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dirkweissenborn / ctakes-server

A simple REST-server around ctakes clinical pipeline.
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Unable to setup server #7

Closed ChaiBapchya closed 7 years ago

ChaiBapchya commented 7 years ago

Followed all the commands for cloning repos and setting up server, Command

java -Dctakes.umlsuser='user' -Dctakes.umlspw='mypass' -Xmx3g -cp target/ctakes-server-0.1.jar:resources/ de.dfki.lt.ctakes.Server localhost 9999 desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml

Error - 

Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/Users/chaitanyabapat/8903/ctakes-server/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)

Error-trace - 

java -Dctakes.umlsuser='user' -Dctakes.umlspw='mypass' -Xmx3g -cp target/ctakes-server-0.1.jar:resources/ de.dfki.lt.ctakes.Server localhost 9999 desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
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].
11 Nov 2017 17:05:47  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = /Users/chaitanyabapat/8903/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
11 Nov 2017 17:05:47  INFO LvgCmdApiResourceImpl -   config file absolute path = /Users/chaitanyabapat/8903/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
11 Nov 2017 17:05:47  INFO LvgCmdApiResourceImpl - cwd = /Users/chaitanyabapat/8903/ctakes-server
11 Nov 2017 17:05:47  INFO LvgCmdApiResourceImpl - cd /Users/chaitanyabapat/8903/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/
java.sql.SQLException: error in script file line: 1 Unexpected token UNIQUE, requires COLLATION in statement [SET DATABASE UNIQUE]
    at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
    at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
    at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
    at org.hsqldb.jdbcDriver.connect(Unknown Source)
    at java.sql.DriverManager.getConnection(DriverManager.java:664)
    at java.sql.DriverManager.getConnection(DriverManager.java:247)
    at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:40)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1479)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1432)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:86)
    at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
    at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
    at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
    at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
    at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
    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 de.dfki.lt.ctakes.Server$.main(Server.scala:35)
    at de.dfki.lt.ctakes.Server.main(Server.scala)
java.sql.SQLException: error in script file line: 1 Unexpected token UNIQUE, requires COLLATION in statement [SET DATABASE UNIQUE]
    at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
    at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
    at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
    at org.hsqldb.jdbcDriver.connect(Unknown Source)
    at java.sql.DriverManager.getConnection(DriverManager.java:664)
    at java.sql.DriverManager.getConnection(DriverManager.java:247)
    at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:40)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1479)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1432)
    at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:86)
    at gov.nih.nlm.nls.lvg.Api.LvgLexItemApi.<init>(LvgLexItemApi.java:80)
    at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:94)
    at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
    at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
    at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
    at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
    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 de.dfki.lt.ctakes.Server$.main(Server.scala:35)
    at de.dfki.lt.ctakes.Server.main(Server.scala)
11 Nov 2017 17:05:47  INFO LvgCmdApiResourceImpl - cd /Users/chaitanyabapat/8903/ctakes-server
11 Nov 2017 17:05:47  INFO ClearNLPDependencyParserAE - using Morphy analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
11 Nov 2017 17:05:59  INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip
11 Nov 2017 17:06:01  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
11 Nov 2017 17:06:01  INFO ConstituencyParser - Initializing parser...
11 Nov 2017 17:06:05  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
11 Nov 2017 17:06:05  INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer
11 Nov 2017 17:06:05  INFO DrugMentionAnnotator - Finite state machines loaded.
11 Nov 2017 17:06:06  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
11 Nov 2017 17:06:06  INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
11 Nov 2017 17:06:06  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 
11 Nov 2017 17:06:06  INFO AbstractJCasTermAnnotator - Using minimum term text span: 3
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/Users/chaitanyabapat/8903/ctakes-server/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 de.dfki.lt.ctakes.Server$.main(Server.scala:35)
    at de.dfki.lt.ctakes.Server.main(Server.scala)
Caused by: java.lang.NullPointerException
    at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
    ... 15 more
dirkweissenborn commented 7 years ago

these errors are CTakes specific errors and have nothing to do with this server. the server simply converts the output CAS to json and provides a REST interface.

ashanideepta commented 6 years ago

I am trying to run the code on a blank new EC2 instance and I get this exact same error. @ChaiBapchya did you find a solution to this error?

ChaiBapchya commented 6 years ago

Umm no. I was stuck on that too.

dermatologist commented 6 years ago

Same here. Any solution yet?

parthnatu commented 6 years ago

change <ctakes.version> tag in pom.xml to 4.0.0

humehta commented 6 years ago

where do we change the pom.xml? where can we find it?

parthnatu commented 6 years ago

It's in the root of this repository.

sakatipomu commented 6 years ago

any solution for this problem?

parthnatu commented 6 years ago

This file is present in the root of the repository when you clone it. Change the version to 4.0.0

sakatipomu commented 6 years ago

@parthnatu, Thank you for the suggestion. But I am not using ctakes-server, I have imported ctakes developer version from ctakes website. So I do not have this pom.xml.But still facing this error.I tried changing ctakes/pom.xml also.

parthnatu commented 6 years ago

Can you paste the log here? Also I suggest following the instructions completely and reinstalling.

sakatipomu commented 6 years ago

@parthnatu , I have given UMLS username and password as VM arguments. I hope that error is solved now. But Currently I am facing another error. Please shed some light if you know about it.

11:33:31.06 - 16: org.apache.uima.tools.cvd.MainFrame.handleException(666): SEVERE: The class org.apache.ctakes.drugner.ae.DrugMentionAnnotator could not be found. (Descriptor: file:/Users/skatipomu/cTAKES/ctakes/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml) org.apache.uima.resource.ResourceInitializationException: The class org.apache.ctakes.drugner.ae.DrugMentionAnnotator could not be found. (Descriptor: file:/Users/skatipomu/cTAKES/ctakes/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml) at org.apache.uima.resource.impl.ResourceManager_impl.loadUserClassOrThrow(ResourceManager_impl.java:874) at org.apache.uima.resource.Resource_ImplBase.loadUserClassOrThrow(Resource_ImplBase.java:334) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:210) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:173) 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:289) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:417) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:435) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192) 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:289) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:381) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1803) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:605) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:66) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886) at java.awt.Component.processMouseEvent(Component.java:6539) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2239) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2297) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476) at java.awt.Container.dispatchEventImpl(Container.java:2283) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) at java.awt.EventQueue$4.run(EventQueue.java:733) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) 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: java.lang.ClassNotFoundException: org.apache.ctakes.drugner.ae.DrugMentionAnnotator at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at org.apache.uima.resource.impl.ResourceManager_impl.loadUserClass(ResourceManager_impl.java:856) at org.apache.uima.resource.impl.ResourceManager_impl.loadUserClassOrThrow(ResourceManager_impl.java:870) ... 57 more

parthnatu commented 6 years ago

I think you should try reinstalling and raising this issue in the ctakes repository.