Hi all,
I'm using cTAKES user to process CDA documents by AggregateCdaProcessor.xml and
AggregateCdaUMLSProcessor.xml located in
/desc/ctakes-clinical-pipeline/desc/analysis_engine/
My script to call this is
java -Dctakes.umlsuser= -Dctakes.umlspw= -cp
$CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/
-Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms2g -Xmx3g
org.apache.ctakes.core.cpe.CmdLineCpeRunner
$CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda_masoud.xml
test_cda_masoud.xml has a proper path to CDA input and output. I'm using the
two CDA files that come with the cTAKES package (testpatient_cn_2.xml and
testpatient_cn_1.xml compatible with NotesIIST_RTF.DTD).
Unfortunately, it seems that CdaCasInitializer cannot run, and I get the
attached errors. I get the same errors when using the GUI with
AggregateCdaProcessor AE
- Am I missing something obvious?
- Does cTAKES *User* installation handle CDA documents?
- Is org.apache.ctakes.core.cpe.CmdLineCpeRunner an appropriate pipeline for
CdaCasInitializer?
Thank you so much for your help in advance.
Masoud
On 11/8/19, 8:30 AM, "Finan, Sean" <[email protected]> wrote:
Hi Masoud,
I think that the CdaCasInitializer is at least 10 years old. I would not
expect it to conform to any recent standards.
Does anybody else have a reader or transformer that can handle HL7 CDA r2?
Sean
p.s.
If anybody is involved with HL7 International, you may want to get some
movement on addressing the typo on the page header(s):
Section 1a: Clinical Document Architcture (CDA®)
________________________________________
From: Masoud Rouhizadeh <[email protected]>
Sent: Thursday, November 7, 2019 5:59 PM
To: [email protected]
Subject: cTAKES handling HL7 CDA Level 1 [EXTERNAL]
Dear cTAKES developer mailing list,
We have been working on a project at Hopkins for converting Epic-generated
RTF notes into Clinical Document Architecture Level One.
We have been using HL7 CDA® Release 2 Schema, and now we plan to use cTAKES
for concept extraction from those documents. The CDA Schema and examples can be
found here
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.hl7.org_implement_standards_product-5Fbrief.cfm-3Fproduct-5Fid-3D7&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=h8q4BiKKL6eDBOGEta7gcpkDGIx5xFPlGrNfUPlzBuc&s=l8HjgDHeywmdkSUkOJBGWNLpJ-bPlw7Lmgzh02w8k2s&e=
In the cTAKES documentation, I see that CdaCasInitializer "does not handle
all CDA documents. The CDA document must conform to the DTD
resources/cda/NotesIIST_RTF.DTD."
Has anyone tested and evaluated cTAKES ability to consume HL7 CDA Level 1
Release 2 documents?
Thank you,
Masoud
----
Masoud Rouhizadeh, PhD
Faculty - Division of Health Science Informatics (DHSI)
NLP Lead - Institute for Clinical and Translational Research (ICTR)
Johns Hopkins University School of Medicine
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cs.jhu.edu_-7Emrou_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=h8q4BiKKL6eDBOGEta7gcpkDGIx5xFPlGrNfUPlzBuc&s=8fvrQoIy8orWYKCJoob5Z0Sbbioe5xyiN7pDMTzImOc&e=
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].
