 May 2017 14:09:44 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 2.355 sec <<< > FAILURE! > Running org.apache.ctakes.temporal.ae.EventAnnotatorTest > 18 May 2017 14:09:45 INFO LvgAnnotator - URL for lvg.properties > =file:/C:/Users/*****/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > 18 May 2017 14:09:46 INFO SentenceDetector - Sentence detector model file: > org/apache/ctakes/core/sentdetect/sd-med-model.zip > 18 May 2017 14:09:46 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.653 sec <<< > FAILURE! > Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest > 18 May 2017 14:09:46 INFO LvgAnnotator - URL for lvg.properties > =file:/C:/Users/*****/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > 18 May 2017 14:09:48 INFO SentenceDetector - Sentence detector model file: > org/apache/ctakes/core/sentdetect/sd-med-model.zip > 18 May 2017 14:09:48 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 2.01 sec <<< > FAILURE! > Running org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest > 18 May 2017 14:09:48 INFO LvgAnnotator - URL for lvg.properties > =file:/C:/Users/*****/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > 18 May 2017 14:09:50 INFO SentenceDetector - Sentence detector model file: > org/apache/ctakes/core/sentdetect/sd-med-model.zip > 18 May 2017 14:09:50 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.965 sec <<< > FAILURE! > > Results : > > Tests in error: > testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest): URI > is not hierarchical > testPipeline(org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest): > URI is not hierarchical > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is not > hierarchical > testPipeline(org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest): > URI is not hierarchical > testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest): > URI is not hierarchical > > Tests run: 5, Failures: 0, Errors: 5, Skipped: 0 > > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > [INFO] Apache cTAKES ...................................... SUCCESS [ 4.706 > s] > [INFO] ctakes-gui-res ..................................... SUCCESS [ 4.121 > s] > [INFO] Apache cTAKES Resources core ....................... SUCCESS [ 0.909 > s] > [INFO] Apache cTAKES common type system ................... SUCCESS [ 12.160 > s] > [INFO] Apache cTAKES utils ................................ SUCCESS [ 3.959 > s] > [INFO] Apache cTAKES core ................................. SUCCESS [ 13.412 > s] > [INFO] ctakes-gui ......................................... SUCCESS [ 5.780 > s] > [INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [ 1.132 > s] > [INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [ 5.202 > s] > [INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [ 1.023 > s] > [INFO] Apache cTAKES chunker .............................. SUCCESS [ 3.919 > s] > [INFO] Apache cTAKES document preprocessor ................ SUCCESS [ 3.413 > s] > [INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 9.365 > s] > [INFO] Apache cTAKES dictionary lookup .................... SUCCESS [ 4.784 > s] > [INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [ 4.595 > s] > [INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 11.133 > s] > [INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [ 4.018 > s] > [INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [ 0.637 > s] > [INFO] Apache cTAKES named entity contexts ................ SUCCESS [ 5.072 > s] > [INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [ 3.367 > s] > [INFO] Apache cTAKES Constituency Parser .................. SUCCESS [ 3.824 > s] > [INFO] Apache cTAKES Resources coreference ................ SUCCESS [ 4.169 > s] > [INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [ 0.707 > s] > [INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 11.739 > s] > [INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 26.007 > s] > [INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 9.707 > s] > [INFO] Apache cTAKES Resources assertion .................. SUCCESS [ 2.856 > s] > [INFO] Apache cTAKES Assertion ............................ SUCCESS [ 8.264 > s] > [INFO] Apache cTAKES Resources temporal ................... SUCCESS [ 1.140 > s] > [INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [ 1.442 > s] > [INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [ 4.489 > s] > [INFO] Apache cTAKES Temporal Information Extraction ...... FAILURE [ 30.803 > s] > [INFO] Apache cTAKES CoReference Resolver ................. SKIPPED > [INFO] Apache cTAKES Resources drug-ner ................... SKIPPED > [INFO] Apache cTAKES Drug NER ............................. SKIPPED > [INFO] Apache cTAKES Resources side-effect ................ SKIPPED > [INFO] Apache cTAKES Side Effects ......................... SKIPPED > [INFO] Apache cTAKES Resources smoking-status ............. SKIPPED > [INFO] Apache cTAKES Smoking Status ....................... SKIPPED > [INFO] Apache cTAKES Resources assertion-zoner ............ SKIPPED > [INFO] Apache cTAKES Assertion's zoner .................... SKIPPED > [INFO] Apache cTAKES Resources ctakes-ytex-res ............ SKIPPED > [INFO] Apache cTAKES YTEX ................................. SKIPPED > [INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED > [INFO] ctakes-clinical-pipeline-res ....................... SKIPPED > [INFO] Apache cTAKES ctakes-clinical-pipeline ............. SKIPPED > [INFO] ctakes-examples-res ................................ SKIPPED > [INFO] ctakes-examples .................................... SKIPPED > [INFO] Apache cTAKES YTEX Web ............................. SKIPPED > [INFO] Apache cTAKES Distribution ......................... SKIPPED > [INFO] Apache cTAKES Regression-test ...................... SKIPPED > [INFO] Apache cTAKES template filler ...................... SKIPPED > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILURE > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 03:30 min > [INFO] Finished at: 2017-05-18T14:09:50-04:00 > [INFO] Final Memory: 76M/798M > [INFO] > ------------------------------------------------------------------------ > [ERROR] Failed to execute goal > org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test (default-test) on > project ctakes-temporal: There are test failures. > [ERROR] > [ERROR] Please refer to > C:\Users\*****\eclipse-workspace-*****\ctakes-4.0.1-SNAPSHOT\ctakes-temporal\target\surefire-reports > for the individual test results. > [ERROR] -> [Help 1] > [ERROR] > [ERROR] To see the full stack trace of the errors, re-run Maven with the -e > switch. > [ERROR] Re-run Maven using the -X switch to enable full debug logging. > [ERROR] > [ERROR] For more information about the errors and possible solutions, please > read the following articles: > [ERROR] [Help 1] > http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException > [ERROR] > [ERROR] After correcting the problems, you can resume the build with the > command > [ERROR] mvn <goals> -rf :ctakes-temporal > > Here is the error from the BackwardsTimeAnnotatorTest test's surefire report: > > <testcase > classname="org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest" > name="testPipeline" time="3.078"> > <error message="URI is not hierarchical" > type="java.lang.IllegalArgumentException">java.lang.IllegalArgumentException: > URI is not hierarchical > at java.io.File.<init>(File.java:418) > at > org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65) > at > org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628) > at > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464) > at > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193) > 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:131) > 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: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: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.produceResource(UIMAFramework.java:331) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448) > at > org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:205) > at > org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:227) > at > org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:260) > at > org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest.testPipeline(BackwardsTimeAnnotatorTest.java:70) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at > org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47) > at > org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12) > at > org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44) > at > org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17) > at > org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271) > at > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70) > at > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50) > at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238) > at > org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63) > at > org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236) > at > org.junit.runners.ParentRunner.access$000(ParentRunner.java:53) > at > org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229) > at org.junit.runners.ParentRunner.run(ParentRunner.java:309) > at > org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249) > at > org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142) > at > org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at > org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189) > at > org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165) > at > org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85) > at > org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104) > at > org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75) > </error>
