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From Pei Chen <chen...@apache.org>
Subject Re: Adding UMLS username and password ....
Date Tue, 24 Dec 2013 03:49:03 GMT
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" <ksarma@ksarma.com> wrote:
>>
>>> Ah, I think I might know the problem. You probably have a percent sign
>>> in your password. If so, you should replace it with a double percent (%%)
>>> in the batch file, as the % sign is a reserved character in batch files.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Karthik Sarma
>>> UCLA Medical Scientist Training Program Class of 20??
>>> Member, UCLA Medical Imaging & Informatics Lab
>>> Member, CA Delegation to the House of Delegates of the American Medical
>>> Association
>>> ksarma@ksarma.com
>>> gchat: ksarma@gmail.com
>>> linkedin: www.linkedin.com/in/ksarma
>>>
>>>
>>> On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner <joshuaweiner2@gmail.com>wrote:
>>>
>>>> when I run the script I get the following error: ((see below the
>>>>
>>>>
>>>> I run: bin\runctakesCVD.bat
>>>> I get:
>>>>
>>>> C:\apache-ctakes-3.1.00>java -Dctakes.umlsuser=joshuawiener2
>>>> -Dctakes.umlspw=mypasswordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
>>>> -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>  Error: Could not find or load main class org.apache.uima.tools.cvd.CVD
>>>>
>>>>
>>>>
>>>> On Mon, Dec 23, 2013 at 10:02 PM, Karthik Sarma <ksarma@ksarma.com>wrote:
>>>>
>>>>> OK, and what is the output when you run the script?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Karthik Sarma
>>>>> UCLA Medical Scientist Training Program Class of 20??
>>>>> Member, UCLA Medical Imaging & Informatics Lab
>>>>> Member, CA Delegation to the House of Delegates of the American
>>>>> Medical Association
>>>>> ksarma@ksarma.com
>>>>> gchat: ksarma@gmail.com
>>>>> linkedin: www.linkedin.com/in/ksarma
>>>>>
>>>>>
>>>>> On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <
>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>
>>>>>> based on the code below I see the home directory as being set to
the
>>>>>> current_dir which is C:\apache-ctakes-3.0.1..............
>>>>>>
>>>>>> I also tried using James code to re-set the directory .. did not
work.
>>>>>>
>>>>>> @REM Guess CTAKES_HOME if not defined
>>>>>> set CURRENT_DIR=%cd%
>>>>>> if not "%CTAKES_HOME%" == "" goto gotHome
>>>>>> set CTAKES_HOME=%CURRENT_DIR%
>>>>>> if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
>>>>>> cd ..
>>>>>> set CTAKES_HOME=%cd%
>>>>>>
>>>>>> :gotHome
>>>>>> if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
>>>>>> echo The CTAKES_HOME environment variable is not defined correctly
>>>>>> echo This environment variable is needed to run this program
>>>>>> goto end
>>>>>>
>>>>>> :okHome
>>>>>> cd %CTAKES_HOME%
>>>>>> java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=56Kmartin% -cp
>>>>>> "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M
>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>
>>>>>> :end
>>>>>>
>>>>>>
>>>>>> On Mon, Dec 23, 2013 at 9:55 PM, Karthik Sarma <ksarma@ksarma.com>wrote:
>>>>>>
>>>>>>> What is your CTAKES_HOME set to?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Karthik Sarma
>>>>>>> UCLA Medical Scientist Training Program Class of 20??
>>>>>>> Member, UCLA Medical Imaging & Informatics Lab
>>>>>>> Member, CA Delegation to the House of Delegates of the American
>>>>>>> Medical Association
>>>>>>> ksarma@ksarma.com
>>>>>>> gchat: ksarma@gmail.com
>>>>>>> linkedin: www.linkedin.com/in/ksarma
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner <
>>>>>>> joshuaweiner2@gmail.com> wrote:
>>>>>>>
>>>>>>>> Where do you see this James?
>>>>>>>>
>>>>>>>> Here is my code... I see the -cp parameter and its arguements
right
>>>>>>>> after "mypassword" ... right?
>>>>>>>>
>>>>>>>> :okHome
>>>>>>>> cd %CTAKES_HOME%
>>>>>>>> java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=mypassword
-cp
>>>>>>>> "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>
>>>>>>>> :end
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Dec 23, 2013 at 9:44 PM, Masanz, James J. <
>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>
>>>>>>>>>  I see now that the java command in your previous post
didn’t
>>>>>>>>> include the -cp parameter and its arguments.
>>>>>>>>>
>>>>>>>>> Please add that back in.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com]
>>>>>>>>> *On Behalf Of *Joshua Weiner
>>>>>>>>> *Sent:* Monday, December 23, 2013 8:12 PM
>>>>>>>>>
>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>> *Subject:* Re: Adding UMLS username and password ....
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> James,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I appreciate your persistence, it means quite a lot.
>>>>>>>>> Unfortunately, even with your latest attempt I still
get the same error:
>>>>>>>>>
>>>>>>>>> Error: Could not find or load main class
>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I am on windows 8, 8gb of ram.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you for your persistence.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Josh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Dec 23, 2013 at 9:07 PM, Masanz, James J. <
>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>
>>>>>>>>> Try this
>>>>>>>>>
>>>>>>>>> CD  C:\apache-ctakes-3.1.0
>>>>>>>>>
>>>>>>>>> set CTAKES_HOME=C:\apache-ctakes-3.1.0
>>>>>>>>>
>>>>>>>>> then enter the java command from the command line that
you were
>>>>>>>>> entering
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Note: in my previous post, it was my mistake of including
the
>>>>>>>>> percent signs in the SET command.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I meant to suggest
>>>>>>>>>
>>>>>>>>> set CTAKES_HOME=""
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com]
>>>>>>>>> *On Behalf Of *Joshua Weiner
>>>>>>>>> *Sent:* Monday, December 23, 2013 7:55 PM
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>> *Subject:* Re: Adding UMLS username and password ....
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> James,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you for your continual prompt responses. Unfortunately,
even
>>>>>>>>> after I did set%CTAKES_HOME%="" I still get the following
errror:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=joshuawiener2
>>>>>>>>> =DCtakes.umlspw=mypasswwordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-ctakes-3.1.0/config/log4j.xml
>>>>>>>>> -Xmd512M -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>> Error: Could not find or load main class
>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> once again my code in the runctakesCVD.bat file is:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> :okHome
>>>>>>>>>
>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>
>>>>>>>>> java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=passwordd
-cp
>>>>>>>>> "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>> -Xmx2048M org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> :end
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Dec 23, 2013 at 8:45 PM, Masanz, James J. <
>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> You might try from the command line
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> echo  %CTAKES_HOME%
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> or even better for debug purposes put it just before
the  CD
>>>>>>>>> %CTAKES_HOME%  line.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> It should respond with the parent of the bin, desc, and
resources
>>>>>>>>> directory.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> If it responds with something else, try clearing %CTAKES_HOME%
by
>>>>>>>>> entering the following on the command line and then trying
the bat file
>>>>>>>>> again.
>>>>>>>>>
>>>>>>>>> set %CTAKES_HOME%=""
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Oh, and you’ll probably want to change -Xmx1024M  to
be  –Xmx2048M
>>>>>>>>> or even larger or you will run into a heap space error
for many
>>>>>>>>> parts of cTAKES.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -- James
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com]
>>>>>>>>> *On Behalf Of *Joshua Weiner
>>>>>>>>> *Sent:* Monday, December 23, 2013 7:36 PM
>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>> *Subject:* Re: Adding UMLS username and password ....
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> James,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks so much for your response. When I remove the brackets
I
>>>>>>>>> still get an error, I get:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> "Error: could not find or load main class
>>>>>>>>> org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you so much for your help. I appreciate your dilligence.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Sincerely,
>>>>>>>>>
>>>>>>>>> Josh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Dec 23, 2013 at 8:32 PM, Masanz, James J. <
>>>>>>>>> Masanz.James@mayo.edu> wrote:
>>>>>>>>>
>>>>>>>>> Sorry for the confusion, don’t include the brackets,
so it should
>>>>>>>>> look like this:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -Dctakes.umlsuser=joshuawiener2  -Dctakes.umlspw=mypassword
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com]
>>>>>>>>> *On Behalf Of *Joshua Weiner
>>>>>>>>> *Sent:* Monday, December 23, 2013 7:28 PM
>>>>>>>>> *To:* user@ctakes.apache.org
>>>>>>>>> *Subject:* Adding UMLS username and password ....
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>   Hey guys,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I know this is probably a dumb question but I can't for
the life
>>>>>>>>> of me figure it out. I finally got a UMLS username and
password, but I
>>>>>>>>> don't think I am updating the BAT files correctly...
here is what I did:
>>>>>>>>> note my username is joshuaweiner2 and my password (for
this example) is
>>>>>>>>> mypasswordd (see below).... I now can't get the CVD to
run.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you for your help...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> :okHome
>>>>>>>>>
>>>>>>>>> cd %CTAKES_HOME%
>>>>>>>>>
>>>>>>>>> java -Dctakes.umlsuser=<joshuawiener2>
>>>>>>>>> -Dctakes.umlspw=<mypasswordd> -cp
>>>>>>>>> "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
>>>>>>>>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M
>>>>>>>>> -Xmx1024M org.apache.uima.tools.cvd.CVD
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> :end
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Joshua S. Weiner
>>>>>>>>>
>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>
>>>>>>>>> 201.638.0047
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Joshua S. Weiner
>>>>>>>>>
>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>
>>>>>>>>> 201.638.0047
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Joshua S. Weiner
>>>>>>>>>
>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>
>>>>>>>>> 201.638.0047
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Joshua S. Weiner
>>>>>>>>>
>>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>>>
>>>>>>>>> 201.638.0047
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Joshua S. Weiner
>>>>>>>> joshuaweiner2@gmail.com
>>>>>>>> 201.638.0047
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Joshua S. Weiner
>>>>>> joshuaweiner2@gmail.com
>>>>>> 201.638.0047
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Joshua S. Weiner
>>>> joshuaweiner2@gmail.com
>>>> 201.638.0047
>>>>
>>>
>>>
>
>
> --
> Joshua S. Weiner
> joshuaweiner2@gmail.com
> 201.638.0047
>

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