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 >
