ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: AggregatePlaintextFastUMLSProcessor.xml will not load
Date Thu, 19 Nov 2015 22:08:16 GMT
Hi Arron,

The stack trace is a  bit of a bear (our fault), but it has the line:
Caused by: java.sql.SQLException: No Hsql DB exists at Url

Your bash output is a little easier to read (thanks!), and it has:
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


Did you download the dictionary from sourceforge and put it in your resources/ directory?

Sean


-----Original Message-----
From: Arron Lacey [mailto:a.s.lacey@swansea.ac.uk] 
Sent: Thursday, November 19, 2015 4:57 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://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=BQIDAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RiIYcr73rLVeNQaQSkl00noyo-r5pbyw7Tbf_CHIwek&s=VYBl5y749hKpyw59I3n83EUvnL4Lhvg7ormepPCdItM&e=
 for user myuser:
....
19 Nov 2015 21:43:59  INFO UmlsUserApprover -   UMLS Account at 
https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=BQIDAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RiIYcr73rLVeNQaQSkl00noyo-r5pbyw7Tbf_CHIwek&s=VYBl5y749hKpyw59I3n83EUvnL4Lhvg7ormepPCdItM&e=
 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 #
#   https://urldefense.proofpoint.com/v2/url?u=http-3A__www.apache.org_licenses_LICENSE-2D2.0&d=BQIDAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RiIYcr73rLVeNQaQSkl00noyo-r5pbyw7Tbf_CHIwek&s=y4oQyGSxfGqR8KkW-M3L_wa1giVpxIGGoYjZAktdZe0&e=

#
# 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.farrinstitute.org_&d=BQIDAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RiIYcr73rLVeNQaQSkl00noyo-r5pbyw7Tbf_CHIwek&s=Nc13vD7UXW5ORb2wuLjHtOSllYcIWnVVRq6jRDS0Pcs&e=
>
*

*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



Mime
View raw message