Meet Dave created CTAKES-516:
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Summary: cTAKES Piper File Submitter doesn't write xmi file to
output directory
Key: CTAKES-516
URL: https://issues.apache.org/jira/browse/CTAKES-516
Project: cTAKES
Issue Type: Bug
Affects Versions: 4.0.1
Environment: Ubuntu 14.04
IntelliJ IDEA 2018.2
Java 1.8
Reporter: Meet Dave
Hi
The Piper File submitter doesn't do anything after the step "Finished assigning
attributes". The output directory doesn't contain xmi files
23 Jul 2018 19:38:06 INFO PiperRunnerPanel - Running Piper File ...
23 Jul 2018 19:38:15 INFO PiperFileReader - Loading Piper File
/home/dave/fall_2018/BMS_CTakes/ctakes-clinical-pipeline-res/target/classes/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
...
23 Jul 2018 19:38:18 INFO PiperFileReader - Loading Piper File
DefaultTokenizerPipeline ...
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.23 Jul 2018 19:39:27 INFO PiperFileReader - Loading Piper File ChunkerSubPipe
...
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23 Jul 2018 19:39:28 INFO PiperFileReader - Loading Piper File
DictionarySubPipe ...
.23 Jul 2018 19:39:28 INFO PropertyAeFactory - Parameter LookupXml has value ;
ignoring empty value
.....
23 Jul 2018 19:39:29 INFO PiperFileReader - Loading Piper File
AttributeCleartkSubPipe ...
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23 Jul 2018 19:39:36 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
23 Jul 2018 19:39:36 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
23 Jul 2018 19:39:36 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
23 Jul 2018 19:39:36 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
23 Jul 2018 19:39:38 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
23 Jul 2018 19:39:39 INFO AbstractJCasTermAnnotator - Using dictionary lookup
window type: org.apache.ctakes.typesystem.type.textspan.Sentence
23 Jul 2018 19:39:39 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
23 Jul 2018 19:39:39 INFO AbstractJCasTermAnnotator - Using minimum term text
span: 3
23 Jul 2018 19:39:39 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
23 Jul 2018 19:39:39 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
23 Jul 2018 19:39:39 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
.....................23 Jul 2018 19:39:46 INFO UmlsUserApprover - UMLS Account
has been validated
23 Jul 2018 19:39:46 INFO JdbcConnectionFactory - Connecting to
jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab:
.23 Jul 2018 19:39:46 INFO ENGINE - open start - state not modified
...................................
23 Jul 2018 19:39:58 INFO JdbcConnectionFactory - Database connected
23 Jul 2018 19:39:58 INFO JdbcRareWordDictionary - Connected to cui and term
table CUI_TERMS
23 Jul 2018 19:39:58 INFO JdbcConceptFactory - Connected to concept table TUI
with class TUI
23 Jul 2018 19:39:58 INFO JdbcConceptFactory - Connected to concept table
RXNORM with class LONG
23 Jul 2018 19:39:58 INFO JdbcConceptFactory - Connected to concept table
PREFTERM with class PREFTERM
23 Jul 2018 19:39:58 INFO JdbcConceptFactory - Connected to concept table
SNOMEDCT_US with class LONG
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
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23 Jul 2018 19:40:14 INFO ClearNLPDependencyParserAE - Initializing ClearNLP
dependency parser, using lemmatizer: true
23 Jul 2018 19:40:14 INFO ClearNLPSemanticRoleLabelerAE - Starting initializing
23 Jul 2018 19:40:14 INFO ClearNLPSemanticRoleLabelerAE - Initializing ClearNLP
semantic role labeler
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23 Jul 2018 19:40:16 INFO ClearNLPSemanticRoleLabelerAE - Finished initializing
23 Jul 2018 19:40:16 INFO CleartkAnalysisEngine - Starting initializing for
Assigning Attributes
23 Jul 2018 19:40:21 INFO CleartkAnalysisEngine - Finished initializing
23 Jul 2018 19:40:22 INFO FileTreeReader - Reading
/home/dave/fall_2018/CTAKES_Data/input/test.txt
23 Jul 2018 19:40:22 INFO SentenceDetector - Starting processing.
23 Jul 2018 19:40:22 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
23 Jul 2018 19:40:22 INFO ContextDependentTokenizerAnnotator - process(JCas)
23 Jul 2018 19:40:22 INFO POSTagger - process(JCas)
23 Jul 2018 19:40:22 INFO Chunker - process(JCas)
23 Jul 2018 19:40:22 INFO ChunkAdjuster - process(JCas)
23 Jul 2018 19:40:22 INFO ChunkAdjuster - process(JCas)
23 Jul 2018 19:40:22 INFO AbstractJCasTermAnnotator - Finding Named Entities ...
23 Jul 2018 19:40:22 INFO AbstractJCasTermAnnotator - Finished processing
23 Jul 2018 19:40:22 INFO ClearNLPDependencyParserAE - Dependency parser
starting with thread:pool-2-thread-1
23 Jul 2018 19:40:22 INFO ClearNLPDependencyParserAE - Dependency parser ending
with thread:pool-2-thread-1
23 Jul 2018 19:40:22 INFO ClearNLPSemanticRoleLabelerAE - Starting processing
...
23 Jul 2018 19:40:22 INFO ClearNLPSemanticRoleLabelerAE - Finished processing
23 Jul 2018 19:40:22 INFO CleartkAnalysisEngine - Assigning Attributes ...
23 Jul 2018 19:40:22 INFO CleartkAnalysisEngine - Finished Assigning Attributes
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