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From Joshua Weiner <joshuawein...@gmail.com>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 02:59:30 GMT
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

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