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 71BF0181B5 for ; Mon, 22 Jun 2015 19:12:10 +0000 (UTC) Received: (qmail 45228 invoked by uid 500); 22 Jun 2015 19:12:10 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 45191 invoked by uid 500); 22 Jun 2015 19:12:10 -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 45180 invoked by uid 99); 22 Jun 2015 19:12:10 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 22 Jun 2015 19:12:10 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of justinzhang.xl@gmail.com designates 209.85.213.176 as permitted sender) Received: from [209.85.213.176] (HELO mail-ig0-f176.google.com) (209.85.213.176) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 22 Jun 2015 19:09:54 +0000 Received: by igin14 with SMTP id n14so23277877igi.1 for ; Mon, 22 Jun 2015 12:11:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=2Dkols4ZFxCsBZAiDcUAtBARE9UOWp1KW2UyoFePn/U=; b=XE3SgjHWSK9b8EiAK/25RqNII10VrqqESTUL3xPHRUQeK09QUCMBPgYJwzzqPf9TVi mHfAZPrxXBNLcU3xms3mamrpnjXT6hLkRIONdh1n6CYDRowRySp1tflxtUrv9I9GOwJQ mY8rIV4eOv/fIGOKcz3jCX3UN5UG3treWw/6IgTRx0F187CwLdWvzL1qw0E3bPwtaMXb E2D9CnhHbWhC6QtyccrJdzuwsSz/uTFVzDCRScSeIiwGCq8mNpAa+7IPIY9wML21WHzp wRWGpdf8iuiS0/5RQyYZwaC51lhQ80qSWu259dzqwSEcqEj8X8+iXDMlGV4m2DgfX1jS JNFg== MIME-Version: 1.0 X-Received: by 10.107.37.69 with SMTP id l66mr41243398iol.76.1435000302497; Mon, 22 Jun 2015 12:11:42 -0700 (PDT) Received: by 10.64.149.230 with HTTP; Mon, 22 Jun 2015 12:11:42 -0700 (PDT) Date: Mon, 22 Jun 2015 14:11:42 -0500 Message-ID: Subject: smoking status - ctakes-3.2.2 error From: Justin Zhang To: user@ctakes.apache.org Content-Type: multipart/alternative; boundary=001a1140ea0248761d0519200bc8 X-Virus-Checked: Checked by ClamAV on apache.org --001a1140ea0248761d0519200bc8 Content-Type: text/plain; charset=UTF-8 Hi All, Any one have run "smoking status pipeline" successfully. I am using Mac machine to run ctakes version3.2.2 1. Start from terminal to run $CTAKES_HOME/bin/runctakesCVD.sh cd $CTAKES_HOME java -Dctakes.umlsuser=userid -Dctakes.umlspw=password -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD "$@" 2. Open text file (xml file) I loaded smoking training set (xml format) requested from i2b2 https://www.i2b2.org/NLP/DataSets/Download.php 3. Load AE ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml I got the following error "analysis_engine.SentenceAdjuster" was found in the class path or data path Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "analysis_engine.SentenceAdjuster" was found in the class path or data path. (Descriptor: file:/Users/justin/vdec_work/ctakes/apache-ctakes-3.2.2/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml) at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147) ... 47 more 4. I added class path in runctakesCVD.sh java -Dctakes.umlsuser=userid -Dctakes.umlspw=password -cp $CTAKES_HOME/desc/ctakes-smoking-status/desc/::$CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD "$@" 5. Open same xml file and load the same *CDA.xml annotator engine. "SentenceAdjuster" error gone, but got the other error "URI is not hierarchical" org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: URI is not hierarchical java.lang.IllegalArgumentException: URI is not hierarchical at java.io.File.(File.java:418) at org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) 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.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6525) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6290) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 6. I also tried plained text Annotator "SimulatedProdSmokingTAE.xml", and got the same error. Any one could help! Thanks a lot, -- Justin --001a1140ea0248761d0519200bc8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi All,

Any one have run "smoking = status pipeline" successfully.=C2=A0
I am using Mac machine = to run ctakes version3.2.2

1. Start from terminal = to run $CTAKES_HOME/bin/runctakesCVD.sh
=C2=A0 =C2=A0 =C2=A0=C2= =A0cd $CTAKES_HOME<= /div>

=C2=A0 =C2=A0java = -Dctakes.umlsuser=3Duserid -Dctakes.umlspw=3Dpassword -cp $CTAKES_HOME/desc= /:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=3Dfile:$= CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD = "$@"


2. Open text file (xml file) I loaded= smoking training set (xml format) requested from i2b2 https://www.i2b2.org/NLP/DataSets/Do= wnload.php=C2=A0

3. Load AE ctakes-smoking-sta= tus/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml

=C2=A0 =C2=A0I got the following error=C2=A0"analysis_engine.Se= ntenceAdjuster" was found in the class path or data path
Caused by: org.apache.uima.util.InvalidXMLException: An im= port could not be resolved.=C2=A0 No .xml file with name "analysis_eng= ine.SentenceAdjuster" was found in the class path or data path. (Descr= iptor: file:/Users/justin/vdec_work/ctakes/apache-ctakes-3.2.2/desc/ctakes-= smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml)
<= div> at org.apache.uima.r= esource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at org.apache.uim= a.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalys= isEngineImports(AnalysisEngineDescription_impl.java:798)
at org.apache.uima.analysis_engi= ne.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports= (AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.Analys= isEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngine= Description_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngin= e_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 47 more

=
4. I added class path in runctakesCVD.sh

=C2=A0 =C2=A0 ja= va -Dctakes.umlsuser=3Duserid -Dctakes.umlspw=3Dpassword -cp $CTAKES_HOME/d= esc/ctakes-smoking-status/desc/::$CTAKES_HOM= E/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=3D= file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cv= d.CVD "$@"


5. Open same xml f= ile and load the same *CDA.xml annotator engine.=C2=A0

=
=C2=A0 =C2=A0 "SentenceAdjuster" error gone, but got the oth= er error "URI is not hierarchical"

= org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: URI is no= t hierarchical
java.lang.IllegalArgumentException: URI is not hie= rarchical
at j= ava.io.File.<init>(File.java:418)
at org.apache.ctakes.core.resource.FileResourceIm= pl.load(FileResourceImpl.java:44)
at org.apache.uima.resource.impl.ResourceManager_impl.r= egisterResource(ResourceManager_impl.java:603)
at org.apache.uima.resource.impl.ResourceM= anager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at org.apache.uima= .resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at org.apache.uima.ana= lysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.= java:157)
at o= rg.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize= (PrimitiveAnalysisEngine_impl.java:123)
at org.apache.uima.impl.AnalysisEngineFactory_imp= l.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeRe= sourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.u= ima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramewor= k.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.im= pl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAna= lysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
<= span class=3D"" style=3D"white-space:pre"> at org.apache.uima.analys= is_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngi= ne(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.Aggreg= ateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.ui= ma.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_im= pl.java:94)
at= org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Composi= teResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFram= ework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)<= /div>
at org.apache.= uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
= at org.apache.uima.tools= .cvd.MainFrame.setupAE(MainFrame.java:1486)
at org.apache.uima.tools.cvd.MainFrame.loadAE= Descriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHan= dler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fir= eActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPe= rformed(AbstractButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(D= efaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonMod= el.java:259)
a= t javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.B= asicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at com.apple.laf.AquaMenuItemUI.doClick(= AquaMenuItemUI.java:157)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(= BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6525)
at javax.swing.J= Component.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Comp= onent.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatch= EventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:229= 2)
at java.awt= .Component.dispatchEvent(Component.java:4703)
at java.awt.LightweightDispatcher.retargetM= ouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Contai= ner.java:4533)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
=
at java.awt.Contain= er.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.ja= va:2750)
at ja= va.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEven= tImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue= $3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
<= span class=3D"" style=3D"white-space:pre"> at java.security.AccessCo= ntroller.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPr= ivilege(ProtectionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivi= lege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue= $4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)=
at java.secur= ity.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.Even= tQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventFo= rFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilte= r(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Ev= entDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThrea= d.java:101)
at= java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
=
at java.awt.EventDi= spatchThread.run(EventDispatchThread.java:82)

6. I also tried plained text Annotator "SimulatedProdSmokingTAE.xml&= quot;, and got the same error.

Any one could help!=

Thanks a lot,

--
Justin
--001a1140ea0248761d0519200bc8--