Hmm looks like there actually might be a typo in the descriptor -- it had to be modified to set for UMLS. Check the aggregate processor xml file for the typo
-- 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 10:28 PM, Pei Chen <[email protected]> wrote: > not sure if it's a email copy and paste error or is it just a typo: > DcitionaryLookupAnnotatorUMLS.xml > instead ??? DictionaryLookupAnnotatorUMLS.xml ??? > Would you be able to go to View > Log > there's usually a bit more info in > the ~/uima.log file. > > > On Mon, Dec 23, 2013 at 11:21 PM, Joshua Weiner > <[email protected]>wrote: > >> 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 >> > >
