Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 81A8010443 for ; Tue, 24 Dec 2013 14:51:51 +0000 (UTC) Received: (qmail 26138 invoked by uid 500); 24 Dec 2013 14:51:35 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 26083 invoked by uid 500); 24 Dec 2013 14:51:31 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 26068 invoked by uid 99); 24 Dec 2013 14:51:28 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 24 Dec 2013 14:51:28 +0000 X-ASF-Spam-Status: No, hits=1.7 required=5.0 tests=FREEMAIL_ENVFROM_END_DIGIT,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of joshuaweiner89@gmail.com designates 209.85.212.47 as permitted sender) Received: from [209.85.212.47] (HELO mail-vb0-f47.google.com) (209.85.212.47) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 24 Dec 2013 14:51:22 +0000 Received: by mail-vb0-f47.google.com with SMTP id q12so3484792vbe.34 for ; Tue, 24 Dec 2013 06:51:01 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:sender:in-reply-to:references:from:date:message-id :subject:to:content-type; bh=MU/PrAoqZi2AGeFGG4p8qG3sgwLcoAFF0uiE1W+osy8=; b=N/8LWxdkUDH2O8mWPPQr06GA1eCz0gNlE+1gBVyjiNlSz1lyzj9RgfkfH825rUth+W FYXiG7XolcHOJgOwtkUVE2KbsL+fDWBjuwWknAh+OMA5vM7wt6Pyn6k/NDVNEXwhDMM9 553Lb+fBpRGgEcZs14/PaQ3UBiKz4/4n4FGVRNoT7Z1TfY2KHrL1o6TKbv/9BX102Cyt cqUfbJ5d416dK483MyqOYJoKOjijl0IR45vGi9OUQMY0Bw8BWzj0uSRTR8qSncmPL87T 438eWv0RumV5gTRqU92AQoYJyBxrggIaRT4b74cROTRdQTYvOMMu32Nl0p/Dn3EbjfkF mk9Q== X-Received: by 10.58.23.33 with SMTP id j1mr1085118vef.27.1387896661167; Tue, 24 Dec 2013 06:51:01 -0800 (PST) MIME-Version: 1.0 Sender: joshuaweiner89@gmail.com Received: by 10.58.214.195 with HTTP; Tue, 24 Dec 2013 06:50:30 -0800 (PST) In-Reply-To: <924DE05C19409B438EB81DE683A942D910639D7A@CHEXMBX1A.CHBOSTON.ORG> References: <996FC801C05DF64A84246A106FACACD0219E61@MSGPEXCHA08A.mfad.mfroot.org> <996FC801C05DF64A84246A106FACACD0219E94@MSGPEXCHA08A.mfad.mfroot.org> <996FC801C05DF64A84246A106FACACD0219EC1@MSGPEXCHA08A.mfad.mfroot.org> <996FC801C05DF64A84246A106FACACD0219EE4@MSGPEXCHA08A.mfad.mfroot.org> <924DE05C19409B438EB81DE683A942D910639D7A@CHEXMBX1A.CHBOSTON.ORG> From: Joshua Weiner Date: Tue, 24 Dec 2013 09:50:30 -0500 X-Google-Sender-Auth: siDYtu7nO7SvhPvkH7h1AoSS348 Message-ID: Subject: Re: Adding UMLS username and password .... To: user@ctakes.apache.org Content-Type: multipart/alternative; boundary=047d7b339df97955de04ee48dfa8 X-Virus-Checked: Checked by ClamAV on apache.org --047d7b339df97955de04ee48dfa8 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Thank you so much . Looks like i am all set now... Damn Kaspersky was unhappy with me trying to help the world. Happy Holidays everyone! Josh On Tue, Dec 24, 2013 at 9:35 AM, Chen, Pei wrote: > Joshua, > > By any chance, are you behind a firewall or proxy server? > > > > This annotator essentially tries to connect to the UMLS web service[1] to > validate your credentials/license=85 > > > > [1] https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser > > > > --Pei > > > > *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On > Behalf Of *Joshua Weiner > *Sent:* Tuesday, December 24, 2013 9:30 AM > > *To:* user@ctakes.apache.org > *Subject:* Re: Adding UMLS username and password .... > > > > Here is what the log file says... hopefully this drives to the answer.. > > > > 12/24/13 9:26:58 AM - 14: > org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: > 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/DictionaryLookupAnnotatorUMLS.xml) > > 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/DictionaryLookupAnnotatorUMLS.xml) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initial= izeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initial= ize(PrimitiveAnalysisEngine_impl.java:156) > > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisE= ngineFactory_impl.java:94) > > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compos= iteResourceFactory_impl.java:62) > > at > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:38= 7) > > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254= ) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB= (AggregateAnalysisEngine_impl.java:431) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initial= izeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initial= ize(AggregateAnalysisEngine_impl.java:185) > > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisE= ngineFactory_impl.java:94) > > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compos= iteResourceFactory_impl.java:62) > > at > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:35= 4) > > at > org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) > > at > org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477) > > at > org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerform= ed(AnnotatorOpenEventHandler.java:52) > > at