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From Joshua Weiner <joshuawein...@gmail.com>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 14:29:25 GMT
Here is what the log file says... hopefully this drives to the answer..

12/24/13 9:26:58 AM - 14:
org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed.  (Descriptor:
file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed.  (Descriptor:
file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.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.produceAnalysisEngine(UIMAFramework.java:354)
 at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
 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$200(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
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:79)
 at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 54 more
Caused by: java.net.ConnectException: connect: Address is invalid on local
machine, or port is not valid on remote machine
at java.net.DualStackPlainSocketImpl.connect0(Native Method)
 at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
 at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
 at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
 at java.net.Socket.connect(Unknown Source)
at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
 at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
 at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
 at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
Source)
 at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
Source)
 at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
Source)
at
sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
Source)
 at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:70)
 ... 55 more



On Tue, Dec 24, 2013 at 12:22 AM, Karthik Sarma <ksarma@ksarma.com> wrote:

> Hmm looks like there actually might be a typo in the descriptor -- it had
> to be modified to set for UMLS. Check the aggregate processor xml file for
> the typo
>
>
>
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab
> Member, CA Delegation to the House of Delegates of the American Medical
> Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma
>
>
> On Mon, Dec 23, 2013 at 10:28 PM, Pei Chen <chenpei@apache.org> wrote:
>
>> not sure if it's a email copy and paste error or is it just a typo:
>> DcitionaryLookupAnnotatorUMLS.xml
>> instead ??? DictionaryLookupAnnotatorUMLS.xml  ???
>> Would you be able to go to View > Log > there's usually a bit more info
>> in the ~/uima.log file.
>>
>>
>> On Mon, Dec 23, 2013 at 11:21 PM, Joshua Weiner <joshuaweiner2@gmail.com>wrote:
>>
>>> I changed my password so it no loner has a %... and I also set the
>>> password in the dictionarylookupannotatorUMLS.xml file as you described...
>>>
>>> I still get the same error...
>>> org.apache.uima.resource.ResourceInitializationException: Initialization
>>> of annotator class
>>> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
>>> failed. (Descriptor:
>>> file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml)
>>> ...
>>>
>>> What is going on???
>>>
>>>
>>> On Mon, Dec 23, 2013 at 10:49 PM, Pei Chen <chenpei@apache.org> wrote:
>>>
>>>> Hi Joshua,
>>>> I just noticed that you figured out the escaping issue.  But based on
>>>> the error, it probably still failed due to invalid umls pw (if you check
>>>> the uima.log files you will probably see the out put.)
>>>> If you want to bypass the entire escaping the environment var issue,
>>>> you can also set the umls credentials within the xml file itself:
>>>> Which should be inside your:
>>>> C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/
>>>> desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml
>>>>
>>>>
>>>> On Mon, Dec 23, 2013 at 10:26 PM, Joshua Weiner <
>>>> joshuaweiner2@gmail.com> wrote:
>>>>
>>>>> Gah .. I am not sure why this is so challenging... Now I try to run;
>>>>> AggregatePlaintextUMLSProcessor.xml
>>>>>
>>>>> and I get the error:
>>>>> org.apache.uima.resource.ResourceInitializationException:
>>>>> Initialization of annotator class
>>>>> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
>>>>> failed. (Descriptor:
>>>>> file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml)
>>>>> ...
>>>>>
>>>>> hopefully this is my last problem!! Thank you for your help.!!!!!!!!!!!
>>>>>
>>>>> Josh
>>>>>
>>>>>
>>>>> On Mon, Dec 23, 2013 at 10:21 PM, Joshua Weiner <
>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>
>>>>>> Smart man karthik. I do have a percent sign in my password. Thank
you
>>>>>> for your help here, both of you.
>>>>>>
>>>>>> Works now! Great tip.
>>>>>> On Dec 23, 2013 7:11 PM, "Karthik Sarma" <ksarma@ksarma.com>
wrote:
>>>>>>
>>>>>>> Ah, I think I might know the problem. You probably have a percent
>>>>>>> sign in your password. If so, you should replace it with a double
percent
>>>>>>> (%%) in the batch file, as the % sign is a reserved character
in batch
>>>>>>> files.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Karthik Sarma
>>>>>>> UCLA Medical Scientist Training Program Class of 20??
>>>>>>> Member, UCLA Medical Imaging & Informatics Lab
>>>>>>> Member, CA Delegation to the House of Delegates of the American
>>>>>>> Medical Association
>>>>>>> ksarma@ksarma.com
>>>>>>> gchat: ksarma@gmail.com
>>>>>>> linkedin: www.linkedin.com/in/ksarma
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner <
>>>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>>>
>>>>>>>> when I run the script I get the following error: ((see below
the
>>>>>>>>
>>>>>>>>
>>>>>>>> I run: bin\runctakesCVD.bat
>>>>>>>> I get:
