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Posted to dev@ctakes.apache.org by shahid ashraf <sh...@trialx.com> on 2017/01/21 12:06:27 UTC
Ctakes Dictionary Gui
Hi I was able to run and produce the new custom umls files. and where put
under ctakes binary (not dev).
I changed the name
under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following
error (not when using old org/apache/ctakes
/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key
Unknown class
org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by:
org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key
Unknown class
org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException:
org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
RE: Ctakes Dictionary Gui
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Shahid,
The error is that java cannot find the class:
org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
I’m not sure why you are seeing that as the class does exist in trunk as it is spelled out. I cannot repeat your error. Are you able to check your repository or .jar to see if that particular class is present?
Sean
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well. Still getting this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com>> wrote:
Hi I was able to run and produce the new custom umls files. and where put under ctakes binary (not dev).
I changed the name under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following error (not when using old org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Sean
I was able to serialize cas to json . the issue was with old uima libraries
were used.
On Thu, Jan 26, 2017 at 1:05 AM, shahid ashraf <sh...@trialx.com> wrote:
> Question 3 was in the Context to below MRCONSO query.
> grep -m 100 'everolimus 2.5 MG' MRCONSO.RRF
> C2920402|ENG|P|L9444011|PF|S11732016|Y|A18087431|3277625|
> 998188||RXNORM|SCDC|998188|everolimus 2.5 MG|0|N|4352|
> C2920403|ENG|P|L9440907|PF|S11732014|N|A24007275|6361783|
> 998189||RXNORM|PSN|998189|everolimus 2.5 MG Oral Tablet|0|N|4352|
> C2920403|ENG|P|L9440907|PF|S11732014|Y|A18086252|3277626|
> 998189||RXNORM|SCD|998189|everolimus 2.5 MG Oral Tablet|0|N|4352|
> C2920404|ENG|P|L9444010|PF|S11732015|Y|A18089772|3277627|
> 998190||RXNORM|SBDC|998190|everolimus 2.5 MG [Afinitor]|0|N|4096|
> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|
> 998191||RXNORM|SBD|998191|everolimus 2.5 MG Oral Tablet
> [Afinitor]|0|N|4352|
> in above we see all these in RXNORM not in fast dictionary.
>
> Is that Dictionary -Gui filter based on *Term Types* --
> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/
> RXNORM/stats.html
> So can we control that ... ?
>
> Also i was thinking to generate the json output from web-client:
> } else if ("json".equalsIgnoreCase(format)) {
> response.setContentType("application/json");
> ByteArrayOutputStream output = new ByteArrayOutputStream();
> // XiCasSerializer.serialize(jcas.getCas(), output);
> JsonCasSerializer.jsonSerialize(jcas.getCas(), output);
> sb.append(output.toString());
> output.close();
>
>
> Pom.xml
>
> <dependency>
> <groupId>org.apache.uima</groupId>
> <artifactId>uimaj-core</artifactId>
> <version>2.4.0</version>
> </dependency>
> <dependency>
> <groupId>org.apache.uima</groupId>
> <artifactId>uimafit-core</artifactId>
> <version>2.1.0</version>
> </dependency>
> <!-- https://mvnrepository.com/artifact/org.apache.uima/uimaj-json -->
> <dependency>
> <groupId>org.apache.uima</groupId>
> <artifactId>uimaj-json</artifactId>
> <version>2.9.0</version>
> </dependency>
>
>
> Getting the following error:
>
>
> WARNING] Error for /DemoServlet
> java.lang.NoClassDefFoundError: org/apache/uima/cas/impl/
> CasSerializerSupport
> at org.apache.uima.json.JsonCasSerializer.<init>(
> JsonCasSerializer.java:155)
> at org.apache.uima.json.JsonCasSerializer.jsonSerialize(
> JsonCasSerializer.java:255)
> at org.apache.uima.json.JsonCasSerializer.jsonSerialize(
> JsonCasSerializer.java:206)
> at org.apache.ctakes.web.client.servlet.DemoServlet.
> formatResults(DemoServlet.java:149)
> at org.apache.ctakes.web.client.servlet.DemoServlet.doPost(
> DemoServlet.java:92)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:800)
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(
> ServletHandler.java:587)
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(
> ScopedHandler.java:143)
> at org.eclipse.jetty.security.SecurityHandler.handle(
> SecurityHandler.java:577)
> at org.eclipse.jetty.server.session.SessionHandler.
> doHandle(SessionHandler.java:223)
> at org.eclipse.jetty.server.handler.ContextHandler.
> doHandle(ContextHandler.java:1125)
> at org.eclipse.jetty.servlet.ServletHandler.doScope(
> ServletHandler.java:515)
> at org.eclipse.jetty.server.session.SessionHandler.
> doScope(SessionHandler.java:185)
> at org.eclipse.jetty.server.handler.ContextHandler.
> doScope(ContextHandler.java:1059)
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(
> ScopedHandler.java:141)
> at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(
> ContextHandlerCollection.java:215)
> at org.eclipse.jetty.server.handler.HandlerCollection.
> handle(HandlerCollection.java:110)
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(
> HandlerWrapper.java:97)
> at org.eclipse.jetty.server.Server.handle(Server.java:497)
> at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:313)
> at org.eclipse.jetty.server.HttpConnection.onFillable(
> HttpConnection.java:248)
> at org.eclipse.jetty.io.AbstractConnection$2.run(
> AbstractConnection.java:540)
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(
> QueuedThreadPool.java:626)
> at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(
> QueuedThreadPool.java:546)
> at java.lang.Thread.run(Thread.java:745)
>
>
> On Thu, Jan 26, 2017 at 12:30 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> Hi Shahid, answers are below.
>>
>>
>>
>> >I am seeing few more FP like MEN :
>>
>> >SENTENCE: MEN
>>
>> NN
>>
>> |======|
>>
>> Disorder
>>
>> C0027662
>>
>> |======|
>>
>> Drug
>>
>> C0127527
>>
>>
>>
>> MEN is an abbreviation for Multiple Endocrine Neoplasia (Disorder C0027662). In is also an abbreviation for the antibiotic Menogaril (Drug C0127527). Strictly speaking, these are not false positives. There is a lot of effort in the nlp community, including by ctakes contributors, on word sense disambiguation (WSD) that would improve mapping of words such as “men”.
>>
>>
>>
>> >Where as it could have been matched to :
>>
>> >Meta Mapping (1000):
>>
>> > 1000 C0025266:Men (Male population group)
>>
>>
>>
>> Ctakes uses a set of semantic types for lookup. Population Group (T098)
>> is not one of them. By default ctakes focuses on clinically-relevant
>> terms. If you create a custom dictionary you can add semantic types like
>> Population Group.
>>
>>
>>
>> > 2) Also is there any way round to match based on spelling mistakes.
>> like
>>
>> >advill ==> advil
>>
>> >neplasm ==> neoplasm
>>
>>
>>
>> Spell correction is another thing that ctakes does not focus upon. There
>> are many approaches and a module could be created to handle spelling.
>>
>>
>>
>> >3) Can we all concepts from MRCONSO into fast matching dictionary.
>>
>>
>>
>> Yes, using the dictionary gui select all vocabulary sources and all
>> semantic types. Get ready for a big database and you may need to bump up
>> your memory allocation for ctakes.
>>
>>
>>
>> Sean
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Jan 25, 2017 at 10:12 PM, Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>> Hi Shahid,
>>
>>
>>
>> I tested LVG on “levels” and it didn’t produce an equivalent singular
>> form. I don’t know of any special lvg parameters that will toggle this on
>> and off – as far as I know it should always attempt it for nouns. Because
>> this may happen quite a bit I started thinking on an alternative solution …
>> but may not get to it for a while and when I do I’ll still need to run some
>> tests to make sure it works.
