I changed my password so it no loner has a %... and I also set the password in the dictionarylookupannotatorUMLS.xml file as you described...
I still get the same 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) ... What is going on??? On Mon, Dec 23, 2013 at 10:49 PM, Pei Chen <[email protected]> wrote: > 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 > <[email protected]>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 >> <[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 >>>>> >>>> >>>> >> >> >> -- >> Joshua S. Weiner >> [email protected] >> 201.638.0047 >> > > -- Joshua S. Weiner [email protected] 201.638.0047