javax.swing.AbstractButton.fireActionPerformed(Unknown Sourc= e) > > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown > Source) > > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown > Source) > > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > > at javax.swing.AbstractButton.doClick(Unknown Source) > > at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Sourc= e) > > at > javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Sour= ce) > > at java.awt.Component.processMouseEvent(Unknown Source) > > at javax.swing.JComponent.processMouseEvent(Unknown Source) > > at java.awt.Component.processEvent(Unknown Source) > > at java.awt.Container.processEvent(Unknown Source) > > at java.awt.Component.dispatchEventImpl(Unknown Source) > > at java.awt.Container.dispatchEventImpl(Unknown Source) > > at java.awt.Component.dispatchEvent(Unknown Source) > > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown > Source) > > at java.awt.LightweightDispatcher.processMouseEvent(Unknown > Source) > > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > > at java.awt.Container.dispatchEventImpl(Unknown Source) > > at java.awt.Window.dispatchEventImpl(Unknown Source) > > at java.awt.Component.dispatchEvent(Unknown Source) > > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > > at java.awt.EventQueue.access$200(Unknown Source) > > at java.awt.EventQueue$3.run(Unknown Source) > > at java.awt.EventQueue$3.run(Unknown Source) > > at java.security.AccessController.doPrivileged(Native Method) > > at > java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > > at > java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > > at java.awt.EventQueue$4.run(Unknown Source) > > at java.awt.EventQueue$4.run(Unknown Source) > > at java.security.AccessController.doPrivileged(Native Method) > > at > java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) > > at java.awt.EventQueue.dispatchEvent(Unknown Source) > > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown > Source) > > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown > Source) > > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown > Source) > > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > > at java.awt.EventDispatchThread.run(Unknown Source) > > Caused by: org.apache.uima.resource.ResourceInitializationException > > at > org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.init= ialize(UmlsDictionaryLookupAnnotator.java:79) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initial= izeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) > > ... 54 more > > Caused by: java.net.ConnectException: connect: Address is invalid on loca= l > machine, or port is not valid on remote machine > > at java.net.DualStackPlainSocketImpl.connect0(Native Method) > > at java.net.DualStackPlainSocketImpl.socketConnect(Unknown > Source) > > at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) > > at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown > Source) > > at java.net.AbstractPlainSocketImpl.connect(Unknown Source) > > at java.net.PlainSocketImpl.connect(Unknown Source) > > at java.net.SocksSocketImpl.connect(Unknown Source) > > at java.net.Socket.connect(Unknown Source) > > at sun.security.ssl.SSLSocketImpl.connect(Unknown Source) > > at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source) > > at sun.net.NetworkClient.doConnect(Unknown Source) > > at sun.net.www.http.HttpClient.openServer(Unknown Source) > > at sun.net.www.http.HttpClient.openServer(Unknown Source) > > at sun.net.www.protocol.https.HttpsClient.(Unknown Source= ) > > at sun.net.www.protocol.https.HttpsClient.New(Unknown Source) > > at > sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpC= lient(Unknown > Source) > > at > sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) > > at > sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unk= nown > Source) > > at > sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Sourc= e) > > at > sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown > Source) > > at > org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isVa= lidUMLSUser(UmlsDictionaryLookupAnnotator.java:93) > > at > org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.init= ialize(UmlsDictionaryLookupAnnotator.java:70) > > ... 