>>>>>>>>
>>>>>>>> C:\apache-ctakes-3.1.00>java -Dctakes.umlsuser=joshuawiener2
>>>>>>>> -Dctakes.umlspw=mypasswordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
>>>>>>>> -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>  Error: Could not find or load main class
>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Dec 23, 2013 at 10:02 PM, Karthik Sarma <ksarma@ksarma.com>wrote:
>>>>>>>>
>>>>>>>>> OK, and what is the output when you run the script?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Karthik Sarma
>>>>>>>>> UCLA Medical Scientist Training Program Class of 20??
>>>>>>>>> Member, UCLA Medical Imaging & Informatics Lab
>>>>>>>>> Member, CA Delegation to the House of Delegates of the
American
>>>>>>>>> Medical Association
>>>>>>>>> ksarma@ksarma.com
>>>>>>>>> gchat: ksarma@gmail.com
>>>>>>>>> linkedin: www.linkedin.com/in/ksarma
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <
>>>>>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> based on the code below I see the home directory
as being set to
>>>>>>>>>> the current_dir which is C:\apache-ctakes-3.0.1..............
>>>>>>>>>>
>>>>>>>>>> I also tried using James code to re-set the directory
.. did not
>>>>>>>>>> work.
>>>>>>>>>>
>>>>>>>>>> @REM Guess CTAKES_HOME if not defined
>>>>>>>>>> set CURRENT_DIR=%cd%
>>>>>>>>>> if not "%CTAKES_HOME%" == "" goto gotHome
>>>>>>>>>> set CTAKES_HOME=%CURRENT_DIR%
>>>>>>>>>> if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto
okHome
>>>>>>>>>> cd ..
>>>>>>>>>> set CTAKES_HOME=%cd%
>>>>>>>>>>
>>>>>>>>>> :gotHome
>>>>>>>>>> if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto
okHome
>>>>>>>>>> echo The CTAKES_HOME environment variable is not
defined correctly
>>>>>>>>>> echo This environment variable is needed to run this
program
>>>>>>>>>> goto end
>>>>>>>>>>
>>>>>>>>>> :okHome
>>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>> java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=56Kmartin%
>>>>>>>>>> -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>>
>>>>>>>>>> :end
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Dec 23, 2013 at 9:55 PM, Karthik Sarma <ksarma@ksarma.com
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> What is your CTAKES_HOME set to?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Karthik Sarma
>>>>>>>>>>> UCLA Medical Scientist Training Program Class
of 20??
>>>>>>>>>>> Member, UCLA Medical Imaging & Informatics
Lab
>>>>>>>>>>> Member, CA Delegation to the House of Delegates
of the American
>>>>>>>>>>> Medical Association
>>>>>>>>>>> ksarma@ksarma.com
>>>>>>>>>>> gchat: ksarma@gmail.com
>>>>>>>>>>> linkedin: www.linkedin.com/in/ksarma
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner
<
>>>>>>>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Where do you see this James?
>>>>>>>>>>>>
>>>>>>>>>>>> Here is my code... I see the -cp parameter
and its arguements
>>>>>>>>>>>> right after "mypassword" ... right?
>>>>>>>>>>>>
>>>>>>>>>>>> :okHome
>>>>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>>>> java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=mypassword
>>>>>>>>>>>> -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>
>>>>>>>>>>>> :end
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Dec 23, 2013 at 9:44 PM, Masanz,
James J. <
>>>>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>  I see now that the java command in your
previous post didn’t
>>>>>>>>>>>>> include the -cp parameter and its arguments.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Please add that back in.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:
>>>>>>>>>>>>> joshuaweiner89@gmail.com] *On Behalf
Of *Joshua Weiner
>>>>>>>>>>>>> *Sent:* Monday, December 23, 2013 8:12
PM
>>>>>>>>>>>>>
>>>>>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>>>>>> *Subject:* Re: Adding UMLS username and
password ....
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> James,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I appreciate your persistence, it means
quite a lot.
>>>>>>>>>>>>> Unfortunately, even with your latest
attempt I still get the same error:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Error: Could not find or load main class
>>>>>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am on windows 8, 8gb of ram.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for your persistence.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Josh
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Dec 23, 2013 at 9:07 PM, Masanz,
James J. <
>>>>>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Try this
>>>>>>>>>>>>>
>>>>>>>>>>>>> CD  C:\apache-ctakes-3.1.0
>>>>>>>>>>>>>
>>>>>>>>>>>>> set CTAKES_HOME=C:\apache-ctakes-3.1.0
>>>>>>>>>>>>>
>>>>>>>>>>>>> then enter the java command from the
command line that you
>>>>>>>>>>>>> were entering
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Note: in my previous post, it was my
mistake of including the
>>>>>>>>>>>>> percent signs in the SET command.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I meant to suggest
>>>>>>>>>>>>>
>>>>>>>>>>>>> set CTAKES_HOME=""
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:
>>>>>>>>>>>>> joshuaweiner89@gmail.com] *On Behalf
Of *Joshua Weiner
>>>>>>>>>>>>> *Sent:* Monday, December 23, 2013 7:55
PM
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>>>>>> *Subject:* Re: Adding UMLS username and
password ....
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> James,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for your continual prompt responses.
Unfortunately,
>>>>>>>>>>>>> even after I did set%CTAKES_HOME%=""
