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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject Re: mvn install error on ctakes-temporal module test
Date Thu, 18 May 2017 19:45:56 GMT
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 <SPM9R@hscmail.mcc.virginia.edu> 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.&lt;init&gt;(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>

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