55 more > > > > > > On Tue, Dec 24, 2013 at 12:22 AM, Karthik Sarma wrote= : > > 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 fo= r > 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 > ksarma@ksarma.com > gchat: ksarma@gmail.com > > linkedin: www.linkedin.com/in/ksarma > > > > On Mon, Dec 23, 2013 at 10:28 PM, Pei Chen 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 i= n > the ~/uima.log file. > > > > On Mon, Dec 23, 2013 at 11:21 PM, Joshua Weiner > 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 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 > 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 > 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" 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 > ksarma@ksarma.com > gchat: ksarma@gmail.com > > linkedin: www.linkedin.com/in/ksarma > > > > On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner > 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=3Djoshuawiener2 > -Dctakes.umlspw=3DmypasswordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apache-c= takes-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 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 > ksarma@ksarma.com > gchat: ksarma@gmail.com > > linkedin: www.linkedin.com/in/ksarma > > > > On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner > 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=3D%cd% > > if not "%CTAKES_HOME%" =3D=3D "" goto gotHome > > set CTAKES_HOME=3D%CURRENT_DIR% > > if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome > > cd .. > > set CTAKES_HOME=3D%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=3Djoshuawiener2 -Dctakes.umlspw=3D56Kmartin% -cp > "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" > -Dlog4j.configuration=3Dfile:/%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 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 > ksarma@ksarma.com > gchat: ksarma@gmail.com > > linkedin: www.linkedin.com/in/ksarma > > > > On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner > 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=3Djoshuawiener2 -Dctakes.umlspw=3Dmypassword -cp > "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" > -Dlog4j.configuration=3Dfile:/%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. > wrote: > > I see now that the java command in your previous post didn=92t include th= e > -cp parameter and its arguments. > > Please add that back in. > > > > > > *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On > Behalf Of *Joshua Weiner > *Sent:* Monday, December 23, 2013 8:12 PM > > > *To:* user@ctakes.apache.org > *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. > wrote: > > Try this > > CD C:\apache-ctakes-3.1.0 > > set CTAKES_HOME=3DC:\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=3D"" > > > > > > *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On > Behalf Of *Joshua Weiner > *Sent:* Monday, December 23, 2013 7:55 PM > > > *To:* user@ctakes.apache.org > *Subject:* Re: Adding UMLS username and password .... > > > > James, > > > Thank you for your continual prompt responses. Unfortunately, even after = I > did set%CTAKES_HOME%=3D"" I still get the following errror: > > > > C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=3Djoshuawiener2 > =3DDCtakes.umlspw=3DmypasswwordCTAKES_HOMECTAKES_HOMECTAKES_HOME/C:\apach= e-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=3Djoshuawiener2 -Dctakes.umlspw=3Dpasswordd -cp > "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" > -Dlog4j.configuration=3Dfile:/%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. > 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 enterin= g > the following on the command line and then trying the bat file again. > > set %CTAKES_HOME%=3D"" > > > > Oh, and you=92ll probably want to change -Xmx1024M to be =96Xmx2048M or > even larger or you will run into a heap space error for many parts of > cTAKES. > > > > -- James > > > > > > *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On > Behalf Of *Joshua Weiner > *Sent:* Monday, December 23, 2013 7:36 PM > *To:* user@ctakes.apache.org > *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. > wrote: > > Sorry for the confusion, don=92t include the brackets, so it should look > like this: > > > > -Dctakes.umlsuser=3Djoshuawiener2 -Dctakes.umlspw=3Dmypassword > > > > *From:* joshuaweiner89@gmail.com [mailto:joshuaweiner89@gmail.com] *On > Behalf Of *Joshua Weiner > *Sent:* Monday, December 23, 2013 7:28 PM > *To:* user@ctakes.apache.org > *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 m= y > username is joshuaweiner2 and my password (for this example) is mypasswor= dd > (see below).... I now can't get the CVD to run. > > > Thank you for your help... > > > > :okHome > > cd %CTAKES_HOME% > > java -Dctakes.umlsuser=3D -Dctakes.umlspw=3D = -cp > "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" > -Dlog4j.configuration=3Dfile:/%CTAKES_HOME%/config/log4j.xml -Xms512M > -Xmx1024M org.apache.uima.tools.cvd.CVD > > > > :end > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > > > > > > > > > > -- > Joshua S. Weiner > > joshuaweiner2@gmail.com > > 201.638.0047 > --=20 Joshua S. Weiner joshuaweiner2@gmail.com 201.638.0047 --047d7b339df97955de04ee48dfa8 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Thank you so much . Looks like i am all set now... Damn Ka= spersky was unhappy with me trying to help the world.

