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 LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 15:41, Finan, Sean <sean.fi...@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 > 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.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 > > > > 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. > > >
