Kyle Rasku created CTAKES-549:
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Summary: java.sql.SQLException: Invalid User for UMLS dictionary
sno_rx_16abTerms
Key: CTAKES-549
URL: https://issues.apache.org/jira/browse/CTAKES-549
Project: cTAKES
Issue Type: Bug
Components: ctakes-dictionary-lookup-fast
Affects Versions: 4.0.0
Environment: Ubuntu linux 18.04 and Windows 10
Reporter: Kyle Rasku
Hi,
I've been trying to set up cTAKES successfully for days. I've tried on both my
Ubuntu 18.04 machine, and on a machine running Windows 10.
In both cases, I get an exception when I try to open the CAS Debugger GUI.
I get an error message reading:
08 Jan 2021 19:29:28 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
08 Jan 2021 19:29:28 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user umls_api_key:
.08 Jan 2021 19:29:29 ERROR UmlsUserApprover - UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user
umls_api_key with a77bf06e-75aa-3cb5-8422-86497ff10856 (Not actually my API
key - though, after you export it to env. variables on linux, it does appear in
the console output, rather than CHANGE ME)
I have tried this 2 ways. One (above) using umls_api_key as the username, as
documented in the 4.0.0.1 release notes at the bottom, and another (on Windows)
passing the API key directly to java using -Dctakes.umls_apikey=\{my_api_key}
Both times, I get the above error, in spite of the fact that this works, and I
receive the right information back at
https://documentation.uts.nlm.nih.gov/rest/authentication.html:
{{curl -X POST https://utslogin.nlm.nih.gov/cas/v1/api-key -H 'content-type:
application/x-www-form-urlencoded' -d apikey=\{your_api_key_here}}}
I really hope you can help me.
Kylie
Log File:
07:29:29.310 - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526):
SEVERE: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/opt/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)07:29:29.310
- 1: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/opt/apache-ctakes-4.0.0/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:/opt/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
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:429)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
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.tools.cvd.MainFrame.setupAE(MainFrame.java:1486) at
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476) at
org.apache.uima.tools.cvd.CVD.main(CVD.java:164)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:131)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 17 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: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)
... 18 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:196)
... 21 moreCaused by: java.sql.SQLException: Invalid User for UMLS dictionary
sno_rx_16abTerms at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29)
... 26 more
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