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Posted to dev@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2018/02/26 19:00:52 UTC
Re: UmlsUserApprover Error [EXTERNAL]
Is it possible there is some network issue preventing connectivity? New
institutional firewall maybe?
Otherwise, it looks like somehow your credentials are not getting into
the right place. Possible a configuration file had them before and it's
been changed out from under you?
One thing you can try, if you are using an IDE, you can directly put
your credentials into the VM options for your run configuration with:
-Dctakes.umlsuser=<user name> -Dctakes.umlspw<password>
and see if you still get the issue.
Tim
On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih
> .gov_restful_isValidUMLSUser&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> ZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=QbqFJzRYGmbPDeAjP62zpOAAeADv_Vn6tyqECTuo
> dRA&e=:
> .............................. 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(DelegatingMethodAcces
> sorImpl.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.ini
> tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:274)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tialize(PrimitiveAnalysisEngine_impl.java:172)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
> sisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
> mpositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
> a: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.ini
> tASB(AggregateAnalysisEngine_impl.java:435)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
> tialize(AggregateAnalysisEngine_impl.java:192)
> at
> org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(Analys
> isEngineFactory.java:711)
> at
> org.apache.uima.fit.factory.AggregateBuilder.createAggregate(Aggregat
> eBuilder.java:207)
> at
> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipelin
> e.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.UmlsJdbcRareWordDicti
> onary
> at
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.ini
> tialize(AbstractJCasTermAnnotator.java:140)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> tializeAnalysisComponent(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.UmlsJdbcRareWordDicti
> onary
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> arser.parseDictionary(DictionaryDescriptorParser.java:198)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> arser.parseDictionaries(DictionaryDescriptorParser.java:155)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> arser.parseDescriptor(DictionaryDescriptorParser.java:127)
> at
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.ini
> tialize(AbstractJCasTermAnnotator.java:138)
> ... 19 more
> Caused by: java.lang.reflect.InvocationTargetException
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct
> orAccessorImpl.java:62)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC
> onstructorAccessorImpl.java:45)
> at
> java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> arser.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.UmlsJdbcRareWordDicti
> onary.<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.UmlsJdbcRareWordDicti
> onary:
> 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]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_
> confluence_display_MAVEN_MojoExecutionExceptio&d=DwIBaQ&c=qS4goWBT7po
> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=Z9Q1v5cl4ubq7HiQZ0gmKI5UNl44aS8XvQYjcd66
> rzs&e=
>
> *Andrew Phillips*
> GitHub: github.com/skeledrew
> LinkedIn: www.linkedin.com/in/aphillipstech