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From Pei Chen <chen...@apache.org>
Subject Re: Invalid username and pw running ctakes error message.
Date Wed, 27 May 2015 18:02:40 GMT
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 <sai.anuroop@abzooba.com>
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 <mminnah@gmail.com> 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 <sai.anuroop@abzooba.com> 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
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>> 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 <chenpei@apache.org> 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 <Yu.Liang@nyumc.org> 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 <chenpei@apache.org> 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 <Yu.Liang@nyumc.org> 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 <
>>>>> Pei.Chen@childrens.harvard.edu> 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 <Yu.Liang@nyumc.org>
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 <
>>>>> Guergana.Savova@childrens.harvard.edu> 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:Yu.Liang@nyumc.org]
>>>>> >>> Sent: Friday, May 15, 2015 11:07 AM
>>>>> >>> To: user@ctakes.apache.org
>>>>> >>> 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
>>>>> >>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>

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