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https://issues.apache.org/jira/browse/CTAKES-542?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649942#comment-17649942
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Sean Finan edited comment on CTAKES-542 at 12/29/22 6:14 PM:
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There is no further information on the error from the log? Was a file named
"ctakes.error.log" created in the ctakes root directory?
!! Did you download a dictionary? The lines right after the last one that you
pasted would have let us know. If you did not get the dictionary from
sourceforge and put it in the right place then dictionary lookup will fail.
was (Author: seanfinan):
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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