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From "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Subject mvn install error on ctakes-temporal module test
Date Thu, 18 May 2017 18:55:15 GMT
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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