Hi,
I'm hoping for some more insights into using the side effect annotator.
As per Pie Chen's suggestion I've added the side effect annotator to the
default AggregatePlaintextFastUMLSProcessor. The xml changes are shown
below.
Initially I was getting 'URI is not hierarchical' errors. After some
searching I thought this might be due to a missing dictionary file and
added sideEffect_dictionary.txt at
'apache-ctakes-3.2.2\resources\org\apache\ctakes\sideeffect\lookup'.
This stopped the URI errors. I put some dummy content in the dictionary
(shown below; using the full content from here didn't help either -
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt).
Now as per the log files, I'm getting null pointer exceptions within
sideEffectAnnotator.java - at 2 different locations as shown below.
Getting an exception is dependent on the text analysed:
'Seen today. On tamoxifen 20 mg daily which caused headaches.' causes an
exception.
'Seen today. On tamoxifen 20 mg daily which caused something.' does not
(of course there is no clinical finding in the second text).
Given that others are using the side effect annotator, I'm guessing this
is some kind of issue with my configuration/dictionary and would
appreciate any advice.
I'm running the latest version of cTakes 'as is'.
Thanks in advance.
Graham Pitson
-----------------------------AggregatePlaintextFastUMLSProcessor.xml---------------------------------------------
<delegateAnalysisEngine key="SideEffectAnnotator">
<import location="SideEffectAnnotator.xml"/>
</delegateAnalysisEngine>
<node>ConstituencyParser</node>
<node>SideEffectAnnotator</node>
<!-- <node>AssertionAnnotator</node> -->
<!-- <node>StatusAnnotator</node> -->
<!-- <node>NegationAnnotator</node> -->
<node>GenericCleartkAnalysisEngine</node>
-------------------------test text-------------------------------
'Seen today. On tamoxifen 20 mg daily which caused headaches.'
-------------------------------------------error logs (2 different
exception
locations)-----------------------------------------------------------
17/12/15 6:21:24 AM - 14:
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Annotator processing failed.
org.apache.uima.analysis_engine.AnalysisEngineProcessException:
Annotator processing failed.
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
at
org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526)
at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:429)
at
org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
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: java.lang.NullPointerException
at
org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.isInAllergySection(SideEffectAnnotator.java:759)
at
org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.getSideEffectsWithPrioritizedRule(SideEffectAnnotator.java:342)
at
org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.process(SideEffectAnnotator.java:180)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
... 47 more
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.lang.NullPointerException
at
org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.getPotentialSideEffects(SideEffectAnnotator.java:296)
at
org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.process(SideEffectAnnotator.java:177)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
... 47 more
--------------------------------------------dummy
dictionary----------------------------------------------------
//FORMAT: generic drug|brand drug|side effect1, side effect2,...
Tamoxifen|Nolvadex,Tam|Hot flushes, nausea, endometrial cancer
