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Posted to commits@ctakes.apache.org by se...@apache.org on 2024/07/31 14:06:17 UTC
(ctakes) branch main updated (1556d13 -> 5e0f7bd)
This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a change to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
from 1556d13 Replaced all logging with log4j2 , including java and commons-logging Removed or pushed back a few dependencies.
add 837666c Issue #20 - Crossgrade to SLF4J
new 5e0f7bd Merge pull request #21 from apache/refactoring/20-Crossgrade-to-SLF4J
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
.../java/org/mitre/medfacts/uima/RunZoner.java | 6 +--
.../org/mitre/medfacts/uima/ZoneAnnotator.java | 6 +--
.../attributes/GenericAttributeAnalysisEngine.java | 6 +--
.../attributes/SubjectAttributeAnalysisEngine.java | 6 +--
.../subject/SubjectAttributeClassifier.java | 14 ++++--
.../cr/I2B2Challenge2010CollectionReader.java | 6 +--
.../assertion/cr/MiPACQKnowtatorXMLReader.java | 6 +--
.../ctakes/assertion/cr/NegExAnnotation.java | 6 +--
.../ctakes/assertion/cr/NegExCorpusReader.java | 6 +--
.../ctakes/assertion/eval/AssertionEvaluation.java | 6 +--
...dViewFromOneCasIntoInitialViewOfAnotherCas.java | 6 +--
.../medfacts/AssertionAnalysisEngine.java | 11 ++---
.../medfacts/AssertionAnalysisEngineFit.java | 6 +--
.../ctakes/assertion/medfacts/CasIndexer.java | 6 +--
.../medfacts/ConceptConverterAnalysisEngine.java | 6 +--
.../ctakes/assertion/medfacts/ConceptLookup.java | 6 +--
.../medfacts/Converti2b2AnnotationsToCTAKES.java | 6 +--
.../cleartk/AssertionCleartkAnalysisEngine.java | 15 +++---
.../cleartk/PolarityCleartkAnalysisEngine.java | 4 +-
.../cleartk/PolarityFedaCleartkAnalysisEngine.java | 4 +-
.../cleartk/SubjectCleartkAnalysisEngine.java | 5 +-
.../medfacts/cleartk/TrainAssertionModel.java | 6 +--
.../medfacts/cleartk/extractors/CueWordTest.java | 6 +--
.../medfacts/cleartk/extractors/CueWordTest2.java | 6 +--
.../cleartk/extractors/SurroundingExtractor.java | 2 +-
.../SubjectCleartkAnalysisEngineWindowed.java | 5 +-
.../WindowedAssertionCleartkAnalysisEngine.java | 6 +--
...racterOffsetToLineTokenConverterCtakesImpl.java | 6 +--
.../i2b2/api/SingleDocumentProcessorCtakes.java | 6 +--
.../GenerateDependencyRepresentation.java | 6 +--
.../pipelines/GenerateTreeRepresentation.java | 6 +--
...ityAndAttributeReaderPipelineForSeedCorpus.java | 16 ++++---
.../ctakes/assertion/stub/AssertionAnnotation.java | 6 +--
.../assertion/stub/AssertionFileProcessor.java | 6 +--
.../apache/ctakes/assertion/stub/BatchRunner.java | 6 +--
.../ctakes/assertion/stub/JarafeMEDecoder.java | 6 +--
.../assertion/stub/SingleDocumentProcessor.java | 6 +--
.../ctakes/assertion/stub/StringHandling.java | 6 +--
.../java/org/apache/ctakes/chunker/ae/Chunker.java | 6 +--
.../ctakes/chunker/ae/adjuster/ChunkAdjuster.java | 6 +--
.../chunker/concurrent/ThreadSafeChunker.java | 6 +--
.../constituency/parser/MaxentParserWrapper.java | 6 +--
.../constituency/parser/ae/ConstituencyParser.java | 6 +--
.../concurrent/ThreadSafeConstituencyParser.java | 6 +--
.../ae/ContextDependentTokenizerAnnotator.java | 6 +--
.../ctakes/core/ae/AbstractCommandRunner.java | 6 +--
.../apache/ctakes/core/ae/BsvRegexSectionizer.java | 6 +--
.../apache/ctakes/core/ae/CDASegmentAnnotator.java | 6 +--
.../org/apache/ctakes/core/ae/CommandRunner.java | 12 ++---
.../org/apache/ctakes/core/ae/CopyAnnotator.java | 6 +--
.../org/apache/ctakes/core/ae/CtakesRunner.java | 6 +--
.../core/ae/DocumentIdPrinterAnalysisEngine.java | 6 +--
.../apache/ctakes/core/ae/EolSentenceFixer.java | 6 +--
.../java/org/apache/ctakes/core/ae/ExitForcer.java | 6 +--
.../org/apache/ctakes/core/ae/LabValueFinder.java | 6 +--
.../org/apache/ctakes/core/ae/ListAnnotator.java | 6 +--
.../apache/ctakes/core/ae/ListEntryNegator.java | 6 +--
.../apache/ctakes/core/ae/ListParagraphFixer.java | 6 +--
.../apache/ctakes/core/ae/ListSentenceFixer.java | 6 +--
.../apache/ctakes/core/ae/MrsDrSentenceJoiner.java | 6 +--
.../apache/ctakes/core/ae/OverlapAnnotator.java | 6 +--
.../apache/ctakes/core/ae/ParagraphAnnotator.java | 6 +--
.../ctakes/core/ae/ParagraphSentenceFixer.java | 6 +--
.../apache/ctakes/core/ae/PiperFileRunEngine.java | 6 +--
.../org/apache/ctakes/core/ae/PythonPipper.java | 6 +--
.../org/apache/ctakes/core/ae/PythonRunner.java | 10 ++--
.../apache/ctakes/core/ae/RegexSectionizer.java | 6 +--
.../ctakes/core/ae/SHARPKnowtatorXMLReader.java | 24 ++++++----
.../ctakes/core/ae/SectionSegmentAnnotator.java | 6 +--
.../apache/ctakes/core/ae/SentenceDetector.java | 8 ++--
.../core/ae/SentenceDetectorAnnotatorBIO.java | 6 +--
.../core/ae/SimpleSegmentWithTagsAnnotator.java | 6 +--
.../apache/ctakes/core/ae/StartFinishLogger.java | 6 +--
.../apache/ctakes/core/ae/SubjectSectionFixer.java | 6 +--
.../ctakes/core/ae/TemplateFillerAnnotator.java | 6 +--
.../apache/ctakes/core/ae/TokenizerAnnotator.java | 6 +--
.../ctakes/core/ae/TokenizerAnnotatorPTB.java | 6 +--
.../apache/ctakes/core/cc/AbstractFileWriter.java | 6 +--
.../apache/ctakes/core/cc/AbstractJdbcWriter.java | 6 +--
.../ctakes/core/cc/AbstractTableFileWriter.java | 6 +--
.../org/apache/ctakes/core/cc/CasConsumer.java | 6 +--
.../apache/ctakes/core/cc/CuiCountFileWriter.java | 6 +--
.../apache/ctakes/core/cc/CuiListFileWriter.java | 6 +--
.../org/apache/ctakes/core/cc/CuiLookupLister.java | 6 +--
.../apache/ctakes/core/cc/FileTreeXmiWriter.java | 6 +--
.../core/cc/FilesInDirectoryCasConsumer.java | 6 +--
.../apache/ctakes/core/cc/JdbcWriterTemplate.java | 6 +--
.../ctakes/core/cc/SemanticTableFileWriter.java | 6 +--
.../ctakes/core/cc/SentenceTokensPrinter.java | 6 +--
.../org/apache/ctakes/core/cc/TextSpanWriter.java | 6 +--
.../ctakes/core/cc/XmiWriterCasConsumerCtakes.java | 6 +--
.../org/apache/ctakes/core/cc/html/CssWriter.java | 6 +--
.../apache/ctakes/core/cc/html/HtmlTextWriter.java | 6 +--
.../org/apache/ctakes/core/cc/html/JsWriter.java | 6 +--
.../ctakes/core/cc/jdbc/AbstractJdbcWriter.java | 6 +--
.../apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java | 6 +--
.../ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java | 6 +--
.../core/cc/jdbc/i2b2/ObservationFactRow.java | 6 +--
.../ctakes/core/cc/jdbc/row/EmptyInitializer.java | 6 +--
.../ctakes/core/cc/pretty/html/CssWriter.java | 6 +--
.../ctakes/core/cc/pretty/html/HtmlTextWriter.java | 6 +--
.../ctakes/core/cc/pretty/html/JsWriter.java | 6 +--
.../core/cc/pretty/plaintext/PrettyTextWriter.java | 6 +--
.../cc/pretty/plaintext/PrettyTextWriterFit.java | 4 +-
.../cc/pretty/plaintext/PrettyTextWriterUima.java | 6 +--
.../cc/property/plaintext/PropertyTextWriter.java | 6 +--
