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 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 LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 07:18, Finan, Sean <sean.fi...@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 > > 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.Miller@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.ap > > > ac > > > h > > > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeF > > > 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_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeF > > > 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.properti > > > 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_3xhKwEW > > > 14 > > > J > > > ZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=QbqFJzRYGmbPDeAjP62zpOAAeADv_Vn6tyqEC > > > Tu > > > 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(DelegatingMethodAc > > > 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.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(An > > > al > > > 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.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(Ana > > > ly > > > s > > > isEngineFactory.java:711) > > > at > > > org.apache.uima.fit.factory.AggregateBuilder.createAggregate(Aggre > > > ga > > > t > > > eBuilder.java:207) > > > at > > > org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipe > > > li > > > 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.UmlsJdbcRareWordDi > > > 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.UmlsJdbcRareWordDi > > > ct > > > i > > > onary > > > at > > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescript > > > or > > > P > > > arser.parseDictionary(DictionaryDescriptorParser.java:198) > > > at > > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescript > > > or > > > P > > > arser.parseDictionaries(DictionaryDescriptorParser.java:155) > > > at > > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescript > > > 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(NativeConstr > > > uc > > > t > > > orAccessorImpl.java:62) > > > at > > > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Delegati > > > ng > > > C > > > onstructorAccessorImpl.java:45) > > > at > > > java.lang.reflect.Constructor.newInstance(Constructor.java:423) > > > at > > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescript > > > 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.UmlsJdbcRareWordDi > > > 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.UmlsJdbcRareWordDi > > > 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=qS4goWBT > > > 7p > > > o > > > plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=Z9Q1v5cl4ubq7HiQZ0gmKI5UNl44aS8XvQYjc > > > 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. If you are not the > intended recipient you are notified that disclosing, copying, > distributing or taking any action in reliance on the contents of this > information is strictly prohibited and against the law. >