>>
>>
>>
>> Andrey Kurdumov recently made an update for ctakes to use LVG 2016
>> (cheers!). The current version is fairly old and the 2016 may very well
>> perform better. I have pasted his email below.
>>
>>
>>
>> As I promise, I udpate cTakes to support LVG version 2016 year.
>>
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
>> ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
>> &m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVh
>> ugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e=
>>
>>
>>
>> Please take a look.
>>
>> In the github following modifications to current version of cTakes
>>
>> - Removed two large files to make project fit GitHub restrictions.
>>
>> - Some very small cleanup which placed in separate commit.
>>
>> - Some fixes to ytex related tests, that's was required for me to pass
>> mvn install command.
>>
>>
>>
>> Assumptions:
>>
>> - User should update ctakesnormx and other databases from HSQLdb 1.8 to
>> HSQLDB 2.3.4
>>
>>
>>
>>
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Wednesday, January 25, 2017 2:11 AM
>>
>>
>> *To:* Finan, Sean
>> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>> *Subject:* Re: Ctakes Dictionary Gui
>>
>>
>>
>> Thanks sean for this insightful information. This is of great help.(i am
>> newbie to ctakes and also come from python background.)
>>
>> I tested on the Fast version. Is it so that ctakes LVG is not currently
>> adding plurals to the terms. Because in logs i see that LVG is being setup
>> before processing the docs in CVD.
>>
>> I guess below logs show ctakes is using LVG:
>>
>>
>>
>> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
>> Lvg with config file = /Users/shahid/projects/workspa
>> ce/ctakes/ctakes-dictionary-lookup/resources/org/apache/
>> ctakes/lvg/data/config/lvg.properties
>>
>> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute
>> path = /Users/shahid/projects/workspace/ctakes/ctakes-dictionary-
>> lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties
>>
>> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd =
>> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>>
>> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
>> /Users/shahid/projects/workspace/ctakes/ctakes-dictionary-
>> lookup/resources/org/apache/ctakes/lvg/
>>
>> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
>> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>>
>> 25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy
>> analysis? true
>>
>> Loading configuration.
>>
>> Loading feature templates.
>>
>> Loading lexica.
>>
>> Loading model:
>>
>> ............................................................
>> ............................
>>
>> 25 Jan 2017 12:31:54 INFO Chunker - Chunker model file:
>> org/apache/ctakes/chunker/models/chunker-model.zip
>>
>> 25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite
>> state machines loaded.
>>
>> 25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser...
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope
>> sizes: 7 , 7
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order:
>> LEFT,RIGHT
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer:
>> org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
>>
>> 25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData()
>> called for ContextInitializer
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer:
>> org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type:
>> org.apache.ctakes.typesystem.type.textspan.Sentence
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type:
>> org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
>>
>> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type:
>> org.apache.ctakes.typesystem.type.syntax.BaseToken
>>
>> 25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines
>> loaded.
>>
>> 25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file:
>> org/apache/ctakes/postagger/models/mayo-pos.zip
>>
>> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary
>> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>>
>> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset
>> loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP
>> VBZ WDT WP WPS WRB
>>
>> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term
>> text span: 3
>>
>> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary
>> Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_appliedvocab
>> .xml
>>
>> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing
>> dictionary specifications:
>>
>> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had
>> build doc
>>
>> FILEPATH: [Document: No DOCTYPE declaration, Root is [Element:
>> <lookupSpecification/>]]
>>
>> 25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and
>> term table CUI_TERMS
>>
>> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser -
>> RareWordDictionary parseDictionaries Done...
>>
>> [Element: <conceptFactories/>]
>>
>> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
>> parseConceptFactories...
>>
>> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
>> parseConceptFactories... Collection
>>
>>
>>
>> Also in FASTAGGREGATE PIPELINE Desc i see
>>
>> <flowConstraints>
>>
>> <fixedFlow>
>>
>> <node>SimpleSegmentAnnotator</node>
>>
>> <node>SentenceDetectorAnnotator</node>
>>
>> <node>TokenizerAnnotator</node>
>>
>> * <node>LvgAnnotator</node>*
>>
>> <node>ContextDependentTokenizerAnnotator</node>
>>
>> <node>POSTagger</node>
>>
>> <!-- <node>ClearPOSTagger</node> -->
>>
>> <node>Chunker</node>
>>
>> <node>AdjustNounPhraseToIncludeFollowingNP</node>
>>
>> <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
>>
>> <node>LookupWindowAnnotator</node>
>>
>> <node>DictionaryLookupAnnotatorDB</node>
>>
>> <node>DependencyParser</node>
>>
>> ...
>>
>> </fixedFlow>
>>
>>
>>
>>
>>
>> Is there any setting that will let LVG generate plurals.
>>
>>
>>
>> On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>> Hi Shahid,
>>
>> You will definitely find instances where the old dictionary finds terms
>> but the fast does not, and vice-versa. The fast lookup uses a more concise
>> dictionary, and the concepts that you noted are probably not in it. There
>> is another thread between myself and Pratik Agarwal (last week in fact) on
>> exactly the topic of drugs identified generically or with dose, route,
>> form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
>>
>> Everolimus is in the dictionary by itself:
>>
>> sql> select * from cui_terms where text like '%everolimus%';
>>
>> CUI RINDEX TCOUNT TEXT RWORD
>>
>> ------ ------ ------ ---------- ----------
>>
>> 541315 0 1 everolimus everolimus
>>
>>
>>
>> The reason why everolimus was not identified by itself is because it was
>> given the part of speech “DT” (Determiner), which is specified as unwanted
>> for lookup. In my test with “… given everolimus 2.5 MG …”:
>>
>> WordToken
>>
>> begin
>>
>> 12
>>
>> end
>>
>> 16
>>
>> tokenNumber
>>
>> 2
>>
>> partOfSpeech
>>
>> VBD
>>
>> capitalization
>>
>> 0
>>
>> numPosition
>>
>> 0
>>
>> WordToken
>>
>> begin
>>
>> 17
>>
>> end
>>
>> 27
>>
>> tokenNumber
>>
>> 3
>>
>> partOfSpeech
>>
>> DT
>>
>> capitalization
>>
>> 0
>>
>> numPosition
>>
>> 0
>>
>> MeasurementAnnotation
>>
>> begin
>>
>> 28
>>
>> end
>>
>> 34
>>
>> id
>>
>> 0
>>
>> typeID
>>
>> 0
>>
>> discoveryTechnique
>>
>> 0
>>
>> polarity
>>
>> 0
>>
>> uncertainty
>>
>> 0
>>
>> conditional
>>
>> false
>>
>> generic
>>
>> false
>>
>> historyOf
>>
>> 0
>>
>>
>>
>> “DT” normally is assigned to things like “the, a, these” and at some
>> point the community decided that words with the DT part of speech should
>> not be considered as candidates for dictionary lookup.
>> http://www.clips.ua.ac.be/pages/mbsp-tags
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.clips.ua.ac.be_pages_mbsp-2Dtags&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3k7SCH8Gvj_palkdWwWeKGysBHTV_K5itUG2DE4icAI&s=xwP78R729SFVEwbCNa_af452uzXvIik2Ob4SYQyNPHw&e=>
>>
>> The default exclusion parts of speech are:
>>
>> “VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
>>
>> To change this, set the parameter “exclusionTags” to this string without
>> DT.
>>
>>
>>
>> As for “higher testosterone levels”, are you running the LVG (Lexical
>> Variant Generator) module? “testosterone level” is in the dictionary, but
>> the plural “testosterone levels” is not. This is done on purpose to keep
>> the database small. The old dictionary may not have the same tactic.
