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From Arron Lacey <a.s.la...@swansea.ac.uk>
Subject Re: AggregatePlaintextFastUMLSProcessor.xml will not load
Date Sun, 22 Nov 2015 22:30:18 GMT
Thanks Tomasz - I now have this working.

Arron.

*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.
*
Please don't print this e-mail unless you really need to. | Peidiwch ag 
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The contents of this email are confidential and for the intended 
recipient only. If you have received this
message in error, please inform the sender and delete the message. | Mae 
cynnwys yr ebost hwn yn gyfrinachol a dim ond y derbynnydd a fwriadwyd a 
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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


On 19/11/15 22:07, Tomasz Oliwa wrote:
> If you look at the bottom of your Exception you will see:
>
> ...
> 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
> ...
>
> It looks like the cTAKES resources are not found, you can get them here:
> http://sourceforge.net/projects/ctakesresources/files/
>
> The guide on how to extract them for a dev install is:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
>
> For a user install:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide
>
> Regards,
> Tomasz
>
>
>
> ________________________________________
> From: Arron Lacey [a.s.lacey@swansea.ac.uk]
> Sent: Thursday, November 19, 2015 3:56 PM
> To: dev@ctakes.apache.org
> Subject: AggregatePlaintextFastUMLSProcessor.xml will not load
>
> 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.
> *
> Please don't print this e-mail unless you really need to. | Peidiwch ag
> argraffu'r e-bost hwn oni bai fod gwir angen gwneud hynny.
>
> The contents of this email are confidential and for the intended
> recipient only. If you have received this
> message in error, please inform the sender and delete the message. | Mae
> cynnwys yr ebost hwn yn gyfrinachol a dim ond y derbynnydd a fwriadwyd a
> ddylai ei ddarllen. Os derbynioch y neges mewn camgymeriad, rhowch wybod
> 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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