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https://issues.apache.org/jira/browse/CTAKES-542?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Sean Finan closed CTAKES-542.
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Resolution: Information Provided
Information on a proper workflow was provided by a user.
> Error : Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> --------------------------------------------------------------------------------------------------------------------
>
> Key: CTAKES-542
> URL: https://issues.apache.org/jira/browse/CTAKES-542
> Project: cTAKES
> Issue Type: Bug
> Components: ctakes-dictionary-lookup
> Affects Versions: 4.0.0
> Environment: Ubuntu
> Reporter: Jamil Z
> Priority: Major
> Attachments: Screenshot_20200406_121736.png
>
>
> Dear everyone,
> I am trying to use cTAKES tools to find UMLS concepts given a clinical text.
> I followed the "Install cTAKES" and "Add UMLS access rights" parts in the
> user guide :
> [https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide]
> Then I tried to run the default clinical pipeline by launching this command :
> ./bin/runClinicalPipeline.sh -i input/ --xmiOut output/ --user <mylogin>
> --pass <mypass>
> However, I am getting this output (and error) - a screenshot is attached :
> 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].
> 06 avr. 2020 12:09:59 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 06 avr. 2020 12:09:59 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 06 avr. 2020 12:09:59 INFO ContextDependentTokenizerAnnotator - Finite state
> machines loaded.
> 06 avr. 2020 12:09:59 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 06 avr. 2020 12:09:59 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
> 06 avr. 2020 12:10:00 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
> 06 avr. 2020 12:10:00 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
> 06 avr. 2020 12:10:00 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
> 06 avr. 2020 12:10:00 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
> 06 avr. 2020 12:10:00 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
> 06 avr. 2020 12:10:00 INFO UmlsUserApprover - Checking UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user zaghirj:
> ..........06 avr. 2020 12:10:04 INFO UmlsUserApprover - UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user zaghirj has been
> validated
> 06 avr. 2020 12:10:04 ERROR PiperFileRunner - Initialization of annotator
> class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
> failed. (Descriptor: <unknown>)
>
> What should I do? Did I forget anything?
>
> Thank you very much for your help.
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