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Posted to user@ctakes.apache.org by Joshua Weiner <jo...@gmail.com> on 2013/12/24 02:27:51 UTC
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
RE: Adding UMLS username and password ....
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I was talking about your previous email where you have a line that starts with
C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=joshuawiener2
Do you have directories
C:\apache-ctakes-3.1.0\bin
C:\apache-ctakes-3.1.0\lib
C:\apache-ctakes-3.1.0\resources
If so, you could try this:
Edit the .bat file and put the following
set CTAKES_HOME=C:\apache-ctakes-3.1.0
just before the line
cd %CTAKES_HOME%
so it looks like
:okHome
set CTAKES_HOME=C:\apache-ctakes-3.1.0
cd %CTAKES_HOME%
then enter the following in your command window
cd C:\apache-ctakes-3.1.0
bin\runcTAKESCVD.bat
hope this helps
From: joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 8:51 PM
To: user@ctakes.apache.org
Subject: Re: Adding UMLS username and password ....
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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 8:12 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:55 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<ma...@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<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047
Re: Adding UMLS username and password ....
Posted by Pei Chen <ch...@apache.org>.
Not sure how windows bat scripts handles escape chars, but if happen to
have a special char such as a % in any of the values, perhaps you may want
to try to double quote it or the windows equivalent of escaping it?
--Pei
On Mon, Dec 23, 2013 at 10:05 PM, Joshua Weiner <jo...@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 <ks...@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 <jo...@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 <ks...@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
>
Re: Adding UMLS username and password ....
Posted by Karthik Sarma <ks...@ksarma.com>.
One of the more interesting problems I've seen on the list to be sure. Glad
it works!
--
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 9:21 PM, Joshua Weiner <jo...@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" <ks...@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 <jo...@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 <ks...@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 <ks...@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
>>>
>>
>>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
Thank you so much . Looks like i am all set now... Damn Kaspersky was
unhappy with me trying to help the world.
Happy Holidays everyone!
Josh
On Tue, Dec 24, 2013 at 9:35 AM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> Joshua,
>
> By any chance, are you behind a firewall or proxy server?
>
>
>
> This annotator essentially tries to connect to the UMLS web service[1] to
> validate your credentials/license…
>
>
>
> [1] https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser
>
>
>
> --Pei
>
>
>
> *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On
> Behalf Of *Joshua Weiner
> *Sent:* Tuesday, December 24, 2013 9:30 AM
>
> *To:* user@ctakes.apache.org
> *Subject:* Re: Adding UMLS username and password ....
>
>
>
> 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 <ks...@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 <ch...@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 <jo...@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 <ch...@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 <jo...@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 <jo...@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" <ks...@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 <jo...@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 <ks...@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 <jo...@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 <ks...@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 <jo...@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. <Ma...@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. <Ma...@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. <Ma...@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. <Ma...@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
>
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
RE: Adding UMLS username and password ....
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Joshua,
By any chance, are you behind a firewall or proxy server?
This annotator essentially tries to connect to the UMLS web service[1] to validate your credentials/license...
[1] https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser
--Pei
From: joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Tuesday, December 24, 2013 9:30 AM
To: user@ctakes.apache.org
Subject: Re: Adding UMLS username and password ....
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 <ks...@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<ma...@ksarma.com>
gchat: ksarma@gmail.com<ma...@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>
On Mon, Dec 23, 2013 at 10:28 PM, Pei Chen <ch...@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 <jo...@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 <ch...@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 <jo...@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 <jo...@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" <ks...@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<ma...@ksarma.com>
gchat: ksarma@gmail.com<ma...@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>
On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner <jo...@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 <ks...@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<ma...@ksarma.com>
gchat: ksarma@gmail.com<ma...@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>
On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <jo...@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 <ks...@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<ma...@ksarma.com>
gchat: ksarma@gmail.com<ma...@gmail.com>
linkedin: www.linkedin.com/in/ksarma<http://www.linkedin.com/in/ksarma>
On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner <jo...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 8:12 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:55 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<ma...@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<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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 <ks...@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 <ch...@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 <jo...@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 <ch...@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" <ks...@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 <ks...@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
Re: Adding UMLS username and password ....
Posted by Karthik Sarma <ks...@ksarma.com>.
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 <ch...@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 <jo...@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 <ch...@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" <ks...@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 <ks...@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 <ks...@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
>>
>
>
Re: Adding UMLS username and password ....
Posted by Pei Chen <ch...@apache.org>.
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 <jo...@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 <ch...@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 <jo...@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" <ks...@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 <ks...@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 <ks...@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
>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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 <ch...@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 <jo...@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 <jo...@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" <ks...@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 <ks...@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 <ks...@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
Re: Adding UMLS username and password ....
Posted by Pei Chen <ch...@apache.org>.
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 <jo...@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 <jo...@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" <ks...@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 <jo...@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 <ks...@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 <ks...@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
>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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 <jo...@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" <ks...@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 <jo...@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 <ks...@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 <ks...@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
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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" <ks...@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 <jo...@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 <ks...@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 <jo...@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 <ks...@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
>>
>
>
Re: Adding UMLS username and password ....
Posted by Karthik Sarma <ks...@ksarma.com>.
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 <jo...@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 <ks...@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 <jo...@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 <ks...@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
>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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 <ks...@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 <jo...@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 <ks...@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 <jo...@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
Re: Adding UMLS username and password ....
Posted by Karthik Sarma <ks...@ksarma.com>.
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 <jo...@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 <ks...@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 <jo...@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
>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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 <ks...@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 <jo...@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. <Ma...@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. <Ma...@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. <Ma...@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. <Ma...@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
Re: Adding UMLS username and password ....
Posted by Karthik Sarma <ks...@ksarma.com>.
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 <jo...@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. <Ma...@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. <Ma...@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. <Ma...@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. <Ma...@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
>
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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. <Ma...@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. <Ma...@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. <Ma...@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. <Ma...@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
RE: Adding UMLS username and password ....
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:55 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<ma...@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<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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. <Ma...@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. <Ma...@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. <Ma...@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
RE: Adding UMLS username and password ....
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user@ctakes.apache.org<ma...@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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<ma...@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<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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. <Ma...@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. <Ma...@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
RE: Adding UMLS username and password ....
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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. <Ma...@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<ma...@gmail.com> [mailto:joshuaweiner89@gmail.com<ma...@gmail.com>] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user@ctakes.apache.org<ma...@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<ma...@gmail.com>
201.638.0047<tel:201.638.0047>
--
Joshua S. Weiner
joshuaweiner2@gmail.com<ma...@gmail.com>
201.638.0047
Re: Adding UMLS username and password ....
Posted by Joshua Weiner <jo...@gmail.com>.
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. <Ma...@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
RE: Adding UMLS username and password ....
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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<ma...@gmail.com>
201.638.0047