Ha= ppy Holidays everyone!

Josh

On Tue, Dec 24, 2013 at 9:35 AM, Chen, Pei <= span dir=3D"ltr"><Pei.Chen@childrens.harvard.edu> wrote:

Joshua,

By any chance, are you be= hind a firewall or proxy server?

=A0<= /p>

This annotator essentiall= y tries to connect to the UMLS web service[1] to validate your credentials/= license=85

=A0<= /p> 

[1] https://uts-ws=
.nlm.nih.gov/restful/isValidUMLSUser
=A0

--Pei

=A0<= /p>

From: joshuaweiner89@gmail= .com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Tuesday, December 24, 2013 9:30 AM


To: user= @ctakes.apache.org
Subject: Re: Adding UMLS username and password ....

=A0

Here is what the log file says... hopefully this dri= ves to the answer..

=A0

12/24/13 9:26:58 AM - 14: org.apache.uima.tools.cvd.= MainFrame.handleException(527): SEVERE: Initialization of annotator class &= quot;org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator&q= uot; failed. =A0(Descriptor: file:/C:/apache-ctakes-3.1.0/desc/ctakes-dicti= onary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)=

org.apache.uima.resource.ResourceInitializationExcep= tion: Initialization of annotator class "org.apache.ctakes.dictionary.= lookup.ae.UmlsDictionaryLookupAnnotator" failed. =A0(Descriptor: file:= /C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/= DictionaryLookupAnnotatorUMLS.xml)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(Pr= imitiveAnalysisEngine_impl.java:252)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEn= gine_impl.java:156)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.impl.= AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:= 94)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.impl.= CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl= .java:62)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.UIMAF= ramework.produceResource(UIMAFramework.java:269)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.UIMAF= ramework.produceAnalysisEngine(UIMAFramework.java:387)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngin= e_impl.java:431)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEng= ine(AggregateAnalysisEngine_impl.java:375)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEn= gine_impl.java:185)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.impl.= AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:= 94)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.impl.= CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl= .java:62)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.UIMAF= ramework.produceResource(UIMAFramework.java:269)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.UIMAF= ramework.produceAnalysisEngine(UIMAFramework.java:354)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.tools= .cvd.MainFrame.setupAE(MainFrame.java:1484)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.tools= .cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.tools= .cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHa= ndler.java:52)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.AbstractB= utton.fireActionPerformed(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.AbstractB= utton$Handler.actionPerformed(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.DefaultBu= ttonModel.fireActionPerformed(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.DefaultBu= ttonModel.setPressed(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.AbstractB= utton.doClick(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.plaf.basi= c.BasicMenuItemUI.doClick(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.plaf.basi= c.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Component.pr= ocessMouseEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at javax.swing.JComponen= t.processMouseEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Component.pr= ocessEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Container.pr= ocessEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Component.di= spatchEventImpl(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Container.di= spatchEventImpl(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Component.di= spatchEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.LightweightD= ispatcher.retargetMouseEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.LightweightD= ispatcher.processMouseEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.LightweightD= ispatcher.dispatchEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Container.di= spatchEventImpl(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Window.dispa= tchEventImpl(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.Component.di= spatchEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue.d= ispatchEventImpl(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue.a= ccess$200(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue$3= .run(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue$3= .run(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.security.AccessC= ontroller.doPrivileged(Native Method)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.security.Protect= ionDomain$1.doIntersectionPrivilege(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.security.Protect= ionDomain$1.doIntersectionPrivilege(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue$4= .run(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue$4= .run(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.security.AccessC= ontroller.doPrivileged(Native Method)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.security.Protect= ionDomain$1.doIntersectionPrivilege(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventQueue.d= ispatchEvent(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.pumpOneEventForFilters(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.pumpEventsForFilter(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.pumpEventsForHierarchy(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.pumpEvents(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.pumpEvents(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.awt.EventDispatc= hThread.run(Unknown Source)

Caused by: org.apache.uima.resource.ResourceInitiali= zationException

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.ctakes.dic= tionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLo= okupAnnotator.java:79)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.uima.analy= sis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(Pr= imitiveAnalysisEngine_impl.java:250)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 ... 54 more

