Hello,
I’m an intern in the Stanford Biomedical Informatics Lab and I've been working
on getting a ctakes page for a week, and I’ve been getting a lot of errors. I
have been getting a filed to initialize error for the last day and a half and I
can not solve it. I will send you the whole log, if you can help me out it
would be greatly appreciated.
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].
/Users/sboussard/Desktop/apache-ctakes-4.0.0/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
09 Aug 2019 11:28:50 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
09 Aug 2019 11:28:50 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
09 Aug 2019 11:28:50 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
09 Aug 2019 11:28:50 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
09 Aug 2019 11:28:51 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using dictionary lookup
window type: org.apache.ctakes.typesystem.type.textspan.Sentence
09 Aug 2019 11:28:52 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
09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using minimum term text
span: 3
09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
09 Aug 2019 11:28:52 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
09 Aug 2019 11:28:52 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard:
..09 Aug 2019 11:28:53 INFO UmlsUserApprover - UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard has been
validated
09 Aug 2019 11:28:53 ERROR ClinicalProcessor - Initialization of annotator
class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed. (Descriptor: <unknown>)