.../property/plaintext/PropertyTextWriterFit.java | 2 +-
.../property/plaintext/PropertyTextWriterUima.java | 6 +--
.../concurrent/ThreadSafeSentenceDetector.java | 6 +--
.../concurrent/ThreadSafeSentenceDetectorBio.java | 6 +--
.../ctakes/core/cr/AbstractFileTreeReader.java | 6 +--
.../org/apache/ctakes/core/cr/FileTreeReader.java | 6 +--
.../core/cr/FilesInDirectoryCollectionReader.java | 6 +--
.../ctakes/core/cr/JdbcCollectionReader.java | 6 +--
.../core/cr/LinesFromFileCollectionReader.java | 6 +--
.../ctakes/core/cr/jdbc/DecryptorWrapper.java | 6 +--
.../ctakes/core/cr/jdbc/JdbcNotesReader.java | 6 +--
.../ctakes/core/cr/jdbc/PassThroughDecryptor.java | 6 +--
.../ctakes/core/knowtator/KnowtatorXMLParser.java | 6 +--
.../core/patient/AbstractPatientConsumer.java | 6 +--
.../core/patient/AbstractPatientFileWriter.java | 6 +--
.../ctakes/core/patient/PatientNoteCollector.java | 6 +--
.../ctakes/core/patient/PatientNoteStore.java | 6 +--
.../ctakes/core/patient/PatientViewUtil.java | 6 +--
.../ctakes/core/pipeline/CliOptionalsHandler.java | 6 +--
.../apache/ctakes/core/pipeline/CuiCollector.java | 6 +--
.../ctakes/core/pipeline/EntityCollector.java | 6 +--
.../ctakes/core/pipeline/PipeBitInfoUtil.java | 6 +--
.../ctakes/core/pipeline/PipeBitLocator.java | 6 +--
.../ctakes/core/pipeline/PipelineBuilder.java | 6 +--
.../ctakes/core/pipeline/PiperFileReader.java | 6 +--
.../ctakes/core/pipeline/PiperFileRunner.java | 6 +--
.../apache/ctakes/core/resource/FileLocator.java | 6 +--
.../ctakes/core/resource/FileReadWriteUtil.java | 6 +--
.../ctakes/core/resource/FileResourceImpl.java | 6 +--
.../core/resource/JdbcConnectionResourceImpl.java | 6 +--
.../resource/LuceneIndexReaderResourceImpl.java | 6 +--
.../resource/StringIntegerMapResourceImpl.java | 6 +--
.../core/resource/StringMapResourceImpl.java | 6 +--
.../org/apache/ctakes/core/util/BannerWriter.java | 6 +--
.../apache/ctakes/core/util/FinishedLogger.java | 4 +-
.../ctakes/core/util/NumberedSuffixComparator.java | 6 +--
.../apache/ctakes/core/util/PropertyAeFactory.java | 8 ++--
.../ctakes/core/util/RelationArgumentUtil.java | 6 +--
.../org/apache/ctakes/core/util/StringUtil.java | 6 +--
.../util/annotation/EssentialAnnotationUtil.java | 6 +--
.../annotation/IdentifiedAnnotationBuilder.java | 6 +--
.../core/util/annotation/OntologyConceptUtil.java | 6 +--
.../ctakes/core/util/annotation/WordTokenUtil.java | 6 +--
.../org/apache/ctakes/core/util/doc/DocIdUtil.java | 6 +--
.../org/apache/ctakes/core/util/doc/NoteSpecs.java | 6 +--
.../ctakes/core/util/doc/SourceMetadataUtil.java | 6 +--
.../ctakes/core/util/external/SystemUtil.java | 6 +--
.../org/apache/ctakes/core/util/log/DotLogger.java | 8 ++--
.../ctakes/core/util/log/FinishedLogger.java | 6 +--
.../ctakes/core/util/regex/RegexSpanFinder.java | 6 +--
.../ctakes/core/util/regex/TimeoutMatcher.java | 6 +--
.../ctakes/core/ae/TokenizerAnnotatorPTBTests.java | 6 +--
.../ctakes/core/cr/FileTreeReaderTester.java | 6 +--
.../core/util/OntologyConceptUtilTester.java | 6 +--
.../coreference/ae/CopyCoreferenceRelations.java | 6 +--
.../ae/DeterministicMarkableAnnotator.java | 6 +--
.../coreference/ae/EventCoreferenceAnnotator.java | 6 +--
.../coreference/ae/MarkableSalienceAnnotator.java | 6 +--
.../ae/MentionClusterCoreferenceAnnotator.java | 6 +--
.../MentionClusterRankingCoreferenceAnnotator.java | 4 +-
.../coreference/ae/MipacqMarkableCreator.java | 6 +--
.../ae/MipacqMarkablePairGenerator.java | 6 +--
.../coreference/ae/MipacqSvmChainCreator.java | 6 +--
.../ae/PatientMentionClusterCoreferencer.java | 6 +--
.../ae/ThymeAnaforaCrossDocCorefXmlReader.java | 6 +--
.../ae/pairing/cluster/HeadwordPairer.java | 6 +--
.../coreference/cc/ODIEVectorFileWriter.java | 6 +--
.../ThreadSafeMarkableSalienceAnnotator.java | 6 +--
.../ThreadSafeMentionClusterCoreferencer.java | 6 +--
.../eval/EvaluationOfEventCoreference.java | 10 ++--
.../coreference/util/AnnotationSelector.java | 2 +-
.../coreference/util/ClusterMentionFetcher.java | 6 +--
.../ctakes/coreference/eval/helpers/SpanTest.java | 15 +++---
.../dependency/parser/DependencyNodeWriter.java | 6 +--
.../parser/ae/ClearNLPDependencyParserAE.java | 8 ++--
.../parser/ae/ClearNLPSemanticRoleLabelerAE.java | 6 +--
.../parser/ae/shared/DependencySharedModel.java | 6 +--
.../parser/ae/shared/LemmatizerSharedModel.java | 6 +--
.../concurrent/ThreadSafeClearNlpDepParser.java | 6 +--
.../ThreadSafeClearNlpSemRoleLabeler.java | 6 +--
.../dependency/parser/util/AnnotationDepUtils.java | 6 +--
.../parser/util/ClearDependencyUtility.java | 6 +--
.../dependency/parser/util/DependencyUtility.java | 6 +--
.../dictionary/cased/ae/CasedAnnotationFinder.java | 6 +--
.../AlikeSubsumingAnnotationCreator.java | 6 +--
.../cased/annotation/AnnotationCreatorUtil.java | 6 +--
.../annotation/NonSubsumingAnnotationCreator.java | 6 +--
.../SemanticSubsumingAnnotationCreator.java | 6 +--
.../dictionary/cased/dictionary/BsvDictionary.java | 6 +--
.../cased/dictionary/BsvListDictionary.java | 6 +--
.../cased/dictionary/JdbcDictionary.java | 6 +--
.../dictionary/cased/encoder/BsvEncoder.java | 6 +--
.../dictionary/cased/encoder/BsvListEncoder.java | 6 +--
.../dictionary/cased/encoder/JdbcEncoder.java | 6 +--
.../cased/lookup/ContiguousLookupEngine.java | 6 +--
.../dictionary/cased/lookup/LookupEngine.java | 6 +--
.../cased/util/tokenize/TokenizedTermMapper.java | 6 +--
.../lookup2/ae/AbstractJCasTermAnnotator.java | 6 +--
.../lookup2/ae/OverlapJCasTermAnnotator.java | 6 +--
.../lookup2/concept/BsvConceptFactory.java | 6 +--
.../lookup2/concept/JdbcConceptFactory.java | 6 +--
.../lookup2/concept/UmlsJdbcConceptFactory.java | 6 +--
.../lookup2/concurrent/ThreadSafeFastLookup.java | 6 +--
.../lookup2/consumer/DefaultTermConsumer.java | 6 +--
.../consumer/DefaultUmlsConceptCreator.java | 6 +--
.../consumer/SemanticCleanupTermConsumer.java | 6 +--
.../lookup2/dictionary/BsvRareWordDictionary.java | 6 +--
.../dictionary/DictionaryDescriptorParser.java | 6 +--
.../lookup2/dictionary/JdbcRareWordDictionary.java | 6 +--
.../dictionary/RareWordDictionaryWrapper.java | 6 +--
.../lookup2/dictionary/RareWordTermMapCreator.java | 6 +--
.../dictionary/UmlsJdbcRareWordDictionary.java | 6 +--
.../lookup2/relation/CuiRelationsJdbc.java | 6 +--
.../dictionary/lookup2/util/CuiCodeUtil.java | 6 +--
.../lookup2/util/JdbcConnectionFactory.java | 10 ++--
.../dictionary/lookup2/util/UmlsUserApprover.java | 6 +--
.../lookup2/ae/TestDictionaryLoadResources.java | 6 +--
.../dictionary/lookup2/util/UmlsUserTest.java | 6 +--
.../lookup/ae/AssertionCuePhraseConsumerImpl.java | 6 +--
.../dictionary/lookup/ae/DebugConsumerImpl.java | 6 +--