Caused by: java.net.ConnectException: connect: Addre= ss is invalid on local machine, or port is not valid on remote machine

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.DualStackPla= inSocketImpl.connect0(Native Method)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.DualStackPla= inSocketImpl.socketConnect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.AbstractPlai= nSocketImpl.doConnect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.AbstractPlai= nSocketImpl.connectToAddress(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.AbstractPlai= nSocketImpl.connect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.PlainSocketI= mpl.connect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.SocksSocketI= mpl.connect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at java.net.Socket.conne= ct(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.security.ssl.SSLS= ocketImpl.connect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.security.ssl.Base= SSLSocketImpl.connect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.NetworkClient= .doConnect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.http.Http= Client.openServer(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.http.Http= Client.openServer(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= https.HttpsClient.<init>(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= https.HttpsClient.New(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= http.HttpURLConnection.plainConnect(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)<= /u>

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= http.HttpURLConnection.getOutputStream(Unknown Source)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at sun.net.www.protocol.= https.HttpsURLConnectionImpl.getOutputStream(Unknown Source)<= /p>

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.ctakes.dic= tionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDiction= aryLookupAnnotator.java:93)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 at org.apache.ctakes.dic= tionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLo= okupAnnotator.java:70)

=A0=A0=A0=A0=A0=A0=A0=A0=A0 ... 55 more

=A0

=A0

On Tue, Dec 24, 2013 at 12:22 AM, Karthik Sarma <= ksarma@ksarma.com> wrote:

Hmm looks like there actually might be a typo in the= descriptor -- it had to be modified to set for UMLS. Check the aggregate p= rocessor xml file for the typo

On Mon, Dec 23, 2013 at 10:28 PM, Pei Chen <chenpei@apache.org&g= t; wrote:

not sure if it's a email copy and paste error or= is it just a typo:

DcitionaryLookupAnnotatorUMLS.xml<= /u>

instead ???=A0DictionaryLookupAnnotatorUMLS.= xml =A0???

Would you be able to go to View > Log >= ; there's usually a bit more info in the ~/uima.log file.=

=A0

On Mon, Dec 23, 2013 at 11:21 PM, Joshua Weiner <= joshuaweiner2@= gmail.com> wrote:

I changed my password so it no loner has a %... and = I also set the password in the dictionarylookupannotatorUMLS.xml file as yo= u described...


I still get the same error...

org.apache.uima.resource.ResourceInitializat= ionException: Initialization of annotator class "org.apache.ctakes.dic= tionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/de= sc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml) ...=

=A0

What is going on???

=A0

On Mon, Dec 23, 2013 at 10:49 PM, Pei Chen <chenpei@apache.org&g= t; wrote:

Hi Joshua,

I just noticed that you figured out the escaping iss= ue. =A0But 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.)=A0=

If you want to bypass the entire escaping the enviro= nment var issue, you can also set the umls credentials within the xml file = itself:

Which should be inside your:=A0

C:/apache-ctakes-3.1.0/desc/ctakes-dictionar= y-lookup/desc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml

=A0

On Mon, Dec 23, 2013 at 10:26 PM, Joshua Weiner <= joshuaweiner2@= gmail.com> wrote:

Gah .. I am not sure why this is so challenging... N= ow I try to run;=A0AggregatePlaintextUMLSProcessor.xml

=A0

and I get the error:

org.apache.uima.resource.ResourceInitializat= ionException: Initialization of annotator class "org.apache.ctakes.dic= tionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/C:/apache-ctakes-3.1.0/desc/ctakes-dictionary-lookup/de= sc/analysis_engine/DcitionaryLookupAnnotatorUMLS.xml) ...<= /u>

=A0

hopefully this is my last problem!! Thank yo= u for your help.!!!!!!!!!!!

=A0

Josh

=A0

On Mon, Dec 23, 2013 at 10:21 PM, Joshua Weiner <= joshuaweiner2@= gmail.com> wrote:

Smart man karthik. I do have a percent sign in my password. Thank you fo= r your help here, both of you.

Works now! Great tip.