18 Dec 2019 13:24:09 INFO CdaCasInitializer - Hyphen dictionary:
org/apache/ctakes/preprocessor/tokenizer/hyphenated.txt
18 Dec 2019 13:24:09 INFO CdaCasInitializer - DTD:
org/apache/ctakes/preprocessor/cda/NotesIIST_RTF.DTD
18 Dec 2019 13:24:09 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using left , right scope sizes: 7
, 7
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
18 Dec 2019 13:24:11 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
18 Dec 2019 13:24:11 INFO NegationContextAnalyzer - initBoundaryData() called
for ContextInitializer
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
18 Dec 2019 13:24:11 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
18 Dec 2019 13:24:11 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
18 Dec 2019 13:24:11 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using left , right scope sizes:
10 , 10
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
18 Dec 2019 13:24:11 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.status.StatusContextAnalyzer
18 Dec 2019 13:24:11 INFO StatusContextAnalyzer - initBoundaryData() called
for ContextInitializer
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.status.StatusContextHitConsumer
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
18 Dec 2019 13:24:11 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
18 Dec 2019 13:24:11 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
18 Dec 2019 13:24:11 INFO LvgCmdApiResourceImpl - config file absolute path
=
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
18 Dec 2019 13:24:11 INFO LvgCmdApiResourceImpl - cwd =
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0
18 Dec 2019 13:24:11 INFO LvgCmdApiResourceImpl - cd
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/
18 Dec 2019 13:24:11 INFO ENGINE - open start - state not modified
18 Dec 2019 13:24:11 INFO ENGINE - dataFileCache open start
18 Dec 2019 13:24:12 INFO LvgCmdApiResourceImpl - cd
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0
18 Dec 2019 13:24:12 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl -
indexDir=org/apache/ctakes/dictionary/lookup/drug_index exists.
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loading Lucene Index
into memory:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/drug_index
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loaded Lucene Index,
# docs=5
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl -
indexDir=org/apache/ctakes/dictionary/lookup/OrangeBook exists.
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loading Lucene Index
into memory:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/OrangeBook
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loaded Lucene Index,
# docs=18889
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl -
indexDir=org/apache/ctakes/dictionary/lookup/snomed-like_sample exists.
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loading Lucene Index
into memory:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/snomed-like_sample
18 Dec 2019 13:24:12 INFO LuceneIndexReaderResourceImpl - Loaded Lucene Index,
# docs=12
18 Dec 2019 13:24:12 INFO DictionaryLookupAnnotator - Parsing descriptor:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/LookupDesc.xml
18 Dec 2019 13:24:12 INFO FirstTokenPermLookupInitializerImpl - Exclusion
tagset loaded: [cc, pp, cd, pdt, prp$, vbn, vbp, pp$, wdt, wrb, ls, vb, vbz,
prp, dt, ex, pos, md, vbd, wp, vbg, to, wps, rp]
18 Dec 2019 13:24:12 INFO UmlsToSnomedLuceneConsumerImpl - Using lucene index:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/snomed-like_codes_sample
18 Dec 2019 13:24:12 INFO UmlsToSnomedLuceneConsumerImpl - Loaded Lucene index
with 15 entries.
18 Dec 2019 13:24:12 INFO FirstTokenPermLookupInitializerImpl - Exclusion
tagset loaded: [cc, pp, cd, pdt, vbn, vbp, pp$, wdt, wrb, ls, vb, vbz, dt, ex,
pos, md, vbd, wp, vbg, to, wps, rp]
18 Dec 2019 13:24:12 INFO AssertionAnalysisEngine - scope model file:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/assertion/models/scope.model
18 Dec 2019 13:24:12 INFO AssertionAnalysisEngine - cue model file:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/assertion/models/cue.model
18 Dec 2019 13:24:12 INFO AssertionAnalysisEngine - pos model file:
/Users/mrou/CCDA-Mac/Tools/apache-ctakes-4.0.0/resources/org/apache/ctakes/assertion/models/pos.model
18 Dec 2019 13:24:12 WARN BatchRunner - This class cannot be used until
CTAKES-76 is implemented.
18 Dec 2019 13:24:12 WARN JarafeMEDecoder - This class cannot be used until
CTAKES-76 is implemented.
Dec 18, 2019 1:24:12 PM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named assertionModelResourceImpl has been
declared multiple times with different definitions. The definition of the
resource in component
/AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be
used. The definition in component
/AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will
be ignored.
Dec 18, 2019 1:24:12 PM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named scopeModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will
be ignored.
