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.la...@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.la...@swansea.ac.uk <mailto:a.s.la...@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. 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