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 [email protected] gchat: [email protected] linkedin: www.linkedin.com/in/ksarma On Mon, Dec 23, 2013 at 9:21 PM, Joshua Weiner <[email protected]>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" <[email protected]> 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 >> [email protected] >> gchat: [email protected] >> linkedin: www.linkedin.com/in/ksarma >> >> >> On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner >> <[email protected]>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 <[email protected]>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 >>>> [email protected] >>>> gchat: [email protected] >>>> linkedin: www.linkedin.com/in/ksarma >>>> >>>> >>>> On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <[email protected] >>>> > 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 <[email protected]>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 >>>>>> [email protected] >>>>>> gchat: [email protected] >>>>>> linkedin: www.linkedin.com/in/ksarma >>>>>> >>>>>> >>>>>> On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner < >>>>>> [email protected]> 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. < >>>>>>> [email protected]> 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:* [email protected] [mailto:[email protected]] *On >>>>>>>> Behalf Of *Joshua Weiner >>>>>>>> *Sent:* Monday, December 23, 2013 8:12 PM >>>>>>>> >>>>>>>> *To:* [email protected] >>>>>>>> *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. < >>>>>>>> [email protected]> 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:* [email protected] [mailto:[email protected]] *On >>>>>>>> Behalf Of *Joshua Weiner >>>>>>>> *Sent:* Monday, December 23, 2013 7:55 PM >>>>>>>> >>>>>>>> >>>>>>>> *To:* [email protected] >>>>>>>> *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. < >>>>>>>> [email protected]> 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:* [email protected] [mailto:[email protected]] *On >>>>>>>> Behalf Of *Joshua Weiner >>>>>>>> *Sent:* Monday, December 23, 2013 7:36 PM >>>>>>>> *To:* [email protected] >>>>>>>> *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. < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>> Sorry for the confusion, don’t include the brackets, so it should >>>>>>>> look like this: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=mypassword >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *From:* [email protected] [mailto:[email protected]] *On >>>>>>>> Behalf Of *Joshua Weiner >>>>>>>> *Sent:* Monday, December 23, 2013 7:28 PM >>>>>>>> *To:* [email protected] >>>>>>>> *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 >>>>>>>> >>>>>>>> [email protected] >>>>>>>> >>>>>>>> 201.638.0047 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Joshua S. Weiner >>>>>>>> >>>>>>>> [email protected] >>>>>>>> >>>>>>>> 201.638.0047 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Joshua S. Weiner >>>>>>>> >>>>>>>> [email protected] >>>>>>>> >>>>>>>> 201.638.0047 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Joshua S. Weiner >>>>>>>> >>>>>>>> [email protected] >>>>>>>> >>>>>>>> 201.638.0047 >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Joshua S. Weiner >>>>>>> [email protected] >>>>>>> 201.638.0047 >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Joshua S. Weiner >>>>> [email protected] >>>>> 201.638.0047 >>>>> >>>> >>>> >>> >>> >>> -- >>> Joshua S. Weiner >>> [email protected] >>> 201.638.0047 >>> >> >>