I still get the following errror:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=joshuawiener2
>>>>>>>>>>>>> =DCtakes.umlspw=mypasswwordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
>>>>>>>>>>>>> -Xmd512M -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>> Error: Could not find or load main class
>>>>>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> once again my code in the runctakesCVD.bat
file is:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> :okHome
>>>>>>>>>>>>>
>>>>>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>>>>>
>>>>>>>>>>>>> java -Dctakes.umlsuser=joshuawiener2
-Dctakes.umlspw=passwordd
>>>>>>>>>>>>> -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> :end
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Dec 23, 2013 at 8:45 PM, Masanz,
James J. <
>>>>>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> You might try from the command line
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> echo  %CTAKES_HOME%
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> or even better for debug purposes put
it just before the  CD
>>>>>>>>>>>>> %CTAKES_HOME%  line.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> It should respond with the parent of
the bin, desc, and
>>>>>>>>>>>>> resources directory.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> If it responds with something else, try
clearing %CTAKES_HOME%
>>>>>>>>>>>>> by entering the following on the command
line and then trying the bat file
>>>>>>>>>>>>> again.
>>>>>>>>>>>>>
>>>>>>>>>>>>> set %CTAKES_HOME%=""
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Oh, and you’ll probably want to change
-Xmx1024M  to be  –Xmx2048M
>>>>>>>>>>>>> or even larger or you will run into a
heap space error for
>>>>>>>>>>>>> many parts of cTAKES.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> -- James
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:
>>>>>>>>>>>>> joshuaweiner89@gmail.com] *On Behalf
Of *Joshua Weiner
>>>>>>>>>>>>> *Sent:* Monday, December 23, 2013 7:36
PM
>>>>>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>>>>>> *Subject:* Re: Adding UMLS username and
password ....
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> James,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks so much for your response. When
I remove the brackets I
>>>>>>>>>>>>> still get an error, I get:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> "Error: could not find or load main class
>>>>>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you so much for your help. I appreciate
your dilligence.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Josh
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Dec 23, 2013 at 8:32 PM, Masanz,
James J. <
>>>>>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sorry for the confusion, don’t include
the brackets, so it
>>>>>>>>>>>>> should look like this:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> -Dctakes.umlsuser=joshuawiener2  -Dctakes.umlspw=mypassword
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:
>>>>>>>>>>>>> joshuaweiner89@gmail.com] *On Behalf
Of *Joshua Weiner
>>>>>>>>>>>>> *Sent:* Monday, December 23, 2013 7:28
PM
>>>>>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>>>>>> *Subject:* Adding UMLS username and password
....
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>   Hey guys,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I know this is probably a dumb question
but I can't for the
>>>>>>>>>>>>> life of me figure it out. I finally got
a UMLS username and password, but I
>>>>>>>>>>>>> don't think I am updating the BAT files
correctly... here is what I did:
>>>>>>>>>>>>> note my username is joshuaweiner2 and
my password (for this example) is
>>>>>>>>>>>>> mypasswordd (see below).... I now can't
get the CVD to run.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for your help...
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> :okHome
>>>>>>>>>>>>>
>>>>>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>>>>>
>>>>>>>>>>>>> java -Dctakes.umlsuser=<joshuawiener2>
>>>>>>>>>>>>> -Dctakes.umlspw=<mypasswordd> -cp
>>>>>>>>>>>>> "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>>>>>> -Xmx1024M org.apache.uima.tools.cvd.CVD
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> :end
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>>>>>
>>>>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>>>>>
>>>>>>>>>>>>> 201.638.0047
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>>>>>
>>>>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>>>>>
>>>>>>>>>>>>> 201.638.0047
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>>>>>
>>>>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>>>>>
>>>>>>>>>>>>> 201.638.0047
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>>>>>
>>>>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>>>>>
>>>>>>>>>>>>> 201.638.0047
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>>>> 201.638.0047
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Joshua S. Weiner
>>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>> 201.638.0047
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Joshua S. Weiner
>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>> 201.638.0047
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Joshua S. Weiner
>>>>> joshuaweiner2@gmail.com
>>>>> 201.638.0047
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Joshua S. Weiner
>>> joshuaweiner2@gmail.com
>>> 201.638.0047
>>>
>>
>>
>


-- 
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047

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