>>
>> sql> select * from cui_terms where text like 'testosterone level%';
>>
>> CUI RINDEX TCOUNT TEXT RWORD
>>
>> ------ ------ ------ ------------------ ------------
>>
>> 523912 0 2 testosterone level testosterone
>>
>>
>>
>> The LVG module –should- add the plural as a variant and the lookup module
>> will use that variant for lookup. The dictionary module (and others) does
>> not stand on its own – its success depends upon the proper output of
>> previous modules in the pipeline. When I test with “… higher testosterone
>> level …” (without LVG) it does find what you are looking for:
>>
>> WordToken
>>
>> begin
>>
>> 18
>>
>> end
>>
>> 24
>>
>> tokenNumber
>>
>> 4
>>
>> partOfSpeech
>>
>> JJR
>>
>> capitalization
>>
>> 0
>>
>> numPosition
>>
>> 0
>>
>> ProcedureMention
>>
>> begin
>>
>> 25
>>
>> end
>>
>> 43
>>
>> id
>>
>> 0
>>
>> codingScheme
>>
>> SNOMEDCT
>>
>> code
>>
>> 104957004
>>
>> score
>>
>> 0.0
>>
>> disambiguated
>>
>> false
>>
>> cui
>>
>> C0523912
>>
>> tui
>>
>> T059
>>
>> preferredText
>>
>> Testosterone measurement
>>
>> typeID
>>
>> 5
>>
>> discoveryTechnique
>>
>> 1
>>
>> polarity
>>
>> 0
>>
>> uncertainty
>>
>> 0
>>
>> conditional
>>
>> false
>>
>> generic
>>
>> false
>>
>> historyOf
>>
>> 0
>>
>> MedicationMention
>>
>> begin
>>
>> 25
>>
>> end
>>
>> 37
>>
>> id
>>
>> 0
>>
>> codingScheme
>>
>> SNOMEDCT
>>
>> code
>>
>> 109033004
>>
>> score
>>
>> 0.0
>>
>> disambiguated
>>
>> false
>>
>> cui
>>
>> C0039601
>>
>> tui
>>
>> T121
>>
>> preferredText
>>
>> Testosterone
>>
>> codingScheme
>>
>>
>>
>> I just ran through with LVG and LVG does not form “level” from “levels”.
>>
>>
>>
>>
>> I hope that helps,
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Tuesday, January 24, 2017 10:17 AM
>>
>>
>> *To:* Finan, Sean
>> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>> *Subject:* Re: Ctakes Dictionary Gui
>>
>>
>>
>> Hi Sean
>>
>>
>>
>> I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow)
>> . I found that one of the drug everolimus 2.5 mg is not found by the
>> fast version. it is actually in RXNORM of my MRCONSO.RRF file.
>>
>> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|998
>> 191||RXNORM|SBD|998191|*everolimus 2.5 MG* Oral Tablet
>> [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
>>
>> Also other case is :
>>
>> SENTENCE: higher testosterone levels
>>
>> JJR NN NNS
>>
>> |==========|
>>
>> Procedure
>>
>> C0202227
>>
>> C0523912
>>
>> |==========|
>>
>> Drug
>>
>> C0039601
>>
>> AggregratePlainTextUMLSProcessor is able to find from higher testosterone levels:
>>
>> *testosterone levels*
>>
>> <refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" tui="T059"/>
>>
>> C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone level|9|N|256|
>>
>> I am not able to understand why fast version is not able to do so.
>>
>>
>>
>> MoreOver in comparison to Metamap, we are not able to do this.
>>
>> Phrase: higher testosterone levels
>>
>> Meta Mapping (966):
>>
>> 966 C1295653:High testosterone level (Increased testosterone level)
>> [Finding]
>>
>>
>>
>> On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>> Hi Shahid,
>>
>>
>>
>> I’m glad that the fix worked!
>>
>> Unfortunately, the fast dictionary format will not work with the old
>> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
>>
>> You can manually create an updated dictionary for the older module, but
>> it is more involved.
>>
>> In our tests and those done by others the new “fast” lookup has as good
>> or better accuracy depending upon the test corpus. Plus it is runs in 1/500
>> th the time. I recommend that you stick to it.
>>
>>
>>
>> Sean
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Tuesday, January 24, 2017 5:50 AM
>> *To:* Finan, Sean
>> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>>
>>
>> *Subject:* Re: Ctakes Dictionary Gui
>>
>>
>>
>> Thanks Sean
>>
>>
>>
>> That was the case for not finding the class. there were space in the xml
>> generated by dictionary-gui.
>>
>> Also i am curious how we can use new umls with normal
>> AggregratePlainTextUMLSProcessor.
>>
>>
>>
>>
>>
>> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>> Ah – there might be an erroneous space in the classname.
>>
>>
>>
>> Go to your dictionary settings xml. In the line:
>>
>> <implementationName>org.apache.ctakes.dictionary.lookup2.
>> concept.JdbcConceptFactory</implementationName>
>>
>>
>>
>> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>>
>> If you see a space, remove it.
>>
>>
>>
>> It looks like I introduced this bug a few weeks ago.
>>
>>
>>
>> Thanks,
>>
>> Sean
>>
>>
>>
>>
>>
>> *From:* shahid ashraf [mailto:shahid@trialx.com]
>> *Sent:* Saturday, January 21, 2017 1:42 PM
>> *To:* dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com;
>> pratik agarwal
>> *Subject:* Re: Ctakes Dictionary Gui
>>
>>
>>
>> Have put username and password (umls) in custom.xml as well. Still
>> getting this error:
>>
>> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526):
>> SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.
>> lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .DefaultJCasTermAnnotator" failed. (Descriptor:
>> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l
>> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>>
>> org.apache.uima.resource.ResourceInitializationException: Initialization
>> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .DefaultJCasTermAnnotator" failed. (Descriptor:
>> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l
>> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>
>> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>>
>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>>
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.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.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>>
>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>>
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.java:354)
>>
>> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>>
>> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra
>> me.java:476)
>>
>> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.
>> actionPerformed(AnnotatorOpenEventHandler.java:52)
>>
>> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto
>> n.java:2022)
>>
>> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB
>> utton.java:2346)
>>
>> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu
>> ttonModel.java:402)
>>
>> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>>
>> at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>>
>> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItem
>> UI.java:833)
>>
>> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
>>
>> at javax.swing.plaf.basic.BasicMenuItemUI$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(Pro
>> tectionDomain.java:75)
>>
>> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro
>> tectionDomain.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(Pro
>> tectionDomain.java:75)
>>
>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
>>
>> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis
>> patchThread.java:201)
>>
>> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat
>> chThread.java:116)
>>
>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis
>> patchThread.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)
>>
>> Caused by: org.apache.uima.resource.ResourceInitializationException:
>> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
>> Can't find resource for bundle java.util.PropertyResourceBundle, key
>> Unknown class org.apache.ctakes.dictionary.l
>> ookup2.concept.JdbcConceptFactory
>>
>> at org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>
>> ... 55 more
>>
>> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
>> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
>> Can't find resource for bundle java.util.PropertyResourceBundle, key
>> Unknown class org.apache.ctakes.dictionary.l
>> ookup2.concept.JdbcConceptFactory
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
>>
>> at org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>>
>> ... 56 more
>>
>> Caused by: java.lang.ClassNotFoundException:
>> org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
>>
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>
>> at java.lang.Class.forName0(Native Method)
>>
>> at java.lang.Class.forName(Class.java:264)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
>>
>> ... 59 more
>>
>>
>>
>>
>>
>> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
>>
>> Hi I was able to run and produce the new custom umls files. and where put
>> under ctakes binary (not dev).
>>
>>
>>
>> I changed the name under apache-ctakes-3.2.2/desc
>> /ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLook
>> upAnnotator.xml
>>
>>
>>
>> <name>DictionaryDescriptorFile</name>
>>
>> <description/>
>>
>> <fileResourceSpecifier>
>>
>> <fileUrl>file:org/apache/ctak
>> es/dictionary/lookup/fast/custom.xml</fileUrl>
>>
>>
>>
>> when running AggregatePlantextFastUmlsProcessor.xml I am getting
>> following error (not when using old org/apache/ctakes/dictiona
>> ry/lookup/fast/cTakesHsql.xml)
>>
>>
>>
>> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
>> Initialization of annotator class "org.apache.ctakes.dictionary.
>> lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .DefaultJCasTermAnnotator" failed. (Descriptor:
>> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l
>> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>>
>> org.apache.uima.resource.ResourceInitializationException: Initialization
>> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .DefaultJCasTermAnnotator" failed. (Descriptor:
>> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-l
>> ookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>>
>> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>>
>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>>
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.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.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>>
>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>>
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.java:354)
>>
>> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>>
>> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra
>> me.java:476)
>>
>> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.
>> actionPerformed(AnnotatorOpenEventHandler.java:52)
>>
>> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto
>> n.java:2022)
>>
>> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB
>> utton.java:2346)
>>
>> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu
>> ttonModel.java:402)
>>
>> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>>
>> at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>>
>> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItem
>> UI.java:833)
>>
>> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
>>
>> at javax.swing.plaf.basic.BasicMenuItemUI$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(Pro
>> tectionDomain.java:75)
>>
>> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro
>> tectionDomain.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(Pro
>> tectionDomain.java:75)
>>
>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
>>
>> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis
>> patchThread.java:201)
>>
>> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat
>> chThread.java:116)
>>
>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis
>> patchThread.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)
>>
>> Caused by: org.apache.uima.resource.ResourceInitializationException:
>> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
>> Can't find resource for bundle java.util.PropertyResourceBundle, key
>> Unknown class org.apache.ctakes.dictionary.l
>> ookup2.concept.JdbcConceptFactory
>>
>> at org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>>
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>
>> ... 55 more
>>
>> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
>> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
>> Can't find resource for bundle java.util.PropertyResourceBundle, key
>> Unknown class org.apache.ctakes.dictionary.l
>> ookup2.concept.JdbcConceptFactory
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
>>
>> at org.apache.ctakes.dictionary.lookup2.ae
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
>> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>>
>> ... 56 more
>>
>> Caused by: java.lang.ClassNotFoundException:
>> org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
>>
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>
>> at java.lang.Class.forName0(Native Method)
>>
>> at java.lang.Class.forName(Class.java:264)
>>
>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe
>> scriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
>>
>> ... 59 more
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>>
>>
>>
>>
>> --
>>
>> with Regards
>>
>> Shahid Ashraf
>>
>
>
>
> --
> with Regards
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Hi Sean
Thanks Again!
I am seeing few more FP like MEN :
SENTENCE: MEN
NN
|======|
Disorder
C0027662
|======|
Drug
C0127527
Where as it could have been matched to :
Meta Mapping (1000):
1000 C0025266:Men (Male population group)
2) Also is there any way round to match based on spelling mistakes. like
advill ==> advil
neplasm ==> neoplasm
3) Can we all concepts from MRCONSO into fast matching dictionary.
On Wed, Jan 25, 2017 at 10:12 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Shahid,
>
>
>
> I tested LVG on “levels” and it didn’t produce an equivalent singular
> form. I don’t know of any special lvg parameters that will toggle this on
> and off – as far as I know it should always attempt it for nouns. Because
> this may happen quite a bit I started thinking on an alternative solution …
> but may not get to it for a while and when I do I’ll still need to run some
> tests to make sure it works.
>
>
>
> Andrey Kurdumov recently made an update for ctakes to use LVG 2016
> (cheers!). The current version is fairly old and the 2016 may very well
> perform better. I have pasted his email below.
>
>
>
> As I promise, I udpate cTakes to support LVG version 2016 year.
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=
> IJWxluJDIVhugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e=
>
>
>
> Please take a look.
>
> In the github following modifications to current version of cTakes
>
> - Removed two large files to make project fit GitHub restrictions.
>
> - Some very small cleanup which placed in separate commit.
>
> - Some fixes to ytex related tests, that's was required for me to pass mvn
> install command.
>
>
>
> Assumptions:
>
> - User should update ctakesnormx and other databases from HSQLdb 1.8 to
> HSQLDB 2.3.4
>
>
>
>
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Wednesday, January 25, 2017 2:11 AM
>
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks sean for this insightful information. This is of great help.(i am
> newbie to ctakes and also come from python background.)
>
> I tested on the Fast version. Is it so that ctakes LVG is not currently
> adding plurals to the terms. Because in logs i see that LVG is being setup
> before processing the docs in CVD.
>
> I guess below logs show ctakes is using LVG:
>
>
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> Lvg with config file = /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/data/
> config/lvg.properties
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute
> path = /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/data/
> config/lvg.properties
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd =
> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>
> 25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true
>
> Loading configuration.
>
> Loading feature templates.
>
> Loading lexica.
>
> Loading model:
>
> ............................................................
> ............................
>
> 25 Jan 2017 12:31:54 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
> 25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
>
> 25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser...
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope
> sizes: 7 , 7
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer:
> org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
>
> 25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData()
> called for ContextInitializer
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer:
> org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type:
> org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type:
> org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type:
> org.apache.ctakes.typesystem.type.syntax.BaseToken
>
> 25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines
> loaded.
>
> 25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset
> loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP
> VBZ WDT WP WPS WRB
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_
> appliedvocab.xml
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had
> build doc
>
> FILEPATH: [Document: No DOCTYPE declaration, Root is [Element:
> <lookupSpecification/>]]
>
> 25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and
> term table CUI_TERMS
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - RareWordDictionary
> parseDictionaries Done...
>
> [Element: <conceptFactories/>]
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
> parseConceptFactories...
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
> parseConceptFactories... Collection
>
>
>
> Also in FASTAGGREGATE PIPELINE Desc i see
>
> <flowConstraints>
>
> <fixedFlow>
>
> <node>SimpleSegmentAnnotator</node>
>
> <node>SentenceDetectorAnnotator</node>
>
> <node>TokenizerAnnotator</node>
>
> * <node>LvgAnnotator</node>*
>
> <node>ContextDependentTokenizerAnnotator</node>
>
> <node>POSTagger</node>
>
> <!-- <node>ClearPOSTagger</node> -->
>
> <node>Chunker</node>
>
> <node>AdjustNounPhraseToIncludeFollowingNP</node>
>
> <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
>
> <node>LookupWindowAnnotator</node>
>
> <node>DictionaryLookupAnnotatorDB</node>
>
> <node>DependencyParser</node>
>
> ...
>
> </fixedFlow>
>
>
>
>
>
> Is there any setting that will let LVG generate plurals.
>
>
>
> On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
> You will definitely find instances where the old dictionary finds terms
> but the fast does not, and vice-versa. The fast lookup uses a more concise
> dictionary, and the concepts that you noted are probably not in it. There
> is another thread between myself and Pratik Agarwal (last week in fact) on
> exactly the topic of drugs identified generically or with dose, route,
> form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
>
> Everolimus is in the dictionary by itself:
>
> sql> select * from cui_terms where text like '%everolimus%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ---------- ----------
>
> 541315 0 1 everolimus everolimus
>
>
>
> The reason why everolimus was not identified by itself is because it was
> given the part of speech “DT” (Determiner), which is specified as unwanted
> for lookup. In my test with “… given everolimus 2.5 MG …”:
>
> WordToken
>
> begin
>
> 12
>
> end
>
> 16
>
> tokenNumber
>
> 2
>
> partOfSpeech
>
> VBD
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> WordToken
>
> begin
>
> 17
>
> end
>
> 27
>
> tokenNumber
>
> 3
>
> partOfSpeech
>
> DT
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> MeasurementAnnotation
>
> begin
>
> 28
>
> end
>
> 34
>
> id
>
> 0
>
> typeID
>
> 0
>
> discoveryTechnique
>
> 0
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
>
>
> “DT” normally is assigned to things like “the, a, these” and at some
> point the community decided that words with the DT part of speech should
> not be considered as candidates for dictionary lookup.
