Hello, My research partner and I have been trying to run piper files in ctakes. We both have the same setup and configuration of cTAKES, but have different operating systems (windows and macOS). On both of our machines, we were successfully able to run HelloWorldPiperRunner. When we try to run the HelloWorldCuiPiperRunner, it runs successfully on the system with the macOS but does not run on the Windows system.
This is the full error: 30 Oct 2019 11:59:59 INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser: ..30 Oct 2019 12:00:00 INFO UmlsUserApprover - UMLS Account has been validated 30 Oct 2019 12:00:00 INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab: .30 Oct 2019 12:00:01 FATAL ENGINE - could not reopen database org.hsqldb.HsqlException: Database lock acquisition failure: lockFile: org.hsqldb.persist.LockFile@b9be1153[file =C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck, exists=false, locked=false, valid=false, ] method: openRAF reason: java.io.FileNotFoundException: C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck (The system cannot find the path specified) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.LockFile.newLockFileLock(Unknown Source) at org.hsqldb.persist.Logger.acquireLock(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.<init>(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:85) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:259) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:292) at org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:433) at org.apache.ctakes.examples.pipeline.HelloWorldCuiPiperRunner.main(HelloWorldCuiPiperRunner.java:46) 30 Oct 2019 12:00:01 FATAL ENGINE - could not reopen database org.hsqldb.HsqlException: Database lock acquisition failure: lockFile: org.hsqldb.persist.LockFile@b9be1153[file =C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck, exists=false, locked=false, valid=false, ] method: openRAF reason: java.io.FileNotFoundException: C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck (The system cannot find the path specified) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.LockFile.newLockFileLock(Unknown Source) at org.hsqldb.persist.Logger.acquireLock(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.<init>(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:85) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:259) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:292) at org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:433) at org.apache.ctakes.examples.pipeline.HelloWorldCuiPiperRunner.main(HelloWorldCuiPiperRunner.java:46) 30 Oct 2019 12:00:01 ERROR JdbcConnectionFactory - Could not create Connection with jdbc:hsqldb:file:/C:/Users/Zach%20Barrett/Documents/Computer%20Science/Junior/Comp%20398/ctakes/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab as sa java.sql.SQLException: Database lock acquisition failure: lockFile: org.hsqldb.persist.LockFile@b9be1153[file =C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck, exists=false, locked=false, valid=false, ] method: openRAF reason: java.io.FileNotFoundException: C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck (The system cannot find the path specified) at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:85) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:259) at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:292) at org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:433) at org.apache.ctakes.examples.pipeline.HelloWorldCuiPiperRunner.main(HelloWorldCuiPiperRunner.java:46) Caused by: org.hsqldb.HsqlException: Database lock acquisition failure: lockFile: org.hsqldb.persist.LockFile@b9be1153[file =C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck, exists=false, locked=false, valid=false, ] method: openRAF reason: java.io.FileNotFoundException: C:\Users\Zach%20Barrett\Documents\Computer%20Science\Junior\Comp%20398\ctakes\resources\org\apache\ctakes\dictionary\lookup\fast\sno_rx_16ab\sno_rx_16ab.lck (The system cannot find the path specified) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.persist.LockFile.newLockFileLock(Unknown Source) at org.hsqldb.persist.Logger.acquireLock(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) ... 45 more 30 Oct 2019 12:00:01 ERROR JdbcRareWordDictionary - Could not Connect to Dictionary sno_rx_16abTerms 30 Oct 2019 12:00:01 ERROR HelloWorldCuiPiperRunner - Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. Not sure what's going on since we both have everything configured the same. Any help would be appreciated! Thank you, Carolina
