Can't run the tests (Could not create JAXB context)

[hgasmi]

I got an error when trying to run the tests (mvn test -Dmaven.test.skip=false). Could you please help?

Initializing JollyDayHoliday for sutime with classpath:edu/stanford/nlp/models/sutime/jollyday/Holidays_sutime.xml
Sep 12, 2018 11:45:59 AM de.jollyday.util.XMLUtil unmarshallConfiguration
WARNING: Could not create JAXB context using the current threads context classloader. Defaulting to ObjectFactory classloader.
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 9.569 sec <<< FAILURE!
testGetGraph(gov.ornl.stucco.RelationExtractorTest) Time elapsed: 9.531 sec <<< ERROR!
edu.stanford.nlp.util.ReflectionLoading$ReflectionLoadingException: Error creating edu.stanford.nlp.time.TimeExpressionExtractorImpl
at edu.stanford.nlp.util.ReflectionLoading.loadByReflection(ReflectionLoading.java:40)
at edu.stanford.nlp.time.TimeExpressionExtractorFactory.create(TimeExpressionExtractorFactory.java:57)
at edu.stanford.nlp.time.TimeExpressionExtractorFactory.createExtractor(TimeExpressionExtractorFactory.java:38)
at edu.stanford.nlp.ie.regexp.NumberSequenceClassifier.(NumberSequenceClassifier.java:79)
at edu.stanford.nlp.ie.NERClassifierCombiner.(NERClassifierCombiner.java:68)
at edu.stanford.nlp.pipeline.AnnotatorImplementations.ner(AnnotatorImplementations.java:99)
at edu.stanford.nlp.pipeline.StanfordCoreNLP$6.create(StanfordCoreNLP.java:627)
at edu.stanford.nlp.pipeline.AnnotatorPool.get(AnnotatorPool.java:85)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.construct(StanfordCoreNLP.java:292)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.(StanfordCoreNLP.java:129)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.(StanfordCoreNLP.java:125)
at gov.ornl.stucco.entity.EntityLabeler.(EntityLabeler.java:26)
at gov.ornl.stucco.RelationExtractorTest.testGetGraph(RelationExtractorTest.java:107)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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:115)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: edu.stanford.nlp.util.MetaClass$ClassCreationException: MetaClass couldn't create public edu.stanford.nlp.time.TimeExpressionExtractorImpl(java.lang.String,java.util.Properties) with args [sutime, {customAnnotatorClass.cyberentity=gov.ornl.stucco.entity.CyberEntityAnnotator, annotators=tokenize, ssplit, pos, cyberheuristics, cyberentity, lemma, ner, parse, customAnnotatorClass.cyberheuristics=gov.ornl.stucco.entity.heuristics.CyberHeuristicAnnotator}]
at edu.stanford.nlp.util.MetaClass$ClassFactory.createInstance(MetaClass.java:233)
at edu.stanford.nlp.util.MetaClass.createInstance(MetaClass.java:378)
at edu.stanford.nlp.util.ReflectionLoading.loadByReflection(ReflectionLoading.java:38)
... 40 more
Caused by: java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at edu.stanford.nlp.util.MetaClass$ClassFactory.createInstance(MetaClass.java:229)
... 42 more
Caused by: java.lang.RuntimeException: Error initializing binder 1
at edu.stanford.nlp.time.Options.(Options.java:92)
at edu.stanford.nlp.time.TimeExpressionExtractorImpl.init(TimeExpressionExtractorImpl.java:45)
at edu.stanford.nlp.time.TimeExpressionExtractorImpl.(TimeExpressionExtractorImpl.java:39)
... 47 more
Caused by: java.lang.IllegalStateException: Cannot instantiate configuration.
at de.jollyday.impl.XMLManager.init(XMLManager.java:286)
at de.jollyday.HolidayManager.createManager(HolidayManager.java:278)
at de.jollyday.HolidayManager.getInstance(HolidayManager.java:194)
at edu.stanford.nlp.time.JollyDayHolidays.init(JollyDayHolidays.java:52)
at edu.stanford.nlp.time.Options.(Options.java:90)
... 49 more
Caused by: java.lang.IllegalStateException: Cannot parse holidays XML file.
at de.jollyday.util.XMLUtil.unmarshallConfiguration(XMLUtil.java:80)
at de.jollyday.impl.XMLManager.init(XMLManager.java:284)
... 53 more
Caused by: javax.xml.bind.JAXBException: Provider com.sun.xml.internal.bind.v2.ContextFactory not found

• with linked exception:
  [java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
  at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:148)
  at javax.xml.bind.ContextFinder.find(ContextFinder.java:361)
  at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:446)
  at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:409)
  at de.jollyday.util.XMLUtil$JAXBContextCreator.create(XMLUtil.java:172)
  at de.jollyday.util.XMLUtil.unmarshallConfiguration(XMLUtil.java:73)
  ... 54 more
  Caused by: java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory
  at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
  at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
  at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
  at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:573)
  at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:145)
  ... 59 more

Results :

Tests in error:
testGetGraph(gov.ornl.stucco.RelationExtractorTest): Error creating edu.stanford.nlp.time.TimeExpressionExtractorImpl

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0

[testak]

It looks like a dependency of the project is not installed. Please run the following commands from the relation-extraction project directory before trying to run the test:

mvn scm:checkout -Dmodule.name=entity-extractor
cd entity-extractor
mvn clean install
cd ..
mvn clean package

Let me know if that helps.