> http://www.clips.ua.ac.be/pages/mbsp-tags
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.clips.ua.ac.be_pages_mbsp-2Dtags&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3k7SCH8Gvj_palkdWwWeKGysBHTV_K5itUG2DE4icAI&s=xwP78R729SFVEwbCNa_af452uzXvIik2Ob4SYQyNPHw&e=>
>
> The default exclusion parts of speech are:
>
> “VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
>
> To change this, set the parameter “exclusionTags” to this string without
> DT.
>
>
>
> As for “higher testosterone levels”, are you running the LVG (Lexical
> Variant Generator) module? “testosterone level” is in the dictionary, but
> the plural “testosterone levels” is not. This is done on purpose to keep
> the database small. The old dictionary may not have the same tactic.
>
> sql> select * from cui_terms where text like 'testosterone level%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ------------------ ------------
>
> 523912 0 2 testosterone level testosterone
>
>
>
> The LVG module –should- add the plural as a variant and the lookup module
> will use that variant for lookup. The dictionary module (and others) does
> not stand on its own – its success depends upon the proper output of
> previous modules in the pipeline. When I test with “… higher testosterone
> level …” (without LVG) it does find what you are looking for:
>
> WordToken
>
> begin
>
> 18
>
> end
>
> 24
>
> tokenNumber
>
> 4
>
> partOfSpeech
>
> JJR
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> ProcedureMention
>
> begin
>
> 25
>
> end
>
> 43
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 104957004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0523912
>
> tui
>
> T059
>
> preferredText
>
> Testosterone measurement
>
> typeID
>
> 5
>
> discoveryTechnique
>
> 1
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
> MedicationMention
>
> begin
>
> 25
>
> end
>
> 37
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 109033004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0039601
>
> tui
>
> T121
>
> preferredText
>
> Testosterone
>
> codingScheme
>
>
>
> I just ran through with LVG and LVG does not form “level” from “levels”.
>
>
>
>
> I hope that helps,
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Tuesday, January 24, 2017 10:17 AM
>
>
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Hi Sean
>
>
>
> I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow)
> . I found that one of the drug everolimus 2.5 mg is not found by the
> fast version. it is actually in RXNORM of my MRCONSO.RRF file.
>
> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|
> 998191||RXNORM|SBD|998191|*everolimus 2.5 MG* Oral Tablet
> [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
>
> Also other case is :
>
> SENTENCE: higher testosterone levels
>
> JJR NN NNS
>
> |==========|
>
> Procedure
>
> C0202227
>
> C0523912
>
> |==========|
>
> Drug
>
> C0039601
>
> AggregratePlainTextUMLSProcessor is able to find from higher testosterone levels:
>
> *testosterone levels*
>
> <refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" tui="T059"/>
>
> C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone level|9|N|256|
>
> I am not able to understand why fast version is not able to do so.
>
>
>
> MoreOver in comparison to Metamap, we are not able to do this.
>
> Phrase: higher testosterone levels
>
> Meta Mapping (966):
>
> 966 C1295653:High testosterone level (Increased testosterone level)
> [Finding]
>
>
>
> On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
>
>
> I’m glad that the fix worked!
>
> Unfortunately, the fast dictionary format will not work with the old
> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
>
> You can manually create an updated dictionary for the older module, but it
> is more involved.
>
> In our tests and those done by others the new “fast” lookup has as good or
> better accuracy depending upon the test corpus. Plus it is runs in 1/500
> th the time. I recommend that you stick to it.
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Tuesday, January 24, 2017 5:50 AM
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>
>
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks Sean
>
>
>
> That was the case for not finding the class. there were space in the xml
> generated by dictionary-gui.
>
> Also i am curious how we can use new umls with normal
> AggregratePlainTextUMLSProcessor.
>
>
>
>
>
> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Ah – there might be an erroneous space in the classname.
>
>
>
> Go to your dictionary settings xml. In the line:
>
> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory</implementationName>
>
>
>
> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>
> If you see a space, remove it.
>
>
>
> It looks like I introduced this bug a few weeks ago.
>
>
>
> Thanks,
>
> Sean
>
>
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Saturday, January 21, 2017 1:42 PM
> *To:* dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik
> agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Have put username and password (umls) in custom.xml as well. Still getting
> this error:
>
> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
> MainFrame.handleException(526): SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
>
>
> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
>
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
>
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
>
>
> <name>DictionaryDescriptorFile</name>
>
> <description/>
>
> <fileResourceSpecifier>
>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
>
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
RE: Ctakes Dictionary Gui
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Shahid,
I tested LVG on “levels” and it didn’t produce an equivalent singular form. I don’t know of any special lvg parameters that will toggle this on and off – as far as I know it should always attempt it for nouns. Because this may happen quite a bit I started thinking on an alternative solution … but may not get to it for a while and when I do I’ll still need to run some tests to make sure it works.
Andrey Kurdumov recently made an update for ctakes to use LVG 2016 (cheers!). The current version is fairly old and the 2016 may very well perform better. I have pasted his email below.
As I promise, I udpate cTakes to support LVG version 2016 year.
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVhugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e=
Please take a look.
In the github following modifications to current version of cTakes
- Removed two large files to make project fit GitHub restrictions.
- Some very small cleanup which placed in separate commit.
- Some fixes to ytex related tests, that's was required for me to pass mvn install command.
Assumptions:
- User should update ctakesnormx and other databases from HSQLdb 1.8 to HSQLDB 2.3.4
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Wednesday, January 25, 2017 2:11 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Thanks sean for this insightful information. This is of great help.(i am newbie to ctakes and also come from python background.)
I tested on the Fast version. Is it so that ctakes LVG is not currently adding plurals to the terms. Because in logs i see that LVG is being setup before processing the docs in CVD.
I guess below logs show ctakes is using LVG:
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = /Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute path = /Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd = /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd /Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
25 Jan 2017 12:31:54 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip
25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser...
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope sizes: 7 , 7
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer: org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer: org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type: org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type: org.apache.ctakes.typesystem.type.syntax.BaseToken
25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines loaded.
25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_appliedvocab.xml
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing dictionary specifications:
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had build doc
FILEPATH: [Document: No DOCTYPE declaration, Root is [Element: <lookupSpecification/>]]
25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and term table CUI_TERMS
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - RareWordDictionary parseDictionaries Done...
[Element: <conceptFactories/>]
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started parseConceptFactories...
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started parseConceptFactories... Collection
Also in FASTAGGREGATE PIPELINE Desc i see
<flowConstraints>
<fixedFlow>
<node>SimpleSegmentAnnotator</node>
<node>SentenceDetectorAnnotator</node>
<node>TokenizerAnnotator</node>
<node>LvgAnnotator</node>
<node>ContextDependentTokenizerAnnotator</node>
<node>POSTagger</node>
<!-- <node>ClearPOSTagger</node> -->
<node>Chunker</node>
<node>AdjustNounPhraseToIncludeFollowingNP</node>
<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
<node>LookupWindowAnnotator</node>
<node>DictionaryLookupAnnotatorDB</node>
<node>DependencyParser</node>
...
</fixedFlow>
Is there any setting that will let LVG generate plurals.
