I am having similar issue.
I created a Dictionary through dictionary creator gui
I got a folder called ICD10 and an XML file called ICD10.XML in
J:\cTAKES\ctakes-dictionary-lookup-fast-res\target\classes\org\apache\ctakes\dictionary\lookup\fast
I am using the default piper DefaultFastPipeline.piper
and I set LookupXml to
J:\cTAKES\ctakes-dictionary-lookup-fast-res\target\classes\org\apache\ctakes\dictionary\lookup\fast\ICD10.XML
But when I run the process I get the error below
Why am I getting this error and how to use the dictionary in my computer
instead of UMLS online?
Thanks
-----------------------------------------------------------------------------------------------------------------------------org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor: <unknown>) at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:274)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172)
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:279) at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) 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:279) at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) 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:279) at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331) at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448) at
org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:166)
at
org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:402)
at org.apache.ctakes.core.pipeline.PiperFileRunner.run(PiperFileRunner.java:82)
at
org.apache.ctakes.gui.pipeline.PiperRunnerPanel$PiperFileRunnable.run(PiperRunnerPanel.java:559)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)Caused by:
org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION
FAILED: 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:139)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267)
... 29 moreCaused by:
org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE
LOCALIZATION FAILED: 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:198)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:137)
... 30 moreCaused 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:423) at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195)
... 33 moreCaused by: java.sql.SQLException: No Hsql DB exists at Url at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:115)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:64)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 38 moreCaused by: java.io.FileNotFoundException: No Resource at
resources/org/apache/ctakes/dictionary/lookup/fast/icd10/icd10.script at
org.apache.ctakes.core.resource.FileLocator.getResource(FileLocator.java:273)
at
org.apache.ctakes.core.resource.FileLocator.getResource(FileLocator.java:254)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:111)
... 42 more
------------------------------------------------------------------------------------------------------------------------------------------------
On Saturday, 28 December 2019, 02:40:38 am AEDT, Finan, Sean
<sean.fi...@childrens.harvard.edu> wrote:
Hi Yatrik,
1. Download the full umls from nlm.
https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
2. Extract everything that you want using MetamorphoSys.
3. Use the ctakes dictionary creator gui to create a ctakes-compatible
database.
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
It sounds like you want to select all of the sources and all of the semantic
types.
Sean
________________________________________
From: Yatrik Buch - Network <buch_yat...@network.lilly.com.INVALID>
Sent: Friday, December 27, 2019 3:09 AM
To: dev@ctakes.apache.org
Subject: Using UMLS full dictionary in cTakes [EXTERNAL]
* External Email - Caution *
Hello,
I am currently using cTakes 4.0.0 web client app with
"/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml" as dictionary and
Clinical Pipeline.
As per my understanding this dictionary is subset of UMLS dictionary.
I require to use full UMLS dictionary. Is it possible access online UMLS
dictionary from cTakes API code ? Or Do I need to download the full dictionary
and use it ?
Thanks,
Yatrik
