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From Karthik Sarma <ksa...@ksarma.com>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 03:02:01 GMT
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
>

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