On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Hi Shahid,
You will definitely find instances where the old dictionary finds terms but the fast does not, and vice-versa. The fast lookup uses a more concise dictionary, and the concepts that you noted are probably not in it. There is another thread between myself and Pratik Agarwal (last week in fact) on exactly the topic of drugs identified generically or with dose, route, form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
Everolimus is in the dictionary by itself:
sql> select * from cui_terms where text like '%everolimus%';
CUI RINDEX TCOUNT TEXT RWORD
------ ------ ------ ---------- ----------
541315 0 1 everolimus everolimus
The reason why everolimus was not identified by itself is because it was given the part of speech “DT” (Determiner), which is specified as unwanted for lookup. In my test with “… given everolimus 2.5 MG …”:
WordToken
begin
12
end
16
tokenNumber
2
partOfSpeech
VBD
capitalization
0
numPosition
0
WordToken
begin
17
end
27
tokenNumber
3
partOfSpeech
DT
capitalization
0
numPosition
0
MeasurementAnnotation
begin
28
end
34
id
0
typeID
0
discoveryTechnique
0
polarity
0
uncertainty
0
conditional
false
generic
false
historyOf
0
“DT” normally is assigned to things like “the, a, these” and at some point the community decided that words with the DT part of speech should not be considered as candidates for dictionary lookup. http://www.clips.ua.ac.be/pages/mbsp-tags<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.clips.ua.ac.be_pages_mbsp-2Dtags&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3k7SCH8Gvj_palkdWwWeKGysBHTV_K5itUG2DE4icAI&s=xwP78R729SFVEwbCNa_af452uzXvIik2Ob4SYQyNPHw&e=>
The default exclusion parts of speech are:
“VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
To change this, set the parameter “exclusionTags” to this string without DT.
As for “higher testosterone levels”, are you running the LVG (Lexical Variant Generator) module? “testosterone level” is in the dictionary, but the plural “testosterone levels” is not. This is done on purpose to keep the database small. The old dictionary may not have the same tactic.
sql> select * from cui_terms where text like 'testosterone level%';
CUI RINDEX TCOUNT TEXT RWORD
------ ------ ------ ------------------ ------------
523912 0 2 testosterone level testosterone
The LVG module –should- add the plural as a variant and the lookup module will use that variant for lookup. The dictionary module (and others) does not stand on its own – its success depends upon the proper output of previous modules in the pipeline. When I test with “… higher testosterone level …” (without LVG) it does find what you are looking for:
WordToken
begin
18
end
24
tokenNumber
4
partOfSpeech
JJR
capitalization
0
numPosition
0
ProcedureMention
begin
25
end
43
id
0
codingScheme
SNOMEDCT
code
104957004
score
0.0
disambiguated
false
cui
C0523912
tui
T059
preferredText
Testosterone measurement
typeID
5
discoveryTechnique
1
polarity
0
uncertainty
0
conditional
false
generic
false
historyOf
0
MedicationMention
begin
25
end
37
id
0
codingScheme
SNOMEDCT
code
109033004
score
0.0
disambiguated
false
cui
C0039601
tui
T121
preferredText
Testosterone
codingScheme
I just ran through with LVG and LVG does not form “level” from “levels”.
I hope that helps,
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Tuesday, January 24, 2017 10:17 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org<ma...@ctakes.apache.org>; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Hi Sean
I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow) . I found that one of the drug everolimus 2.5 mg is not found by the fast version. it is actually in RXNORM of my MRCONSO.RRF file.
C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|998191||RXNORM|SBD|998191|everolimus 2.5 MG Oral Tablet [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
Also other case is :
SENTENCE: higher testosterone levels
JJR NN NNS
|==========|
Procedure
C0202227
C0523912
|==========|
Drug
C0039601
AggregratePlainTextUMLSProcessor is able to find from higher testosterone levels:
testosterone levels
<refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" tui="T059"/>
C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone level|9|N|256|
I am not able to understand why fast version is not able to do so.
MoreOver in comparison to Metamap, we are not able to do this.
Phrase: higher testosterone levels
Meta Mapping (966):
966 C1295653:High testosterone level (Increased testosterone level) [Finding]
On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Hi Shahid,
I’m glad that the fix worked!
Unfortunately, the fast dictionary format will not work with the old Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
You can manually create an updated dictionary for the older module, but it is more involved.
In our tests and those done by others the new “fast” lookup has as good or better accuracy depending upon the test corpus. Plus it is runs in 1/500th the time. I recommend that you stick to it.
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Tuesday, January 24, 2017 5:50 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org<ma...@ctakes.apache.org>; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Thanks Sean
That was the case for not finding the class. there were space in the xml generated by dictionary-gui.
Also i am curious how we can use new umls with normal AggregratePlainTextUMLSProcessor.
On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Ah – there might be an erroneous space in the classname.
Go to your dictionary settings xml. In the line:
<implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
Look for a space between “JdbcConceptFactory” and “</implementationName>”
If you see a space, remove it.
It looks like I introduced this bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>; Finan, Sean; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well. Still getting this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com>> wrote:
Hi I was able to run and produce the new custom umls files. and where put under ctakes binary (not dev).
I changed the name under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following error (not when using old org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Thanks sean for this insightful information. This is of great help.(i am
newbie to ctakes and also come from python background.)
I tested on the Fast version. Is it so that ctakes LVG is not currently
adding plurals to the terms. Because in logs i see that LVG is being setup
before processing the docs in CVD.
I guess below logs show ctakes is using LVG:
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute
path =
/Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/data/config/lvg.properties
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd =
/Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
/Users/shahid/projects/workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/lvg/
25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
/Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy
analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
25 Jan 2017 12:31:54 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser...
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope
sizes: 7 , 7
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines
loaded.
25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset
loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP
VBZ WDT WP WPS WRB
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_appliedvocab.xml
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had
build doc
FILEPATH: [Document: No DOCTYPE declaration, Root is [Element:
<lookupSpecification/>]]
25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and
term table CUI_TERMS
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - RareWordDictionary
parseDictionaries Done...
[Element: <conceptFactories/>]
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
parseConceptFactories...
25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
parseConceptFactories... Collection
Also in FASTAGGREGATE PIPELINE Desc i see
<flowConstraints>
<fixedFlow>
<node>SimpleSegmentAnnotator</node>
<node>SentenceDetectorAnnotator</node>
<node>TokenizerAnnotator</node>
* <node>LvgAnnotator</node>*
<node>ContextDependentTokenizerAnnotator</node>
<node>POSTagger</node>
<!-- <node>ClearPOSTagger</node> -->
<node>Chunker</node>
<node>AdjustNounPhraseToIncludeFollowingNP</node>
<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
<node>LookupWindowAnnotator</node>
<node>DictionaryLookupAnnotatorDB</node>
<node>DependencyParser</node>
...
</fixedFlow>
Is there any setting that will let LVG generate plurals.
On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Shahid,
>
> You will definitely find instances where the old dictionary finds terms
> but the fast does not, and vice-versa. The fast lookup uses a more concise
> dictionary, and the concepts that you noted are probably not in it. There
> is another thread between myself and Pratik Agarwal (last week in fact) on
> exactly the topic of drugs identified generically or with dose, route,
> form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
>
> Everolimus is in the dictionary by itself:
>
> sql> select * from cui_terms where text like '%everolimus%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ---------- ----------
>
> 541315 0 1 everolimus everolimus
>
>
>
> The reason why everolimus was not identified by itself is because it was
> given the part of speech “DT” (Determiner), which is specified as unwanted
> for lookup. In my test with “… given everolimus 2.5 MG …”:
>
> WordToken
>
> begin
>
> 12
>
> end
>
> 16
>
> tokenNumber
>
> 2
>
> partOfSpeech
>
> VBD
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> WordToken
>
> begin
>
> 17
>
> end
>
> 27
>
> tokenNumber
>
> 3
>
> partOfSpeech
>
> DT
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> MeasurementAnnotation
>
> begin
>
> 28
>
> end
>
> 34
>
> id
>
> 0
>
> typeID
>
> 0
>
> discoveryTechnique
>
> 0
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
>
>
> “DT” normally is assigned to things like “the, a, these” and at some
> point the community decided that words with the DT part of speech should
> not be considered as candidates for dictionary lookup.
> http://www.clips.ua.ac.be/pages/mbsp-tags
>
> The default exclusion parts of speech are:
>
> “VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
>
> To change this, set the parameter “exclusionTags” to this string without
> DT.
