Hello, I am getting an error after recompiling a script in my pipeline. My setup was working fine the last time I did a compile several months ago, and I have logged into my UMLS account to ensure it isn't an issue with my credentials, as well as done a complete reinstall from the GitHub repo and checked out the 4.0.0 release. The minor change I made in the script was just uncommenting something that I've used before, so I know there are no errors in it. Any insights as to what the issue may be? I've included the complete output below. Thank you.
[INFO] Scanning for projects... [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies could not be resolved: Failure to find org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in https://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies could not be resolved: Failure to find org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in https://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced [INFO] [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @ ctakes-misc >>> [INFO] [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @ ctakes-misc <<< [INFO] [INFO] [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc --- 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]. 24 Feb 2018 18:22:23 INFO LvgAnnotator - URL for lvg.properties =/home/aphillips5/ctakes/ctakes-misc/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties 24 Feb 2018 18:22:23 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 24 Feb 2018 18:22:24 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae. TokenizerAnnotatorPTB 24 Feb 2018 18:22:24 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 24 Feb 2018 18:22:24 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 24 Feb 2018 18:22:24 INFO Chunker - Chunker model file: /home/aphillips5/ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip 24 Feb 2018 18:22:24 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 24 Feb 2018 18:22:24 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB 24 Feb 2018 18:22:24 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 24 Feb 2018 18:22:24 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml 24 Feb 2018 18:22:24 INFO DictionaryDescriptorParser - Parsing dictionary specifications: 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser: .............................. 10 ............... 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov [WARNING] java.lang.reflect.InvocationTargetException 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.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297) at java.lang.Thread.run(Thread.java:745) Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:274) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipeline.java:101) ... 6 more 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.UmlsJdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:140) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267) ... 18 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.UmlsJdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:198) 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) ... 19 more Caused by: java.lang.reflect.InvocationTargetException 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) ... 22 more Caused by: java.sql.SQLException: Invalid User for UMLS dictionary sno_rx_16abTerms at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29) ... 27 more [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 18.100 s [INFO] Finished at: 2018-02-24T18:22:40-06:00 [INFO] Final Memory: 174M/1150M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:java (default-cli) on project ctakes-misc: An exception occured while executing the Java class. null: InvocationTargetException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>): MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary: Invalid User for UMLS dictionary sno_rx_16abTerms -> [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/MojoExecutionExceptio *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech
