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Posted to commits@ctakes.apache.org by re...@apache.org on 2024/07/27 00:29:40 UTC
(ctakes) 01/01: Issue #20 - Crossgrade to SLF4J
This is an automated email from the ASF dual-hosted git repository.
rec pushed a commit to branch refactoring/20-Crossgrade-to-SLF4J
in repository https://gitbox.apache.org/repos/asf/ctakes.git
commit 320cbefb37bf22b460ad437b7e6fbe85e853c384
Author: Richard Eckart de Castilho <re...@apache.org>
AuthorDate: Fri Jul 26 21:29:04 2024 -0300
Issue #20 - Crossgrade to SLF4J
- Use the SLF4J API instead of the Log4J API
---
.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 | 6 +--
.../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, 1484 insertions(+), 1463 deletions(-)
diff --git a/.gitignore b/.gitignore
index 172a541..ec78bf6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,3 +37,4 @@ cTAKES.error.log
Web ARchives - built by ctakes
*.war
+.factorypath
diff --git a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
index 2775b0d..f5621d2 100644
--- a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
+++ b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
import org.apache.ctakes.core.cc.FileTreeXmiWriter;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.cr.TextReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReader;
@@ -43,7 +43,7 @@ import java.util.List;
public class RunZoner
{
- private static Logger LOGGER = LogManager.getLogger(RunZoner.class.getName());
+ private static Logger LOGGER = LoggerFactory.getLogger(RunZoner.class.getName());
File inputDirectory;
List<File> inputFiles;
diff --git a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
index 840b8d1..fc3349b 100644
--- a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
+++ b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
@@ -26,8 +26,8 @@ import java.util.Iterator;
import java.util.List;
import org.apache.ctakes.assertion.zoner.types.Heading;
import org.apache.ctakes.assertion.zoner.types.Zone;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -64,7 +64,7 @@ public class ZoneAnnotator extends JCasAnnotator_ImplBase {
mandatory = false)
protected Boolean includeGenerics = Boolean.FALSE;
- static private final Logger LOGGER = LogManager.getLogger( "ZoneAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ZoneAnnotator" );
@Override
public void initialize (UimaContext aContext) throws ResourceInitializationException {
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
index 5e6e7bc..2904a7f 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.assertion.attributes;
import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -45,7 +45,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
public class GenericAttributeAnalysisEngine extends JCasAnnotator_ImplBase {
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
index 15eeb01..dd61455 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.assertion.attributes;
import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -39,7 +39,7 @@ import org.apache.uima.resource.ResourceInitializationException;
public class SubjectAttributeAnalysisEngine extends JCasAnnotator_ImplBase {
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
index b452af9..d092247 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
@@ -18,6 +18,12 @@
*/
package org.apache.ctakes.assertion.attributes.subject;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Objects;
+
import org.apache.ctakes.dependency.parser.util.DependencyPath;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.typesystem.type.constants.CONST;
@@ -26,13 +32,11 @@ import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
-
-import java.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
@@ -57,7 +61,7 @@ public class SubjectAttributeClassifier {
public static final String OTHER_DEPTOK = "other_depsrl";
public static final String OTHER_OR = "other_or";
public static ArrayList<String> FeatureIndex = new ArrayList<String>();
- private static final Logger LOGGER = LogManager.getLogger( "SubjectAttributeClassifier" );
+ private static final Logger LOGGER = LoggerFactory.getLogger( "SubjectAttributeClassifier" );
static{
FeatureIndex.add(DONOR_TOKEN);
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java
index 7e1de1a..df4f41d 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CollectionException;
@@ -62,7 +62,7 @@ public class I2B2Challenge2010CollectionReader extends CollectionReader_ImplBase
private String mEncoding = null;
// Pattern conPatt = Pattern.compile("c=\"(.*)\" (\\d+):(\\d+) (\\d+):(\\d+)\\|\\|t=\"(.*)\"");
Pattern astPatt = Pattern.compile("c=\"(.*)\" (\\d+):(\\d+) (\\d+):(\\d+)\\|\\|t=\"(.*)\"\\|\\|a=\"(.*)\"");
- Logger LOGGER = LogManager.getLogger(this.getClass());
+ Logger LOGGER = LoggerFactory.getLogger(this.getClass());
HashMap<String,String> conLocs = new HashMap<String, String>();
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java
index d66ca97..f207519 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java
@@ -32,8 +32,8 @@ import org.apache.ctakes.typesystem.type.refsem.*;
import org.apache.ctakes.typesystem.type.relation.*;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textsem.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.Feature;
@@ -66,7 +66,7 @@ import java.util.*;
products = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.GENERIC_RELATION }
)
public class MiPACQKnowtatorXMLReader extends JCasAnnotator_ImplBase {
- static Logger LOGGER = LogManager.getLogger(MiPACQKnowtatorXMLReader.class);
+ static Logger LOGGER = LoggerFactory.getLogger(MiPACQKnowtatorXMLReader.class);
public static final String PARAM_TEXT_DIRECTORY = "TextDirectory";
@ConfigurationParameter(
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java
index 1d38255..c1aad7e 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.assertion.cr;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Date;
@@ -29,7 +29,7 @@ import java.util.Date;
* some mistakes in gold standard (e.g. where entity is longer than the sentence!)
*/
public class NegExAnnotation {
- static Logger LOGGER = LogManager.getLogger(NegExAnnotation.class);
+ static Logger LOGGER = LoggerFactory.getLogger(NegExAnnotation.class);
/**
* Each line consist of following fields
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java
index b9dfd23..04c7a9e 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java
@@ -26,8 +26,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CollectionException;
@@ -56,7 +56,7 @@ import java.util.List;
products = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
public class NegExCorpusReader extends CollectionReader_ImplBase {
- static Logger LOGGER = LogManager.getLogger(NegExCorpusReader.class);
+ static Logger LOGGER = LoggerFactory.getLogger(NegExCorpusReader.class);
private boolean skipReadingValuesJustReadText = false;
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
index 63130e6..3481664 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
@@ -37,8 +37,8 @@ import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.Modifier;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -83,7 +83,7 @@ import java.util.*;
public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatisticsCompact<String>>> {
-private static final Logger LOGGER = LogManager.getLogger( AssertionEvaluation.class );
+private static final Logger LOGGER = LoggerFactory.getLogger( AssertionEvaluation.class );
private static final String YTEX_NEGATION_DESCRIPTOR = "ytex.uima.NegexAnnotator";
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
index ed81ef2..725de26 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -76,7 +76,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.IDENTIFIED
)
public class MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas extends JCasAnnotator_ImplBase {
- static final Logger LOGGER = LogManager.getLogger(MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.class.getName());
+ static final Logger LOGGER = LoggerFactory.getLogger(MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.class.getName());
private static final String dirWithGoldViews = AssertionConst.testDirectories.get("polarity");// TODO parameterize this
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
index 4aa4cc3..74e3ddb 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
@@ -25,9 +25,8 @@ import org.apache.ctakes.assertion.stub.*;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Level;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -62,7 +61,7 @@ import java.util.Set;
@Deprecated
public class AssertionAnalysisEngine extends JCasAnnotator_ImplBase
{
- private static Logger LOGGER = LogManager.getLogger(AssertionAnalysisEngine.class.getName());
+ private static Logger LOGGER = LoggerFactory.getLogger(AssertionAnalysisEngine.class.getName());
AssertionDecoderConfiguration assertionDecoderConfiguration;
@@ -285,7 +284,7 @@ public class AssertionAnalysisEngine extends JCasAnnotator_ImplBase
{
String message = "current assertion type is null; this is a problem!!";
System.err.println(message);
- LOGGER.log(Level.ERROR,message);
+ // LOGGER.log(Level.ERROR,message);
// Exception runtimeException = new RuntimeException(message);
// throw new AnalysisEngineProcessException(runtimeException);
@@ -365,7 +364,7 @@ public class AssertionAnalysisEngine extends JCasAnnotator_ImplBase
String message = String.format(
"unexpected assertion value returned!! \"%s\"",
assertionType);
- LOGGER.log(Level.ERROR,message);
+ // LOGGER.log(Level.ERROR,message);
// System.err.println(message);
Exception runtimeException = new RuntimeException(message);
throw new AnalysisEngineProcessException(runtimeException);
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
index 657f5f9..35f85c5 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.assertion.stub.*;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -41,7 +41,7 @@ import static org.apache.ctakes.typesystem.type.constants.CONST.ATTR_SUBJECT_PAT
)
public class AssertionAnalysisEngineFit extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "AssertionAnalysisEngineFit" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AssertionAnalysisEngineFit" );
static public final String ASSERTION_MODEL_PARAM = "assertionModelResource";
static public final String SCOPE_MODEL_PARAM = "scopeModelResource";
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java
index 13812a2..26ad232 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.assertion.medfacts;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.Type;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
@@ -34,7 +34,7 @@ import java.util.TreeSet;
public class CasIndexer<T extends Annotation>
{
- private Logger LOGGER = LogManager.getLogger(CasIndexer.class.getName());
+ private Logger LOGGER = LoggerFactory.getLogger(CasIndexer.class.getName());
private JCas jcas;
protected Map<Integer, T> mapByAddress;
protected Type targetType;
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
index 4c80776..e457c44 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FeatureStructure;
@@ -41,7 +41,7 @@ import org.apache.uima.jcas.tcas.Annotation;
)
public class ConceptConverterAnalysisEngine extends JCasAnnotator_ImplBase
{
- public static final Logger LOGGER = LogManager.getLogger(ConceptConverterAnalysisEngine.class.getName());
+ public static final Logger LOGGER = LoggerFactory.getLogger(ConceptConverterAnalysisEngine.class.getName());
public ConceptConverterAnalysisEngine()
{
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
index 06519fa..b2e9b8c 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.assertion.medfacts;
import org.apache.ctakes.assertion.stub.ConceptType;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.FeatureStructure;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
@@ -32,7 +32,7 @@ import java.util.HashSet;
public class ConceptLookup
{
- public static final Logger LOGGER = LogManager.getLogger(ConceptConverterAnalysisEngine.class.getName());
+ public static final Logger LOGGER = LoggerFactory.getLogger(ConceptConverterAnalysisEngine.class.getName());
protected static HashSet<String> problemSet = new HashSet<String>();
protected static HashSet<String> testSet = new HashSet<String>();
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
index 19a981c..febd6fb 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -56,7 +56,7 @@ import java.util.List;
*/
public class Converti2b2AnnotationsToCTAKES {
- private static Logger LOGGER = LogManager.getLogger(Converti2b2AnnotationsToCTAKES.class);
+ private static Logger LOGGER = LoggerFactory.getLogger(Converti2b2AnnotationsToCTAKES.class);
private static CAS getTypeSystemFromDescriptor(String descriptor) throws InvalidXMLException, IOException, ResourceInitializationException, CASException {
XMLParser xmlParser = UIMAFramework.getXMLParser();
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
index d299247..3824612 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
@@ -29,8 +29,6 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -62,8 +60,6 @@ import java.util.*;
*/
public abstract class AssertionCleartkAnalysisEngine extends
CleartkAnnotator<String> {
- Logger LOGGER = LogManager.getLogger( AssertionCleartkAnalysisEngine.class );
-
public static final String PARAM_GOLD_VIEW_NAME = "GoldViewName";
public enum FEATURE_CONFIG {
@@ -310,7 +306,7 @@ public abstract class AssertionCleartkAnalysisEngine extends
@Override
public void process( JCas jCas ) throws AnalysisEngineProcessException {
- LOGGER.info( "Processing ..." );
+ getLogger().info( "Processing ..." );
String documentId = DocIdUtil.getDocumentID( jCas );
String domainId = "";
String domainFeature = null;
@@ -320,7 +316,7 @@ public abstract class AssertionCleartkAnalysisEngine extends
}
if ( documentId != null ) {
- LOGGER.debug( "processing next doc: " + documentId );
+ getLogger().debug( "processing next doc: " + documentId );
// set the domain to be FeatureFunction'ed into all extractors
if ( !fileToDomain.isEmpty() && ffDomainAdaptor != null ) {
domainId = fileToDomain.get( documentId );
@@ -330,7 +326,7 @@ public abstract class AssertionCleartkAnalysisEngine extends
domainFeature = fileToDomain.get( documentId );
}
} else {
- LOGGER.debug( "processing next doc (doc id is null)" );
+ getLogger().debug( "processing next doc (doc id is null)" );
}
this.lastLabel = "<BEGIN>";
@@ -385,7 +381,7 @@ public abstract class AssertionCleartkAnalysisEngine extends
for ( IdentifiedAnnotation identifiedAnnotation : entities ) {
if ( identifiedAnnotation.getPolarity() == -1 ) {
- LOGGER.debug( String.format( " - identified annotation: [%d-%d] polarity %d (%s)",
+ getLogger().debug( String.format( " - identified annotation: [%d-%d] polarity %d (%s)",
identifiedAnnotation.getBegin(),
identifiedAnnotation.getEnd(),
identifiedAnnotation.getPolarity(),
@@ -668,7 +664,8 @@ public abstract class AssertionCleartkAnalysisEngine extends
*/
// Object.finalize() was deprecated in jdk 9. Given the manner of this code, this is a -reasonable- replacement.
- public void collectionProcessComplete() throws AnalysisEngineProcessException {
+ @Override
+public void collectionProcessComplete() throws AnalysisEngineProcessException {
super.collectionProcessComplete();
if ( classifier instanceof AutoCloseable ) {
try {
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
index 8c4a9df..dc97ad6 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
@@ -108,7 +108,7 @@ public class PolarityCleartkAnalysisEngine extends AssertionCleartkAnalysisEngin
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if (NEGATED.equals(polarity))
{
- LOGGER.debug("TRAINING: " + polarity);
+ getLogger().debug("TRAINING: " + polarity);
}
if (NOT_NEGATED.equals(polarity)
&& coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) {
@@ -127,7 +127,7 @@ public class PolarityCleartkAnalysisEngine extends AssertionCleartkAnalysisEngin
} else if (NEGATED.equals(label))
{
polarity = CONST.NE_POLARITY_NEGATION_PRESENT;
- LOGGER.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName()));
+ getLogger().debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName()));
}
entityOrEventMention.setPolarity(polarity);
}
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
index 289e2ca..f0afeac 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
@@ -74,7 +74,7 @@ public class PolarityFedaCleartkAnalysisEngine extends PolarityCleartkAnalysisEn
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if (NEGATED.equals(polarity))
{
- LOGGER.debug("TRAINING: " + polarity);
+ getLogger().debug("TRAINING: " + polarity);
}
if (NOT_NEGATED.equals(polarity)
&& coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) {
@@ -93,7 +93,7 @@ public class PolarityFedaCleartkAnalysisEngine extends PolarityCleartkAnalysisEn
} else if (NEGATED.equals(label))
{
polarity = CONST.NE_POLARITY_NEGATION_PRESENT;
- LOGGER.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName()));
+ getLogger().debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName()));
}
entityOrEventMention.setPolarity(polarity);
}
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
index f5b8a3e..522b8ca 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
@@ -22,7 +22,6 @@ import org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor;
import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Level;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -71,7 +70,7 @@ public class SubjectCleartkAnalysisEngine extends
return;
}
instance.setOutcome(subj);
- LOGGER.log(Level.DEBUG, String.format("[%s] expected: ''; actual: ''; features: %s",
+ getLogger().debug(String.format("[%s] expected: ''; actual: ''; features: %s",
this.getClass().getSimpleName(),
instance.toString()
));
@@ -79,7 +78,7 @@ public class SubjectCleartkAnalysisEngine extends
{
String label = this.classifier.classify(instance.getFeatures());
entityOrEventMention.setSubject(label);
- LOGGER.log(Level.DEBUG, "SUBJECT is being set on an IdentifiedAnnotation: "+label+" "+entityOrEventMention.getSubject());
+ getLogger().debug("SUBJECT is being set on an IdentifiedAnnotation: "+label+" "+entityOrEventMention.getSubject());
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java
index 62ffe1c..b5388cc 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotations
import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier;
import org.apache.ctakes.core.cc.FileTreeXmiWriter;
import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.factory.AggregateBuilder;
@@ -55,7 +55,7 @@ public class TrainAssertionModel {
public static final String PARAM_NAME_MODEL_DIRECTORY = "model-directory";
- protected static final Logger LOGGER = LogManager.getLogger(TrainAssertionModel.class.getName());
+ protected static final Logger LOGGER = LoggerFactory.getLogger(TrainAssertionModel.class.getName());
/**
* @param args
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
index d4aa888..77f7a64 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.JCasFactory;
@@ -47,7 +47,7 @@ import java.util.Map;
public class CueWordTest
{
- Logger LOGGER = LogManager.getLogger(CueWordTest.class.getName());
+ Logger LOGGER = LoggerFactory.getLogger(CueWordTest.class.getName());
/**
* @param args
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
index 0ac6e8b..8c64e58 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.JCasFactory;
@@ -48,7 +48,7 @@ import java.util.Map;
@SuppressWarnings("unchecked")
public class CueWordTest2
{
- Logger LOGGER = LogManager.getLogger(CueWordTest2.class.getName());
+ Logger LOGGER = LoggerFactory.getLogger(CueWordTest2.class.getName());
/**
* @param args
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
index d3abeb2..b279d39 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
@@ -30,7 +30,7 @@ import java.util.List;
public class SurroundingExtractor implements FeatureExtractor1
{
-// protected static final Logger LOGGER = LogManager.getLogger(SurroundingExtractor.class);
+// protected static final Logger LOGGER = LoggerFactory.getLogger(SurroundingExtractor.class);
//
//// Class<? extends Annotation> ancestorAnnotationClass;
////
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/SubjectCleartkAnalysisEngineWindowed.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/SubjectCleartkAnalysisEngineWindowed.java
index 6c25fc2..24db0ea 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/SubjectCleartkAnalysisEngineWindowed.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/SubjectCleartkAnalysisEngineWindowed.java
@@ -22,7 +22,6 @@ import org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor;
import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Level;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -70,14 +69,14 @@ public class SubjectCleartkAnalysisEngineWindowed extends
return;
}
instance.setOutcome( subj );
- LOGGER.log( Level.DEBUG, String.format( "[%s] expected: ''; actual: ''; features: %s",
+ getLogger().debug(String.format( "[%s] expected: ''; actual: ''; features: %s",
this.getClass().getSimpleName(),
instance.toString()
) );
} else {
String label = this.classifier.classify( instance.getFeatures() );
entityOrEventMention.setSubject( label );
- LOGGER.log( Level.DEBUG,
+ getLogger().debug(
"SUBJECT is being set on an IdentifiedAnnotation: " + label + " " + entityOrEventMention.getSubject() );
}
}
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
index 634588b..21ea3cc 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
@@ -34,8 +34,8 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -65,7 +65,7 @@ import java.util.*;
*/
public abstract class WindowedAssertionCleartkAnalysisEngine extends
CleartkAnnotator<String> {
- Logger LOGGER = LogManager.getLogger( WindowedAssertionCleartkAnalysisEngine.class );
+ Logger LOGGER = LoggerFactory.getLogger( WindowedAssertionCleartkAnalysisEngine.class );
public static final String PARAM_GOLD_VIEW_NAME = "GoldViewName";
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
index 8b1ad35..0c9e0b0 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.assertion.stub.LineAndTokenPosition;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.cas.Type;
import org.apache.uima.cas.text.AnnotationIndex;
@@ -35,7 +35,7 @@ import org.apache.uima.jcas.tcas.Annotation;
import java.util.*;
public class CharacterOffsetToLineTokenConverterCtakesImpl implements CharacterOffsetToLineTokenConverter {
- protected Logger LOGGER = LogManager.getLogger(CharacterOffsetToLineTokenConverterCtakesImpl.class.getName());
+ protected Logger LOGGER = LoggerFactory.getLogger(CharacterOffsetToLineTokenConverterCtakesImpl.class.getName());
protected JCas jcas;
protected TreeMap<Integer, Sentence> beginTreeMap;
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
index f085d07..50c8de1 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.assertion.stub.SingleDocumentProcessor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
@@ -37,7 +37,7 @@ import java.util.List;
public class SingleDocumentProcessorCtakes extends SingleDocumentProcessor
{
- Logger LOGGER = LogManager.getLogger(SingleDocumentProcessorCtakes.class.getName());
+ Logger LOGGER = LoggerFactory.getLogger(SingleDocumentProcessorCtakes.class.getName());
protected JCas jcas;
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
index 1822b97..4cf0917 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
@@ -32,8 +32,8 @@ import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.utils.tree.SimpleTree;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.factory.CollectionReaderFactory;
@@ -74,7 +74,7 @@ public class GenerateDependencyRepresentation {
protected static Options options = new Options();
private static SemanticClasses sems = null;
private static PrintStream out = null;
- private static final Logger LOGGER = LogManager.getLogger( "GenerateDependencyRepresentation" );
+ private static final Logger LOGGER = LoggerFactory.getLogger( "GenerateDependencyRepresentation" );
public static final int UP_NODES = 2;
/**
* @param args
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
index 6afa4d6..5d6871d 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.utils.tree.SimpleTree;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.factory.CollectionReaderFactory;
@@ -73,7 +73,7 @@ public class GenerateTreeRepresentation{
protected static Options options = new Options();
private static SemanticClasses sems = null;
private static PrintStream out = null;
- private static final Logger LOGGER = LogManager.getLogger( "GenerateTreeRepresentation" );
+ private static final Logger LOGGER = LoggerFactory.getLogger( "GenerateTreeRepresentation" );
/**
* @param args
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java
index d3a9aed..904d263 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java
@@ -28,8 +28,8 @@ import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
import org.apache.ctakes.core.cc.FileTreeXmiWriter;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.cr.FileTreeReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReaderDescription;
@@ -57,7 +57,7 @@ import java.util.HashMap;
*/
public class GoldEntityAndAttributeReaderPipelineForSeedCorpus {
- static final Logger LOGGER = LogManager.getLogger(GoldEntityAndAttributeReaderPipelineForSeedCorpus.class.getName());
+ static final Logger LOGGER = LoggerFactory.getLogger(GoldEntityAndAttributeReaderPipelineForSeedCorpus.class.getName());
public static void main(String[] args) throws UIMAException, IOException {
@@ -87,7 +87,7 @@ public class GoldEntityAndAttributeReaderPipelineForSeedCorpus {
// File parentDirectory = new File(parentDirectoryString);
if (!parentDirectory.exists())
{
- LOGGER.fatal(String.format("parent directory %s does not exist! exiting!", parentDirectory.getAbsolutePath()));
+ LOGGER.error(String.format("parent directory %s does not exist! exiting!", parentDirectory.getAbsolutePath()));
return;
}
@@ -107,7 +107,7 @@ public class GoldEntityAndAttributeReaderPipelineForSeedCorpus {
if (!currentBatchDirectory.exists())
{
- LOGGER.fatal(String.format("current batch directory does not exist! exiting! [\"%s\"]", currentBatchDirectory.toString()));
+ LOGGER.error(String.format("current batch directory does not exist! exiting! [\"%s\"]", currentBatchDirectory.toString()));
continue;
}
@@ -223,7 +223,8 @@ public class GoldEntityAndAttributeReaderPipelineForSeedCorpus {
readSharpUmls(new File[] {mayoStrat}, trainDirectory, testDirectory, devDirectory,
new Function<File,Subcorpus>(){
- public Subcorpus apply(File f){
+ @Override
+ public Subcorpus apply(File f){
return SharpCorpusSplit.splitStratified(f);
}
});
@@ -233,7 +234,8 @@ public class GoldEntityAndAttributeReaderPipelineForSeedCorpus {
File seed1 = new File(releaseDirectory, "SHARP/SeedSet1/by-batch/umls");
readSharpUmls(new File[] {seed1}, trainDirectory, testDirectory, devDirectory,
new Function<File,Subcorpus>(){
- public Subcorpus apply(File f){
+ @Override
+ public Subcorpus apply(File f){
return SharpCorpusSplit.splitSeed(f);
}
});
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java
index bfa142e..680f580 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java
@@ -1,11 +1,11 @@
package org.apache.ctakes.assertion.stub;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
public class AssertionAnnotation extends ConceptAnnotation {
- static private final Logger LOGGER = LogManager.getLogger( "AssertionAnnotation" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AssertionAnnotation" );
public ConceptType getConceptType() {
LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java
index 6c8d943..bff86b1 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java
@@ -1,14 +1,14 @@
package org.apache.ctakes.assertion.stub;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
import java.util.List;
public class AssertionFileProcessor {
- static private final Logger LOGGER = LogManager.getLogger( "AssertionFileProcessor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AssertionFileProcessor" );
public List<Annotation> processAnnotationFile(File assertionFile) {
LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java
index c61fa4a..1f545d2 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java
@@ -1,14 +1,14 @@
package org.apache.ctakes.assertion.stub;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
import java.util.Set;
public class BatchRunner {
- static private final Logger LOGGER = LogManager.getLogger( "BatchRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BatchRunner" );
public static Set<String> loadEnabledFeaturesFromFile(File enabledFeaturesFile) {
LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java
index 5940f30..eed80bc 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java
@@ -1,13 +1,13 @@
package org.apache.ctakes.assertion.stub;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
public class JarafeMEDecoder {
- static private final Logger LOGGER = LogManager.getLogger( "JarafeMEDecoder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JarafeMEDecoder" );
public JarafeMEDecoder(File assertionModelFile) {
LOGGER.warn("This class cannot be used until CTAKES-76 is implemented.");
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java
index 62a5873..a9000bf 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java
@@ -1,14 +1,14 @@
package org.apache.ctakes.assertion.stub;
import org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.List;
import java.util.Map;
public class SingleDocumentProcessor {
- static private final Logger LOGGER = LogManager.getLogger( "SingleDocumentProcessor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SingleDocumentProcessor" );
protected CharacterOffsetToLineTokenConverterCtakesImpl converter2;
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java
index d48ff0a..be7e1fe 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java
@@ -1,12 +1,12 @@
package org.apache.ctakes.assertion.stub;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
public class StringHandling {
- static private final Logger LOGGER = LogManager.getLogger( "StringHandling" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "StringHandling" );
public static String readEntireContents(File file) {
// TODO Auto-generated method stub
diff --git a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java
index a218c1b..ead4c52 100644
--- a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java
+++ b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -59,7 +59,7 @@ import java.util.List;
public class Chunker extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- private final Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private final Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
/**
diff --git a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
index 668b717..ecf02df 100644
--- a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
+++ b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.chunker.ae.adjuster;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.syntax.Chunk;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -97,7 +97,7 @@ public class ChunkAdjuster extends JCasAnnotator_ImplBase {
// pattern within, instead of always Sentence
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
/**
* Performs initialization logic. This implementation just reads values for
diff --git a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/concurrent/ThreadSafeChunker.java b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/concurrent/ThreadSafeChunker.java
index 757fc04..74abbd4 100644
--- a/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/concurrent/ThreadSafeChunker.java
+++ b/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/concurrent/ThreadSafeChunker.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.chunker.concurrent;
import org.apache.ctakes.chunker.ae.Chunker;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -29,7 +29,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeChunker extends Chunker {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeChunker" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeChunker" );
/**
* {@inheritDoc}
diff --git a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
index a4b2c5e..8966913 100644
--- a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
+++ b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.fit.util.JCasUtil;
@@ -46,7 +46,7 @@ public class MaxentParserWrapper implements ParserWrapper {
Parser parser = null;
private String parseStr = "";
- static private final Logger LOGGER = LogManager.getLogger( "MaxentParserWrapper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MaxentParserWrapper" );
private int maxTokens;
public MaxentParserWrapper(InputStream in){
diff --git a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
index c684e65..e918e09 100644
--- a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
+++ b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.constituency.parser.ParserWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.log.DotLogger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -62,7 +62,7 @@ public class ConstituencyParser extends JCasAnnotator_ImplBase {
private ParserWrapper parser = null;
- static private final Logger LOGGER = LogManager.getLogger( "ConstituencyParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ConstituencyParser" );
@Override
public void initialize( final UimaContext aContext ) throws ResourceInitializationException {
diff --git a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/concurrent/ThreadSafeConstituencyParser.java b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/concurrent/ThreadSafeConstituencyParser.java
index 8c3939b..2fd4e04 100644
--- a/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/concurrent/ThreadSafeConstituencyParser.java
+++ b/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/concurrent/ThreadSafeConstituencyParser.java
@@ -10,8 +10,8 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Normally I would use composition and a singleton, but here extension is done for @ConfigurationParameter discovery.
@@ -29,7 +29,7 @@ import org.apache.logging.log4j.LogManager;
)
public class ThreadSafeConstituencyParser extends ConstituencyParser {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeConstituencyParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeConstituencyParser" );
/**
* {@inheritDoc}
diff --git a/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/context/tokenizer/ae/ContextDependentTokenizerAnnotator.java b/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/context/tokenizer/ae/ContextDependentTokenizerAnnotator.java
index e3fc7e7..2c51e6d 100644
--- a/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/context/tokenizer/ae/ContextDependentTokenizerAnnotator.java
+++ b/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/context/tokenizer/ae/ContextDependentTokenizerAnnotator.java
@@ -28,8 +28,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.syntax.*;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -53,7 +53,7 @@ import java.util.*;
)
public class ContextDependentTokenizerAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
private DateFSM iv_dateFSM;
private TimeFSM iv_timeFSM;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java
index 7835cd0..90d9325 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.resource.ResourceInitializationException;
@@ -16,7 +16,7 @@ import java.io.IOException;
*/
abstract public class AbstractCommandRunner extends PausableFileLoggerAE {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractCommandRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractCommandRunner" );
// This parameter is not mandatory so that extending classes can have fixed commands.
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java
index 62cbcdc..4bbdc1b 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -27,7 +27,7 @@ import java.io.InputStreamReader;
)
public class BsvRegexSectionizer extends RegexSectionizer {
- static private final Logger LOGGER = LogManager.getLogger( "BsvRegexSectionizer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvRegexSectionizer" );
static public final String SECTION_TYPES_PATH = "SectionsBsv";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
index b733960..6291abb 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -52,7 +52,7 @@ import java.util.regex.Pattern;
)
public class CDASegmentAnnotator extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "CDASegmentAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CDASegmentAnnotator" );
protected static HashMap<String, Pattern> patterns = new HashMap<>();
protected static HashMap<String, String> section_names = new HashMap<>();
protected static final String DEFAULT_SECTION_FILE_NAME = "src/user/resources/org/apache/ctakes/core/sections"
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
index 2b67488..2aedb25 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -25,7 +25,7 @@ import java.io.IOException;
)
public class CommandRunner extends AbstractCommandRunner {
- static private final Logger LOGGER = LogManager.getLogger( "CommandRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CommandRunner" );
static public final String SET_JAVAHOME_PARAM = "SetJavaHome";
@@ -106,14 +106,14 @@ public class CommandRunner extends AbstractCommandRunner {
private Logger getRunLogger() {
final String logName = getLogName();
if ( logName != null && !logName.isEmpty() ) {
- return LogManager.getLogger( logName );
+ return LoggerFactory.getLogger( logName );
}
final String command = getCommand().trim();
final int spaceIndex = command.indexOf( ' ' );
if ( spaceIndex < 0 ) {
- return LogManager.getLogger( command );
+ return LoggerFactory.getLogger( command );
}
- return LogManager.getLogger( command.substring( 0, spaceIndex ) );
+ return LoggerFactory.getLogger( command.substring( 0, spaceIndex ) );
}
static public AnalysisEngineDescription createEngineDescription( final String command )
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
index 0a0a20e..211ca60 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.ParamUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -79,7 +79,7 @@ public class CopyAnnotator extends JCasAnnotator_ImplBase {
private Class<? extends TOP> srcClass;
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "CopyAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CopyAnnotator" );
// constructor used to create a new instance of the destination
// JCas object
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
index ad5e318..bdb3f62 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -26,7 +26,7 @@ import java.io.IOException;
)
public class CtakesRunner extends PausableFileLoggerAE {
- static private final Logger LOGGER = LogManager.getLogger( "CtakesRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CtakesRunner" );
static public final String PIPE_PARAM = "Pipeline";
static public final String PIPE_DESC = "Piper parameters. Make sure to quote.";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
index 9e83083..723aaaa 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
@@ -35,7 +35,7 @@ import org.apache.uima.jcas.JCas;
)
public class DocumentIdPrinterAnalysisEngine extends JCasAnnotator_ImplBase
{
- static private final Logger LOGGER = LogManager.getLogger( "DocumentIdPrinterAnalysisEngine" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DocumentIdPrinterAnalysisEngine" );
@Override
public void process(JCas jcas) throws AnalysisEngineProcessException
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java
index 2f9f56c..13acc66 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -27,7 +27,7 @@ import java.util.regex.Pattern;
)
final public class EolSentenceFixer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "EolSentenceFixer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "EolSentenceFixer" );
static private final Pattern WHITESPACE = Pattern.compile( "\\s+" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java
index 96d8afa..518fffd 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.ae.inert.PausableAE;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -24,7 +24,7 @@ import java.awt.*;
)
public class ExitForcer extends PausableAE {
- static private final Logger LOGGER = LogManager.getLogger( "ExitForcer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ExitForcer" );
static public final String FORCE_PARAM = "ForceExit";
static public final String FORCE_DESC = "Forcibly exits the system when the value is yes. Yes by default.";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
index 48f2ad6..3858f3e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
@@ -11,8 +11,8 @@ import org.apache.ctakes.typesystem.type.syntax.NumToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -66,7 +66,7 @@ final public class LabValueFinder extends JCasAnnotator_ImplBase {
"C1715372", // "Medical problem"
"C1441604" }; // "High sensitivity"
- static final Logger LOGGER = LogManager.getLogger( "LabValueFinder" );
+ static final Logger LOGGER = LoggerFactory.getLogger( "LabValueFinder" );
@ConfigurationParameter( name = PARAM_ALL_SECTIONS,
description = "Use all Annotatable sections. This ignores the value of " + PARAM_SECTIONS,
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
index 335f808..d6b5bff 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.core.util.regex.RegexSpanFinder;
import org.apache.ctakes.typesystem.type.textspan.ListEntry;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -43,7 +43,7 @@ import java.util.stream.Collectors;
)
final public class ListAnnotator extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ListAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ListAnnotator" );
static public final String LIST_TYPES_PATH = "LIST_TYPES_PATH";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
index b190e18..d931f40 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.ctakes.typesystem.type.textspan.List;
import org.apache.ctakes.typesystem.type.textspan.ListEntry;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.text.AnnotationFS;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -38,7 +38,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.LIST;
)
public class ListEntryNegator extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ListEntryNegator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ListEntryNegator" );
static private final Pattern NEGATIVE_PATTERN
= Pattern
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
index 26ebd63..6aafd5c 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textspan.List;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -27,7 +27,7 @@ import java.util.regex.Pattern;
)
final public class ListParagraphFixer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ListSentenceFixer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ListSentenceFixer" );
static private final Pattern WHITESPACE = Pattern.compile( "\\s+" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java
index f937cf1..aa2f4db 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textspan.List;
import org.apache.ctakes.typesystem.type.textspan.ListEntry;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -28,7 +28,7 @@ import java.util.regex.Pattern;
)
final public class ListSentenceFixer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ListSentenceFixer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ListSentenceFixer" );
static private final Pattern WHITESPACE = Pattern.compile( "\\s+" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
index 7997f31..15e1a5e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -30,7 +30,7 @@ import java.util.stream.Collectors;
)
final public class MrsDrSentenceJoiner extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "MrsDrSentenceJoiner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MrsDrSentenceJoiner" );
/**
* Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java
index fe7646d..608e9e2 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.JCasUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -62,7 +62,7 @@ import java.util.*;
)
public class OverlapAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "OverlapAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "OverlapAnnotator" );
/**
* No overlap at all between A and B
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java
index 16aa0d2..6d14953 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.core.util.regex.RegexSpanFinder;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -35,7 +35,7 @@ import java.util.regex.Pattern;
)
final public class ParagraphAnnotator extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ParagraphAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParagraphAnnotator" );
static public final String PARAGRAPH_TYPES_PATH = "PARAGRAPH_TYPES_PATH";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java
index 0cb5a63..917c5d3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -29,7 +29,7 @@ import java.util.stream.Collectors;
)
final public class ParagraphSentenceFixer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ParagraphSentenceFixer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParagraphSentenceFixer" );
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java
index b751ede..37988db 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.pipeline.CliOptionals;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -36,7 +36,7 @@ import java.nio.file.Paths;
)
public class PiperFileRunEngine extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PiperFileRunEngine" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperFileRunEngine" );
@ConfigurationParameter(
name = "PiperParams",
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java
index 51abfb9..6762fd5 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.MutableUimaContext;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -21,7 +21,7 @@ import org.apache.uima.resource.ResourceInitializationException;
role = PipeBitInfo.Role.SPECIAL
)
public class PythonPipper extends PythonRunner {
- static private final Logger LOGGER = LogManager.getLogger( "PythonPipper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PythonPipper" );
static public final String PIP_PACKAGE_PARAM = "PipPackage";
static public final String PIP_PACKAGE_DESC = "Path of the python package to pip.";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
index eccb4dc..30b987f 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -26,7 +26,7 @@ import java.io.IOException;
)
public class PythonRunner extends AbstractCommandRunner {
- static private final Logger LOGGER = LogManager.getLogger( "PythonRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PythonRunner" );
static public final String VENV_PARAM = "VirtualEnv";
static public final String VENV_DESC = "Path to Python virtual environment.";
@@ -147,9 +147,9 @@ public class PythonRunner extends AbstractCommandRunner {
private Logger getRunLogger() {
final String logName = getLogName();
if ( logName != null && !logName.isEmpty() ) {
- return LogManager.getLogger( logName );
+ return LoggerFactory.getLogger( logName );
}
- return LogManager.getLogger( getModuleName() );
+ return LoggerFactory.getLogger( getModuleName() );
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java
index abeb042..00aaf49 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.core.util.regex.RegexSpanFinder;
import org.apache.ctakes.core.util.regex.TimeoutMatcher;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -33,7 +33,7 @@ import java.util.stream.Collectors;
)
abstract public class RegexSectionizer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "RegexSectionizer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RegexSectionizer" );
static public final String PARAM_TAG_DIVIDERS = "TagDividers";
@ConfigurationParameter(
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
index e86b250..5536a49 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
@@ -33,8 +33,8 @@ import org.apache.ctakes.typesystem.type.refsem.*;
import org.apache.ctakes.typesystem.type.relation.*;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textsem.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CASRuntimeException;
@@ -65,7 +65,7 @@ import java.util.*;
PipeBitInfo.TypeProduct.DEGREE_RELATION, PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
)
public class SHARPKnowtatorXMLReader extends JCasAnnotator_ImplBase {
- static Logger LOGGER = LogManager.getLogger(SHARPKnowtatorXMLReader.class);
+ static Logger LOGGER = LoggerFactory.getLogger(SHARPKnowtatorXMLReader.class);
public static final String PARAM_TEXT_DIRECTORY = "TextDirectory";
@ConfigurationParameter(
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
index 2925d34..69ff2fb 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.core.resource.FileResource;
import org.apache.ctakes.core.util.DocumentSection;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -55,7 +55,7 @@ public class SectionSegmentAnnotator extends JCasAnnotator_ImplBase {
private StructFinder structureFinder;
private String templateFile= null;
- static private final Logger LOGGER = LogManager.getLogger( "SectionSegmentAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SectionSegmentAnnotator" );
public HashMap<Integer, DocumentSection> sections;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
index b4542c1..b2ecc0b 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
@@ -31,8 +31,8 @@ import org.apache.ctakes.core.sentence.SentenceDetectorCtakes;
import org.apache.ctakes.core.sentence.SentenceSpan;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -103,7 +103,7 @@ public class SentenceDetector extends JCasAnnotator_ImplBase {
private String NEWLINE = "\n";
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "SentenceDetector" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SentenceDetector" );
@Override
public void initialize(UimaContext aContext)
@@ -271,7 +271,7 @@ public class SentenceDetector extends JCasAnnotator_ImplBase {
* @throws IOException
*/
public static void main(String[] args) throws IOException {
- final Logger LOGGER = LogManager.getLogger(SentenceDetector.class.getName()
+ final Logger LOGGER = LoggerFactory.getLogger(SentenceDetector.class.getName()
+ ".main()");
// Handle arguments
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java
index f91a6f6..c3b1b2c 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.utils.struct.CounterMap;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -59,7 +59,7 @@ import java.util.*;
)
public class SentenceDetectorAnnotatorBIO extends CleartkAnnotator<String>{
- static private final Logger LOGGER = LogManager.getLogger( "SentenceDetectorAnnotatorBIO" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SentenceDetectorAnnotatorBIO" );
private static final int WINDOW_SIZE = 3;
public static enum FEAT_CONFIG {GILLICK, CHAR, SHAPE, LINE_POS, CHAR_SHAPE, CHAR_POS, CHAR_SHAPE_POS }
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
index 1999449..82ac782 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -47,7 +47,7 @@ import java.io.StringReader;
public class SimpleSegmentWithTagsAnnotator extends JCasAnnotator_ImplBase {
private String segmentId;
- static private final Logger LOGGER = LogManager.getLogger( "SimpleSegmentWithTagsAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SimpleSegmentWithTagsAnnotator" );
@Override
public void initialize( UimaContext aContext )
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
index e6f6277..71f1cf3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.AnalysisComponent;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -65,7 +65,7 @@ public class StartFinishLogger extends JCasAnnotator_ImplBase {
public void initialize( final UimaContext context )
throws ResourceInitializationException {
super.initialize( context );
- _logger = LogManager.getLogger( _loggerName );
+ _logger = LoggerFactory.getLogger( _loggerName );
if ( _isStart != null && _isStart ) {
if ( _loggerTask == null || _loggerTask.equals( DEFAULT_TASK ) ) {
_logger.info( "Starting initializing" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java
index b4e4323..b5b9f69 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -20,7 +20,7 @@ import java.util.Collection;
*/
final public class SubjectSectionFixer extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "SubjectSectionFixer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SubjectSectionFixer" );
static private final Collection<String> FAMILY_HISTORY = Arrays.asList(
// "FamilyAndSocialHistory_Section", "FamilyEnviroment_Section", "FamilyMedicalHistory_Section" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
index 02694c2..8d411f5 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -47,7 +47,7 @@ import java.util.Map;
public class TemplateFillerAnnotator extends JCasAnnotator_ImplBase{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "TemplateFillerAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TemplateFillerAnnotator" );
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java
index 7347fa9..0c3f021 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.core.resource.StringIntegerMapResource;
import org.apache.ctakes.core.util.ParamUtil;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -55,7 +55,7 @@ import java.util.Set;
)
public class TokenizerAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "TokenizerAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TokenizerAnnotator" );
public static final int TOKEN_CAP_NONE = 0;
public static final int TOKEN_CAP_FIRST_ONLY = 1;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
index 202b05e..f2847e0 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -54,7 +54,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
public class TokenizerAnnotatorPTB extends JCasAnnotator_ImplBase
{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "TokenizerAnnotatorPTB" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TokenizerAnnotatorPTB" );
/**
* Value is "SegmentsToSkip". This parameter specifies which segments to skip. The parameter should be
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
index 6ed8d01..2003126 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
import org.apache.ctakes.typesystem.type.structured.DocumentPath;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -26,7 +26,7 @@ import java.util.Collection;
*/
abstract public class AbstractFileWriter<T> extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractOutputFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractOutputFileWriter" );
/**
* Name of configuration parameter that must be set to the path of a directory into which the
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
index d0c7c48..977b5cf 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.resource.JdbcConnectionResource;
import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.typesystem.type.structured.SourceData;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -29,7 +29,7 @@ import java.util.Map;
*/
abstract public class AbstractJdbcWriter extends CasConsumer_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractJdbcWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractJdbcWriter" );
// Parameter names for the desc file
static public final String PARAM_DB_CONN_RESRC = "DbConnResrcName";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java
index b9c674c..212d8b6 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.cc;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.jcas.JCas;
@@ -14,7 +14,7 @@ import java.util.List;
abstract public class AbstractTableFileWriter
extends AbstractFileWriter<List<List<String>>> {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractTableFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractTableFileWriter" );
protected enum TableType {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
index 5292a84..b641901 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.impl.XCASSerializer;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -47,7 +47,7 @@ import java.io.OutputStream;
)
public class CasConsumer extends CasConsumer_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "CasConsumer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasConsumer" );
private String iv_outputDir = null;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
index 498f383..1981c5e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -43,7 +43,7 @@ import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPU
// TODO extend AbstractOutputFileWriter
public class CuiCountFileWriter extends CasConsumer_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "CuiCountFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiCountFileWriter" );
static private final String FILE_EXTENSION = ".cuicount.bsv";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
index 92f01b3..bc50235 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
@@ -9,8 +9,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -34,7 +34,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
)
public class CuiListFileWriter extends AbstractJCasFileWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CuiListFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiListFileWriter" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
index cd06c37..7d693a8 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -25,7 +25,7 @@ import java.util.Map;
*/
public class CuiLookupLister extends AbstractJCasFileWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CuiLookupLister" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiLookupLister" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java
index c15c034..f3e4d31 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.impl.XmiCasSerializer;
@@ -31,7 +31,7 @@ import java.io.*;
// TODO Create and extend AbstractInputFileReader a'la the abstract writer
final public class FileTreeXmiWriter extends AbstractJCasFileWriter {
- static private final Logger LOGGER = LogManager.getLogger( "FileTreeXmiWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileTreeXmiWriter" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
index d8d9008..10dfdd0 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CasConsumer_ImplBase;
import org.apache.uima.jcas.JCas;
@@ -53,7 +53,7 @@ public class FilesInDirectoryCasConsumer extends CasConsumer_ImplBase {
public static final String PARAM_OUTPUTDIR = "OutputDirectory";
- static private final Logger LOGGER = LogManager.getLogger( "FilesInDirectoryCasConsumer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FilesInDirectoryCasConsumer" );
File iv_outputDirectory;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
index 38de963..77c7311 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -49,7 +49,7 @@ import java.util.*;
)
public class JdbcWriterTemplate extends AbstractJdbcWriter {
- static private final Logger LOGGER = LogManager.getLogger( "JdbcWriterTemplate" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcWriterTemplate" );
// Parameter names for the desc file
static public final String PARAM_VECTOR_TABLE = "VectorTable";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java
index c5a7e16..b5c8105 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -32,7 +32,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
)
public class SemanticTableFileWriter extends AbstractTableFileWriter {
- static private final Logger LOGGER = LogManager.getLogger( "SemanticTableFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SemanticTableFileWriter" );
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
index 6db8fcc..d6a2478 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.JCasUtil;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.cas.text.AnnotationIndex;
@@ -46,7 +46,7 @@ import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPU
public class SentenceTokensPrinter extends CasConsumer_ImplBase {
// LOG4J logger based on interface name
- final static private Logger LOGGER = LogManager.getLogger( "SentenceTokensPrinter" );
+ final static private Logger LOGGER = LoggerFactory.getLogger( "SentenceTokensPrinter" );
private String _outputDirPath;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
index df678b9..455f9ab 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.refsem.Entity;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -38,7 +38,7 @@ import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPU
)
public class TextSpanWriter extends CasConsumer_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "TextSpanWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TextSpanWriter" );
static private final String FILE_EXTENSION = ".textspan.bsv";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
index e9d1225..b3a721a 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
@@ -39,8 +39,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -99,7 +99,7 @@ public class XmiWriterCasConsumerCtakes extends CasConsumer_ImplBase {
@Override
public void initialize( UimaContext context ) throws ResourceInitializationException {
super.initialize( context );
- LogManager.getLogger( getClass().getSimpleName() ).warn( "Deprecated. Please use FileTreeXmiWriter instead." );
+ LoggerFactory.getLogger( getClass().getSimpleName() ).warn( "Deprecated. Please use FileTreeXmiWriter instead." );
mDocNum = 0;
if ( !mOutputDir.exists() ) {
mOutputDir.mkdirs();
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/CssWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/CssWriter.java
index dc1d3c0..2010201 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/CssWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/CssWriter.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.html;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedWriter;
import java.io.File;
@@ -19,7 +19,7 @@ import static org.apache.ctakes.core.cc.html.HtmlTextWriter.*;
*/
final class CssWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CssWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CssWriter" );
private CssWriter() {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
index f403421..15e5932 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
@@ -21,8 +21,8 @@ import org.apache.ctakes.typesystem.type.textspan.ListEntry;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.FSCollectionFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -76,7 +76,7 @@ final public class HtmlTextWriter extends AbstractJCasFileWriter {
static final String WIKI_CENTER = "_WK_";
static final String WIKI_END = "_WIK";
- static private final Logger LOGGER = LogManager.getLogger( "HtmlTextWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HtmlTextWriter" );
static private final String PREFERRED_TERM_UNKNOWN = "Unknown Preferred Term";
static private final String CTAKES_VERSION = "6.0.0-SNAPSHOT";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java
index 6601930..eea1b76 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.html;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedWriter;
import java.io.File;
@@ -18,7 +18,7 @@ import static org.apache.ctakes.core.cc.html.HtmlTextWriter.*;
*/
final class JsWriter {
- static private final Logger LOGGER = LogManager.getLogger( "JsWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JsWriter" );
private JsWriter() {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
index 12d3e7a..15cbf0d 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.cc.jdbc;
import org.apache.ctakes.core.cc.jdbc.db.JdbcDb;
import org.apache.ctakes.core.cc.jdbc.table.JdbcTable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -22,7 +22,7 @@ import java.util.Collection;
*/
abstract public class AbstractJdbcWriter<T> extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "AstractJdbcWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AstractJdbcWriter" );
static public final String PARAM_DB_DRIVER = "DbDriver";
@ConfigurationParameter(
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java
index ad13702..da7b1e3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.jdbc.i2b2;
import org.apache.ctakes.core.cc.jdbc.db.AbstractJdbcDb;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.ResourceInitializationException;
import java.sql.SQLException;
@@ -17,7 +17,7 @@ import static org.apache.ctakes.core.cc.jdbc.i2b2.ObservationFactTable.CorpusSet
*/
public class I2b2Db extends AbstractJdbcDb {
- static private final Logger LOGGER = LogManager.getLogger( "I2b2Db" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "I2b2Db" );
public I2b2Db( final String driver,
final String url,
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java
index 7c6ccfe..0ec857e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.cc.jdbc.i2b2;
import org.apache.ctakes.core.cc.jdbc.AbstractJCasJdbcWriter;
import org.apache.ctakes.core.cc.jdbc.db.JdbcDb;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.jcas.JCas;
@@ -26,7 +26,7 @@ import java.sql.SQLException;
)
public class I2b2JdbcWriter extends AbstractJCasJdbcWriter {
- static private final Logger LOGGER = LogManager.getLogger( "I2b2JdbcWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "I2b2JdbcWriter" );
static public final String PARAM_TABLE_NAME = "FactOutputTable";
@ConfigurationParameter(
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
index 30bf82d..1051513 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.structured.SourceData;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceProcessException;
@@ -32,7 +32,7 @@ import static org.apache.ctakes.core.cc.jdbc.i2b2.ObservationFactTable.CorpusSet
public class ObservationFactRow
implements JdbcRow<CorpusSettings, JCas, JCas, IdentifiedAnnotation, UmlsConcept> {
- static private final Logger LOGGER = LogManager.getLogger( "ObservationFactRow" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ObservationFactRow" );
static private final String PATIENT_NUM = "patient_num";
static private final String PROVIDER_ID = "provider_id";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java
index 7a6534b..82b0adf 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.jdbc.row;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Does nothing. Can be passed to JdbcRow to do nothing for patient, document initialization.
@@ -13,6 +13,6 @@ import org.apache.logging.log4j.LogManager;
*/
final public class EmptyInitializer {
- static private final Logger LOGGER = LogManager.getLogger( "EmptyInitializer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "EmptyInitializer" );
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/CssWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/CssWriter.java
index 9cdb0fd..ca9ced0 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/CssWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/CssWriter.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.cc.pretty.html;
import org.apache.ctakes.core.cc.pretty.SemanticGroup;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedWriter;
import java.io.File;
@@ -19,7 +19,7 @@ import static org.apache.ctakes.core.cc.pretty.html.HtmlTextWriter.*;
*/
final class CssWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CssWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CssWriter" );
private CssWriter() {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
index 1ea626a..1e4d4ea 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
@@ -20,8 +20,8 @@ import org.apache.ctakes.typesystem.type.textspan.ListEntry;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.FSCollectionFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -76,7 +76,7 @@ final public class HtmlTextWriter extends AbstractJCasFileWriter {
static final String WIKI_CENTER = "_WK_";
static final String WIKI_END = "_WIK";
- static private final Logger LOGGER = LogManager.getLogger( "HtmlTextWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HtmlTextWriter" );
static private final String PREFERRED_TERM_UNKNOWN = "Unknown Preferred Term";
static private final String CTAKES_VERSION = "6.0.0-SNAPSHOT";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/JsWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/JsWriter.java
index ffe2619..302595b 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/JsWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/JsWriter.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.cc.pretty.html;
import org.apache.ctakes.core.cc.pretty.SemanticGroup;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedWriter;
import java.io.File;
@@ -19,7 +19,7 @@ import static org.apache.ctakes.core.cc.pretty.html.HtmlTextWriter.*;
*/
final class JsWriter {
- static private final Logger LOGGER = LogManager.getLogger( "JsWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JsWriter" );
private JsWriter() {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
index 3106915..607c810 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
@@ -17,8 +17,8 @@ import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.text.AnnotationFS;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -42,7 +42,7 @@ import java.util.stream.Collectors;
final public class PrettyTextWriter {
- static private final Logger LOGGER = LogManager.getLogger( "PrettyTextWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PrettyTextWriter" );
static private final String FILE_EXTENSION = ".pretty.txt";
private String _outputDirPath;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java
index b10b6d6..ea8f90e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.cc.pretty.plaintext;
-//import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+//import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java
index 15c3d9e..bed4db4 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.pretty.plaintext;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
@@ -33,7 +33,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
final public class PrettyTextWriterUima extends CasConsumer_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PrettyTextWriterUima" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PrettyTextWriterUima" );
// delegate
final private PrettyTextWriter _prettyTextWriter;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
index b116442..0ec59f2 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.typesystem.type.refsem.*;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.text.AnnotationFS;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -30,7 +30,7 @@ import java.util.*;
*/
public class PropertyTextWriter {
- static private final Logger LOGGER = LogManager.getLogger( "PropertyTextWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PropertyTextWriter" );
static private final String FILE_EXTENSION = ".properties.txt";
private String _outputDirPath;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java
index 47a4b6e..ab7a7a3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java
@@ -43,7 +43,7 @@ public class PropertyTextWriterFit extends CasConsumer_ImplBase {
)
private String fitOutputDirectoryPath;
-// static private final Logger LOGGER = LogManager.getLogger( "PropertyTextWriterFit" );
+// static private final Logger LOGGER = LoggerFactory.getLogger( "PropertyTextWriterFit" );
// delegate
final private PropertyTextWriter _propertyTextWriter;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java
index feeccc5..3013e06 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc.property.plaintext;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
@@ -32,7 +32,7 @@ import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPU
public class PropertyTextWriterUima extends CasConsumer_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PrettyTextWriterUima" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PrettyTextWriterUima" );
// delegate
final private PropertyTextWriter _propertyTextWriter;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java b/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java
index d47198c..a729bd5 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.concurrent;
import org.apache.ctakes.core.ae.SentenceDetector;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -27,7 +27,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeSentenceDetector extends SentenceDetector {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadedSentenceDetector" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadedSentenceDetector" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java b/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java
index 95f1ff0..1b6e4c1 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.concurrent;
import org.apache.ctakes.core.ae.SentenceDetectorAnnotatorBIO;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -29,7 +29,7 @@ import org.cleartk.ml.jar.GenericJarClassifierFactory;
)
final public class ThreadSafeSentenceDetectorBio extends SentenceDetectorAnnotatorBIO {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeSentenceDetectorBio" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeSentenceDetectorBio" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
index 46d91f6..f992ad8 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
@@ -10,8 +10,8 @@ import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.core.util.doc.JCasBuilder;
import org.apache.ctakes.core.util.doc.NoteSpecs;
import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.collection.CollectionException;
import org.apache.uima.collection.impl.CollectionReaderDescription_impl;
@@ -55,7 +55,7 @@ import java.util.stream.Collectors;
*/
abstract public class AbstractFileTreeReader extends JCasCollectionReader_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractFileTreeReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractFileTreeReader" );
static public final String PARAM_WRITE_BANNER = "WriteBanner";
@ConfigurationParameter(
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
index 8438726..11d72b3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.cr;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.factory.CollectionReaderFactory;
import org.apache.uima.jcas.JCas;
@@ -36,7 +36,7 @@ import java.util.stream.Stream;
)
final public class FileTreeReader extends AbstractFileTreeReader {
- static private final Logger LOGGER = LogManager.getLogger( "FileTreeReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileTreeReader" );
/**
* @param jCas unpopulated jcas
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
index 9b7f144..8b18477 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
@@ -43,8 +43,8 @@ import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CollectionException;
@@ -113,7 +113,7 @@ public class FilesInDirectoryCollectionReader extends CollectionReader_ImplBase
*/
@Override
public void initialize() throws ResourceInitializationException {
- LogManager.getLogger( getClass().getSimpleName() ).warn( "Deprecated. Please use FileTreeReader instead." );
+ LoggerFactory.getLogger( getClass().getSimpleName() ).warn( "Deprecated. Please use FileTreeReader instead." );
final String inputDirPath = (String)getConfigParameterValue( ConfigParameterConstants.PARAM_INPUTDIR );
File directory;
try {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
index d72f45b..feaf7f0 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileResource;
import org.apache.ctakes.core.resource.JdbcConnectionResource;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.collection.CollectionException;
import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
@@ -57,7 +57,7 @@ import java.util.StringTokenizer;
public class JdbcCollectionReader extends JCasCollectionReader_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "JdbcCollectionReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcCollectionReader" );
/**
* SQL statement to retrieve the document.
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java
index 37d6e2c..e41051b 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.cr;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CollectionException;
@@ -103,7 +103,7 @@ public class LinesFromFileCollectionReader extends CollectionReader_ImplBase {
String iv_language;
String iv_delimeter;
- static private final Logger LOGGER = LogManager.getLogger( "LinesFromFileCollectionReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LinesFromFileCollectionReader" );
@Override
public void initialize() throws ResourceInitializationException {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/DecryptorWrapper.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/DecryptorWrapper.java
index 1643efe..79c62bf 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/DecryptorWrapper.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/DecryptorWrapper.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cr.jdbc;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
@@ -17,7 +17,7 @@ import java.lang.reflect.Method;
*/
final public class DecryptorWrapper implements Decryptor {
- static private final Logger LOGGER = LogManager.getLogger( "DecryptorWrapper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DecryptorWrapper" );
private final Object _decryptorThing;
private final Method _decryptionMethod;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/JdbcNotesReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/JdbcNotesReader.java
index 6a38720..bc6c225 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/JdbcNotesReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/JdbcNotesReader.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.typesystem.type.structured.Demographics;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.structured.Metadata;
import org.apache.ctakes.typesystem.type.structured.SourceData;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.cas.CASRuntimeException;
import org.apache.uima.collection.CollectionException;
@@ -41,7 +41,7 @@ import java.sql.*;
)
final public class JdbcNotesReader extends JCasCollectionReader_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "JdbcNoteTableReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcNoteTableReader" );
static public final String PARAM_DB_DRIVER = "DbDriver";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/PassThroughDecryptor.java b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/PassThroughDecryptor.java
index 7bb0770..93db78c 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/PassThroughDecryptor.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/PassThroughDecryptor.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cr.jdbc;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Performs no decrpytion, just returns the note text
@@ -13,7 +13,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class PassThroughDecryptor implements Decryptor {
- static private final Logger LOGGER = LogManager.getLogger( "PassThroughDecryptor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PassThroughDecryptor" );
/**
* Performs no decryption, just returns the note text
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java b/ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java
index 8320d42..c800277 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.knowtator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
@@ -31,7 +31,7 @@ import java.util.*;
public class KnowtatorXMLParser {
- private static final Logger LOGGER = LogManager.getLogger(KnowtatorXMLParser.class.getName());
+ private static final Logger LOGGER = LoggerFactory.getLogger(KnowtatorXMLParser.class.getName());
private XMLOutputter xmlOutputter = new XMLOutputter();
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java
index 36ae72a..0ec09e3 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.patient;
import org.apache.ctakes.core.ae.NamedEngine;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -54,7 +54,7 @@ abstract public class AbstractPatientConsumer extends JCasAnnotator_ImplBase imp
protected AbstractPatientConsumer( final String aeName, final String action ) {
_action = action;
- _logger = LogManager.getLogger( aeName );
+ _logger = LoggerFactory.getLogger( aeName );
}
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java
index 2ef377f..3d9c059 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.patient;
import org.apache.ctakes.core.ae.NamedEngine;
import org.apache.ctakes.core.cc.AbstractFileWriter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
@@ -23,7 +23,7 @@ abstract public class AbstractPatientFileWriter
extends AbstractFileWriter<Collection<JCas>>
implements NamedEngine {
- static private final Logger LOGGER = LogManager.getLogger( "AbstractPatientFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AbstractPatientFileWriter" );
static private final Object DATA_LOCK = new Object();
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java
index 164fe6d..6235a6e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.patient;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
@@ -22,7 +22,7 @@ import org.apache.uima.jcas.JCas;
)
final public class PatientNoteCollector extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PatientNoteCollector" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PatientNoteCollector" );
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
index fbd2ca3..3a2d594 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
import org.apache.ctakes.typesystem.type.structured.Metadata;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.cas.CASException;
import org.apache.uima.cas.CASRuntimeException;
@@ -34,7 +34,7 @@ public enum PatientNoteStore {
}
- static private final Logger LOGGER = LogManager.getLogger( "PatientNoteStore" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PatientNoteStore" );
static private final String GENERIC_PATIENT = "Generic";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java
index f3a4c6a..f01176d 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.patient;
import org.apache.ctakes.core.util.NumberedSuffixComparator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.jcas.JCas;
@@ -29,7 +29,7 @@ final public class PatientViewUtil {
static private final Predicate<String> isNameGold = s -> s.startsWith( GOLD_PREFIX );
static private final Predicate<JCas> isCasGold = c -> c.getViewName().startsWith( GOLD_PREFIX );
- static private final Logger LOGGER = LogManager.getLogger( "PatientViewUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PatientViewUtil" );
private PatientViewUtil() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
index bed10ed..cd95a76 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.pipeline;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
/**
@@ -11,7 +11,7 @@ import org.apache.logging.log4j.Logger;
*/
final public class CliOptionalsHandler {
- static private final Logger LOGGER = LogManager.getLogger( "CliOptionalsHandler" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CliOptionalsHandler" );
private CliOptionalsHandler() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
index 20148fc..32d3cbc 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.pipeline;
import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.core.util.doc.DocIdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
@@ -25,7 +25,7 @@ public enum CuiCollector {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "CuiCollector" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiCollector" );
private final Map<String, Map<String, Long>> _cuiCountMap = new HashMap<>();
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
index 53e0f36..9c2c6d5 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.pipeline;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -29,7 +29,7 @@ public enum EntityCollector {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "EntityCollector" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "EntityCollector" );
private final Map<String, Collection<Entity>> _entityMap = new HashMap<>();
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java
index 30c260a..cdaf40e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.pipeline;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.collection.CasConsumer_ImplBase;
import org.apache.uima.collection.CollectionReader_ImplBase;
@@ -22,7 +22,7 @@ import java.util.stream.Collectors;
@Immutable
final public class PipeBitInfoUtil {
- static private final Logger LOGGER = LogManager.getLogger( "PipeBitInfoUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipeBitInfoUtil" );
static private final String UNKNOWN_PIPE_BIT = "! Unfamiliar";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java
index 883238f..9f14cef 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.pipeline;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_component.AnalysisComponent;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReader;
@@ -31,7 +31,7 @@ public enum PipeBitLocator {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "PipeBitFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipeBitFinder" );
static private final Object[] EMPTY_OBJECT_ARRAY = new Object[ 0 ];
static private final String[] CTAKES_PACKAGES
= { "core",
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
index 7b54f26..62470ca 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.cr.FileTreeReader;
import org.apache.ctakes.core.util.PropertyAeFactory;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_component.AnalysisComponent;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -42,7 +42,7 @@ import java.util.List;
*/
final public class PipelineBuilder {
- static private final Logger LOGGER = LogManager.getLogger( "PipelineBuilder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipelineBuilder" );
private CollectionReaderDescription _readerDesc;
// TODO replace pairs of 3 lists with 2 instances of a single class. Put a build() (sub) method in class?
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
index 4f3f012..3a4935e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.pipeline;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.log.DotLogger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -46,7 +46,7 @@ import java.util.regex.Pattern;
@SuppressWarnings( "unchecked" )
final public class PiperFileReader {
- static private final Logger LOGGER = LogManager.getLogger( "PiperFileReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperFileReader" );
static public final String AE_VIEW_NAMES = "AeViews";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
index 4b19f15..95347d0 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.pipeline;
import com.lexicalscope.jewel.cli.CliFactory;
import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.FileNotFoundException;
@@ -19,7 +19,7 @@ import java.nio.file.Paths;
*/
final public class PiperFileRunner {
- static private final Logger LOGGER = LogManager.getLogger( "PiperFileRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperFileRunner" );
private PiperFileRunner() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java
index 3b3b882..b2fca5d 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.*;
import java.net.*;
@@ -33,7 +33,7 @@ import java.util.*;
*/
final public class FileLocator {
- static private final Logger LOGGER = LogManager.getLogger( "FileLocator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileLocator" );
/**
* $CTAKES_HOME is an environment variable that may be set to indicate
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileReadWriteUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileReadWriteUtil.java
index 08eb5db..0ca0fdb 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileReadWriteUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileReadWriteUtil.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.*;
import java.nio.file.Files;
@@ -21,7 +21,7 @@ final public class FileReadWriteUtil {
private FileReadWriteUtil() {
}
- static private final Logger LOGGER = LogManager.getLogger( "FileReadWriteUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileReadWriteUtil" );
/**
* Reading text from a file or resource is done everywhere, but a common implementation is missing from ctakes.
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResourceImpl.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResourceImpl.java
index 7fe7369..4919abb 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResourceImpl.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResourceImpl.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -34,7 +34,7 @@ import java.net.URL;
public class FileResourceImpl implements FileResource, SharedResourceObject
{
private File iv_file;
- static private final Logger LOGGER = LogManager.getLogger( "FileResourceImpl" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileResourceImpl" );
public void load(DataResource dr) throws ResourceInitializationException
{
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResourceImpl.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResourceImpl.java
index 0fab0f5..d2fca30 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResourceImpl.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResourceImpl.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -39,7 +39,7 @@ import java.sql.DriverManager;
public class JdbcConnectionResourceImpl implements JdbcConnectionResource,
SharedResourceObject
{
- static private final Logger LOGGER = LogManager.getLogger( "JdbcConnectionResourceImpl" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcConnectionResourceImpl" );
/**
* JDBC driver ClassName.
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResourceImpl.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResourceImpl.java
index db71a6a..b30294c 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResourceImpl.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResourceImpl.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.index.DirectoryReader;
import org.apache.lucene.index.IndexReader;
import org.apache.lucene.store.*;
@@ -38,7 +38,7 @@ public class LuceneIndexReaderResourceImpl
implements LuceneIndexReaderResource, SharedResourceObject {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "LuceneIndexReaderResourceImpl" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LuceneIndexReaderResourceImpl" );
private IndexReader iv_indexReader;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java
index d59230e..7a6c4b6 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -41,7 +41,7 @@ public class StringIntegerMapResourceImpl
implements StringIntegerMapResource, SharedResourceObject
{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "StringIntegerMapResourceImpl" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "StringIntegerMapResourceImpl" );
private final String DELIMITER = "|";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResourceImpl.java b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResourceImpl.java
index 4fe5af2..1b8cce8 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResourceImpl.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResourceImpl.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.core.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -40,7 +40,7 @@ public class StringMapResourceImpl
implements StringMapResource, SharedResourceObject
{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "StringMapResourceImpl" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "StringMapResourceImpl" );
private final String DELIMITER = "|";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java
index 723a35c..654f1f8 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -10,7 +10,7 @@ import org.apache.logging.log4j.LogManager;
final public class BannerWriter {
// The ProgressDone logger in our ctakes log4j configuration hides the name of the logger.
- static private final Logger EOL_LOGGER = LogManager.getLogger( "ProgressDone" );
+ static private final Logger EOL_LOGGER = LoggerFactory.getLogger( "ProgressDone" );
private BannerWriter() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
index 7cdef89..97c8c14 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.util;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -29,7 +29,7 @@ final public class FinishedLogger extends JCasAnnotator_ImplBase {
*/
@Override
public void initialize( final UimaContext context ) throws ResourceInitializationException {
- LogManager.getLogger( "FinishedLogger" ).warn( "Deprecated use FinishedLogger in (sub) package log." );
+ LoggerFactory.getLogger( "FinishedLogger" ).warn( "Deprecated use FinishedLogger in (sub) package log." );
_delegate.initialize( context );
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java
index d75f760..97d6566 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Comparator;
@@ -15,7 +15,7 @@ import java.util.Comparator;
* @since 8/25/2017
*/
public class NumberedSuffixComparator implements Comparator<String> {
- static private final Logger LOGGER = LogManager.getLogger( "NumberedSuffixComparator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "NumberedSuffixComparator" );
/**
* {@inheritDoc}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
index 9b0970f..7a84e3c 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.util;
import org.apache.ctakes.core.ae.StartFinishLogger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_component.AnalysisComponent;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -32,7 +32,7 @@ public enum PropertyAeFactory {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "PropertyAeFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PropertyAeFactory" );
// Use a single hashmap so that multiple properties files can be used
@@ -43,7 +43,7 @@ public enum PropertyAeFactory {
try {
_typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription();
} catch ( ResourceInitializationException riE ) {
- LogManager.getLogger( "PropertyAeFactory" )
+ LoggerFactory.getLogger( "PropertyAeFactory" )
.error( "Could not initialize cTAKES Type System\n" + riE.getMessage() );
System.exit( -1 );
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java
index 8fa532a..fde801e 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -26,7 +26,7 @@ final public class RelationArgumentUtil {
private RelationArgumentUtil() {
}
- static private final Logger LOGGER = LogManager.getLogger( "RelationUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RelationUtil" );
/**
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/StringUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/StringUtil.java
index 5f150e3..a1b844a 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/StringUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/StringUtil.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Arrays;
@@ -13,7 +13,7 @@ import java.util.Arrays;
*/
final public class StringUtil {
- static private final Logger LOGGER = LogManager.getLogger( "StringUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "StringUtil" );
private StringUtil() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
index 8418f05..c20d10f 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
@@ -9,8 +9,8 @@ import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.FSCollectionFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -28,7 +28,7 @@ import java.util.stream.Collectors;
*/
final public class EssentialAnnotationUtil {
- static private final Logger LOGGER = LogManager.getLogger( "EssentialAnnotationUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "EssentialAnnotationUtil" );
private EssentialAnnotationUtil() {
}
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java
index 06d0a1c..b360f99 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
@@ -25,7 +25,7 @@ import java.util.stream.Collectors;
*/
final public class IdentifiedAnnotationBuilder {
- static private final Logger LOGGER = LogManager.getLogger( "IdentifiedAnnotationBuilder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IdentifiedAnnotationBuilder" );
static private final Pair<Integer> NULL_SPAN = new Pair<>( -1, -1 );
private Pair<Integer> _textSpan = NULL_SPAN;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
index e93b1f3..bcceda2 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.util.annotation;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.FeatureStructure;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -25,7 +25,7 @@ import java.util.stream.Stream;
*/
final public class OntologyConceptUtil {
- static private final Logger LOGGER = LogManager.getLogger( "IdentifiedAnnotationUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IdentifiedAnnotationUtil" );
static private final FeatureStructure[] EMPTY_FEATURE_ARRAY = new FeatureStructure[ 0 ];
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java
index f78c187..427c3c4 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.util.annotation;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.annotation.concurrent.Immutable;
@@ -15,7 +15,7 @@ import javax.annotation.concurrent.Immutable;
@Immutable
final public class WordTokenUtil {
- static private final Logger LOGGER = LogManager.getLogger( "WordTokenUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "WordTokenUtil" );
static private final String MISSING_WORDTOKEN_TEXT = "MISSING_WORDTOKEN_TEXT";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
index d95f463..6ca9611 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.util.doc;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CASException;
import org.apache.uima.cas.CASRuntimeException;
import org.apache.uima.fit.util.JCasUtil;
@@ -40,7 +40,7 @@ final public class DocIdUtil {
static public final String NO_DOCUMENT_ID = "UnknownDocument";
static public final String NO_DOCUMENT_ID_PREFIX = "UnknownDocumentPrefix";
- static private final Logger LOGGER = LogManager.getLogger( "DocumentIDAnnotationUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DocumentIDAnnotationUtil" );
static private final Pattern FILE_FIX_PATTERN = Pattern.compile( "[^A-Za-z0-9\\.]" );
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java
index d5138cd..aa6b73d 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.util.doc;
import org.apache.ctakes.typesystem.type.structured.SourceData;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -28,7 +28,7 @@ import static org.apache.ctakes.core.util.doc.SourceMetadataUtil.UNKNOWN_PATIENT
*/
final public class NoteSpecs {
- static private final Logger LOGGER = LogManager.getLogger( "NoteSpecs" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "NoteSpecs" );
// ClinicalNote is not yet a fhir resource, but it may be in the future and is the best fit.
// http://wiki.hl7.org/index.php?title=ClinicalNote_FHIR_Resource_Proposal
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java
index 41cc7ba..e63c308 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.util.doc;
import org.apache.ctakes.typesystem.type.structured.Metadata;
import org.apache.ctakes.typesystem.type.structured.SourceData;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceProcessException;
@@ -21,7 +21,7 @@ import java.util.Collection;
*/
final public class SourceMetadataUtil {
- static private final Logger LOGGER = LogManager.getLogger( "SourceMetadataUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SourceMetadataUtil" );
static public final String UNKNOWN_PATIENT = "UnknownPatient";
static public final long UNKNOWN_PATIENT_NUM = -1;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/external/SystemUtil.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/external/SystemUtil.java
index 6a03b64..a967a8f 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/external/SystemUtil.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/external/SystemUtil.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.util.external;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.*;
@@ -26,7 +26,7 @@ import java.util.zip.ZipInputStream;
final public class SystemUtil {
- static private final Logger LOGGER = LogManager.getLogger( "SystemUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SystemUtil" );
private SystemUtil() {
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
index f0fed29..a7d208f 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.util.log;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import java.io.Closeable;
import java.io.IOException;
@@ -20,8 +20,8 @@ import java.util.concurrent.TimeUnit;
*/
final public class DotLogger implements Closeable {
- static private final Logger DOT_LOGGER = LogManager.getLogger( "ProgressAppender" );
- static private final Logger EOL_LOGGER = LogManager.getLogger( "ProgressDone" );
+ static private final Logger DOT_LOGGER = LoggerFactory.getLogger( "ProgressAppender" );
+ static private final Logger EOL_LOGGER = LoggerFactory.getLogger( "ProgressDone" );
private final ExecutorService _timer;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java
index 11e2ed4..d136b31 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.util.log;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.ProgressManager;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -31,7 +31,7 @@ import java.util.jar.Manifest;
)
final public class FinishedLogger extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ProgressDone" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ProgressDone" );
static private final String BUILD_VERSION = "Implementation-Version";
static private final String BUILD_DATE = "Implementation-Build-Date";
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/RegexSpanFinder.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/RegexSpanFinder.java
index b3f86fb..9f20c34 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/RegexSpanFinder.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/RegexSpanFinder.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.core.util.regex;
import org.apache.ctakes.core.util.Pair;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.Closeable;
import java.util.ArrayList;
@@ -37,7 +37,7 @@ import java.util.regex.PatternSyntaxException;
*/
final public class RegexSpanFinder implements Closeable {
- static private final Logger LOGGER = LogManager.getLogger( "RegexSpanFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RegexSpanFinder" );
static private final int DEFAULT_TIMEOUT_MILLIS = 1000;
static private final int MIN_TIMEOUT_MILLIS = 100;
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/TimeoutMatcher.java b/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/TimeoutMatcher.java
index 5dbfd65..b9b6361 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/TimeoutMatcher.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/TimeoutMatcher.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.util.regex;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.Closeable;
import java.util.concurrent.*;
@@ -37,7 +37,7 @@ import java.util.regex.PatternSyntaxException;
*/
public class TimeoutMatcher implements Closeable {
- static private final Logger LOGGER = LogManager.getLogger( "TimeoutMatcher" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TimeoutMatcher" );
static private final int DEFAULT_TIMEOUT_MILLIS = 1000;
static private final int MIN_TIMEOUT_MILLIS = 100;
diff --git a/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java b/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java
index 609ed6d..b861850 100644
--- a/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java
+++ b/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.typesystem.type.syntax.*;
import org.apache.ctakes.utils.test.TestUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
@@ -33,7 +33,7 @@ import java.util.Date;
public class TokenizerAnnotatorPTBTests {
TestData<SimpleToken []>[] tests;
- private static final Logger LOGGER = LogManager.getLogger(TokenizerAnnotatorPTBTests.class.getName());
+ private static final Logger LOGGER = LoggerFactory.getLogger(TokenizerAnnotatorPTBTests.class.getName());
public TokenizerAnnotatorPTBTests() {
diff --git a/ctakes-core/src/test/java/org/apache/ctakes/core/cr/FileTreeReaderTester.java b/ctakes-core/src/test/java/org/apache/ctakes/core/cr/FileTreeReaderTester.java
index 196d2c5..57c6853 100644
--- a/ctakes-core/src/test/java/org/apache/ctakes/core/cr/FileTreeReaderTester.java
+++ b/ctakes-core/src/test/java/org/apache/ctakes/core/cr/FileTreeReaderTester.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.cr;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.junit.Test;
import java.io.File;
@@ -18,7 +18,7 @@ import static org.junit.Assert.*;
*/
public class FileTreeReaderTester {
- static private final Logger LOGGER = LogManager.getLogger( "FileTreeReaderTester" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileTreeReaderTester" );
static private final String DOCUMENT_ID = "someFile";
static private final String PREFIX_SHORT = "subdir";
diff --git a/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java b/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
index 51f6b6e..260e425 100644
--- a/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
+++ b/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.jcas.JCas;
@@ -26,7 +26,7 @@ import static org.junit.Assert.assertTrue;
*/
public class OntologyConceptUtilTester {
- static private final Logger LOGGER = LogManager.getLogger( "IdentifiedAnnotationUtilTester" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IdentifiedAnnotationUtilTester" );
static private final String TUI_1 = "T001";
static private final String TUI_2 = "T002";
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java
index f23ca48..255b220 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java
@@ -10,8 +10,8 @@ import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.Markable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CASException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -32,7 +32,7 @@ import java.util.*;
dependencies = { PipeBitInfo.TypeProduct.MARKABLE, PipeBitInfo.TypeProduct.COREFERENCE_RELATION, PipeBitInfo.TypeProduct.DEPENDENCY_NODE }
)
public class CopyCoreferenceRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
- private static final Logger LOGGER = LogManager.getLogger( "CopyCoreferenceRelations" );
+ private static final Logger LOGGER = LoggerFactory.getLogger( "CopyCoreferenceRelations" );
private static final double DROPOUT_RATE = 0.1;
// TODO - make document aware for mention-cluster coreference? Not as easy as relation remover because this should work for
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java
index 4afa1e3..5b3225a 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java
@@ -10,8 +10,8 @@ import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.Markable;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -36,7 +36,7 @@ import static org.apache.ctakes.dependency.parser.util.DependencyUtility.*;
products = { MARKABLE }
)
public class DeterministicMarkableAnnotator extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "DeterministicMarkableAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DeterministicMarkableAnnotator" );
// list starters like A. or #1 or 3)
static Pattern headerPatt = Pattern.compile("^(([A-Z][\\.\\:\\)])|(#\\d+)|(\\d+[\\.\\:\\)])) *");
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/EventCoreferenceAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/EventCoreferenceAnnotator.java
index 7dd2e6b..52dee08 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/EventCoreferenceAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/EventCoreferenceAnnotator.java
@@ -17,8 +17,8 @@ import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -74,7 +74,7 @@ public class EventCoreferenceAnnotator extends RelationExtractorAnnotator {
private double lastScore;
- private Logger LOGGER = LogManager.getLogger(EventCoreferenceAnnotator.class);
+ private Logger LOGGER = LoggerFactory.getLogger(EventCoreferenceAnnotator.class);
public static AnalysisEngineDescription createDataWriterDescription(
Class<? extends DataWriter<String>> dataWriterClass,
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java
index 1d7e147..e537bd7 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.coreference.ae.features.salience.GrammaticalRoleFeature
import org.apache.ctakes.coreference.ae.features.salience.MorphosyntacticFeatureExtractor;
import org.apache.ctakes.coreference.ae.features.salience.SemanticEnvironmentFeatureExtractor;
import org.apache.ctakes.typesystem.type.textsem.Markable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -39,7 +39,7 @@ import java.util.Map;
)
public class MarkableSalienceAnnotator extends CleartkAnnotator<Boolean> {
- static private final Logger LOGGER = LogManager.getLogger( "MarkableSalienceAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MarkableSalienceAnnotator" );
List<FeatureExtractor1<Markable>> extractors = new ArrayList<>();
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
index 071347c..ed95f99 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.utils.struct.CounterMap;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -59,7 +59,7 @@ import static org.apache.ctakes.coreference.util.ClusterMentionFetcher.Collectio
products = { COREFERENCE_RELATION }
)
public class MentionClusterCoreferenceAnnotator extends CleartkAnnotator<String> implements NamedEngine {
- static private final Logger LOGGER = LogManager.getLogger( MentionClusterCoreferenceAnnotator.class.getSimpleName() );
+ static private final Logger LOGGER = LoggerFactory.getLogger( MentionClusterCoreferenceAnnotator.class.getSimpleName() );
public static final String NO_RELATION_CATEGORY = "-NONE-";
public static final String PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE =
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java
index 6dc497a..19d38ad 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java
@@ -19,7 +19,7 @@ import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -321,7 +321,7 @@ public class MentionClusterRankingCoreferenceAnnotator extends CleartkAnnotator<
ConllDependencyNode headNode = DependencyUtility.getNominalHeadNode(jcas, mention);
if(headNode == null){
- LogManager.getLogger(MentionClusterRankingCoreferenceAnnotator.class).warn("There is a markable with no dependency node covering it.");
+ LoggerFactory.getLogger(MentionClusterRankingCoreferenceAnnotator.class).warn("There is a markable with no dependency node covering it.");
return pairs;
}
String head = headNode.getCoveredText().toLowerCase();
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java
index f9bfd8f..ef8ee0e 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.coreference.type.PronounMarkable;
import org.apache.ctakes.coreference.util.AnnotationSelector;
import org.apache.ctakes.typesystem.type.syntax.Chunk;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -67,7 +67,7 @@ public class MipacqMarkableCreator extends JCasAnnotator_ImplBase {
Set<String> otherVerb;
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
@Override
public void initialize(UimaContext uc) throws ResourceInitializationException {
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java
index c3393a2..f1b08ab 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java
@@ -26,8 +26,8 @@ import org.apache.ctakes.coreference.util.PairAttributeCalculator;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.Chunk;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -58,7 +58,7 @@ public class MipacqMarkablePairGenerator extends JCasAnnotator_ImplBase {
HashSet<String> stopwords;
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
int numVecs = 0;
@Override
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
index 43298d3..451e5a4 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FSIterator;
@@ -67,7 +67,7 @@ public class MipacqSvmChainCreator extends JCasAnnotator_ImplBase {
File modelFile = null;
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
// svm models
// private AbstractClassifier mod_pron, mod_dem, mod_coref;
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientMentionClusterCoreferencer.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientMentionClusterCoreferencer.java
index 9cd06ea..8119874 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientMentionClusterCoreferencer.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientMentionClusterCoreferencer.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.coreference.ae;
import org.apache.ctakes.core.patient.AbstractPatientConsumer;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.analysis_engine.ResultSpecification;
@@ -17,7 +17,7 @@ import org.apache.uima.resource.ResourceInitializationException;
*/
public class PatientMentionClusterCoreferencer extends AbstractPatientConsumer {
- static private final Logger LOGGER = LogManager.getLogger( "PatientMentionClusterCoreferencer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PatientMentionClusterCoreferencer" );
private final MentionClusterCoreferenceAnnotator _delegate;
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
index 2716f5e..fb9963a 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
@@ -17,8 +17,8 @@ import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.Markable;
import org.apache.ctakes.utils.struct.CounterMap;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -66,7 +66,7 @@ public class ThymeAnaforaCrossDocCorefXmlReader extends AbstractPatientConsumer
)boolean isTraining;
private static final String NAME = ThymeAnaforaCrossDocCorefXmlReader.class.getSimpleName();
- private static final Logger LOGGER = LogManager.getLogger(ThymeAnaforaCrossDocCorefXmlReader.class);
+ private static final Logger LOGGER = LoggerFactory.getLogger(ThymeAnaforaCrossDocCorefXmlReader.class);
public ThymeAnaforaCrossDocCorefXmlReader(){
super(NAME,
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/HeadwordPairer.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/HeadwordPairer.java
index 17a08f9..8ab8536 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/HeadwordPairer.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/HeadwordPairer.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.coreference.util.ClusterMentionFetcher;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.Markable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import java.util.*;
@@ -30,7 +30,7 @@ public class HeadwordPairer extends ClusterMentionPairer_ImplBase {
ConllDependencyNode headNode = DependencyUtility.getNominalHeadNode(jcas, mention);
if(headNode == null){
- LogManager.getLogger(MentionClusterCoreferenceAnnotator.class).warn("There is a markable with no dependency node covering it.");
+ LoggerFactory.getLogger(MentionClusterCoreferenceAnnotator.class).warn("There is a markable with no dependency node covering it.");
return pairs;
}
String head = headNode.getCoveredText().toLowerCase();
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
index ab612a3..e869181 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
@@ -29,8 +29,8 @@ import org.apache.ctakes.coreference.util.*;
import org.apache.ctakes.relationextractor.eval.XMIReader;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.utils.tree.SimpleTree;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -59,7 +59,7 @@ import java.util.Scanner;
)
public class ODIEVectorFileWriter extends JCasAnnotator_ImplBase {
- private Logger LOGGER = LogManager.getLogger(this.getClass());
+ private Logger LOGGER = LoggerFactory.getLogger(this.getClass());
// private static final Integer NGRAM_THRESHOLD = 0;
private String outputDir = null;
private String goldStandardDir = null;
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMarkableSalienceAnnotator.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMarkableSalienceAnnotator.java
index ecb5668..9ace638 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMarkableSalienceAnnotator.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMarkableSalienceAnnotator.java
@@ -16,8 +16,8 @@ import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import java.io.File;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Normally I would use composition and a singleton, but here extension is done for @ConfigurationParameter discovery.
@@ -37,7 +37,7 @@ import org.apache.logging.log4j.LogManager;
)
public class ThreadSafeMarkableSalienceAnnotator extends MarkableSalienceAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeMarkableSalienceAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeMarkableSalienceAnnotator" );
/**
* {@inheritDoc}
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMentionClusterCoreferencer.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMentionClusterCoreferencer.java
index b63561f..b3989f4 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMentionClusterCoreferencer.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMentionClusterCoreferencer.java
@@ -16,8 +16,8 @@ import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import java.io.File;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
@@ -37,7 +37,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
)
public class ThreadSafeMentionClusterCoreferencer extends MentionClusterCoreferenceAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeMentionClusterCoreferencer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeMentionClusterCoreferencer" );
/**
* {@inheritDoc}
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
index eaf3429..6cda02c 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
@@ -42,8 +42,8 @@ import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.utils.distsem.WordEmbeddings;
import org.apache.ctakes.utils.distsem.WordVector;
import org.apache.ctakes.utils.distsem.WordVectorReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -119,7 +119,7 @@ public class EvaluationOfEventCoreference extends EvaluationOfTemporalRelations_
public boolean getSkipTest();
}
- private static final Logger LOGGER = LogManager.getLogger(EvaluationOfEventCoreference.class);
+ private static final Logger LOGGER = LoggerFactory.getLogger(EvaluationOfEventCoreference.class);
public static float COREF_PAIRS_DOWNSAMPLE = 0.5f;
public static float COREF_CLUSTER_DOWNSAMPLE=0.5f;
private static final int NUM_SAMPLES = 0;
@@ -509,7 +509,7 @@ public class EvaluationOfEventCoreference extends EvaluationOfTemporalRelations_
}
}
public static class DocumentIDPrinter extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
- static Logger LOGGER = LogManager.getLogger(DocumentIDPrinter.class);
+ static Logger LOGGER = LoggerFactory.getLogger(DocumentIDPrinter.class);
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
String docId = DocIdUtil.getDocumentID( jCas );
@@ -871,7 +871,7 @@ public class EvaluationOfEventCoreference extends EvaluationOfTemporalRelations_
public static class EvaluationPatientNoteCollector extends JCasAnnotator_ImplBase {
- private final Logger LOGGER = LogManager.getLogger( "EvaluationPatientNoteCollector" );
+ private final Logger LOGGER = LoggerFactory.getLogger( "EvaluationPatientNoteCollector" );
/**
* Adds the primary view of this cas to a cache of views for patients.
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java
index 36351bc..ef59404 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java
@@ -23,7 +23,7 @@ import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.Logger;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
diff --git a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterMentionFetcher.java b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterMentionFetcher.java
index fc1d256..3ee0423 100644
--- a/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterMentionFetcher.java
+++ b/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterMentionFetcher.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
import org.apache.ctakes.typesystem.type.relation.CollectionTextRelationIdentifiedAnnotationRelation;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.Markable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -26,7 +26,7 @@ import java.util.Map;
*/
final public class ClusterMentionFetcher {
- static private final Logger LOGGER = LogManager.getLogger( "ClusterMentionFetcher" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ClusterMentionFetcher" );
private ClusterMentionFetcher() {
}
diff --git a/ctakes-coreference/src/test/java/org/apache/ctakes/coreference/eval/helpers/SpanTest.java b/ctakes-coreference/src/test/java/org/apache/ctakes/coreference/eval/helpers/SpanTest.java
index 9bf14e3..f791d1c 100644
--- a/ctakes-coreference/src/test/java/org/apache/ctakes/coreference/eval/helpers/SpanTest.java
+++ b/ctakes-coreference/src/test/java/org/apache/ctakes/coreference/eval/helpers/SpanTest.java
@@ -18,18 +18,19 @@
*/
package org.apache.ctakes.coreference.eval.helpers;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import java.lang.invoke.MethodHandles;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
-import static org.junit.Assert.assertEquals;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
public class SpanTest {
- private Logger log = Logger.getLogger(SpanTest.class);
+ private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
@Test
public void testSpanCreation () {
@@ -50,9 +51,9 @@ public class SpanTest {
int[] id1 = sa.get1();
String line1 = IntStream.of(sa.get1()).boxed().map(i -> i.toString()).collect(Collectors.joining(" "));
assertEquals("1 2 3 4", line1);
- log.info( line1 );
+ LOG.info( line1 );
String line2 = IntStream.of(sa.get2()).boxed().map(i -> i.toString()).collect(Collectors.joining(" "));
assertEquals("1 2 3 5", line2);
- log.info( line2 );
+ LOG.info( line2 );
}
}
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
index d50b1d4..6913613 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
@@ -46,8 +46,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.cas.text.AnnotationIndex;
@@ -74,7 +74,7 @@ import java.io.FileWriter;
)
public class DependencyNodeWriter extends CasConsumer_ImplBase {
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
private String iv_outputDir = null;
private String iv_outputFormat = null;
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
index 957b687..3263f2f 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
@@ -33,8 +33,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -87,8 +87,8 @@ public class ClearNLPDependencyParserAE extends JCasAnnotator_ImplBase {
public final static Object LOCK = new Object();
final String language = AbstractReader.LANG_EN;
- // public Logger LOGGER = LogManager.getLogger(getClass().getName());
- static private final Logger LOGGER = LogManager.getLogger( ClearNLPDependencyParserAE.class.getSimpleName() );
+ // public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
+ static private final Logger LOGGER = LoggerFactory.getLogger( ClearNLPDependencyParserAE.class.getSimpleName() );
// single class-based model:
// protected static ExternalResourceDescription defaultParserResource = ExternalResourceFactory.createExternalResourceDescription(
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java
index d51fcd4..401a25e 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java
@@ -33,8 +33,8 @@ import org.apache.ctakes.typesystem.type.textsem.Predicate;
import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -88,7 +88,7 @@ import java.util.Map;
)
public class ClearNLPSemanticRoleLabelerAE extends JCasAnnotator_ImplBase {
final String language = AbstractReader.LANG_EN;
- public Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ public Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
public static final String SRL_PRED_MODEL_KEY = "SrlPredModel";
@ExternalResource(key = SRL_PRED_MODEL_KEY, mandatory=false)
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/DependencySharedModel.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/DependencySharedModel.java
index fce8eb8..14d862d 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/DependencySharedModel.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/DependencySharedModel.java
@@ -5,8 +5,8 @@ import com.googlecode.clearnlp.engine.EngineGetter;
import com.googlecode.clearnlp.nlp.NLPLib;
import com.googlecode.clearnlp.reader.AbstractReader;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -22,7 +22,7 @@ public class DependencySharedModel implements SharedResourceObject {
static public final String DEFAULT_LANGUAGE = AbstractReader.LANG_EN;
// If this is final then why don't we just use a default such as above? Future mutability?
final String language = DEFAULT_LANGUAGE;
- public Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ public Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
@Override
public void load( final DataResource aData ) throws ResourceInitializationException {
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/LemmatizerSharedModel.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/LemmatizerSharedModel.java
index 4d5c181..4cf1ee0 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/LemmatizerSharedModel.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/LemmatizerSharedModel.java
@@ -4,8 +4,8 @@ import com.googlecode.clearnlp.engine.EngineGetter;
import com.googlecode.clearnlp.morphology.AbstractMPAnalyzer;
import com.googlecode.clearnlp.reader.AbstractReader;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -22,7 +22,7 @@ public class LemmatizerSharedModel implements SharedResourceObject {
static public final String DEFAULT_LANGUAGE = AbstractReader.LANG_EN;
// If this is final then why don't we just use a default such as above? Future mutability?
final String language = DEFAULT_LANGUAGE;
- public Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ public Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
@Override
public void load( final DataResource aData ) throws ResourceInitializationException {
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpDepParser.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpDepParser.java
index 5ef58c2..4180f2c 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpDepParser.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpDepParser.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.dependency.parser.concurrent;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -41,7 +41,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeClearNlpDepParser extends ClearNLPDependencyParserAE {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeClearNlpSemRoleLabeler" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeClearNlpSemRoleLabeler" );
/**
* {@inheritDoc}
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpSemRoleLabeler.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpSemRoleLabeler.java
index 15c955a..3e0707f 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpSemRoleLabeler.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpSemRoleLabeler.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.dependency.parser.concurrent;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -42,7 +42,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeClearNlpSemRoleLabeler extends ClearNLPSemanticRoleLabelerAE {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeClearNlpSemRoleLabeler" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeClearNlpSemRoleLabeler" );
/**
* {@inheritDoc}
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
index 2f9ae8e..2bf28b1 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
@@ -23,8 +23,8 @@ import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.utils.tree.SimpleTree;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -32,7 +32,7 @@ import org.apache.uima.jcas.tcas.Annotation;
import java.util.*;
public class AnnotationDepUtils {
- private static Logger LOGGER = LogManager.getLogger(AnnotationDepUtils.class);
+ private static Logger LOGGER = LoggerFactory.getLogger(AnnotationDepUtils.class);
public static String getTokenRelTreeString(JCas jCas, List<ConllDependencyNode> nodes, Annotation[] annotations, String[] labels){
return getTokenRelTreeString(jCas, nodes, annotations, labels, false);
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java
index cb84b2b..c525744 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java
@@ -23,8 +23,8 @@ import com.googlecode.clearnlp.dependency.DEPTree;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -40,7 +40,7 @@ public class ClearDependencyUtility extends DependencyUtility {
// public static UimaDepNode DUMMY_PARENT = new UimaDepNode();
// LOG4J logger based on class name
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
// public static UimaDepTree getDepTreeFromArray(ArrayList<ConllDependencyNode> nodes) {
// UimaDepTree tree = new UimaDepTree();
diff --git a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
index 826a8d1..45622ee 100644
--- a/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
+++ b/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.dependency.parser.util;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.fit.util.JCasUtil;
@@ -38,7 +38,7 @@ import java.util.regex.Pattern;
*/
public abstract class DependencyUtility {
- public static final Logger LOGGER = LogManager.getLogger("DependencyUtility");
+ public static final Logger LOGGER = LoggerFactory.getLogger("DependencyUtility");
static private final Pattern N_DOT_PATTERN = Pattern.compile( "N..?" );
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java
index 34d6a7b..0febecb 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java
@@ -20,8 +20,8 @@ import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -67,7 +67,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
)
final public class CasedAnnotationFinder extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "CasedAnnotationFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasedAnnotationFinder" );
static public final String DICTIONARY_TYPE = "_type";
static public final String ENCODER_TYPE = "_type";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AlikeSubsumingAnnotationCreator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AlikeSubsumingAnnotationCreator.java
index 10417df..9e88365 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AlikeSubsumingAnnotationCreator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AlikeSubsumingAnnotationCreator.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.dictionary.cased.encoder.TermEncoding;
import org.apache.ctakes.dictionary.cased.lookup.DiscoveredTerm;
import org.apache.ctakes.dictionary.cased.util.textspan.MagicTextSpan;
import org.apache.ctakes.dictionary.cased.wsd.WsdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import javax.annotation.concurrent.Immutable;
@@ -24,7 +24,7 @@ import java.util.*;
@Immutable
final public class AlikeSubsumingAnnotationCreator implements AnnotationCreator {
- static private final Logger LOGGER = LogManager.getLogger( "AlikeSubsumingAnnotationCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AlikeSubsumingAnnotationCreator" );
public AlikeSubsumingAnnotationCreator() {
}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreatorUtil.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreatorUtil.java
index 696759a..e7d8b61 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreatorUtil.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreatorUtil.java
@@ -13,8 +13,8 @@ import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
@@ -32,7 +32,7 @@ import java.util.stream.Collectors;
@Immutable
final public class AnnotationCreatorUtil {
- static private final Logger LOGGER = LogManager.getLogger( "AnnotationCreatorUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AnnotationCreatorUtil" );
static private final TermEncoding NULL_CODE = new TermEncoding( "", "" );
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/NonSubsumingAnnotationCreator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/NonSubsumingAnnotationCreator.java
index 919ebb0..8d5c95a 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/NonSubsumingAnnotationCreator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/NonSubsumingAnnotationCreator.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.annotation.SemanticGroup;
import org.apache.ctakes.core.util.annotation.SemanticTui;
import org.apache.ctakes.dictionary.cased.encoder.TermEncoding;
import org.apache.ctakes.dictionary.cased.lookup.DiscoveredTerm;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import javax.annotation.concurrent.Immutable;
@@ -22,7 +22,7 @@ import java.util.Map;
@Immutable
final public class NonSubsumingAnnotationCreator implements AnnotationCreator {
- static private final Logger LOGGER = LogManager.getLogger( "NonSubsumingAnnotationCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "NonSubsumingAnnotationCreator" );
public NonSubsumingAnnotationCreator() {
}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SemanticSubsumingAnnotationCreator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SemanticSubsumingAnnotationCreator.java
index 610ae10..09ee617 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SemanticSubsumingAnnotationCreator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SemanticSubsumingAnnotationCreator.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.dictionary.cased.encoder.TermEncoding;
import org.apache.ctakes.dictionary.cased.lookup.DiscoveredTerm;
import org.apache.ctakes.dictionary.cased.util.textspan.MagicTextSpan;
import org.apache.ctakes.dictionary.cased.wsd.WsdUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import javax.annotation.concurrent.Immutable;
@@ -25,7 +25,7 @@ import static org.apache.ctakes.core.util.annotation.SemanticGroup.*;
@Immutable
final public class SemanticSubsumingAnnotationCreator implements AnnotationCreator {
- static private final Logger LOGGER = LogManager.getLogger( "SemanticSubsumingAnnotationCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SemanticSubsumingAnnotationCreator" );
public SemanticSubsumingAnnotationCreator() {
}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvDictionary.java
index 5a357e7..d723909 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvDictionary.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.dictionary.cased.util.bsv.BsvObjectCreator;
import org.apache.ctakes.dictionary.cased.util.tokenize.TokenizedTerm;
import org.apache.ctakes.dictionary.cased.util.tokenize.TokenizedTermMapper;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.IOException;
@@ -28,7 +28,7 @@ final public class BsvDictionary implements CasedDictionary {
static public final String DICTIONARY_TYPE = "BSV";
- static private final Logger LOGGER = LogManager.getLogger( "BsvDictionary" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvDictionary" );
