RE: Regarding cTakes version upadtion [EXTERNAL]
I just checked the wiki on 3.2 for information on setting the umls values. "[it] has been weighed, it has been measured, and it has been found wanting." We need to remedy this. There are instructions here https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide#cTAKES3.2UserInstallGuide-(Recommended)AddUMLSaccessrights but as it is so important it should have its own page with pervasive links. In the 4.0 docs it should be much more obvious. It is on the page about the Default Clinical Pipeline: https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline and the bottom of the page for piper files: https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files Sean -Original Message- From: Ks Sunder [mailto:shyam...@gmail.com] Sent: Friday, December 01, 2017 8:31 AM To: dev@ctakes.apache.org Subject: Re: Regarding cTakes version upadtion [EXTERNAL] Hi, when i am using cTakes3.2.2 after maven install , cTakes all modules available at src folder in that i changed username and pwd. but cTakes4.0 is jsut created war file of cTakes modules .. i am confused how can change username and pwd in cTakes4.0..? can we have any properties files for that...? please help me.. On Thu, Nov 30, 2017 at 7:42 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Shyam k, > > Are you sure that you changed your umls credentials? How did you change > them? It doesn't look like your change went through since your error is > still: > > is not valid for user CHANGE_ME with CHANGE_ME > > Sean > > -Original Message- > From: Ks Sunder [mailto:shyam...@gmail.com] > Sent: Thursday, November 30, 2017 3:41 AM > To: dev@ctakes.apache.org > Subject: Re: Regarding cTakes version upadtion [EXTERNAL] > > Hi, > > I commented in Pipeline : > \org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar > > stitll i am getting this error : UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME , > I changed UMLusername and password its notworking, but cTakes 3.x is > working properly through current Uml credentials, > we need any other credential for cTakes4.0...? > > Error > > > 30 Nov 2017 14:07:16 INFO DictionaryDescriptorParser - Parsing dictionary > specifications: > 30 Nov 2017 14:07:16 INFO UmlsUserApprover - Checking UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= for user CHANGE_ME: > 30 Nov 2017 14:07:18 ERROR UmlsUserApprover - UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME > > 2017-11-30 14:07:18.867:WARN:/:unavailable > org.apache.uima.resource.ResourceInitializationException: Initialization > of > annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: ) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initialize(PrimitiveAnalysisEngine_impl.java:156) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource( > AnalysisEngineFactory_impl.java:94) > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource( > CompositeResourceFactory_impl.java:62) > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine( > UIMAFramework.java:387) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB( > AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.Aggregat
RE: Regarding cTakes version upadtion [EXTERNAL]
You can explode the war file to a folder and edit the xml file under WEB-INF\classes\org\apache\ctakes\dictionary\lookup\fast with proper UMLS username and password. Then you can deploy the exploded folder in Tomcat. Regards, Gandhi -Original Message- From: Ks Sunder [mailto:shyam...@gmail.com] Sent: Friday, December 01, 2017 7:01 PM To: dev@ctakes.apache.org Subject: Re: Regarding cTakes version upadtion [EXTERNAL] Hi, when i am using cTakes3.2.2 after maven install , cTakes all modules available at src folder in that i changed username and pwd. but cTakes4.0 is jsut created war file of cTakes modules .. i am confused how can change username and pwd in cTakes4.0..? can we have any properties files for that...? please help me.. On Thu, Nov 30, 2017 at 7:42 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Shyam k, > > Are you sure that you changed your umls credentials? How did you change > them? It doesn't look like your change went through since your error is > still: > > is not valid for user CHANGE_ME with CHANGE_ME > > Sean > > -Original Message- > From: Ks Sunder [mailto:shyam...@gmail.com] > Sent: Thursday, November 30, 2017 3:41 AM > To: dev@ctakes.apache.org > Subject: Re: Regarding cTakes version upadtion [EXTERNAL] > > Hi, > > I commented in Pipeline : > \org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar > > stitll i am getting this error : UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME , > I changed UMLusername and password its notworking, but cTakes 3.x is > working properly through current Uml credentials, > we need any other credential for cTakes4.0...? > > Error > > > 30 Nov 2017 14:07:16 INFO DictionaryDescriptorParser - Parsing dictionary > specifications: > 30 Nov 2017 14:07:16 INFO UmlsUserApprover - Checking UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= for user CHANGE_ME: > 30 Nov 2017 14:07:18 ERROR UmlsUserApprover - UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME > > 2017-11-30 14:07:18.867:WARN:/:unavailable > org.apache.uima.resource.ResourceInitializationException: Initialization > of > annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: ) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initialize(PrimitiveAnalysisEngine_impl.java:156) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource( > AnalysisEngineFactory_impl.java:94) > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource( > CompositeResourceFactory_impl.java:62) > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine( > UIMAFramework.java:387) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB( > AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > initialize(AggregateAnalysisEngine_impl.java:185) > at > org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine( > AnalysisEngineFactory.java:711) > at > org.apache.uima.fit.factory.AggregateBuilder.createAggregate( > AggregateBuilder.java:207) > at com.app.webservlet.cTakesWebClass.init(cTakesWebClass.java:36) > at > org.eclipse.jetty.servlet.ServletHolder.initServlet( > ServletHolder.java:532) > at org.eclipse.jetty.s
