Hi Sean and everybody, I just wanted to confirm that I intermittently run into the same issue. I was able to fix it yesterday by removing a bunch of files from /tmp (such as conn.xml, which dictionary lookup apparently creates there under my user name). However, today, the problem returned and I haven’t found a way to fix it.
Again, the same pipeline runs fine on my laptop (Mac OS) and another machine that runs Linux. Dima On Mar 13, 2018, at 14:13, Andrew Phillips <aphilli...@luc.edu<mailto:aphilli...@luc.edu>> wrote: Hi Sean, I looked into changing the relevant configs to non-checking, but didn't have much success. I am back to primarily trying to troubleshoot the original error. I have tried removing files from /tmp (especially conn.xml) as they seemed to be contributing to the issue. I also tried setting up cTAKES with a freshly created account, and am still encountering this issue. Other users on the server also have varying mileage with the same task. Do you have any more ideas of anything else I can try? Thank you. *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 17:45, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Andrew, If you created your own dictionary then you are already bound by your own license credentials used to get the umls download. You do not need to use the ctakes license check. In your lookup configuration xml file you can change the UmlsJdbc** to the non-checking Jdbc**. There are several email threads with associated information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/ 201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe% 3DW6qm6Vw%40mail.gmail.com<http://40mail.gmail.com>%3E Sean -----Original Message----- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 5:13 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 15:41, Finan, Sean <Sean.Finan@childrens.harvard<mailto:Sean.Finan@childrens.harvard>. edu> wrote: Hi Andrew, As far as I know there isn't an explicit timeout imposed by ctakes. There is probably a java or system timeout, but I don't know of an easy way to change it. If you use the default dictionary then you should allow the account check. Sean -----Original Message----- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 4:27 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] @Gandhi: I have always skipped the tests whenever I run the install command. @Sean: 2 of the 4 folders I ran on were eventually processed, and only after running the script multiple times, so it does seem to be a connection issue. However I am trying to run the commands for the last couple of folders manually and the error has been consistent. Is there any way to bypass the account check, or increase the timeout? Or can I just have a loop that continually retries until the operation succeeds? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 07:18, Finan, Sean <Sean.Finan@childrens.harvard<mailto:Sean.Finan@childrens.harvard>. edu> wrote: 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<http://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<mailto: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<mailto: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<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 26 February 2018 at 13:00, Miller, Timothy < Timothy.Miller@childrens. harvard.edu<http://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. ap ac h e.org<http://e.org>_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx eF U& 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. ap ac h e.org<http://e.org>_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx eF U& 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.proper ti es 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_3xhKw EW 14 J ZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=QbqFJzRYGmbPDeAjP62zpOAAeADv_Vn6tyq EC Tu o dRA&e=: .............................. 10 ............... 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov<http://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(DelegatingMethod Ac ce 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.ResourceInitializationExceptio n: 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( An al y sisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResour ce (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 .j av 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(A na ly s isEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(Agg re ga t eBuilder.java:207) at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPi pe li n e.java:101) ... 6 more Caused by: org.apache.uima.resource.ResourceInitializationExceptio n: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWord Di ct 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.UmlsJdbcRareWord Di ct i onary at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescri pt or P arser.parseDictionary(DictionaryDescriptorParser.java:198) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescri pt or P arser.parseDictionaries(DictionaryDescriptorParser.java:155) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescri pt or 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(NativeCons tr uc t orAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Delega ti ng C onstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescri pt or 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.UmlsJdbcRareWord Di ct 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.UmlsJdbcRareWord Di ct 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 .o rg _ confluence_display_MAVEN_MojoExecutionExceptio&d=DwIBaQ&c=qS4goW BT 7p o plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=Z9Q1v5cl4ubq7HiQZ0gmKI5UNl44aS8XvQY jc d6 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. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. 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