.../lookup/ae/DictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/DirectLookupInitializerImpl.java | 6 +--
.../ae/FirstTokenPermLookupInitializerImpl.java | 6 +--
.../lookup/ae/LookupParseUtilitiesRefactor.java | 6 +--
.../lookup/ae/OrangeBookFilterConsumerImpl.java | 6 +--
.../ae/ThreadedDictionaryLookupAnnotator.java | 6 +--
.../ae/ThreadedUmlsDictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/UmlsDictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/UmlsToSnomedLuceneConsumerImpl.java | 6 +--
.../algorithms/FirstTokenPermutationImpl.java | 6 +--
.../lookup/lucene/LuceneDictionaryImpl.java | 6 +--
.../ctakes/drugner/ae/DrugMentionAnnotator.java | 6 +--
.../apache/ctakes/examples/ae/BodySideFinder.java | 6 +--
.../ctakes/examples/ae/ConfigParameterExample.java | 6 +--
.../apache/ctakes/examples/ae/RegexBpFinder.java | 6 +--
.../ctakes/examples/cc/FileTreeViewXmiWriter.java | 6 +--
.../apache/ctakes/examples/cc/TokenPrinter.java | 6 +--
.../apache/ctakes/examples/cc/TokenSpanWriter.java | 6 +--
.../ctakes/examples/cr/LetterColumnReader.java | 6 +--
.../examples/pipeline/HelloWorldBuilderRunner.java | 6 +--
.../pipeline/HelloWorldCuiPiperRunner.java | 6 +--
.../pipeline/HelloWorldPropsPiperRunner.java | 6 +--
.../examples/pipeline/ProcessDirBuilderRunner.java | 6 +--
.../examples/pipeline/ProcessDirPiperRunner.java | 6 +--
.../pipeline/ProcessLinesClinicalRunner.java | 6 +--
.../fhir/backbone/CompositionSectionCreator.java | 6 +--
.../org/apache/ctakes/fhir/cc/FhirDocComposer.java | 6 +--
.../apache/ctakes/fhir/cc/FhirJsonFileWriter.java | 6 +--
.../org/apache/ctakes/fhir/cc/FhirJsonWriter.java | 6 +--
.../org/apache/ctakes/fhir/cr/BundleReader.java | 6 +--
.../apache/ctakes/fhir/cr/FhirJsonFileReader.java | 6 +--
.../apache/ctakes/fhir/cr/FhirXmlFileReader.java | 6 +--
.../ctakes/fhir/element/FhirElementFactory.java | 6 +--
.../ctakes/fhir/element/FhirElementParser.java | 6 +--
.../ctakes/fhir/resource/AnnotationParser.java | 6 +--
.../ctakes/fhir/resource/BaseTokenParser.java | 6 +--
.../apache/ctakes/fhir/resource/BundleCreator.java | 6 +--
.../ctakes/fhir/resource/CompositionCreator.java | 6 +--
.../ctakes/fhir/resource/CompositionParser.java | 6 +--
.../ctakes/fhir/resource/FhirBasicParser.java | 4 +-
.../fhir/resource/IdentifiedAnnotationCreator.java | 6 +--
.../fhir/resource/IdentifiedAnnotationParser.java | 6 +--
.../ctakes/fhir/resource/ParagraphParser.java | 6 +--
.../ctakes/fhir/resource/SectionCreator.java | 6 +--
.../apache/ctakes/fhir/resource/SectionParser.java | 6 +--
.../ctakes/fhir/resource/SentenceParser.java | 6 +--
.../org/apache/ctakes/fhir/util/FhirNoteSpecs.java | 6 +--
.../ctakes/gui/action/GlobalHotKeyManager.java | 6 +--
.../ctakes/gui/component/CellRendererLabel.java | 6 +--
.../ctakes/gui/component/CellRendererPanel.java | 6 +--
.../apache/ctakes/gui/component/DisablerPane.java | 6 +--
.../ctakes/gui/component/FileChooserPanel.java | 6 +--
.../ctakes/gui/component/FileTableCellEditor.java | 6 +--
.../ctakes/gui/component/PositionedSplitPane.java | 6 +--
.../ctakes/gui/component/SystemOutPanel.java | 6 +--
.../ctakes/gui/dictionary/DictionaryBuilder.java | 6 +--
.../ctakes/gui/dictionary/DictionaryCreator.java | 6 +--
.../gui/dictionary/DictionaryDownloader.java | 6 +--
.../ctakes/gui/dictionary/DictionaryXmlWriter.java | 6 +--
.../apache/ctakes/gui/dictionary/MainPanel.java | 6 +--
.../dictionary/cased/CasedDictionaryCreator.java | 6 +--
.../gui/dictionary/cased/CasedMainPanel.java | 6 +--
.../gui/dictionary/cased/CasedPiperWriter.java | 6 +--
.../gui/dictionary/cased/CasedReadmeWriter.java | 6 +--
.../ctakes/gui/dictionary/cased/HsqlWriter.java | 6 +--
.../gui/dictionary/cased/umls/UmlsParser.java | 6 +--
.../gui/dictionary/umls/AutoTermExtractor.java | 6 +--
.../gui/dictionary/umls/ConceptMapFactory.java | 6 +--
.../ctakes/gui/dictionary/umls/CuiCodeUtil.java | 6 +--
.../ctakes/gui/dictionary/umls/DoseUtil.java | 6 +--
.../gui/dictionary/umls/LanguageTableModel.java | 6 +--
.../ctakes/gui/dictionary/umls/MrconsoParser.java | 6 +--
.../ctakes/gui/dictionary/umls/MrstyParser.java | 6 +--
.../gui/dictionary/umls/SourceTableModel.java | 6 +--
.../gui/dictionary/umls/TuiCellRenderer.java | 6 +--
.../ctakes/gui/dictionary/umls/TuiTableModel.java | 6 +--
.../gui/dictionary/umls/VocabularyStore.java | 6 +--
.../ctakes/gui/dictionary/util/FileUtil.java | 6 +--
.../ctakes/gui/dictionary/util/HsqlUtil.java | 6 +--
.../ctakes/gui/dictionary/util/JdbcUtil.java | 6 +--
.../gui/dictionary/util/RareWordDbWriter.java | 6 +--
.../ctakes/gui/generic/GenericRunnerGui.java | 6 +--
.../org/apache/ctakes/gui/generic/MainPanel.java | 6 +--
.../org/apache/ctakes/gui/pipeline/MainPanel.java | 6 +--
.../org/apache/ctakes/gui/pipeline/MainPanel2.java | 6 +--
.../apache/ctakes/gui/pipeline/PiperCreator.java | 6 +--
.../ctakes/gui/pipeline/PiperDisplayModel.java | 6 +--
.../apache/ctakes/gui/pipeline/PiperRunnerGui.java | 6 +--
.../ctakes/gui/pipeline/PiperRunnerPanel.java | 6 +--
.../ctakes/gui/pipeline/bit/BitCellRenderer.java | 6 +--
.../ctakes/gui/pipeline/bit/BitInfoPanel.java | 6 +--
.../ctakes/gui/pipeline/bit/PipeBitFinder.java | 6 +--
.../ctakes/gui/pipeline/bit/PipeBitPainter.java | 6 +--
.../bit/available/AvailablesListModel.java | 6 +--
.../pipeline/bit/available/AvailablesRenderer.java | 6 +--
.../gui/pipeline/bit/info/PipeBitInfoPanel.java | 6 +--
.../gui/pipeline/bit/info/PipeBitInfoRenderer.java | 6 +--
.../ctakes/gui/pipeline/bit/info/RoleRenderer.java | 6 +--
.../pipeline/bit/info/TypeProductListModel.java | 6 +--
.../gui/pipeline/bit/info/TypeProductRenderer.java | 6 +--
.../bit/parameter/DefaultParameterHolder.java | 6 +--
.../bit/parameter/ParameterCellRenderer.java | 6 +--
.../pipeline/bit/parameter/ParameterInfoPanel.java | 6 +--
.../pipeline/bit/parameter/ParameterMapper.java | 6 +--
.../bit/parameter/ParameterTableModel.java | 6 +--
.../gui/pipeline/bit/user/DefaultUserBit.java | 6 +--
.../gui/pipeline/bit/user/UserBitInfoPanel.java | 6 +--
.../gui/pipeline/bit/user/UserBitListModel.java | 6 +--
.../gui/pipeline/bit/user/UserBitRenderer.java | 6 +--
.../pipeline/bit/user/UserParameterInfoPanel.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperFinder.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperInfo.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperTextFilter.java | 6 +--
.../org/apache/ctakes/gui/util/ColorFactory.java | 6 +--
.../org/apache/ctakes/gui/util/IconLoader.java | 6 +--
.../org/apache/ctakes/lvg/ae/LvgAnnotator.java | 10 ++--
.../ctakes/lvg/ae/LvgBaseTokenAnnotator.java | 6 +--
.../org/apache/ctakes/lvg/ae/LvgSingleton.java | 6 +--
.../org/apache/ctakes/lvg/ae/ThreadSafeLvg.java | 6 +--
