Sai, Just curious, Did you download and unpack/merge the separate UMLS resources into the resources folder?
UMLS® Dictionary Zipped copy of the cTAKES™ UMLS® dictionary. Please refer to the Dictionary Install Guide <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dictionary+Lookup> for assistance. Install fast version if only running ctakes-fast. All Versions <http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.1.1-bin.zip/download> Fast Version <http://sourceforge.net/projects/ctakesresources/files/ctakessnorx-3.2.1.1.zip/download> On Tue, May 26, 2015 at 8:15 AM, Sai Anuroop <[email protected]> wrote: > Hi Murali, > > Presently i am using the most recent version ctakes 3.2.2 pointed out in > this mail thread by Pei.Still i am running into the same error.Here is the > java command i have used: > > :okHome > @set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64 > cd %CTAKES_HOME% > java -Dctakes.umlsuser=saianuroop -Dctakes.umlspw=password -cp > "%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/;%CTAKES_HOME%/lib/*" > -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx3g > org.apache.uima.tools.cvd.CVD > cd %CURRENT_DIR% > :end > > but when i am trying to run AggregatePlainTextfastUMLSProcessor i am > facing following error: > > org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: > Initialization of annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: > file:/C:/Users/Abzooba/apache-ctakes-3.2.1/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) > org.apache.uima.resource.ResourceInitializationException: Initialization > of annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: > file:/C:/Users/Abzooba/apache-ctakes-3.2.1/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) > 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.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.produceResource(UIMAFramework.java:314) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) > at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486) > at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476) > at > org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.AbstractButton.doClick(Unknown Source) > at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) > at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown > Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > at java.awt.EventQueue.access$500(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > Caused by: org.apache.uima.resource.ResourceInitializationException: > EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: > Can't find resource for bundle java.util.PropertyResourceBundle, key Could > not construct > org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:134) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) > ... 55 more > Caused by: > org.apache.uima.analysis_engine.annotator.AnnotatorContextException: > EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: > Can't find resource for bundle java.util.PropertyResourceBundle, key Could > not construct > org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary > at > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:203) > at > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:160) > at > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:131) > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132) > ... 56 more > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) > at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown > Source) > at java.lang.reflect.Constructor.newInstance(Unknown Source) > at > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200) > ... 59 more > Caused by: java.sql.SQLException: Invalid User for UMLS dictionary > UmlsHsqlRareWord > at > org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29) > ... 64 more > > My password doesnot contain any special characters and i can login with my > present credentials in UMLS website.There is no blockage made by > firewall.So Can you please explain where is the problem. > > Regards, > > Vetsa Sai Anuroop > > Abzooba India Infotech Private Limited > > 10th Floor, Infinity Benchmark, Block EP GP, Sector V, Salt Lake, Kolkata > – 700 091, West Bengal, India > > > > > On Thu, May 21, 2015 at 4:19 PM, Murali <[email protected]> wrote: > >> Sai >> >> This issue has been resolved. Please check the responses posted earlier >> regarding the specifics of the build. >> >> Murali >> Wired Informatics >> >> >> >> On May 21, 2015, at 4:00 AM, Sai Anuroop <[email protected]> wrote: >> >> Hi Pei, >> >> Is this issue yet resolved officially? I am still getting the same error >> with the new version.i wanted to know whether it is mistake from my side or >> not.? >> >> Regards, >> >> Vetsa Sai Anuroop >> >> Abzooba India Infotech Private Limited >> >> 10th Floor, Infinity Benchmark, Block EP GP, Sector V, Salt