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acstevens / ctakes-standalone-application

cTAKES standalone application
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Failed to Execute Goal Error #3

Open humehta opened 6 years ago

humehta commented 6 years ago

Getting an issue while running the following command:

mvn -Dmaven.test.skip=true clean package assembly:single

Error:

[INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to C:\Users\harsh\ctakes-standalone-application\target\classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] Source option 1.5 is no longer supported. Use 1.6 or later. [ERROR] Target option 1.5 is no longer supported. Use 1.6 or later. [INFO] 2 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 07:17 min [INFO] Finished at: 2018-07-02T17:14:58-07:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project ctakes-standalone-application: Compilation failure: Compilation failure: [ERROR] Source option 1.5 is no longer supported. Use 1.6 or later. [ERROR] Target option 1.5 is no longer supported. Use 1.6 or later. [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

acstevens commented 6 years ago

Check you java version.

java -version

The error is saying you have java version 1.5 and you should use 1.6 or later.

humehta commented 6 years ago

I figured out the error it was not java, you will have to edit your pom.xml file to include the maven 1.6 version

humehta commented 6 years ago

But when implementing the ">startup.bat --text "diabetes"" command I am getting the following error:

02 Jul 2018 18:16:21 FATAL ENGINE - could not reopen database org.hsqldb.HsqlException: wrong database file version at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.HsqlDatabaseProperties.load(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:72) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at com.sentimetrix.ctakes.service.ClinicalEntityRecognizer.(ClinicalEntityRecognizer.java:48) at com.sentimetrix.ctakes.application.CTakesApp.main(CTakesApp.java:145) 02 Jul 2018 18:16:21 FATAL ENGINE - could not reopen database org.hsqldb.HsqlException: wrong database file version at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.HsqlDatabaseProperties.load(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:72) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at com.sentimetrix.ctakes.service.ClinicalEntityRecognizer.(ClinicalEntityRecognizer.java:48) at com.sentimetrix.ctakes.application.CTakesApp.main(CTakesApp.java:145)

02 Jul 2018 18:16:21 ERROR JdbcConnectionFactory - Could not create Connection with jdbc:hsqldb:file:C:\Users\harsh\ctakes-standalone-application\target\ctakes-standalone-application-0.0.1-SNAPSHOT-bin\ctakes-standalone-application-0.0.1-SNAPSHOT\org\apache\ctakes\dictionary\lookup\fast\ctakessnorx\ctakessnorx as sa java.sql.SQLException: wrong database file version at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:72) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at com.sentimetrix.ctakes.service.ClinicalEntityRecognizer.(ClinicalEntityRecognizer.java:48) at com.sentimetrix.ctakes.application.CTakesApp.main(CTakesApp.java:145) Caused by: org.hsqldb.HsqlException: wrong database file version at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.HsqlDatabaseProperties.load(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) ... 30 more 02 Jul 2018 18:16:21 ERROR JdbcRareWordDictionary - Could not Connect to Dictionary UmlsHsqlRareWord 02 Jul 2018 18:16:21 ERROR ClinicalEntityRecognizer - unable to create pipeline: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: ) Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: ) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at com.sentimetrix.ctakes.service.ClinicalEntityRecognizer.(ClinicalEntityRecognizer.java:48) at com.sentimetrix.ctakes.application.CTakesApp.main(CTakesApp.java:145) Caused by: org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) ... 13 more Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:199) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) ... 14 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) ... 17 more Caused by: java.sql.SQLException: wrong database file version at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.(JdbcRareWordDictionary.java:72) ... 22 more Caused by: org.hsqldb.HsqlException: wrong database file version at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.HsqlDatabaseProperties.load(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) ... 30 more

Any inputs on this?