ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Matt Work Coarr <mattcoarr.w...@gmail.com>
Subject drug ner in ctakes 3.2.1
Date Tue, 16 Dec 2014 16:04:54 GMT
I'm getting an error when I try to load the Drug NER pipeline in the ctakes
3.2.1 CVD.

I received a similar error in ctakes 3.2.0 for the clinical pipeline, but
the clinical pipeline is working for me now in 3.2.1. :-)

Is Drug NER supported in 3.2.1 and can it use the new fast dictionary
lookup?  Or is there more work required there?

FYI...

I'm loading
desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml

Here's the error message:

java.lang.IllegalArgumentException: URI is not hierarchical
More detailed information is in the log file.


Here's the stack trace:

12/15/14 4:57:45 PM - 15:
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.produceAnalysisEngine(UIMAFramework.java:354)

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

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:3321)

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:2739)

at java.awt.Component.dispatchEvent(Component.java:4703)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746)

at java.awt.EventQueue.access$400(EventQueue.java:97)

at java.awt.EventQueue$3.run(EventQueue.java:697)

at java.awt.EventQueue$3.run(EventQueue.java:691)

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:719)

at java.awt.EventQueue$4.run(EventQueue.java:717)

at java.security.AccessController.doPrivileged(Native Method)

at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:716)

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)



Matt

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message