Hi Pei, Could you help me some information to set up the absolute paths for all file references? For example, I am using Analysis Engine "SimulatedProdSmokingTAE_CDA.xml" from "runctakesCVD.sh"
Thanks, Justin On Tue, Jun 23, 2015 at 8:56 AM, Chen, Pei <[email protected]> wrote: > Justin, > > There’s an outstanding Jira item to update the smoking status config[1]. > > In the interim, you may have to use absolute paths for all of the file > references in the smoking status descriptor xml’s. > > > > --Pei > > > > [1] https://issues.apache.org/jira/browse/CTAKES-363 > > > > *From:* Justin Zhang [mailto:[email protected]] > *Sent:* Monday, June 22, 2015 3:12 PM > *To:* [email protected] > *Subject:* smoking status - ctakes-3.2.2 error > > > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.i2b2.org_NLP_DataSets_Download.php&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=eX43uMBIHoGxaLgv5sccMzG8lXanT7JVR2habAts79E&s=bKfvQqf4kjYnVZAKI06ZZZQuitijyp0h4Rkonue52ic&e=> > > > > > 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.<init>(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 > -- Justin
