[jira] [Commented] (CTAKES-542) Error : Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.

["Sean Finan (Jira)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/CTAKES-542?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649942#comment-17649942 ] 

Sean Finan commented on CTAKES-542:
-----------------------------------

There is no further information on the error from the log?  Was a file named "ctakes.error.log" created in the ctakes root directory?

> 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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