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From Arron Lacey <a.s.la...@swansea.ac.uk>
Subject AggregatePlaintextFastUMLSProcessor.xml will not load
Date Thu, 19 Nov 2015 21:56:33 GMT
Hi - I am trying to load AE "AggregatePlaintextFastUMLSProcessor.xml" 
but it will not load. Here I include my log file, bash output and 
runctakesCVD.sh. I am using version 3.2.2 (downloaded and installed today)

Any help would be appreciated thanks.

*** LOG FILE ***

19/11/15 21:46:37 - 13: 
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: 
Initialization of annotator class 
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" 
failed.  (Descriptor: 
file:/home/arron/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:/home/arron/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$Handler.actionPerformed(AbstractButton.java:2346)
     at 
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
     at 
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
     at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
     at 
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
     at 
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
     at java.awt.Component.processMouseEvent(Component.java:6525)
     at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
     at java.awt.Component.processEvent(Component.java:6290)
     at java.awt.Container.processEvent(Container.java:2234)
     at java.awt.Component.dispatchEventImpl(Component.java:4881)
     at java.awt.Container.dispatchEventImpl(Container.java:2292)
     at java.awt.Component.dispatchEvent(Component.java:4703)
     at 
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
     at 
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
     at java.awt.Container.dispatchEventImpl(Container.java:2278)
     at java.awt.Window.dispatchEventImpl(Window.java:2739)
     at java.awt.Component.dispatchEvent(Component.java:4703)
     at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746)
     at java.awt.EventQueue.access$400(EventQueue.java:97)
     at java.awt.EventQueue$3.run(EventQueue.java:697)
     at java.awt.EventQueue$3.run(EventQueue.java:691)
     at java.security.AccessController.doPrivileged(Native Method)
     at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
     at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
     at java.awt.EventQueue$4.run(EventQueue.java:719)
     at java.awt.EventQueue$4.run(EventQueue.java:717)
     at java.security.AccessController.doPrivileged(Native Method)
     at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
     at java.awt.EventQueue.dispatchEvent(EventQueue.java:716)
     at 
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
     at 
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
     at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
     at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
     at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
     at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
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:132)
     at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
     ... 54 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:130)
     ... 55 more
Caused by: java.lang.reflect.InvocationTargetException
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
     at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
     at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
     at 
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200)
     ... 58 more
Caused by: java.sql.SQLException: No Hsql DB exists at Url
     at 
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:109)
     at 
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:60)
     at 
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:93)
     at 
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:75)
     at 
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
     ... 63 more
Caused by: java.io.FileNotFoundException: No File exists at 
resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script
     at 
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
     at 
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:106)
     ... 67 more