>
>
>
> As for “higher testosterone levels”, are you running the LVG (Lexical
> Variant Generator) module? “testosterone level” is in the dictionary, but
> the plural “testosterone levels” is not. This is done on purpose to keep
> the database small. The old dictionary may not have the same tactic.
>
> sql> select * from cui_terms where text like 'testosterone level%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ------------------ ------------
>
> 523912 0 2 testosterone level testosterone
>
>
>
> The LVG module –should- add the plural as a variant and the lookup module
> will use that variant for lookup. The dictionary module (and others) does
> not stand on its own – its success depends upon the proper output of
> previous modules in the pipeline. When I test with “… higher testosterone
> level …” (without LVG) it does find what you are looking for:
>
> WordToken
>
> begin
>
> 18
>
> end
>
> 24
>
> tokenNumber
>
> 4
>
> partOfSpeech
>
> JJR
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> ProcedureMention
>
> begin
>
> 25
>
> end
>
> 43
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 104957004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0523912
>
> tui
>
> T059
>
> preferredText
>
> Testosterone measurement
>
> typeID
>
> 5
>
> discoveryTechnique
>
> 1
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
> MedicationMention
>
> begin
>
> 25
>
> end
>
> 37
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 109033004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0039601
>
> tui
>
> T121
>
> preferredText
>
> Testosterone
>
> codingScheme
>
>
>
> I just ran through with LVG and LVG does not form “level” from “levels”.
>
>
>
>
> I hope that helps,
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Tuesday, January 24, 2017 10:17 AM
>
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Hi Sean
>
>
>
> I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow)
> . I found that one of the drug everolimus 2.5 mg is not found by the
> fast version. it is actually in RXNORM of my MRCONSO.RRF file.
>
> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|
> 998191||RXNORM|SBD|998191|*everolimus 2.5 MG* Oral Tablet
> [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
>
> Also other case is :
>
> SENTENCE: higher testosterone levels
>
> JJR NN NNS
>
> |==========|
>
> Procedure
>
> C0202227
>
> C0523912
>
> |==========|
>
> Drug
>
> C0039601
>
> AggregratePlainTextUMLSProcessor is able to find from higher testosterone levels:
>
> *testosterone levels*
>
> <refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" tui="T059"/>
>
> C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone level|9|N|256|
>
> I am not able to understand why fast version is not able to do so.
>
>
>
> MoreOver in comparison to Metamap, we are not able to do this.
>
> Phrase: higher testosterone levels
>
> Meta Mapping (966):
>
> 966 C1295653:High testosterone level (Increased testosterone level)
> [Finding]
>
>
>
> On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
>
>
> I’m glad that the fix worked!
>
> Unfortunately, the fast dictionary format will not work with the old
> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
>
> You can manually create an updated dictionary for the older module, but it
> is more involved.
>
> In our tests and those done by others the new “fast” lookup has as good or
> better accuracy depending upon the test corpus. Plus it is runs in 1/500
> th the time. I recommend that you stick to it.
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Tuesday, January 24, 2017 5:50 AM
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>
>
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks Sean
>
>
>
> That was the case for not finding the class. there were space in the xml
> generated by dictionary-gui.
>
> Also i am curious how we can use new umls with normal
> AggregratePlainTextUMLSProcessor.
>
>
>
>
>
> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Ah – there might be an erroneous space in the classname.
>
>
>
> Go to your dictionary settings xml. In the line:
>
> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory</implementationName>
>
>
>
> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>
> If you see a space, remove it.
>
>
>
> It looks like I introduced this bug a few weeks ago.
>
>
>
> Thanks,
>
> Sean
>
>
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Saturday, January 21, 2017 1:42 PM
> *To:* dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik
> agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Have put username and password (umls) in custom.xml as well. Still getting
> this error:
>
> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
> MainFrame.handleException(526): SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
>
>
> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
>
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
>
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
>
>
> <name>DictionaryDescriptorFile</name>
>
> <description/>
>
> <fileResourceSpecifier>
>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
>
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
RE: Ctakes Dictionary Gui
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Shahid,
You will definitely find instances where the old dictionary finds terms but the fast does not, and vice-versa. The fast lookup uses a more concise dictionary, and the concepts that you noted are probably not in it. There is another thread between myself and Pratik Agarwal (last week in fact) on exactly the topic of drugs identified generically or with dose, route, form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
Everolimus is in the dictionary by itself:
sql> select * from cui_terms where text like '%everolimus%';
CUI RINDEX TCOUNT TEXT RWORD
------ ------ ------ ---------- ----------
541315 0 1 everolimus everolimus
The reason why everolimus was not identified by itself is because it was given the part of speech “DT” (Determiner), which is specified as unwanted for lookup. In my test with “… given everolimus 2.5 MG …”:
WordToken
begin
12
end
16
tokenNumber
2
partOfSpeech
VBD
capitalization
0
numPosition
0
WordToken
begin
17
end
27
tokenNumber
3
partOfSpeech
DT
capitalization
0
numPosition
0
MeasurementAnnotation
begin
28
end
34
id
0
typeID
0
discoveryTechnique
0
polarity
0
uncertainty
0
conditional
false
generic
false
historyOf
0
“DT” normally is assigned to things like “the, a, these” and at some point the community decided that words with the DT part of speech should not be considered as candidates for dictionary lookup. http://www.clips.ua.ac.be/pages/mbsp-tags
The default exclusion parts of speech are:
“VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
To change this, set the parameter “exclusionTags” to this string without DT.
As for “higher testosterone levels”, are you running the LVG (Lexical Variant Generator) module? “testosterone level” is in the dictionary, but the plural “testosterone levels” is not. This is done on purpose to keep the database small. The old dictionary may not have the same tactic.
sql> select * from cui_terms where text like 'testosterone level%';
CUI RINDEX TCOUNT TEXT RWORD
------ ------ ------ ------------------ ------------
523912 0 2 testosterone level testosterone
The LVG module –should- add the plural as a variant and the lookup module will use that variant for lookup. The dictionary module (and others) does not stand on its own – its success depends upon the proper output of previous modules in the pipeline. When I test with “… higher testosterone level …” (without LVG) it does find what you are looking for:
WordToken
begin
18
end
24
tokenNumber
4
partOfSpeech
JJR
capitalization
0
numPosition
0
ProcedureMention
begin
25
end
43
id
0
codingScheme
SNOMEDCT
code
104957004
score
0.0
disambiguated
false
cui
C0523912
tui
T059
preferredText
Testosterone measurement
typeID
5
discoveryTechnique
1
polarity
0
uncertainty
0
conditional
false
generic
false
historyOf
0
MedicationMention
begin
25
end
37
id
0
codingScheme
SNOMEDCT
code
109033004
score
0.0
disambiguated
false
cui
C0039601
tui
T121
preferredText
Testosterone
codingScheme
I just ran through with LVG and LVG does not form “level” from “levels”.
I hope that helps,
Sean
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Tuesday, January 24, 2017 10:17 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Hi Sean
I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow) . I found that one of the drug everolimus 2.5 mg is not found by the fast version. it is actually in RXNORM of my MRCONSO.RRF file.
C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|998191||RXNORM|SBD|998191|everolimus 2.5 MG Oral Tablet [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
Also other case is :
SENTENCE: higher testosterone levels
JJR NN NNS
|==========|
Procedure
C0202227
C0523912
|==========|
Drug
C0039601
AggregratePlainTextUMLSProcessor is able to find from higher testosterone levels:
testosterone levels
<refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004" oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912" tui="T059"/>
C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone level|9|N|256|
I am not able to understand why fast version is not able to do so.
MoreOver in comparison to Metamap, we are not able to do this.
Phrase: higher testosterone levels
Meta Mapping (966):
966 C1295653:High testosterone level (Increased testosterone level) [Finding]
On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Hi Shahid,
I’m glad that the fix worked!
