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From Joshua Weiner <joshuawein...@gmail.com>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 03:21:49 GMT
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
>>
>
>

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