Lake, >> Kolkata – 700 091, West Bengal, India >> >> >> This e-mail and any attachments transmitted with it are confidential and >> may be legally privileged. If you are not the intended recipient or if you >> have received this e-mail in error, you must destroy all copies incl. >> attachments and notify the sender by return e-mail or by phone. Any >> dissemination, distribution or other use of the contents of this message by >> anyone other than the intended recipient is strictly prohibited. Abzooba >> does not guarantee that this email has not been monitored, intercepted and >> amended or that it is virus or error free. Any views expressed in this >> message are those of the individual sender. All liabilities of the Abzooba >> Group and its entities for any damages resulting from e-mail use are >> excluded. >> >> On Tue, May 19, 2015 at 5:46 PM, Pei Chen <[email protected]> wrote: >> >>> Yu, >>> The change is in: >>> >>> ctakes-dictionary-lookup-3.2.2.jar >>> ctakes-dictionary-lookup-fast-3.2.2.jar >>> You can find it in the lib dir of the binary artifact of the release >>> candidate or in staging repo: >>> https://repository.apache.org/#view-repositories;staging~browsestorage >>> >>> More details are in: >>> https://issues.apache.org/jira/browse/CTAKES-359 >>> https://svn.apache.org/viewvc?view=revision&revision=1678940 >>> >>> On Tue, May 19, 2015 at 12:27 AM, Liang, Yu <[email protected]> wrote: >>> >>>> which file did you update to solve the invalid username problem, I am >>>> getting confused since when download the new version, I GOT THE ERROR that >>>> I debugged before for a long time again. I just want to replace the file >>>> you update and keep the others the same. >>>> Yu Liang >>>> >>>> CHIBI >>>> >>>> >>>> >>>> >>>> >>>> On May 18, 2015, at 2:16 PM, Pei Chen <[email protected]> wrote: >>>> >>>> Yu, >>>> Are you using the binaries from the RC2[1] from the vote thread [1]? >>>> >>>> [1] https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2 >>>> [2] >>>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3CCAPqz87p-%3D6DEmsxG5AMgHhetmG7%3Dh%2B-TU2F_%2B_yn7BcbUhMrjw%40mail.gmail.com%3E >>>> --Pei >>>> >>>> On Mon, May 18, 2015 at 12:40 PM, Liang, Yu <[email protected]> wrote: >>>> >>>>> Hi Pei, >>>>> >>>>> I vote it. >>>>> Is it working right now? I still run into the same error message. >>>>> Thank you. >>>>> Yu Liang >>>>> >>>>> CHIBI >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> > On May 15, 2015, at 4:20 PM, Chen, Pei < >>>>> [email protected]> wrote: >>>>> > >>>>> > There's a release candidate out already. We just need 3 +1 votes to >>>>> make it official. >>>>> > >>>>> > Sent from my iPhone >>>>> > >>>>> >> On May 15, 2015, at 11:35 AM, Liang, Yu <[email protected]> wrote: >>>>> >> >>>>> >> Do you have any idea what is the estimated time that will release >>>>> the patch? >>>>> >> Yu Liang >>>>> >> >>>>> >> CHIBI >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >>> On May 15, 2015, at 11:09 AM, Savova, Guergana < >>>>> [email protected]> wrote: >>>>> >>> >>>>> >>> This happened because NLM introduced some changes. There has been >>>>> a lot of discussion on this topic in the cTAKES user and dev lists in the >>>>> last several days. Please, check these discussions. >>>>> >>> >>>>> >>> A patch has already been created and is scheduled to be released. >>>>> >>> --Guergana >>>>> >>> >>>>> >>> -----Original Message----- >>>>> >>> From: Liang, Yu [mailto:[email protected]] >>>>> >>> Sent: Friday, May 15, 2015 11:07 AM >>>>> >>> To: [email protected] >>>>> >>> Subject: Invalid username and pw running ctakes error message. >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> I run the command line and get this error message this morning >>>>> that never happened before. I definitely have a valid username and >>>>> password. >>>>> >>> Do you know what is going on? I run ctakes a couple of days ago, >>>>> and there is no problem. >>>>> >>> >>>>> >>> Thank you so much. Looking forward to hearing back ASAP!!! >>>>> >>> >>>>> >>> >>>>> >>> Using ctakes.umlsaddr: >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser-3A&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=LMUm5dEjNmfWgEanWU2ABsF-cDEmV05VYvJ_q19zymc&s=k8oQSNfvyDKyjK1iz_tFqIDvi3ShxjIu4VVRJ4YpgOc&e= >>>>> teqyuyl >>>>> >>> 15 May 2015 10:45:19 ERROR UmlsDictionaryLookupAnnotator - Error: >>>>> Invalid UMLS License. A UMLS License is required to use the UMLS >>>>> dictionary lookup. >>>>> >>> Error: You may request one at: >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_license.html&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=LMUm5dEjNmfWgEanWU2ABsF-cDEmV05VYvJ_q19zymc&s=hSI-p-B6bXZdEMlyW-8UoIORwwroBvJsjs84Zdrt4GI&e= >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> Yu Liang >>>>> >>> >>>>> >>> CHIBI >>>>> >> >>>>> >>>>> >>>> >>>> >>> >> >