Unfortunately, the fast dictionary format will not work with the old Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
You can manually create an updated dictionary for the older module, but it is more involved.
In our tests and those done by others the new “fast” lookup has as good or better accuracy depending upon the test corpus. Plus it is runs in 1/500th the time. I recommend that you stick to it.
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Tuesday, January 24, 2017 5:50 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org<ma...@ctakes.apache.org>; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Thanks Sean
That was the case for not finding the class. there were space in the xml generated by dictionary-gui.
Also i am curious how we can use new umls with normal AggregratePlainTextUMLSProcessor.
On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Ah – there might be an erroneous space in the classname.
Go to your dictionary settings xml. In the line:
<implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
Look for a space between “JdbcConceptFactory” and “</implementationName>”
If you see a space, remove it.
It looks like I introduced this bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>; Finan, Sean; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well. Still getting this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com>> wrote:
Hi I was able to run and produce the new custom umls files. and where put under ctakes binary (not dev).
I changed the name under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following error (not when using old org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Hi Sean
I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow)
. I found that one of the drug everolimus 2.5 mg is not found by the fast
version. it is actually in RXNORM of my MRCONSO.RRF file.
C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|998191||RXNORM|SBD|998191|*everolimus
2.5 MG* Oral Tablet [Afinitor]|0|N|4352|. Let me know if you have any
inputs on this.
Also other case is :
SENTENCE: higher testosterone levels
JJR NN NNS
|==========|
Procedure
C0202227
C0523912
|==========|
Drug
C0039601
AggregratePlainTextUMLSProcessor is able to find from higher
testosterone levels:
*testosterone levels*
<refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED"
code="104957004" oid="104957004#SNOMED" score="0.0"
disambiguated="false" cui="C0523912" tui="T059"/>
C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone
level|9|N|256|
I am not able to understand why fast version is not able to do so.
MoreOver in comparison to Metamap, we are not able to do this.
Phrase: higher testosterone levels
Meta Mapping (966):
966 C1295653:High testosterone level (Increased testosterone level)
[Finding]
On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Shahid,
>
>
>
> I’m glad that the fix worked!
>
> Unfortunately, the fast dictionary format will not work with the old
> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
>
> You can manually create an updated dictionary for the older module, but it
> is more involved.
>
> In our tests and those done by others the new “fast” lookup has as good or
> better accuracy depending upon the test corpus. Plus it is runs in 1/500
> th the time. I recommend that you stick to it.
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Tuesday, January 24, 2017 5:50 AM
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
>
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks Sean
>
>
>
> That was the case for not finding the class. there were space in the xml
> generated by dictionary-gui.
>
> Also i am curious how we can use new umls with normal
> AggregratePlainTextUMLSProcessor.
>
>
>
>
>
> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> Ah – there might be an erroneous space in the classname.
>
>
>
> Go to your dictionary settings xml. In the line:
>
> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory</implementationName>
>
>
>
> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>
> If you see a space, remove it.
>
>
>
> It looks like I introduced this bug a few weeks ago.
>
>
>
> Thanks,
>
> Sean
>
>
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Saturday, January 21, 2017 1:42 PM
> *To:* dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik
> agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Have put username and password (umls) in custom.xml as well. Still getting
> this error:
>
> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
> MainFrame.handleException(526): SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
>
>
> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
>
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
>
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
>
>
> <name>DictionaryDescriptorFile</name>
>
> <description/>
>
> <fileResourceSpecifier>
>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
>
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
RE: Ctakes Dictionary Gui
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Shahid,
I’m glad that the fix worked!
Unfortunately, the fast dictionary format will not work with the old Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
You can manually create an updated dictionary for the older module, but it is more involved.
In our tests and those done by others the new “fast” lookup has as good or better accuracy depending upon the test corpus. Plus it is runs in 1/500th the time. I recommend that you stick to it.
Sean
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Tuesday, January 24, 2017 5:50 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; kant2002@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Thanks Sean
That was the case for not finding the class. there were space in the xml generated by dictionary-gui.
Also i am curious how we can use new umls with normal AggregratePlainTextUMLSProcessor.
On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Ah – there might be an erroneous space in the classname.
Go to your dictionary settings xml. In the line:
<implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
Look for a space between “JdbcConceptFactory” and “</implementationName>”
If you see a space, remove it.
It looks like I introduced this bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:shahid@trialx.com<ma...@trialx.com>]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>; Finan, Sean; kant2002@googlemail.com<ma...@googlemail.com>; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well. Still getting this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com>> wrote:
Hi I was able to run and produce the new custom umls files. and where put under ctakes binary (not dev).
I changed the name under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following error (not when using old org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Thanks Sean
That was the case for not finding the class. there were space in the xml
generated by dictionary-gui.
Also i am curious how we can use new umls with normal
AggregratePlainTextUMLSProcessor.
On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Ah – there might be an erroneous space in the classname.
>
>
>
> Go to your dictionary settings xml. In the line:
>
> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory</implementationName>
>
>
>
> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>
> If you see a space, remove it.
>
>
>
> It looks like I introduced this bug a few weeks ago.
>
>
>
> Thanks,
>
> Sean
>
>
>
>
>
> *From:* shahid ashraf [mailto:shahid@trialx.com]
> *Sent:* Saturday, January 21, 2017 1:42 PM
> *To:* dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik
> agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Have put username and password (umls) in custom.xml as well. Still getting
> this error:
>
> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
> MainFrame.handleException(526): SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
>
>
> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
>
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
>
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
>
>
> <name>DictionaryDescriptorFile</name>
>
> <description/>
>
> <fileResourceSpecifier>
>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
>
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> 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: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)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
RE: Ctakes Dictionary Gui
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Ah – there might be an erroneous space in the classname.
Go to your dictionary settings xml. In the line:
<implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
Look for a space between “JdbcConceptFactory” and “</implementationName>”
If you see a space, remove it.
It looks like I introduced this bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:shahid@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2002@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well. Still getting this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com>> wrote:
Hi I was able to run and produce the new custom umls files. and where put under ctakes binary (not dev).
I changed the name under apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
<name>DictionaryDescriptorFile</name>
<description/>
<fileResourceSpecifier>
<fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/custom.xml</fileUrl>
when running AggregatePlantextFastUmlsProcessor.xml I am getting following error (not when using old org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml)
5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Unknown class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.java:253)
... 59 more
--
with Regards
Shahid Ashraf
--
with Regards
Shahid Ashraf
Re: Ctakes Dictionary Gui
Posted by shahid ashraf <sh...@trialx.com>.
Have put username and password (umls) in custom.xml as well. Still getting
this error:
1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
MainFrame.handleException(526): SEVERE: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor: file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed. (Descriptor: file:/usr/local/apache-ctakes-
3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_
engine/UmlsLookupAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
initialize(PrimitiveAnalysisEngine_impl.java:156)
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: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)
Caused by: org.apache.uima.resource.ResourceInitializationException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key
Unknown class org.apache.ctakes.dictionary.lookup2.concept.
JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
initialize(AbstractJCasTermAnnotator.java:132)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key
Unknown class org.apache.ctakes.dictionary.lookup2.concept.
JdbcConceptFactory
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
java:255)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser.
java:226)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
lookup2.concept.JdbcConceptFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
java:253)
... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sh...@trialx.com> wrote:
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
> <name>DictionaryDescriptorFile</name>
> <description/>
> <fileResourceSpecifier>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
> failed. (Descriptor: file:/usr/local/apache-ctakes-
> 3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_
> engine/UmlsLookupAnnotator.xml)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
> 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: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)
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
> initialize(AbstractJCasTermAnnotator.java:132)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 55 more
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
> initialize(AbstractJCasTermAnnotator.java:130)
> ... 56 more
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> at java.lang.Class.forName0(Native Method)
> at java.lang.Class.forName(Class.java:264)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
> ... 59 more
>
> --
> with Regards
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf