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tmills / ctakes-docker

Apache License 2.0
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Error on UMLS connection #37

Open Vortex10 opened 3 years ago

Vortex10 commented 3 years ago

Hi Tim,

I was trying to configure following the steps on the tutorial, however UMLS replaced the username and password to SSO, is this tutorial still valid?

What should be the configuration for the following file?

https://github.com/tmills/ctakes-docker/blob/master/env_file_sample.txt

Thanks


Certificate was added to keystore
>>> Setting defaultBrokerURL to:https://192.168.68.103:61616
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/apache-ctakes-4.0.0/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/apache-uima-as-2.10.3/apache-activemq/lib/slf4j-log4j12-1.7.13.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
  UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user <username> with <password>

org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
    at org.apache.uima.aae.controller.PrimitiveAnalysisEngineController_impl.initializeAnalysisEngine(PrimitiveAnalysisEngineController_impl.java:376)
    at org.apache.uima.aae.UimaAsPriorityBasedThreadFactory$1.run(UimaAsPriorityBasedThreadFactory.java:141)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/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: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)
tmills commented 3 years ago

You're right, the tutorial is probably not valid anymore. I have a new docker image I use for the SSO change, but it probably won't fit with the rest of the tutorial.

On Mon, Dec 28, 2020 at 3:12 PM Pedro Santos notifications@github.com wrote:

Hi Tim,

I was trying to configure following the steps on the tutorial, however UMLS replaced the username and password to SSO, is this tutorial still valid?

What should be the configuration for the following file?

https://github.com/tmills/ctakes-docker/blob/master/env_file_sample.txt

Thanks

Certificate was added to keystore

Setting defaultBrokerURL to:https://192.168.68.103:61616 SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/apache-ctakes-4.0.0/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/apache-uima-as-2.10.3/apache-activemq/lib/slf4j-log4j12-1.7.13.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user with

org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) at org.apache.uima.aae.controller.PrimitiveAnalysisEngineController_impl.initializeAnalysisEngine(PrimitiveAnalysisEngineController_impl.java:376) at org.apache.uima.aae.UimaAsPriorityBasedThreadFactory$1.run(UimaAsPriorityBasedThreadFactory.java:141) at java.lang.Thread.run(Thread.java:748) Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/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: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)

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Vortex10 commented 3 years ago

Would you have the process to build the file with the SSO or the docker build file? And the new repo

tmills commented 3 years ago

Here is the repo: https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container

On Mon, Dec 28, 2020 at 3:23 PM Pedro Santos notifications@github.com wrote:

Would you have the process to build the file with the SSO or the docker build file? And the new repo

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chen-yifu commented 3 years ago

Hi, is this repo still available anywhere? Thank you!

tmills commented 3 years ago

Hi @chen-yifu , I've re-created it so the link above should work now.

chen-yifu commented 3 years ago

Thank you very much!