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From Sai Anuroop <sai.anur...@abzooba.com>
Subject Re: Invalid username and pw running ctakes error message.
Date Thu, 28 May 2015 07:32:19 GMT
Hi Pei,

Yes, I have downloaded and added the seperate UMLS resources into resource
folder.

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 Wed, May 27, 2015 at 11:32 PM, Pei Chen <chenpei@apache.org> wrote:

> 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
>>> 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 <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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