Dec 18, 2019 1:24:12 PM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named cueModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will
be ignored.
Dec 18, 2019 1:24:12 PM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named enabledFeaturesResourceImpl has been
declared multiple times with different definitions. The definition of the
resource in component
/AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be
used. The definition in component
/AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will
be ignored.
18 Dec 2019 13:24:12 INFO ClearNLPDependencyParserAE - using Morphy analysis?
true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
CPM Initialization Complete
18 Dec 2019 13:24:24 INFO CdaCasInitializer - process(JCas)
[Fatal Error] :1:1: Content is not allowed in prolog.
Dec 18, 2019 1:24:24 PM
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
callAnalysisComponentProcess(430)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:230)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1;
Content is not allowed in prolog.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175)
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:168)
... 10 more
Dec 18, 2019 1:24:24 PM
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
processAndOutputNewCASes(273)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:230)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1;
Content is not allowed in prolog.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175)
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:168)
... 10 more
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:230)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1;
Content is not allowed in prolog.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175)
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:168)
... 10 more
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit process
SEVERE: The container AggregateCdaProcessor returned the following error
message: null (Thread Name: [Procesing Pipeline#1 Thread]::)
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit
maybeLogSevereException(2500)
SEVERE: Thread: [Procesing Pipeline#1 Thread]::, message: null
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:230)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1;
Content is not allowed in prolog.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175)
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:168)
... 10 more
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:230)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1;
Content is not allowed in prolog.
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175)
at
org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:168)
... 10 more
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.container.ProcessingContainer_Impl process
SEVERE: The CPM stopped because the configured error threshold 0 was exceeded.
(Thread Name: [Procesing Pipeline#1 Thread]::) Component Name:
AggregateCdaProcessor
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit process
SEVERE: The CPM is terminating. The current component is AggregateCdaProcessor.
(Thread Name: [Procesing Pipeline#1 Thread]::)
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit process
WARNING: The CPM cannot be stopped by force. The current container is
AggregateCdaProcessor. (Thread Name: [Procesing Pipeline#1 Thread]::) Reason:
The CAS processor AggregateCdaProcessor is configured to stop the CPM when
excessive errors are encountered. (Thread Name: [Procesing Pipeline#1
Thread]::)
Dec 18, 2019 1:24:24 PM
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit
maybeLogSevereException(2500)
SEVERE: Thread: [Procesing Pipeline#1 Thread]::, message:
org.apache.uima.collection.base_cpm.AbortCPMException:
at
org.apache.uima.collection.impl.cpm.container.ProcessingContainer_Impl.incrementCasProcessorErrors(ProcessingContainer_Impl.java:795)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:1039)
at
org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
Dec 18, 2019 1:24:24 PM org.apache.uima.collection.impl.cpm.engine.CPMEngine
process
INFO: The collection reader thread state is: 1004 (Thread Name: [Procesing
Pipeline#1 Thread]::)
Dec 18, 2019 1:24:24 PM org.apache.uima.collection.impl.cpm.engine.CPMEngine
process
INFO: The CPM processing unit is 0 and processing state 2003. (Thread Name:
[Procesing Pipeline#1 Thread]::)
Dec 18, 2019 1:24:24 PM org.apache.uima.collection.impl.cpm.engine.CPMEngine
process
INFO: The CAS consumer thread state is 2001. (Thread Name: [Procesing
Pipeline#1 Thread]::)
Dec 18, 2019 1:24:24 PM org.apache.uima.collection.impl.cpm.engine.CPMEngine
process
INFO: The application stopped the CPM. (Thread Name: [Procesing Pipeline#1
Thread]::)
Dec 18, 2019 1:24:24 PM org.apache.uima.collection.impl.cpm.engine.CPMEngine
process
INFO: The CPM engine is stopping. An end-of-file token is added to the worker
queue. (Thread Name: [Procesing Pipeline#1 Thread]::) Forced stop: true
Aborted
