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  1. cTAKES
  2. CTAKES-516

cTAKES Piper File Submitter doesn't write xmi file to output directory

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Not A Bug
    • Affects Version/s: 4.0.1
    • Fix Version/s: None
    • Component/s: None
    • Labels:
      None
    • Environment:
      Ubuntu 14.04
      IntelliJ IDEA 2018.2
      Java 1.8

      Description

      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:
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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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            • Assignee:
              Unassigned
              Reporter:
              meetdave06 Meet Dave
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              Dates

              • Created:
                Updated:
                Resolved: