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 <[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 >
