Can't retrieve data back from UMLS

Question

I have been trying to run the ctakes-temporal-demo on github. Currently I have configured everything in eclipse correctly. I have set the correct password and id for UMLS account. When I try to run it I get the following error:

Exception in thread "main" java.lang.Exception: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: <unknown>)
       at com.optum.cda.Main.main(Main.java:103)
Caused by: 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: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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
       at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
       at com.optum.cda.Main.main(Main.java:101)
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:131)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
       ... 12 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:199)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128)
       at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
       ... 13 more
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
       at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196)
       ... 16 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -7
       at java.lang.String.substring(Unknown Source)
       at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
       at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
       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)
       ... 21 more

Can someone familiar with ctakes help me find out the error. I have tried the mailing list, but no replies.

Answer 1

Have you put the data of ctakesnorx.script into the database?
Also we do need to update the following attribute values :

<property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx"/>
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="rareWordTable" value="cui_terms"/>

Answer 2

Finally found a solution ! It seems like the path to the XML descriptor of the dictionary-fast is not reachable. Thus after validating an UMLS user the database setup could not be proceeded.

One of the solution I used was to use a static address for the database (which I will have to change always if the project is moved.). This is not very elegant but works.

Love to hear if anyone has another solution.