[hgasmi]

Thanks, testak but what I am getting is a runtime error when I run the tests, not a compilation issue. I already installed the dependency and the code is compiling fine. Are you able to run the test fine?

[testak]

Which branch of the relation-extractor are you working with?

It appears I need to update the expected output within the test. However, when I run the tests on both develop and master branches I get an AssertionError because the expected output does not match the actual output of the test. Here is a section of my output that starts with initializing JollyDayHoliday:

Initializing JollyDayHoliday for sutime with classpath:edu/stanford/nlp/models/sutime/jollyday/Holidays_sutime.xml
Reading TokensRegex rules from edu/stanford/nlp/models/sutime/defs.sutime.txt
Reading TokensRegex rules from edu/stanford/nlp/models/sutime/english.sutime.txt
Oct 03, 2018 8:43:22 AM edu.stanford.nlp.ling.tokensregex.CoreMapExpressionExtractor appendRules
INFO: Ignoring inactive rule: null
Oct 03, 2018 8:43:22 AM edu.stanford.nlp.ling.tokensregex.CoreMapExpressionExtractor appendRules
INFO: Ignoring inactive rule: temporal-composite-8:ranges
Reading TokensRegex rules from edu/stanford/nlp/models/sutime/english.holidays.sutime.txt
Adding annotator parse
Loading parser from serialized file edu/stanford/nlp/models/lexparser/englishPCFG.ser.gz ...done [0.5 sec].
Annotating 'My Doc'...
Annotating with heuristic cyber labels ... 
Annotating with cyber labels ... 
Loading relationship patterns from 'src/main/resources/patterns_relations_abbrev.json'...
Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 16.491 sec <<< FAILURE!
testGetGraph(gov.ornl.stucco.RelationExtractorTest)  Time elapsed: 16.459 sec  <<< FAILURE!
java.lang.AssertionError
	at gov.ornl.stucco.RelationExtractorTest.testGetGraph(RelationExtractorTest.java:111)

I understand you are seeing your error at runtime, but according to your output it's due to a missing class, which is a dependency for Stanford's CoreNLP library used by the entity-extractor:

Caused by: javax.xml.bind.JAXBException: Provider com.sun.xml.internal.bind.v2.ContextFactory not found

[hgasmi]

I am working on master. I did make sure the dependency is installed but I am still getting the same error.

C:\IEcode\stucco-entity-extractor>mvn clean install
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------< gov.ornl.stucco:entity-extractor >------------------
[INFO] Building entity-extractor 1.0.0
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ entity-extractor ---
[INFO] Deleting C:\IEcode\stucco-entity-extractor\target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ entity-extractor ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 6 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ entity-extractor ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 12 source files to C:\IEcode\stucco-entity-extractor\target\classes
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default) @ entity-extractor ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 12 source files to C:\IEcode\stucco-entity-extractor\target\classes
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ entity-extractor ---
[INFO] Not copying test resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ entity-extractor ---
[INFO] Not compiling test sources
[INFO]
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ entity-extractor ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ entity-extractor ---
[INFO] Building jar: C:\IEcode\stucco-entity-extractor\target\entity-extractor-1.0.0.jar
[INFO]
[INFO] --- maven-install-plugin:2.4:install (default-install) @ entity-extractor ---
[INFO] Installing C:\IEcode\stucco-entity-extractor\target\entity-extractor-1.0.0.jar to C:\Users\Houssem.m2\repository\gov\ornl\stucco\entity-extractor\1.0.0\entity-extractor-1.0.0.jar
[INFO] Installing C:\IEcode\stucco-entity-extractor\pom.xml to C:\Users\Houssem.m2\repository\gov\ornl\stucco\entity-extractor\1.0.0\entity-extractor-1.0.0.pom
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8.950 s
[INFO] Finished at: 2018-10-05T11:56:27+03:00
[INFO] ------------------------------------------------------------------------

[hgasmi]

Fixed the error. It was happening because the jaxb libraries are not included by default in java 9 and 10. So I added them to the pom and it worked fine. Now am I getting the assertion error you mentioned above. Did you get anywhere with it?