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 >
