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

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Information Provided
• Affects Version/s: 4.0.0
• Component/s: ctakes-dictionary-lookup
• Environment: Ubuntu
• Assignee: Unassigned
• Reporter: Jamil Z
• Created: 06/Apr/20 10:18
• Updated: 23/May/23 17:33
• Resolved: 23/May/23 17:33

Description

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.