Trying to run AggregatePlainTextFastUMLSProcessor

[Sai Anuroop <sa...@abzooba.com>]

Hi,

As given in user install guide i made an account in UMLS and received
username and password. then using the java command given in the install
guide i have added credentials.then i am trying to run
AggregatePlainTextFastUMLSProcessor but i am receiving the following error

15/5/15 11:04:00 AM - 15:
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
 (Descriptor:
file:/D:/abzooba/ctakes/apache-ctakes-3.2.1/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:/D:/abzooba/ctakes/apache-ctakes-3.2.1/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.produceResource(UIMAFramework.java:314)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.apache.uima.resource.ResourceInitializationException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key Could
not construct
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:134)
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 Could
not construct
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:203)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:160)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:131)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
... 56 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200)
... 59 more
Caused by: java.sql.SQLException: Invalid User for UMLS dictionary
UmlsHsqlRareWord
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29)
... 64 more

does it mean that i could not add UMLS credentials, because i have entered
for sure valid username and password .Please can anyone tell how to check
it and if not added how to add.(please give the exact java command also)
Regards,

Vetsa Sai Anuroop

Abzooba India Infotech Private Limited

10th Floor, Infinity Benchmark, Block EP GP, Sector V, Salt Lake, Kolkata –
700 091, West Bengal, India


This e-mail and any attachments transmitted with it are confidential and
may be legally privileged. If you are not the intended recipient or if you
have received this e-mail in error, you must destroy all copies incl.
attachments and notify the sender by return e-mail or by phone. Any
dissemination, distribution or other use of the contents of this message by
anyone other than the intended recipient is strictly prohibited. Abzooba
does not guarantee that this email has not been monitored, intercepted and
amended or that it is virus or error free. Any views expressed in this
message are those of the individual sender. All liabilities of the Abzooba
Group and its entities for any damages resulting from e-mail use are
excluded.

RE: Trying to run AggregatePlainTextFastUMLSProcessor

["Miller, Timothy" <Ti...@childrens.harvard.edu>]

Hi Sai,
The problem is probably related to the NLM recently changing the response their server gives to the license check. We have checked in a fix to trunk and there is a new release candidate being tested right now that should hopefully be released soon.
Tim


________________________________
From: Sai Anuroop [sai.anuroop@abzooba.com]
Sent: Friday, May 15, 2015 1:45 AM
To: user@ctakes.apache.org
Subject: Trying to run AggregatePlainTextFastUMLSProcessor

Hi,

As given in user install guide i made an account in UMLS and received username and password. then using the java command given in the install guide i have added credentials.then i am trying to run AggregatePlainTextFastUMLSProcessor but i am receiving the following error

15/5/15 11:04:00 AM - 15: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/D:/abzooba/ctakes/apache-ctakes-3.2.1/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:/D:/abzooba/ctakes/apache-ctakes-3.2.1/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.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:134)
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 Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:203)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:160)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:131)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
... 56 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200)
... 59 more
Caused by: java.sql.SQLException: Invalid User for UMLS dictionary UmlsHsqlRareWord
at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29)
... 64 more

does it mean that i could not add UMLS credentials, because i have entered for sure valid username and password .Please can anyone tell how to check it and if not added how to add.(please give the exact java command also)
Regards,

Vetsa Sai Anuroop

Abzooba India Infotech Private Limited

10th Floor, Infinity Benchmark, Block EP GP, Sector V, Salt Lake, Kolkata – 700 091, West Bengal, India


This e-mail and any attachments transmitted with it are confidential and may be legally privileged. If you are not the intended recipient or if you have received this e-mail in error, you must destroy all copies incl. attachments and notify the sender by return e-mail or by phone. Any dissemination, distribution or other use of the contents of this message by anyone other than the intended recipient is strictly prohibited. Abzooba does not guarantee that this email has not been monitored, intercepted and amended or that it is virus or error free. Any views expressed in this message are those of the individual sender. All liabilities of the Abzooba Group and its entities for any damages resulting from e-mail use are excluded.