.../ctakes/lvg/resource/LvgCmdApiResourceImpl.java | 6 +--
ctakes-mastif-zoner/pom.xml | 5 +-
.../zoner/LineTokenToCharacterOffsetConverter.java | 6 +--
.../java/org/mitre/medfacts/zoner/ZonerCli.java | 55 ++++++++++++----------
.../java/org/mitre/medfacts/zoner/ZonerRunner.java | 6 +--
.../apache/ctakes/necontexts/ContextAnnotator.java | 6 +--
.../necontexts/NamedEntityContextAnalyzer.java | 6 +--
.../concurrent/ThreadSafeContextAnnotator.java | 6 +--
.../org/apache/ctakes/pbj/ae/ArtemisStarter.java | 6 +--
.../org/apache/ctakes/pbj/ae/ArtemisStopper.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjJmsSender.java | 6 +--
.../java/org/apache/ctakes/pbj/ae/PbjPipper.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjReceiverAE.java | 6 +--
.../java/org/apache/ctakes/pbj/ae/PbjSender.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjStompSender.java | 6 +--
.../java/org/apache/ctakes/pbj/cr/PbjReceiver.java | 6 +--
.../apache/ctakes/pbj/util/ArtemisController.java | 6 +--
.../ctakes/postagger/ClearNLPPOSTaggerAE.java | 6 +--
.../org/apache/ctakes/postagger/POSTagger.java | 6 +--
.../postagger/concurrent/ThreadSafePosTagger.java | 6 +--
.../preprocessor/ClinicalNotePreProcessor.java | 6 +--
.../ctakes/preprocessor/ae/CdaCasInitializer.java | 6 +--
.../ctakes/core/ae/LabValueFinderTester.java | 11 ++---
.../regression/test/RegressionPipelineTest.java | 6 +--
.../ae/DegreeOfRelationExtractorAnnotator.java | 6 +--
.../ae/LocationOfRelationExtractorAnnotator.java | 6 +--
.../ae/ModifierExtractorAnnotator.java | 6 +--
.../ae/RelationExtractorAnnotator.java | 6 +--
.../concurrent/ThreadSafeDegreeExtractor.java | 6 +--
.../concurrent/ThreadSafeLocationExtractor.java | 6 +--
.../concurrent/ThreadSafeModifierExtractor.java | 6 +--
.../ctakes/relationextractor/eval/DeepPheXMI.java | 6 +--
.../metastasis/MetastasisAnaforaXMLReader.java | 6 +--
.../smokingstatus/ae/ClassifiableEntries.java | 6 +--
.../ctakes/smokingstatus/ae/PcsClassifier.java | 6 +--
.../smokingstatus/ae/ResolutionAnnotator.java | 6 +--
.../ctakes/smokingstatus/ae/SentenceAdjuster.java | 6 +--
.../cc/RecordResolutionCasConsumer.java | 6 +--
.../filler/ae/TemplateFillerAnnotator.java | 6 +--
.../ctakes/temporal/ae/BackwardsTimeAnnotator.java | 6 +--
.../ae/ConstituencyBasedTimeAnnotator.java | 6 +--
.../temporal/ae/DeepPheAnaforaXMLReader.java | 6 +--
.../ctakes/temporal/ae/DocTimeApproximator.java | 6 +--
.../ctakes/temporal/ae/DocTimeRelAnnotator.java | 6 +--
.../apache/ctakes/temporal/ae/EventAnnotator.java | 6 +--
.../ae/EventEventCRFRelationAnnotator.java | 4 +-
.../temporal/ae/EventEventRelationAnnotator.java | 6 +--
.../temporal/ae/EventTimeRelationAnnotator.java | 6 +--
.../ctakes/temporal/ae/SimpleMedDatesFinder.java | 6 +--
.../ctakes/temporal/ae/THYMEAnaforaXMLReader.java | 6 +--
.../temporal/ae/THYMEQAAnaforaXMLReader.java | 6 +--
.../ctakes/temporal/ae/THYMETreebankReader.java | 6 +--
.../ae/TemporalRelationExtractorAnnotator.java | 4 +-
.../temporal/ae/feature/ClosestVerbExtractor.java | 2 +-
.../ae/feature/CoveredTextToValuesExtractor.java | 6 +--
.../ae/feature/EventPositionFeatureExtractor.java | 2 +-
.../ae/feature/EventPropertyExtractor.java | 6 +--
.../IdentifiedAnnotationFeatureExtractor.java | 6 +--
.../ae/feature/NearbyVerbTenseXExtractor.java | 2 +-
.../ae/feature/SectionHeaderExtractor.java | 2 +-
.../ctakes/temporal/ae/feature/TimeXExtractor.java | 2 +-
.../ctakes/temporal/cc/SimpleMedDatesPrinter.java | 6 +--
.../concurrent/ThreadSafeBackTimeAnnotator.java | 6 +--
.../concurrent/ThreadSafeDocTimeRelAnnotator.java | 6 +--
.../concurrent/ThreadSafeEventAnnotator.java | 6 +--
.../ThreadSafeEventEventRelAnnotator.java | 6 +--
.../ThreadSafeEventTimeRelAnnotator.java | 6 +--
.../eval/EvaluationOfEventPropertiesTk.java | 4 +-
.../ctakes/temporal/eval/Evaluation_ImplBase.java | 6 +--
.../temporal/eval/RemoveTreeAlignedMentions.java | 6 +--
.../apache/ctakes/temporal/utils/CalendarUtil.java | 4 +-
.../temporal/ae/BackwardsTimeAnnotatorTest.java | 6 +--
.../ae/ContextualModalityAnnotatorTest.java | 6 +--
.../temporal/ae/DocTimeRelAnnotatorTest.java | 6 +--
.../ctakes/temporal/ae/EventAnnotatorTest.java | 6 +--
.../ae/EventEventRelationAnnotatorTest.java | 6 +--
.../ae/EventTimeRelationAnnotatorTest.java | 6 +--
.../ctakes/rest/service/RestPipelineRunner.java | 8 ++--
.../apache/ctakes/rest/service/TinyController.java | 6 +--
.../ctakes/rest/service/CtakesRestController.java | 6 +--
.../ctakes/ytex/tools/SetupAuiFirstWord.java | 6 +--
.../ytex/uima/annotators/SentenceDetector.java | 21 +++++----
.../ae/FirstTokenPermLookupInitializerImpl.java | 6 +--
.../InitableJdbcConnectionResourceImpl.java | 6 +--
.../ytex/uima/annotators/DateAnnotatorTest.java | 6 +--
.../ctakes/ytex/web/search/ConceptLookupBean.java | 6 +--
.../ytex/web/search/DocumentSearchServiceImpl.java | 6 +--
.../ctakes/ytex/web/search/SemanticSearchBean.java | 19 ++++----
ctakes-ytex/pom.xml | 4 ++
.../main/java/org/apache/ctakes/jdl/AppJdl.java | 6 +--
.../apache/ctakes/jdl/data/loader/CsvLoader.java | 6 +--
.../apache/ctakes/util/JdbcOperationsHelper.java | 6 +--
.../java/org/apache/ctakes/ytex/dao/DBUtil.java | 6 +--
.../kernel/BaseClassifierEvaluationParser.java | 6 +--
.../ctakes/ytex/kernel/ClassifierEvalUtil.java | 6 +--
.../ytex/kernel/ClassifierEvaluationImporter.java | 6 +--
.../ctakes/ytex/kernel/FoldGeneratorImpl.java | 6 +--
.../ytex/kernel/ImputedFeatureEvaluatorImpl.java | 6 +--
.../kernel/IntrinsicInfoContentEvaluatorImpl.java | 6 +--
.../apache/ctakes/ytex/kernel/KernelUtilImpl.java | 6 +--
.../ctakes/ytex/kernel/SVMLinFormatterFactory.java | 6 +--
.../ctakes/ytex/kernel/SparseDataExporterImpl.java | 6 +--
.../ctakes/ytex/kernel/SvmlinEvaluationParser.java | 6 +--
.../ctakes/ytex/kernel/dao/ConceptDaoImpl.java | 6 +--
.../ytex/kernel/dao/KernelEvaluationDaoImpl.java | 6 +--
.../ctakes/ytex/kernel/dao/SortedSetUserType.java | 6 +--
.../evaluator/CorpusKernelEvaluatorImpl.java | 6 +--
.../ctakes/ytex/kernel/evaluator/NormKernel.java | 6 +--
.../ytex/kernel/evaluator/ProductKernel.java | 19 ++++----
.../ytex/kernel/evaluator/SemanticSimKernel.java | 6 +--
.../ytex/kernel/evaluator/SemanticTypeKernel.java | 6 +--
.../metric/ConceptSimilarityServiceImpl.java | 6 +--
.../apache/ctakes/ytex/kernel/model/ConcRel.java | 6 +--
.../ytex/kernel/pagerank/PageRankServiceImpl.java | 6 +--
.../ytex/kernel/tree/InstanceTreeBuilderImpl.java | 6 +--
.../ctakes/ytex/semil/SemiLEvaluationParser.java | 6 +--
.../ytex/weka/DocumentResultInstanceImporter.java | 6 +--
.../ytex/weka/WekaAttributeEvaluatorImpl.java | 6 +--
.../org/apache/ctakes/ytex/ConceptDaoTest.java | 6 +--
.../apache/ctakes/ytex/umls/dao/UMLSDaoTest.java | 8 ++--
pom.xml | 43 ++++++++---------
467 files changed, 1497 insertions(+), 1468 deletions(-)
(ctakes) 01/01: Merge pull request #21 from apache/refactoring/20-Crossgrade-to-SLF4J
Posted by se...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
commit 5e0f7bd0c240391899a2668e7fb1f69d95e10057
Merge: 1556d13 837666c
Author: Sean Finan <se...@childrens.harvard.edu>
AuthorDate: Wed Jul 31 09:06:12 2024 -0500
Merge pull request #21 from apache/refactoring/20-Crossgrade-to-SLF4J
Issue #20 - Crossgrade to SLF4J
.gitignore | 1 +
.../java/org/mitre/medfacts/uima/RunZoner.java | 6 +--
.../org/mitre/medfacts/uima/ZoneAnnotator.java | 6 +--
.../attributes/GenericAttributeAnalysisEngine.java | 6 +--
.../attributes/SubjectAttributeAnalysisEngine.java | 6 +--
.../subject/SubjectAttributeClassifier.java | 14 ++++--
.../cr/I2B2Challenge2010CollectionReader.java | 6 +--
.../assertion/cr/MiPACQKnowtatorXMLReader.java | 6 +--
.../ctakes/assertion/cr/NegExAnnotation.java | 6 +--
.../ctakes/assertion/cr/NegExCorpusReader.java | 6 +--
.../ctakes/assertion/eval/AssertionEvaluation.java | 6 +--
...dViewFromOneCasIntoInitialViewOfAnotherCas.java | 6 +--
.../medfacts/AssertionAnalysisEngine.java | 11 ++---
.../medfacts/AssertionAnalysisEngineFit.java | 6 +--
.../ctakes/assertion/medfacts/CasIndexer.java | 6 +--
.../medfacts/ConceptConverterAnalysisEngine.java | 6 +--
.../ctakes/assertion/medfacts/ConceptLookup.java | 6 +--
.../medfacts/Converti2b2AnnotationsToCTAKES.java | 6 +--
.../cleartk/AssertionCleartkAnalysisEngine.java | 15 +++---
.../cleartk/PolarityCleartkAnalysisEngine.java | 4 +-
.../cleartk/PolarityFedaCleartkAnalysisEngine.java | 4 +-
.../cleartk/SubjectCleartkAnalysisEngine.java | 5 +-
.../medfacts/cleartk/TrainAssertionModel.java | 6 +--
.../medfacts/cleartk/extractors/CueWordTest.java | 6 +--
.../medfacts/cleartk/extractors/CueWordTest2.java | 6 +--
.../cleartk/extractors/SurroundingExtractor.java | 2 +-
.../SubjectCleartkAnalysisEngineWindowed.java | 5 +-
.../WindowedAssertionCleartkAnalysisEngine.java | 6 +--
...racterOffsetToLineTokenConverterCtakesImpl.java | 6 +--
.../i2b2/api/SingleDocumentProcessorCtakes.java | 6 +--
.../GenerateDependencyRepresentation.java | 6 +--
.../pipelines/GenerateTreeRepresentation.java | 6 +--
...ityAndAttributeReaderPipelineForSeedCorpus.java | 16 ++++---
.../ctakes/assertion/stub/AssertionAnnotation.java | 6 +--
.../assertion/stub/AssertionFileProcessor.java | 6 +--
.../apache/ctakes/assertion/stub/BatchRunner.java | 6 +--
.../ctakes/assertion/stub/JarafeMEDecoder.java | 6 +--
.../assertion/stub/SingleDocumentProcessor.java | 6 +--
.../ctakes/assertion/stub/StringHandling.java | 6 +--
.../java/org/apache/ctakes/chunker/ae/Chunker.java | 6 +--
.../ctakes/chunker/ae/adjuster/ChunkAdjuster.java | 6 +--
.../chunker/concurrent/ThreadSafeChunker.java | 6 +--
.../constituency/parser/MaxentParserWrapper.java | 6 +--
.../constituency/parser/ae/ConstituencyParser.java | 6 +--
.../concurrent/ThreadSafeConstituencyParser.java | 6 +--
.../ae/ContextDependentTokenizerAnnotator.java | 6 +--
.../ctakes/core/ae/AbstractCommandRunner.java | 6 +--
.../apache/ctakes/core/ae/BsvRegexSectionizer.java | 6 +--
.../apache/ctakes/core/ae/CDASegmentAnnotator.java | 6 +--
.../org/apache/ctakes/core/ae/CommandRunner.java | 12 ++---
.../org/apache/ctakes/core/ae/CopyAnnotator.java | 6 +--
.../org/apache/ctakes/core/ae/CtakesRunner.java | 6 +--
.../core/ae/DocumentIdPrinterAnalysisEngine.java | 6 +--
.../apache/ctakes/core/ae/EolSentenceFixer.java | 6 +--
.../java/org/apache/ctakes/core/ae/ExitForcer.java | 6 +--
.../org/apache/ctakes/core/ae/LabValueFinder.java | 6 +--
.../org/apache/ctakes/core/ae/ListAnnotator.java | 6 +--
.../apache/ctakes/core/ae/ListEntryNegator.java | 6 +--
.../apache/ctakes/core/ae/ListParagraphFixer.java | 6 +--
.../apache/ctakes/core/ae/ListSentenceFixer.java | 6 +--
.../apache/ctakes/core/ae/MrsDrSentenceJoiner.java | 6 +--
.../apache/ctakes/core/ae/OverlapAnnotator.java | 6 +--
.../apache/ctakes/core/ae/ParagraphAnnotator.java | 6 +--
.../ctakes/core/ae/ParagraphSentenceFixer.java | 6 +--
.../apache/ctakes/core/ae/PiperFileRunEngine.java | 6 +--
.../org/apache/ctakes/core/ae/PythonPipper.java | 6 +--
.../org/apache/ctakes/core/ae/PythonRunner.java | 10 ++--
.../apache/ctakes/core/ae/RegexSectionizer.java | 6 +--
.../ctakes/core/ae/SHARPKnowtatorXMLReader.java | 24 ++++++----
.../ctakes/core/ae/SectionSegmentAnnotator.java | 6 +--
.../apache/ctakes/core/ae/SentenceDetector.java | 8 ++--
.../core/ae/SentenceDetectorAnnotatorBIO.java | 6 +--
.../core/ae/SimpleSegmentWithTagsAnnotator.java | 6 +--
.../apache/ctakes/core/ae/StartFinishLogger.java | 6 +--
.../apache/ctakes/core/ae/SubjectSectionFixer.java | 6 +--
.../ctakes/core/ae/TemplateFillerAnnotator.java | 6 +--
.../apache/ctakes/core/ae/TokenizerAnnotator.java | 6 +--
.../ctakes/core/ae/TokenizerAnnotatorPTB.java | 6 +--
.../apache/ctakes/core/cc/AbstractFileWriter.java | 6 +--
.../apache/ctakes/core/cc/AbstractJdbcWriter.java | 6 +--
.../ctakes/core/cc/AbstractTableFileWriter.java | 6 +--
.../org/apache/ctakes/core/cc/CasConsumer.java | 6 +--
.../apache/ctakes/core/cc/CuiCountFileWriter.java | 6 +--
.../apache/ctakes/core/cc/CuiListFileWriter.java | 6 +--
.../org/apache/ctakes/core/cc/CuiLookupLister.java | 6 +--
.../apache/ctakes/core/cc/FileTreeXmiWriter.java | 6 +--
.../core/cc/FilesInDirectoryCasConsumer.java | 6 +--
.../apache/ctakes/core/cc/JdbcWriterTemplate.java | 6 +--
.../ctakes/core/cc/SemanticTableFileWriter.java | 6 +--
.../ctakes/core/cc/SentenceTokensPrinter.java | 6 +--
.../org/apache/ctakes/core/cc/TextSpanWriter.java | 6 +--
.../ctakes/core/cc/XmiWriterCasConsumerCtakes.java | 6 +--
.../org/apache/ctakes/core/cc/html/CssWriter.java | 6 +--
.../apache/ctakes/core/cc/html/HtmlTextWriter.java | 6 +--
.../org/apache/ctakes/core/cc/html/JsWriter.java | 6 +--
.../ctakes/core/cc/jdbc/AbstractJdbcWriter.java | 6 +--
.../apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java | 6 +--
.../ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java | 6 +--
.../core/cc/jdbc/i2b2/ObservationFactRow.java | 6 +--
.../ctakes/core/cc/jdbc/row/EmptyInitializer.java | 6 +--
.../ctakes/core/cc/pretty/html/CssWriter.java | 6 +--
.../ctakes/core/cc/pretty/html/HtmlTextWriter.java | 6 +--
.../ctakes/core/cc/pretty/html/JsWriter.java | 6 +--
.../core/cc/pretty/plaintext/PrettyTextWriter.java | 6 +--
.../cc/pretty/plaintext/PrettyTextWriterFit.java | 4 +-
.../cc/pretty/plaintext/PrettyTextWriterUima.java | 6 +--
.../cc/property/plaintext/PropertyTextWriter.java | 6 +--
.../property/plaintext/PropertyTextWriterFit.java | 2 +-
.../property/plaintext/PropertyTextWriterUima.java | 6 +--
.../concurrent/ThreadSafeSentenceDetector.java | 6 +--
.../concurrent/ThreadSafeSentenceDetectorBio.java | 6 +--
.../ctakes/core/cr/AbstractFileTreeReader.java | 6 +--
.../org/apache/ctakes/core/cr/FileTreeReader.java | 6 +--
.../core/cr/FilesInDirectoryCollectionReader.java | 6 +--
.../ctakes/core/cr/JdbcCollectionReader.java | 6 +--
.../core/cr/LinesFromFileCollectionReader.java | 6 +--
.../ctakes/core/cr/jdbc/DecryptorWrapper.java | 6 +--
.../ctakes/core/cr/jdbc/JdbcNotesReader.java | 6 +--
.../ctakes/core/cr/jdbc/PassThroughDecryptor.java | 6 +--
.../ctakes/core/knowtator/KnowtatorXMLParser.java | 6 +--
.../core/patient/AbstractPatientConsumer.java | 6 +--
.../core/patient/AbstractPatientFileWriter.java | 6 +--
.../ctakes/core/patient/PatientNoteCollector.java | 6 +--
.../ctakes/core/patient/PatientNoteStore.java | 6 +--
.../ctakes/core/patient/PatientViewUtil.java | 6 +--
.../ctakes/core/pipeline/CliOptionalsHandler.java | 6 +--
.../apache/ctakes/core/pipeline/CuiCollector.java | 6 +--
.../ctakes/core/pipeline/EntityCollector.java | 6 +--
.../ctakes/core/pipeline/PipeBitInfoUtil.java | 6 +--
.../ctakes/core/pipeline/PipeBitLocator.java | 6 +--
.../ctakes/core/pipeline/PipelineBuilder.java | 6 +--
.../ctakes/core/pipeline/PiperFileReader.java | 6 +--
.../ctakes/core/pipeline/PiperFileRunner.java | 6 +--
.../apache/ctakes/core/resource/FileLocator.java | 6 +--
.../ctakes/core/resource/FileReadWriteUtil.java | 6 +--
.../ctakes/core/resource/FileResourceImpl.java | 6 +--
.../core/resource/JdbcConnectionResourceImpl.java | 6 +--
.../resource/LuceneIndexReaderResourceImpl.java | 6 +--
.../resource/StringIntegerMapResourceImpl.java | 6 +--
.../core/resource/StringMapResourceImpl.java | 6 +--
.../org/apache/ctakes/core/util/BannerWriter.java | 6 +--
.../apache/ctakes/core/util/FinishedLogger.java | 4 +-
.../ctakes/core/util/NumberedSuffixComparator.java | 6 +--
.../apache/ctakes/core/util/PropertyAeFactory.java | 8 ++--
.../ctakes/core/util/RelationArgumentUtil.java | 6 +--
.../org/apache/ctakes/core/util/StringUtil.java | 6 +--
.../util/annotation/EssentialAnnotationUtil.java | 6 +--
.../annotation/IdentifiedAnnotationBuilder.java | 6 +--
.../core/util/annotation/OntologyConceptUtil.java | 6 +--
.../ctakes/core/util/annotation/WordTokenUtil.java | 6 +--
.../org/apache/ctakes/core/util/doc/DocIdUtil.java | 6 +--
.../org/apache/ctakes/core/util/doc/NoteSpecs.java | 6 +--
.../ctakes/core/util/doc/SourceMetadataUtil.java | 6 +--
.../ctakes/core/util/external/SystemUtil.java | 6 +--
.../org/apache/ctakes/core/util/log/DotLogger.java | 8 ++--
.../ctakes/core/util/log/FinishedLogger.java | 6 +--
.../ctakes/core/util/regex/RegexSpanFinder.java | 6 +--
.../ctakes/core/util/regex/TimeoutMatcher.java | 6 +--
.../ctakes/core/ae/TokenizerAnnotatorPTBTests.java | 6 +--
.../ctakes/core/cr/FileTreeReaderTester.java | 6 +--
.../core/util/OntologyConceptUtilTester.java | 6 +--
.../coreference/ae/CopyCoreferenceRelations.java | 6 +--
.../ae/DeterministicMarkableAnnotator.java | 6 +--
.../coreference/ae/EventCoreferenceAnnotator.java | 6 +--
.../coreference/ae/MarkableSalienceAnnotator.java | 6 +--
.../ae/MentionClusterCoreferenceAnnotator.java | 6 +--
.../MentionClusterRankingCoreferenceAnnotator.java | 4 +-
.../coreference/ae/MipacqMarkableCreator.java | 6 +--
.../ae/MipacqMarkablePairGenerator.java | 6 +--
.../coreference/ae/MipacqSvmChainCreator.java | 6 +--
.../ae/PatientMentionClusterCoreferencer.java | 6 +--
.../ae/ThymeAnaforaCrossDocCorefXmlReader.java | 6 +--
.../ae/pairing/cluster/HeadwordPairer.java | 6 +--
.../coreference/cc/ODIEVectorFileWriter.java | 6 +--
.../ThreadSafeMarkableSalienceAnnotator.java | 6 +--
.../ThreadSafeMentionClusterCoreferencer.java | 6 +--
.../eval/EvaluationOfEventCoreference.java | 10 ++--
.../coreference/util/AnnotationSelector.java | 2 +-
.../coreference/util/ClusterMentionFetcher.java | 6 +--
.../ctakes/coreference/eval/helpers/SpanTest.java | 15 +++---
.../dependency/parser/DependencyNodeWriter.java | 6 +--
.../parser/ae/ClearNLPDependencyParserAE.java | 8 ++--
.../parser/ae/ClearNLPSemanticRoleLabelerAE.java | 6 +--
.../parser/ae/shared/DependencySharedModel.java | 6 +--
.../parser/ae/shared/LemmatizerSharedModel.java | 6 +--
.../concurrent/ThreadSafeClearNlpDepParser.java | 6 +--
.../ThreadSafeClearNlpSemRoleLabeler.java | 6 +--
.../dependency/parser/util/AnnotationDepUtils.java | 6 +--
.../parser/util/ClearDependencyUtility.java | 6 +--
.../dependency/parser/util/DependencyUtility.java | 6 +--
.../dictionary/cased/ae/CasedAnnotationFinder.java | 6 +--
.../AlikeSubsumingAnnotationCreator.java | 6 +--
.../cased/annotation/AnnotationCreatorUtil.java | 6 +--
.../annotation/NonSubsumingAnnotationCreator.java | 6 +--
.../SemanticSubsumingAnnotationCreator.java | 6 +--
.../dictionary/cased/dictionary/BsvDictionary.java | 6 +--
.../cased/dictionary/BsvListDictionary.java | 6 +--
.../cased/dictionary/JdbcDictionary.java | 6 +--
.../dictionary/cased/encoder/BsvEncoder.java | 6 +--
.../dictionary/cased/encoder/BsvListEncoder.java | 6 +--
.../dictionary/cased/encoder/JdbcEncoder.java | 6 +--
.../cased/lookup/ContiguousLookupEngine.java | 6 +--
.../dictionary/cased/lookup/LookupEngine.java | 6 +--
.../cased/util/tokenize/TokenizedTermMapper.java | 6 +--
.../lookup2/ae/AbstractJCasTermAnnotator.java | 6 +--
.../lookup2/ae/OverlapJCasTermAnnotator.java | 6 +--
.../lookup2/concept/BsvConceptFactory.java | 6 +--
.../lookup2/concept/JdbcConceptFactory.java | 6 +--
.../lookup2/concept/UmlsJdbcConceptFactory.java | 6 +--
.../lookup2/concurrent/ThreadSafeFastLookup.java | 6 +--
.../lookup2/consumer/DefaultTermConsumer.java | 6 +--
.../consumer/DefaultUmlsConceptCreator.java | 6 +--
.../consumer/SemanticCleanupTermConsumer.java | 6 +--
.../lookup2/dictionary/BsvRareWordDictionary.java | 6 +--
.../dictionary/DictionaryDescriptorParser.java | 6 +--
.../lookup2/dictionary/JdbcRareWordDictionary.java | 6 +--
.../dictionary/RareWordDictionaryWrapper.java | 6 +--
.../lookup2/dictionary/RareWordTermMapCreator.java | 6 +--
.../dictionary/UmlsJdbcRareWordDictionary.java | 6 +--
.../lookup2/relation/CuiRelationsJdbc.java | 6 +--
.../dictionary/lookup2/util/CuiCodeUtil.java | 6 +--
.../lookup2/util/JdbcConnectionFactory.java | 10 ++--
.../dictionary/lookup2/util/UmlsUserApprover.java | 6 +--
.../lookup2/ae/TestDictionaryLoadResources.java | 6 +--
.../dictionary/lookup2/util/UmlsUserTest.java | 6 +--
.../lookup/ae/AssertionCuePhraseConsumerImpl.java | 6 +--
.../dictionary/lookup/ae/DebugConsumerImpl.java | 6 +--
.../lookup/ae/DictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/DirectLookupInitializerImpl.java | 6 +--
.../ae/FirstTokenPermLookupInitializerImpl.java | 6 +--
.../lookup/ae/LookupParseUtilitiesRefactor.java | 6 +--
.../lookup/ae/OrangeBookFilterConsumerImpl.java | 6 +--
.../ae/ThreadedDictionaryLookupAnnotator.java | 6 +--
.../ae/ThreadedUmlsDictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/UmlsDictionaryLookupAnnotator.java | 6 +--
.../lookup/ae/UmlsToSnomedLuceneConsumerImpl.java | 6 +--
.../algorithms/FirstTokenPermutationImpl.java | 6 +--
.../lookup/lucene/LuceneDictionaryImpl.java | 6 +--
.../ctakes/drugner/ae/DrugMentionAnnotator.java | 6 +--
.../apache/ctakes/examples/ae/BodySideFinder.java | 6 +--
.../ctakes/examples/ae/ConfigParameterExample.java | 6 +--
.../apache/ctakes/examples/ae/RegexBpFinder.java | 6 +--
.../ctakes/examples/cc/FileTreeViewXmiWriter.java | 6 +--
.../apache/ctakes/examples/cc/TokenPrinter.java | 6 +--
.../apache/ctakes/examples/cc/TokenSpanWriter.java | 6 +--
.../ctakes/examples/cr/LetterColumnReader.java | 6 +--
.../examples/pipeline/HelloWorldBuilderRunner.java | 6 +--
.../pipeline/HelloWorldCuiPiperRunner.java | 6 +--
.../pipeline/HelloWorldPropsPiperRunner.java | 6 +--
.../examples/pipeline/ProcessDirBuilderRunner.java | 6 +--
.../examples/pipeline/ProcessDirPiperRunner.java | 6 +--
.../pipeline/ProcessLinesClinicalRunner.java | 6 +--
.../fhir/backbone/CompositionSectionCreator.java | 6 +--
.../org/apache/ctakes/fhir/cc/FhirDocComposer.java | 6 +--
.../apache/ctakes/fhir/cc/FhirJsonFileWriter.java | 6 +--
.../org/apache/ctakes/fhir/cc/FhirJsonWriter.java | 6 +--
.../org/apache/ctakes/fhir/cr/BundleReader.java | 6 +--
.../apache/ctakes/fhir/cr/FhirJsonFileReader.java | 6 +--
.../apache/ctakes/fhir/cr/FhirXmlFileReader.java | 6 +--
.../ctakes/fhir/element/FhirElementFactory.java | 6 +--
.../ctakes/fhir/element/FhirElementParser.java | 6 +--
.../ctakes/fhir/resource/AnnotationParser.java | 6 +--
.../ctakes/fhir/resource/BaseTokenParser.java | 6 +--
.../apache/ctakes/fhir/resource/BundleCreator.java | 6 +--
.../ctakes/fhir/resource/CompositionCreator.java | 6 +--
.../ctakes/fhir/resource/CompositionParser.java | 6 +--
.../ctakes/fhir/resource/FhirBasicParser.java | 4 +-
.../fhir/resource/IdentifiedAnnotationCreator.java | 6 +--
.../fhir/resource/IdentifiedAnnotationParser.java | 6 +--
.../ctakes/fhir/resource/ParagraphParser.java | 6 +--
.../ctakes/fhir/resource/SectionCreator.java | 6 +--
.../apache/ctakes/fhir/resource/SectionParser.java | 6 +--
.../ctakes/fhir/resource/SentenceParser.java | 6 +--
.../org/apache/ctakes/fhir/util/FhirNoteSpecs.java | 6 +--
.../ctakes/gui/action/GlobalHotKeyManager.java | 6 +--
.../ctakes/gui/component/CellRendererLabel.java | 6 +--
.../ctakes/gui/component/CellRendererPanel.java | 6 +--
.../apache/ctakes/gui/component/DisablerPane.java | 6 +--
.../ctakes/gui/component/FileChooserPanel.java | 6 +--
.../ctakes/gui/component/FileTableCellEditor.java | 6 +--
.../ctakes/gui/component/PositionedSplitPane.java | 6 +--
.../ctakes/gui/component/SystemOutPanel.java | 6 +--
.../ctakes/gui/dictionary/DictionaryBuilder.java | 6 +--
.../ctakes/gui/dictionary/DictionaryCreator.java | 6 +--
.../gui/dictionary/DictionaryDownloader.java | 6 +--
.../ctakes/gui/dictionary/DictionaryXmlWriter.java | 6 +--
.../apache/ctakes/gui/dictionary/MainPanel.java | 6 +--
.../dictionary/cased/CasedDictionaryCreator.java | 6 +--
.../gui/dictionary/cased/CasedMainPanel.java | 6 +--
.../gui/dictionary/cased/CasedPiperWriter.java | 6 +--
.../gui/dictionary/cased/CasedReadmeWriter.java | 6 +--
.../ctakes/gui/dictionary/cased/HsqlWriter.java | 6 +--
.../gui/dictionary/cased/umls/UmlsParser.java | 6 +--
.../gui/dictionary/umls/AutoTermExtractor.java | 6 +--
.../gui/dictionary/umls/ConceptMapFactory.java | 6 +--
.../ctakes/gui/dictionary/umls/CuiCodeUtil.java | 6 +--
.../ctakes/gui/dictionary/umls/DoseUtil.java | 6 +--
.../gui/dictionary/umls/LanguageTableModel.java | 6 +--
.../ctakes/gui/dictionary/umls/MrconsoParser.java | 6 +--
.../ctakes/gui/dictionary/umls/MrstyParser.java | 6 +--
.../gui/dictionary/umls/SourceTableModel.java | 6 +--
.../gui/dictionary/umls/TuiCellRenderer.java | 6 +--
.../ctakes/gui/dictionary/umls/TuiTableModel.java | 6 +--
.../gui/dictionary/umls/VocabularyStore.java | 6 +--
.../ctakes/gui/dictionary/util/FileUtil.java | 6 +--
.../ctakes/gui/dictionary/util/HsqlUtil.java | 6 +--
.../ctakes/gui/dictionary/util/JdbcUtil.java | 6 +--
.../gui/dictionary/util/RareWordDbWriter.java | 6 +--
.../ctakes/gui/generic/GenericRunnerGui.java | 6 +--
.../org/apache/ctakes/gui/generic/MainPanel.java | 6 +--
.../org/apache/ctakes/gui/pipeline/MainPanel.java | 6 +--
.../org/apache/ctakes/gui/pipeline/MainPanel2.java | 6 +--
.../apache/ctakes/gui/pipeline/PiperCreator.java | 6 +--
.../ctakes/gui/pipeline/PiperDisplayModel.java | 6 +--
.../apache/ctakes/gui/pipeline/PiperRunnerGui.java | 6 +--
.../ctakes/gui/pipeline/PiperRunnerPanel.java | 6 +--
.../ctakes/gui/pipeline/bit/BitCellRenderer.java | 6 +--
.../ctakes/gui/pipeline/bit/BitInfoPanel.java | 6 +--
.../ctakes/gui/pipeline/bit/PipeBitFinder.java | 6 +--
.../ctakes/gui/pipeline/bit/PipeBitPainter.java | 6 +--
.../bit/available/AvailablesListModel.java | 6 +--
.../pipeline/bit/available/AvailablesRenderer.java | 6 +--
.../gui/pipeline/bit/info/PipeBitInfoPanel.java | 6 +--
.../gui/pipeline/bit/info/PipeBitInfoRenderer.java | 6 +--
.../ctakes/gui/pipeline/bit/info/RoleRenderer.java | 6 +--
.../pipeline/bit/info/TypeProductListModel.java | 6 +--
.../gui/pipeline/bit/info/TypeProductRenderer.java | 6 +--
.../bit/parameter/DefaultParameterHolder.java | 6 +--
.../bit/parameter/ParameterCellRenderer.java | 6 +--
.../pipeline/bit/parameter/ParameterInfoPanel.java | 6 +--
.../pipeline/bit/parameter/ParameterMapper.java | 6 +--
.../bit/parameter/ParameterTableModel.java | 6 +--
.../gui/pipeline/bit/user/DefaultUserBit.java | 6 +--
.../gui/pipeline/bit/user/UserBitInfoPanel.java | 6 +--
.../gui/pipeline/bit/user/UserBitListModel.java | 6 +--
.../gui/pipeline/bit/user/UserBitRenderer.java | 6 +--
.../pipeline/bit/user/UserParameterInfoPanel.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperFinder.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperInfo.java | 6 +--
.../ctakes/gui/pipeline/piper/PiperTextFilter.java | 6 +--
.../org/apache/ctakes/gui/util/ColorFactory.java | 6 +--
.../org/apache/ctakes/gui/util/IconLoader.java | 6 +--
.../org/apache/ctakes/lvg/ae/LvgAnnotator.java | 10 ++--
.../ctakes/lvg/ae/LvgBaseTokenAnnotator.java | 6 +--
.../org/apache/ctakes/lvg/ae/LvgSingleton.java | 6 +--
.../org/apache/ctakes/lvg/ae/ThreadSafeLvg.java | 6 +--
.../ctakes/lvg/resource/LvgCmdApiResourceImpl.java | 6 +--
ctakes-mastif-zoner/pom.xml | 5 +-
.../zoner/LineTokenToCharacterOffsetConverter.java | 6 +--
.../java/org/mitre/medfacts/zoner/ZonerCli.java | 55 ++++++++++++----------
.../java/org/mitre/medfacts/zoner/ZonerRunner.java | 6 +--
.../apache/ctakes/necontexts/ContextAnnotator.java | 6 +--
.../necontexts/NamedEntityContextAnalyzer.java | 6 +--
.../concurrent/ThreadSafeContextAnnotator.java | 6 +--
.../org/apache/ctakes/pbj/ae/ArtemisStarter.java | 6 +--
.../org/apache/ctakes/pbj/ae/ArtemisStopper.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjJmsSender.java | 6 +--
.../java/org/apache/ctakes/pbj/ae/PbjPipper.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjReceiverAE.java | 6 +--
.../java/org/apache/ctakes/pbj/ae/PbjSender.java | 6 +--
.../org/apache/ctakes/pbj/ae/PbjStompSender.java | 6 +--
.../java/org/apache/ctakes/pbj/cr/PbjReceiver.java | 6 +--
.../apache/ctakes/pbj/util/ArtemisController.java | 6 +--
.../ctakes/postagger/ClearNLPPOSTaggerAE.java | 6 +--
.../org/apache/ctakes/postagger/POSTagger.java | 6 +--
.../postagger/concurrent/ThreadSafePosTagger.java | 6 +--
.../preprocessor/ClinicalNotePreProcessor.java | 6 +--
.../ctakes/preprocessor/ae/CdaCasInitializer.java | 6 +--
.../ctakes/core/ae/LabValueFinderTester.java | 11 ++---
.../regression/test/RegressionPipelineTest.java | 6 +--
.../ae/DegreeOfRelationExtractorAnnotator.java | 6 +--
.../ae/LocationOfRelationExtractorAnnotator.java | 6 +--
.../ae/ModifierExtractorAnnotator.java | 6 +--
.../ae/RelationExtractorAnnotator.java | 6 +--
.../concurrent/ThreadSafeDegreeExtractor.java | 6 +--
.../concurrent/ThreadSafeLocationExtractor.java | 6 +--
.../concurrent/ThreadSafeModifierExtractor.java | 6 +--
.../ctakes/relationextractor/eval/DeepPheXMI.java | 6 +--
.../metastasis/MetastasisAnaforaXMLReader.java | 6 +--
.../smokingstatus/ae/ClassifiableEntries.java | 6 +--
.../ctakes/smokingstatus/ae/PcsClassifier.java | 6 +--
.../smokingstatus/ae/ResolutionAnnotator.java | 6 +--
.../ctakes/smokingstatus/ae/SentenceAdjuster.java | 6 +--
.../cc/RecordResolutionCasConsumer.java | 6 +--
.../filler/ae/TemplateFillerAnnotator.java | 6 +--
.../ctakes/temporal/ae/BackwardsTimeAnnotator.java | 6 +--
.../ae/ConstituencyBasedTimeAnnotator.java | 6 +--
.../temporal/ae/DeepPheAnaforaXMLReader.java | 6 +--
.../ctakes/temporal/ae/DocTimeApproximator.java | 6 +--
.../ctakes/temporal/ae/DocTimeRelAnnotator.java | 6 +--
.../apache/ctakes/temporal/ae/EventAnnotator.java | 6 +--
.../ae/EventEventCRFRelationAnnotator.java | 4 +-
.../temporal/ae/EventEventRelationAnnotator.java | 6 +--
.../temporal/ae/EventTimeRelationAnnotator.java | 6 +--
.../ctakes/temporal/ae/SimpleMedDatesFinder.java | 6 +--
.../ctakes/temporal/ae/THYMEAnaforaXMLReader.java | 6 +--
.../temporal/ae/THYMEQAAnaforaXMLReader.java | 6 +--
.../ctakes/temporal/ae/THYMETreebankReader.java | 6 +--
.../ae/TemporalRelationExtractorAnnotator.java | 4 +-
.../temporal/ae/feature/ClosestVerbExtractor.java | 2 +-
.../ae/feature/CoveredTextToValuesExtractor.java | 6 +--
.../ae/feature/EventPositionFeatureExtractor.java | 2 +-
.../ae/feature/EventPropertyExtractor.java | 6 +--
.../IdentifiedAnnotationFeatureExtractor.java | 6 +--
.../ae/feature/NearbyVerbTenseXExtractor.java | 2 +-
.../ae/feature/SectionHeaderExtractor.java | 2 +-
.../ctakes/temporal/ae/feature/TimeXExtractor.java | 2 +-
.../ctakes/temporal/cc/SimpleMedDatesPrinter.java | 6 +--
.../concurrent/ThreadSafeBackTimeAnnotator.java | 6 +--
.../concurrent/ThreadSafeDocTimeRelAnnotator.java | 6 +--
.../concurrent/ThreadSafeEventAnnotator.java | 6 +--
.../ThreadSafeEventEventRelAnnotator.java | 6 +--
.../ThreadSafeEventTimeRelAnnotator.java | 6 +--
.../eval/EvaluationOfEventPropertiesTk.java | 4 +-
.../ctakes/temporal/eval/Evaluation_ImplBase.java | 6 +--
.../temporal/eval/RemoveTreeAlignedMentions.java | 6 +--
.../apache/ctakes/temporal/utils/CalendarUtil.java | 4 +-
.../temporal/ae/BackwardsTimeAnnotatorTest.java | 6 +--
.../ae/ContextualModalityAnnotatorTest.java | 6 +--
.../temporal/ae/DocTimeRelAnnotatorTest.java | 6 +--
.../ctakes/temporal/ae/EventAnnotatorTest.java | 6 +--
.../ae/EventEventRelationAnnotatorTest.java | 6 +--
.../ae/EventTimeRelationAnnotatorTest.java | 6 +--
.../ctakes/rest/service/RestPipelineRunner.java | 8 ++--
.../apache/ctakes/rest/service/TinyController.java | 6 +--
.../ctakes/rest/service/CtakesRestController.java | 6 +--
.../ctakes/ytex/tools/SetupAuiFirstWord.java | 6 +--
.../ytex/uima/annotators/SentenceDetector.java | 21 +++++----
.../ae/FirstTokenPermLookupInitializerImpl.java | 6 +--
.../InitableJdbcConnectionResourceImpl.java | 6 +--
.../ytex/uima/annotators/DateAnnotatorTest.java | 6 +--
.../ctakes/ytex/web/search/ConceptLookupBean.java | 6 +--
.../ytex/web/search/DocumentSearchServiceImpl.java | 6 +--
.../ctakes/ytex/web/search/SemanticSearchBean.java | 19 ++++----
ctakes-ytex/pom.xml | 4 ++
.../main/java/org/apache/ctakes/jdl/AppJdl.java | 6 +--
.../apache/ctakes/jdl/data/loader/CsvLoader.java | 6 +--
.../apache/ctakes/util/JdbcOperationsHelper.java | 6 +--
.../java/org/apache/ctakes/ytex/dao/DBUtil.java | 6 +--
.../kernel/BaseClassifierEvaluationParser.java | 6 +--
.../ctakes/ytex/kernel/ClassifierEvalUtil.java | 6 +--
.../ytex/kernel/ClassifierEvaluationImporter.java | 6 +--
.../ctakes/ytex/kernel/FoldGeneratorImpl.java | 6 +--
.../ytex/kernel/ImputedFeatureEvaluatorImpl.java | 6 +--
.../kernel/IntrinsicInfoContentEvaluatorImpl.java | 6 +--
.../apache/ctakes/ytex/kernel/KernelUtilImpl.java | 6 +--
.../ctakes/ytex/kernel/SVMLinFormatterFactory.java | 6 +--
.../ctakes/ytex/kernel/SparseDataExporterImpl.java | 6 +--
.../ctakes/ytex/kernel/SvmlinEvaluationParser.java | 6 +--
.../ctakes/ytex/kernel/dao/ConceptDaoImpl.java | 6 +--
.../ytex/kernel/dao/KernelEvaluationDaoImpl.java | 6 +--
.../ctakes/ytex/kernel/dao/SortedSetUserType.java | 6 +--
.../evaluator/CorpusKernelEvaluatorImpl.java | 6 +--
.../ctakes/ytex/kernel/evaluator/NormKernel.java | 6 +--
.../ytex/kernel/evaluator/ProductKernel.java | 19 ++++----
.../ytex/kernel/evaluator/SemanticSimKernel.java | 6 +--
.../ytex/kernel/evaluator/SemanticTypeKernel.java | 6 +--
.../metric/ConceptSimilarityServiceImpl.java | 6 +--
.../apache/ctakes/ytex/kernel/model/ConcRel.java | 6 +--
.../ytex/kernel/pagerank/PageRankServiceImpl.java | 6 +--
.../ytex/kernel/tree/InstanceTreeBuilderImpl.java | 6 +--
.../ctakes/ytex/semil/SemiLEvaluationParser.java | 6 +--
.../ytex/weka/DocumentResultInstanceImporter.java | 6 +--
.../ytex/weka/WekaAttributeEvaluatorImpl.java | 6 +--
.../org/apache/ctakes/ytex/ConceptDaoTest.java | 6 +--
.../apache/ctakes/ytex/umls/dao/UMLSDaoTest.java | 8 ++--
pom.xml | 43 ++++++++---------
467 files changed, 1497 insertions(+), 1468 deletions(-)