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From Sai Anuroop <sai.anur...@abzooba.com>
Subject Re: Invalid username and pw running ctakes error message.
Date Tue, 26 May 2015 12:15:47 GMT
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
>
>
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> 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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