On Dec 23, 2013 7:11 PM, "Karthik Sarma" &= lt;ksarma@ksarma.com= > wrote:

Ah, I think I might know the problem. You probably h= ave a percent sign in your password. If so, you should replace it with a do= uble 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 Ass= ociation
ksarma@ksarma.com
gchat: ksarma@gmail.c= om

=A0

On Mon, Dec 23, 2013 at 9:05 PM, Joshua Weiner <<= a href=3D"mailto:joshuaweiner2@gmail.com" target=3D"_blank">joshuaweiner2@g= mail.com> wrote:

when I run the script I get the following error: ((s= ee below the=A0

=A0

=A0

I run: bin\runctakesCVD.bat

I get:

=A0

C:\apache-ctakes-3.1.00>java -Dctakes.umlsuser=3D= joshuawiener2 -Dctakes.umlspw=3DmypasswordCTAKES_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

=A0

=A0

On Mon, Dec 23, 2013 at 10:02 PM, Karthik Sarma <= ksarma@ksarma.com> wrote:

OK, and what is the output when you run the script?<= u>

On Mon, Dec 23, 2013 at 8:59 PM, Joshua Weiner <<= a href=3D"mailto:joshuaweiner2@gmail.com" target=3D"_blank">joshuaweiner2@g= mail.com> 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..............<= u>

=A0

I also tried using James code to re-set the director= y .. did not work.

=A0

@REM Guess CTAKES_HOME if not defined<= /p>

set CURRENT_DIR=3D%cd%

if not "%CTAKES_HOME%" =3D=3D ""= goto gotHome

set CTAKES_HOME=3D%CURRENT_DIR%

if exist "%CTAKES_HOME%\bin\runctakesCVD.bat&qu= ot; goto okHome

cd ..

set CTAKES_HOME=3D%cd%

=A0

:gotHome

if exist "%CTAKES_HOME%\bin\runctakesCVD.bat&qu= ot; goto okHome

echo The CTAKES_HOME environment variable is not def= ined correctly

echo This environment variable is needed to run this= program

goto end

=A0

:okHome

cd %CTAKES_HOME%

java -Dctakes.umlsuser=3Djoshuawiener2 -Dctakes.umls= pw=3D56Kmartin% -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_H= OME%/resources/" -Dlog4j.configuration=3Dfile:/%CTAKES_HOME%/config/lo= g4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

=A0

:end

=A0

On Mon, Dec 23, 2013 at 9:55 PM, Karthik Sarma <<= a href=3D"mailto:ksarma@ksarma.com" target=3D"_blank">ksarma@ksarma.com= > 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 Ass= ociation
ksarma@ksarma.com
gchat: ksarma@gmail.c= om

=A0

On Mon, Dec 23, 2013 at 8:50 PM, Joshua Weiner <<= a href=3D"mailto:joshuaweiner2@gmail.com" target=3D"_blank">joshuaweiner2@g= mail.com> wrote:

Where do you see this James?

=A0

Here is my code... I see the -cp parameter and its a= rguements right after "mypassword" ... right?

=A0

:okHome

cd %CTAKES_HOME%

java -Dctakes.umlsuser=3Djoshuawiener2 -Dctakes.umls= pw=3Dmypassword -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_H= OME%/resources/" -Dlog4j.configuration=3Dfile:/%CTAKES_HOME%/config/lo= g4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

=A0

:end

=A0

On Mon, Dec 23, 2013 at 9:44 PM, Masanz, James J. &l= t;Masanz.James@m= ayo.edu> wrote:

I see now that the java c= ommand in your previous post didn=92t include the -cp parameter and its arg= uments.

Please add that back in.<= /span>

=A0<= /p>

=A0<= /p>

From: joshuaweiner8= 9@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 8:12 PM


To: user= @ctakes.apache.org
Subject: Re: Adding UMLS username and password ....

=A0

James,

=A0

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.=A0

=A0

Thank you for your persistence.


Josh

=A0

On Mon, Dec 23, 2013 at 9:07 PM, Masanz, James J. &l= t;Masanz.James@m= ayo.edu> wrote:

Try this=

CD=A0 C:\apache-ctakes-3.= 1.0

set CTAKES_HOME=3DC:\apac= he-ctakes-3.1.0

then enter the java comma= nd from the command line that you were entering

=A0<= /p>

Note: in my previous post= , it was my mistake of including the percent signs in the SET command.

