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