*** OUTPUT FROM BASH ***

bin/runctakesCVD.sh
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is  [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} 
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
19 Nov 2015 21:43:39  INFO LvgCmdApiResourceImpl - Loading NLM Norm and 
Lvg with config file = 
/home/arron/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
19 Nov 2015 21:43:39  INFO LvgCmdApiResourceImpl -   config file 
absolute path = 
/home/arron/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
19 Nov 2015 21:43:39  INFO LvgCmdApiResourceImpl - cwd = 
/home/arron/apache-ctakes-3.2.2
19 Nov 2015 21:43:39  INFO LvgCmdApiResourceImpl - cd 
/home/arron/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/
19 Nov 2015 21:43:39  INFO LvgCmdApiResourceImpl - cd 
/home/arron/apache-ctakes-3.2.2
19 Nov 2015 21:43:39  INFO ClearNLPDependencyParserAE - using Morphy 
analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
19 Nov 2015 21:43:51  INFO Chunker - Chunker model file: 
org/apache/ctakes/chunker/models/chunker-model.zip
19 Nov 2015 21:43:53  INFO ContextDependentTokenizerAnnotator - Finite 
state machines loaded.
19 Nov 2015 21:43:53  INFO ConstituencyParser - Initializing parser...
19 Nov 2015 21:43:56  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
19 Nov 2015 21:43:56  INFO NegationContextAnalyzer - initBoundaryData() 
called for ContextInitializer
19 Nov 2015 21:43:56  INFO DrugMentionAnnotator - Finite state machines 
loaded.
19 Nov 2015 21:43:57  INFO POSTagger - POS tagger model file: 
org/apache/ctakes/postagger/models/mayo-pos.zip
19 Nov 2015 21:43:57  INFO AbstractJCasTermAnnotator - Using dictionary 
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
19 Nov 2015 21:43:57  INFO AbstractJCasTermAnnotator - Exclusion tagset 
loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG 
VBN VBP VBZ WDT WP WPS WRB
19 Nov 2015 21:43:57  INFO AbstractJCasTermAnnotator - Using minimum 
term text span: 3
19 Nov 2015 21:43:57  INFO DictionaryDescriptorParser - Parsing 
dictionary specifications: 
/home/arron/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml
19 Nov 2015 21:43:57  INFO UmlsUserApprover - Checking UMLS Account at 
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user myuser:
....
19 Nov 2015 21:43:59  INFO UmlsUserApprover -   UMLS Account at 
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user myuser has 
been validated
19 Nov 2015 21:43:59 ERROR FileLocator - Could not find 
resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script 
as absolute or in
/home/arron/apache-ctakes-3.2.2 or in any parent thereof or in $CTAKES_HOME
null
19 Nov 2015 21:43:59 ERROR JdbcRareWordDictionary - Could not Connect to 
Dictionary UmlsHsqlRareWord


*** RUNCTAKESCVD.SH FILE ***

#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied.  See the License for the
# specific language governing permissions and limitations
# under the License.
#

# Requires JAVA JDK 1.6+
# If you plan to use the UMLS Resources, set/export env variables
#
export ctakes_umlsuser=myuser
export ctakes_umlspw=mypassword
# or add the properties
#-Dctakes.umlsuser=myuser -Dctakes.umlspw=mypassword

# You can also pass in the name of the XML descriptor to auto load as an 
arugement
# -desc 
$CTAKES_HOME/ctakes-clinical-pipeline/desc/AggregatePlaintextUMLSProcessor.xml

PRG="$0"
while [ -h "$PRG" ]; do
   ls=`ls -ld "$PRG"`
   link=`expr "$ls" : '.*-> \(.*\)$'`
   if expr "$link" : '/.*' > /dev/null; then
     PRG="$link"
   else
     PRG=`dirname "$PRG"`/"$link"
   fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* 
-Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g 
org.apache.uima.tools.cvd.CVD "$@"

-- 

*Arron Lacey
**Research Data Analyst/Research Assistant |
Dadansoddwr Data Ymchwil/Cynorthwyydd Ymchwil
*______________________________________________


Data Science Building (Third Floor) | Yr Adeilad Gwyddor Data (Trydydd 
Llawr)

Swansea University Medical School | Ysgol Feddygaeth Prifysgol Abertawe

Singleton Park | Parc Singleton

SWANSEA SA2 8PP | ABERTAWE SA2 8PP

Wales, United Kingdom | Cymru, Y Deyrnas Unedig


*Phone | Ffôn*+44 (0) 1792 60 2023
*Email | Ebost*a.s.lacey@swansea.ac.uk <mailto:a.s.lacey@swansea.ac.uk>

*www.farrinstitute.org <http://www.farrinstitute.org/>
*

*The University welcomes correspondence in Welsh and English | Mae'r 
Brifysgol yn croesawu gohebiaeth yn Gymraeg ac yn Saesneg.
*
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i'r anfonydd a dilëwch y neges.

Swansea University is a registered charity. No. 1138342 | Mae Prifysgol 
Abertawe yn elusen gofrestredig. Rhif. 1138342



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