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Posted to notifications@ctakes.apache.org by "Sean Finan (JIRA)" <ji...@apache.org> on 2018/12/25 16:38:00 UTC
[jira] [Commented] (CTAKES-516) cTAKES Piper File Submitter doesn't
write xmi file to output directory
[ https://issues.apache.org/jira/browse/CTAKES-516?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16728765#comment-16728765 ]
Sean Finan commented on CTAKES-516:
-----------------------------------
You need to specify that you want to output .xmi files. Either edit a piper and add writeXmis or explicitly add a writer or use the --xmiOut command line parameter.
[https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files]
> 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
> Priority: Major
>
> 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 ...
> ..... 70
> 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 ...
> ....................................
> 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:
> ........................................................................................
> 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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