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From Karthik Sarma <ksa...@ksarma.com>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 02:55:58 GMT
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
>

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