Re: Regarding cTakes version upadtion [EXTERNAL]
Hi, when i am using cTakes3.2.2 after maven install , cTakes all modules available at src folder in that i changed username and pwd. but cTakes4.0 is jsut created war file of cTakes modules .. i am confused how can change username and pwd in cTakes4.0..? can we have any properties files for that...? please help me.. On Thu, Nov 30, 2017 at 7:42 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Shyam k, > > Are you sure that you changed your umls credentials? How did you change > them? It doesn't look like your change went through since your error is > still: > > is not valid for user CHANGE_ME with CHANGE_ME > > Sean > > -Original Message- > From: Ks Sunder [mailto:shyam...@gmail.com] > Sent: Thursday, November 30, 2017 3:41 AM > To: dev@ctakes.apache.org > Subject: Re: Regarding cTakes version upadtion [EXTERNAL] > > Hi, > > I commented in Pipeline : > \org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar > > stitll i am getting this error : UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME , > I changed UMLusername and password its notworking, but cTakes 3.x is > working properly through current Uml credentials, > we need any other credential for cTakes4.0...? > > Error > > > 30 Nov 2017 14:07:16 INFO DictionaryDescriptorParser - Parsing dictionary > specifications: > 30 Nov 2017 14:07:16 INFO UmlsUserApprover - Checking UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= for user CHANGE_ME: > 30 Nov 2017 14:07:18 ERROR UmlsUserApprover - UMLS Account at > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts- > 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc= > le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user > CHANGE_ME with CHANGE_ME > > 2017-11-30 14:07:18.867:WARN:/:unavailable > org.apache.uima.resource.ResourceInitializationException: Initialization > of > annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: ) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > initialize(PrimitiveAnalysisEngine_impl.java:156) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource( > AnalysisEngineFactory_impl.java:94) > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource( > CompositeResourceFactory_impl.java:62) > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine( > UIMAFramework.java:387) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB( > AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > initialize(AggregateAnalysisEngine_impl.java:185) > at > org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine( > AnalysisEngineFactory.java:711) > at > org.apache.uima.fit.factory.AggregateBuilder.createAggregate( > AggregateBuilder.java:207) > at com.app.webservlet.cTakesWebClass.init(cTakesWebClass.java:36) > at > org.eclipse.jetty.servlet.ServletHolder.initServlet( > ServletHolder.java:532) > at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344) > at > org.eclipse.jetty.util.component.AbstractLifeCycle. > start(AbstractLifeCycle.java:64) > at > org.eclipse.jetty.servlet.ServletHandler.initialize( > ServletHandler.java:791) > at > org.eclipse.jetty.servlet.ServletContextHandler.startContext( > ServletContextHandler.java:265) > at > org.eclipse.jetty.webapp.WebAppContext.startContext( > Web
RE: Regarding cTakes version upadtion [EXTERNAL]
Hi Shyam k, Are you sure that you changed your umls credentials? How did you change them? It doesn't look like your change went through since your error is still: > is not valid for user CHANGE_ME with CHANGE_ME Sean -Original Message- From: Ks Sunder [mailto:shyam...@gmail.com] Sent: Thursday, November 30, 2017 3:41 AM To: dev@ctakes.apache.org Subject: Re: Regarding cTakes version upadtion [EXTERNAL] Hi, I commented in Pipeline : \org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar stitll i am getting this error : UMLS Account at https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc=le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user CHANGE_ME with CHANGE_ME , I changed UMLusername and password its notworking, but cTakes 3.x is working properly through current Uml credentials, we need any other credential for cTakes4.0...? Error 30 Nov 2017 14:07:16 INFO DictionaryDescriptorParser - Parsing dictionary specifications: 30 Nov 2017 14:07:16 INFO UmlsUserApprover - Checking UMLS Account at https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc=le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= for user CHANGE_ME: 30 Nov 2017 14:07:18 ERROR UmlsUserApprover - UMLS Account at https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=GMS7z6wXokcMqQHAUda8o3XxG1M868mv_PRYbKeB0Zc=le1pEnmgizyhdYQnzNGbDFgXFy53cl2Jj51E-IjkQck= is not valid for user CHANGE_ME with CHANGE_ME 2017-11-30 14:07:18.867:WARN:/:unavailable org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: ) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at com.app.webservlet.cTakesWebClass.init(cTakesWebClass.java:36) at org.eclipse.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:532) at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344) at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64) at org.eclipse.jetty.servlet.ServletHandler.initialize(ServletHandler.java:791) at org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:265) at org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1242) at org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:717) at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494) at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64) at org.eclipse.jetty.server.handler.HandlerWrapper.doStart(HandlerWrapper.java:95) at org.eclipse.jetty.server.Server.doStart(Server.java:282) at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64) at net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedAdapter.start(JettyEmbeddedAdapter.java:67) at net.sourceforge.eclipsejetty.starter.common.AbstractJettyLauncherMain.launch(AbstractJettyLauncherMain.java:84) at net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedLauncherMain.main(JettyEmbeddedLauncherMain.java:42) Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALI
