Hi Andrew, You wrote: > I ran my script earlier, [...]and only the first run was successful.
Are you saying that one run did succeed? If that is the case then the problem probably is your network. The umls credential check will print dots in the log as time progresses, such as the dots from your log below: > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account [ ... ] > > .............................. 10 > > ............... > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov It looks like the credential check took several (~15?) seconds, which might indicate a slow connection or an eventual connection refused. That does not mean that the slowdown is on your side. It could be that the nih server that handles the credential checks is rarely getting to your request. I'm not sure why that would be (No net neutrality rants, please). Anyway, if the credential check works even once then that is a good indication that the problem is outside ctakes. Sean -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Tuesday, February 27, 2018 7:49 AM To: dev@ctakes.apache.org Subject: RE: UmlsUserApprover Error [EXTERNAL] I guess you are running the build with test cases as I see the below messages in my case only while running build with test cases: >> 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 Could you try building ' ctakes-temporal' module by skipping test case using the command - " mvn clean install -Dmaven.test.skip=true" ? Regards, Gandhi -----Original Message----- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 7:08 AM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] Thanks for the ideas. There hasn't been any such changes, and network connectivity shouldn't be an issue. I ran my script earlier, which automatically runs the same pipeline on several different folders, and only the first run was successful. The others failed with the same error. My latest attempt is to remove the .m2 directory and recompile and reinstall, and it is currently processing the first directory, so I don't know if it will fail on the next as yet. My primary interface is over SSH to a remote server, and this is the script: UmlsLP () { mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" -Dctakes.umlsuser=<user> -Dctakes.umlspw=<pass> > out.tmp ; mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" -Dctakes.umlsuser=<user> -Dctakes.umlspw=<pass> >> out.tmp ; echo Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 26 February 2018 at 13:00, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > 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.apac > > h > > 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.apac > > h > > 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.ni > > h > > .gov_restful_isValidUMLSUser&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14 > > J > > ZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=QbqFJzRYGmbPDeAjP62zpOAAeADv_Vn6tyqECTu > > o > > 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(DelegatingMethodAcce > > s > > 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.in > > i > > tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:274) > > at > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.in > > i > > tialize(PrimitiveAnalysisEngine_impl.java:172) > > at > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal > > y > > sisEngineFactory_impl.java:94) > > at > > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > o > > mpositeResourceFactory_impl.java:62) > > at > > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) > > at > > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja > > v > > a:407) > > at > > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.jav > > a > > :256) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in > > i > > tASB(AggregateAnalysisEngine_impl.java:435) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in > > i > > tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in > > i > > tialize(AggregateAnalysisEngine_impl.java:192) > > at > > org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(Analy > > s > > isEngineFactory.java:711) > > at > > org.apache.uima.fit.factory.AggregateBuilder.createAggregate(Aggrega > > t > > eBuilder.java:207) > > at > > org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipeli > > n > > 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.UmlsJdbcRareWordDict > > i > > onary > > at > > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.in > > i > > tialize(AbstractJCasTermAnnotator.java:140) > > at > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.in > > i > > 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.UmlsJdbcRareWordDict > > i > > onary > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptor > > P > > arser.parseDictionary(DictionaryDescriptorParser.java:198) > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptor > > P > > arser.parseDictionaries(DictionaryDescriptorParser.java:155) > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptor > > P > > arser.parseDescriptor(DictionaryDescriptorParser.java:127) > > at > > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.in > > i > > tialize(AbstractJCasTermAnnotator.java:138) > > ... 19 more > > Caused by: java.lang.reflect.InvocationTargetException > > at > > sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native > > Method) > > at > > sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruc > > t > > orAccessorImpl.java:62) > > at > > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Delegating > > C > > onstructorAccessorImpl.java:45) > > at > > java.lang.reflect.Constructor.newInstance(Constructor.java:423) > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptor > > P > > 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.UmlsJdbcRareWordDict > > i > > 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.UmlsJdbcRareWordDict > > i > > 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=qS4goWBT7p > > o > > plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=Z9Q1v5cl4ubq7HiQZ0gmKI5UNl44aS8XvQYjcd6 > > 6 > > rzs&e= > > > > *Andrew Phillips* > > GitHub: github.com/skeledrew > > LinkedIn: www.linkedin.com/in/aphillipstech This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. 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