=A0<= /p>

I meant to suggest=

set CTAKES_HOME=3D""

=A0<= /p>

=A0<= /p>

From: joshuaweiner8= 9@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:55 PM


To: user= @ctakes.apache.org
Subject: Re: Adding UMLS username and password ....

=A0

James,


Thank you for your continual prompt responses. Unfortunately, even after I = did set%CTAKES_HOME%=3D"" I still get the following errror:

=A0

C:\apache-ctakes-3.1.0>java -Dctakes.umlsuser=3Dj= oshuawiener2 =3DDCtakes.umlspw=3DmypasswwordCTAKES_HOMECTAKES_HOMECTAKES_HO= ME/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

=A0

once again my code in the runctakesCVD.bat file is:<= u>

=A0

=A0

:okHome

cd %CTAKES_HOME%

java -Dctakes.umlsuser=3Djoshuawiener2 -Dctakes.umls= pw=3Dpasswordd -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HO= ME%/resources/" -Dlog4j.configuration=3Dfile:/%CTAKES_HOME%/config/log= 4j.xml -Xms512M -Xmx2048M org.apache.uima.tools.cvd.CVD

=A0

:end

=A0

On Mon, Dec 23, 2013 at 8:45 PM, Masanz, James J. &l= t;Masanz.James@m= ayo.edu> wrote:

=A0<= /p>

You might try from the co= mmand line

=A0<= /p>

echo=A0 %CTAKES_HOME%

=A0<= /p>

or even better for debug = purposes put it just before the =A0CD %CTAKES_HOME% =A0line.

=A0<= /p>

It should respond with th= e parent of the bin, desc, and resources directory.

=A0<= /p>

If it responds with somet= hing else, try clearing %CTAKES_HOME% by entering the following on the comm= and line and then trying the bat file again.

set %CTAKES_HOME%=3D""=

=A0<= /p>

Oh, and you=92ll probably= want to change -Xmx1024M=A0 to be =A0=96Xmx2048M or even larger or you will run into a heap space error for many parts of cT= AKES.

=A0<= /p>

-- James=

=A0

=A0<= /p>

From: joshuaweiner8= 9@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:36 PM
To: user= @ctakes.apache.org
Subject: Re: Adding UMLS username and password ....=

=A0

James,


Thanks so much for your response. When I remove the brackets I still get an= error, I get:

=A0

"Error: could not find or load main class org.a= pache.uima.tools.cvd.CVD

=A0

=A0

Thank you so much for your help. I appreciate your d= illigence.


Sincerely,

Josh

=A0

On Mon, Dec 23, 2013 at 8:32 PM, Masanz, James J. &l= t;Masanz.James@m= ayo.edu> wrote:

Sorry for the confusion, = don=92t include the brackets, so it should look like this:=

=A0<= /p>

-Dctakes.umlsuser=3Djoshuawiener2 =A0-Dctakes.umlspw= =3Dmypassword

=A0<= /p>

From: joshuaweiner8= 9@gmail.com [mailto:joshuaweiner89@gmail.com] On Behalf Of Joshua Weiner
Sent: Monday, December 23, 2013 7:28 PM
To: user= @ctakes.apache.org
Subject: Adding UMLS username and password ....=

=A0

=A0

Hey guys,

=A0

I know this is probably a dumb question but I can= 9;t for the life of me figure it out. I finally got a UMLS username and pas= sword, 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 t= o run.=A0


Thank you for your help...=A0

=A0

:okHome

cd %CTAKES_HOME%

java -Dctakes.umlsuser=3D<joshuawiener2> -Dcta= kes.umlspw=3D<mypasswordd> -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME= %/desc/;%CTAKES_HOME%/resources/" -Dlog4j.configuration=3Dfile:/%CTAKE= S_HOME%/config/log4j.xml -Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD

=A0

:end=A0


=A0

--
Joshua S. Weiner



=A0

--
Joshua S. Weiner



=A0

--
Joshua S. Weiner



=A0

--
Joshua S. Weiner



=A0

--
Joshua S. Weiner

=A0



=A0

--
Joshua S. Weiner

=A0



=A0

--
Joshua S. Weiner

=A0



=A0

--
Joshua S. Weiner

=A0



=A0

--
Joshua S. Weiner

=A0

=A0



=A0

--
Joshua S. Weiner




--
Joshua S. We= iner
201.638.0047
--047d7b339df97955de04ee48dfa8--