final private CasedDictionary _delegateDictionary;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvListDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvListDictionary.java
index ed268dd..bb5c0f0 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvListDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvListDictionary.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.dictionary.cased.lookup.LookupToken;
import org.apache.ctakes.dictionary.cased.util.tokenize.TokenizedTerm;
import org.apache.ctakes.dictionary.cased.util.tokenize.TokenizedTermMapper;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.util.*;
@@ -23,7 +23,7 @@ final public class BsvListDictionary implements CasedDictionary {
static public final String DICTIONARY_TYPE = "BSV_LIST";
- static private final Logger LOGGER = LogManager.getLogger( "BsvListDictionary" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvListDictionary" );
final private CasedDictionary _delegateDictionary;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/JdbcDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/JdbcDictionary.java
index 5563c6b..55b08d8 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/JdbcDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/JdbcDictionary.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.dictionary.cased.dictionary;
import org.apache.ctakes.dictionary.cased.lookup.CandidateTerm;
import org.apache.ctakes.dictionary.cased.lookup.LookupToken;
import org.apache.ctakes.dictionary.cased.util.jdbc.JdbcUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.PreparedStatement;
@@ -29,7 +29,7 @@ final public class JdbcDictionary implements CasedDictionary {
static public final String DICTIONARY_TYPE = "JDBC";
- static private final Logger LOGGER = LogManager.getLogger( "JdbcDictionary" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcDictionary" );
static private final String snomed_rxnorm_2020aa_url
= "jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/cased/sno_rx_2020aa/sno_rx_2020aa";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvEncoder.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvEncoder.java
index 398eacd..7d00a71 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvEncoder.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvEncoder.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.dictionary.cased.util.bsv.BsvFileParser;
import org.apache.ctakes.dictionary.cased.util.bsv.StringArrayCreator;
import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.IOException;
@@ -21,7 +21,7 @@ final public class BsvEncoder implements TermEncoder {
static public final String ENCODER_TYPE = "BSV";
- static private final Logger LOGGER = LogManager.getLogger( "BsvEncoder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvEncoder" );
private final InMemoryEncoder _delegate;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvListEncoder.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvListEncoder.java
index a9d9361..5ba66f3 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvListEncoder.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvListEncoder.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.dictionary.cased.encoder;
import org.apache.ctakes.core.util.StringUtil;
import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.util.*;
@@ -19,7 +19,7 @@ final public class BsvListEncoder implements TermEncoder {
static public final String ENCODER_TYPE = "BSV_LIST";
- static private final Logger LOGGER = LogManager.getLogger( "BsvListEncoder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvListEncoder" );
private final InMemoryEncoder _delegate;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/JdbcEncoder.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/JdbcEncoder.java
index a109f42..798c8f2 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/JdbcEncoder.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/JdbcEncoder.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.dictionary.cased.encoder;
import org.apache.ctakes.dictionary.cased.table.column.CodeType;
import org.apache.ctakes.dictionary.cased.table.column.SchemaCode;
import org.apache.ctakes.dictionary.cased.util.jdbc.JdbcUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.PreparedStatement;
@@ -27,7 +27,7 @@ final public class JdbcEncoder implements TermEncoder {
static public final String ENCODER_TYPE = "JDBC";
- static private final Logger LOGGER = LogManager.getLogger( "JdbcEncoder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcEncoder" );
private final String _name;
private final PreparedStatement _selectCodeStatement;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java
index 0e98261..3040eba 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.dictionary.cased.lookup;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.dictionary.cased.dictionary.CasedDictionary;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.*;
@@ -14,7 +14,7 @@ import java.util.*;
*/
final public class ContiguousLookupEngine {
- static private final Logger LOGGER = LogManager.getLogger( "ContiguousLookupEngine" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ContiguousLookupEngine" );
/**
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java
index 42498f9..3e554ab 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.dictionary.cased.lookup;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.dictionary.cased.dictionary.CasedDictionary;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.*;
@@ -15,7 +15,7 @@ import java.util.*;
*/
public class LookupEngine {
- static private final Logger LOGGER = LogManager.getLogger( "LookupEngine" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LookupEngine" );
/**
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTermMapper.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTermMapper.java
index 7818fea..7078fff 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTermMapper.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTermMapper.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.dictionary.cased.util.tokenize;
import org.apache.ctakes.dictionary.cased.lookup.CandidateTerm;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.*;
import java.util.function.Function;
@@ -38,7 +38,7 @@ import java.util.stream.Collectors;
*/
final public class TokenizedTermMapper {
- static private final Logger LOGGER = LogManager.getLogger( "TokenizedTermMapper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TokenizedTermMapper" );
private TokenizedTermMapper() {
}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
index 741aa61..6304e8b 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
@@ -30,8 +30,8 @@ import org.apache.ctakes.dictionary.lookup2.textspan.TextSpan;
import org.apache.ctakes.dictionary.lookup2.util.DictionarySpec;
import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken;
import org.apache.ctakes.typesystem.type.syntax.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.analysis_engine.annotator.AnnotatorContextException;
@@ -57,7 +57,7 @@ abstract public class AbstractJCasTermAnnotator extends JCasAnnotator_ImplBase
implements JCasTermAnnotator, WindowProcessor {
// LOG4J logger based on interface name
- final static private Logger LOGGER = LogManager.getLogger( "AbstractJCasTermAnnotator" );
+ final static private Logger LOGGER = LoggerFactory.getLogger( "AbstractJCasTermAnnotator" );
// private int _lookupWindowType;
private Class<? extends Annotation> _lookupClass;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
index 4393faf..4a65a23 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan;
import org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan;
import org.apache.ctakes.dictionary.lookup2.textspan.TextSpan;
import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -55,7 +55,7 @@ import java.util.List;
final public class OverlapJCasTermAnnotator extends AbstractJCasTermAnnotator {
// LOG4J logger based on interface name
- final private Logger _LOGGER = LogManager.getLogger( "OverlapJCasTermAnnotator" );
+ final private Logger _LOGGER = LoggerFactory.getLogger( "OverlapJCasTermAnnotator" );
/**
* specifies the number of consecutive non-comma tokens that can be skipped
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
index c5b96bf..7d996c8 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.util.collection.CollectionMap;
import org.apache.ctakes.core.util.collection.HashSetMap;
import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.BufferedReader;
@@ -22,7 +22,7 @@ import java.util.*;
*/
final public class BsvConceptFactory implements ConceptFactory {
- static private final Logger LOGGER = LogManager.getLogger( "BsvConceptFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvConceptFactory" );
static private final String BSV_FILE_PATH = "bsvPath";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java
index d56b7a6..2523464 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.collection.HashSetMap;
import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
import org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory;
import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.*;
@@ -22,7 +22,7 @@ import static org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.*;
public class JdbcConceptFactory extends AbstractConceptFactory {
// LOG4J logger based on class name
- static final private Logger LOGGER = LogManager.getLogger( "JdbcConceptFactory" );
+ static final private Logger LOGGER = LoggerFactory.getLogger( "JdbcConceptFactory" );
static private final String TABLE_KEY_SUFFIX = "TABLE";
static private final String INT_CLASS = "INT";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/UmlsJdbcConceptFactory.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/UmlsJdbcConceptFactory.java
index 9443173..449904f 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/UmlsJdbcConceptFactory.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/UmlsJdbcConceptFactory.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.dictionary.lookup2.concept;
import org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.SQLException;
@@ -17,7 +17,7 @@ import java.util.Properties;
*/
final public class UmlsJdbcConceptFactory implements ConceptFactory {
- static private final Logger LOGGER = LogManager.getLogger( "UmlsJdbcConceptFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UmlsJdbcConceptFactory" );
final private ConceptFactory _delegateConceptFactory;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concurrent/ThreadSafeFastLookup.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concurrent/ThreadSafeFastLookup.java
index 3b9cfce..3776492 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concurrent/ThreadSafeFastLookup.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concurrent/ThreadSafeFastLookup.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -29,7 +29,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeFastLookup extends DefaultJCasTermAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeFastLookup" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeFastLookup" );
/**
* {@inheritDoc}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
index c70112f..d20f054 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
@@ -30,8 +30,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CASRuntimeException;
@@ -51,7 +51,7 @@ import java.util.*;
* Date: 1/9/14
*/
final public class DefaultTermConsumer extends AbstractTermConsumer {
- static private final Logger LOGGER = LogManager.getLogger( "DefaultTermConsumer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DefaultTermConsumer" );
// case insensitive blacklist
static private final String BLACKLIST_KEY = "Blacklist";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultUmlsConceptCreator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultUmlsConceptCreator.java
index d2dcc4b..a7b7e71 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultUmlsConceptCreator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultUmlsConceptCreator.java
@@ -6,8 +6,8 @@ import org.apache.uima.jcas.JCas;
import java.util.ArrayList;
import java.util.Collection;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -16,7 +16,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class DefaultUmlsConceptCreator implements UmlsConceptCreator {
- static private final Logger LOGGER = LogManager.getLogger( "DefaultUmlsConceptCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DefaultUmlsConceptCreator" );
/**
* {@inheritDoc}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
index 801fc1f..580d9c0 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.dictionary.lookup2.concept.Concept;
import org.apache.ctakes.dictionary.lookup2.dictionary.RareWordDictionary;
import org.apache.ctakes.dictionary.lookup2.textspan.TextSpan;
import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
@@ -28,7 +28,7 @@ import java.util.*;
*/
public class SemanticCleanupTermConsumer extends AbstractTermConsumer {
- static private final Logger LOGGER = LogManager.getLogger( "SemanticCleanupTermConsumer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SemanticCleanupTermConsumer" );
private final TermConsumer _idHitConsumer;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java
index 3dbb9e4..310b1ee 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.util.StringUtil;
import org.apache.ctakes.core.util.collection.CollectionMap;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.BufferedReader;
@@ -47,7 +47,7 @@ import static org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCre
*/
final public class BsvRareWordDictionary implements RareWordDictionary {
- static private final Logger LOGGER = LogManager.getLogger( "BsvRareWordDictionary" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BsvRareWordDictionary" );
static private final String BSV_FILE_PATH = "bsvPath";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java
index 6ec5bb7..dcf118e 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java
@@ -22,8 +22,8 @@ import org.apache.ctakes.dictionary.lookup2.concept.ConceptFactory;
import org.apache.ctakes.dictionary.lookup2.consumer.TermConsumer;
import org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec;
import org.apache.ctakes.dictionary.lookup2.util.DictionarySpec;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorContextException;
import org.jdom2.Document;
@@ -53,7 +53,7 @@ import java.util.*;
final public class DictionaryDescriptorParser {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "DictionaryDescriptorParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DictionaryDescriptorParser" );
/**
* A <B>Utility Class</B> cannot be instantiated
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
index 96fbe53..07d4438 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.dictionary.lookup2.dictionary;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
import org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.Connection;
@@ -59,7 +59,7 @@ final public class JdbcRareWordDictionary extends AbstractRareWordDictionary {
}
// LOG4J logger based on class name
- static final private Logger LOGGER = LogManager.getLogger( "JdbcRareWordDictionary" );
+ static final private Logger LOGGER = LoggerFactory.getLogger( "JdbcRareWordDictionary" );
static public final String RARE_WORD_TABLE = "rareWordTable";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java
index caea290..1f21381 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java
@@ -21,8 +21,8 @@
//import org.apache.ctakes.dictionary.lookup.Dictionary;
//import org.apache.ctakes.dictionary.lookup.DictionaryException;
//import org.apache.ctakes.dictionary.lookup.MetaDataHit;
-//import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
//
//import java.util.Collection;
//import java.util.Collections;
@@ -36,7 +36,7 @@ import org.apache.logging.log4j.LogManager;
//public class RareWordDictionaryWrapper extends AbstractRareWordDictionary implements Dictionary {
//
// // LOG4J logger based on class name
-// final private Logger _LOGGER = LogManager.getLogger( getClass().getName() );
+// final private Logger _LOGGER = LoggerFactory.getLogger( getClass().getName() );
//
// final private Dictionary _metaDataHitDictionary;
//
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java
index 75d3b57..de91afc 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.util.collection.ArrayListMap;
import org.apache.ctakes.core.util.collection.CollectionMap;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.*;
@@ -40,7 +40,7 @@ import java.util.*;
*/
final public class RareWordTermMapCreator {
- static private final Logger LOGGER = LogManager.getLogger( "RareWordTermMapCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RareWordTermMapCreator" );
private RareWordTermMapCreator() {
}
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/UmlsJdbcRareWordDictionary.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/UmlsJdbcRareWordDictionary.java
index 13ff58e..d563d6b 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/UmlsJdbcRareWordDictionary.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/UmlsJdbcRareWordDictionary.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.dictionary.lookup2.dictionary;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken;
import org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.sql.SQLException;
@@ -18,7 +18,7 @@ import java.util.Properties;
*/
final public class UmlsJdbcRareWordDictionary implements RareWordDictionary {
- static private final Logger LOGGER = LogManager.getLogger( "UmlsJdbcRareWordDictionary" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UmlsJdbcRareWordDictionary" );
final private RareWordDictionary _delegateDictionary;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java
index 75c6ade..84def97 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java
@@ -18,8 +18,8 @@
// */
//package org.apache.ctakes.dictionary.lookup2.relation;
//
-//import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
//
//import java.sql.Connection;
//import java.sql.PreparedStatement;
@@ -55,7 +55,7 @@ import org.apache.logging.log4j.LogManager;
// }
//
// // LOG4J logger based on class name
-// final private Logger _LOGGER = LogManager.getLogger( getClass().getName() );
+// final private Logger _LOGGER = LoggerFactory.getLogger( getClass().getName() );
//
// final private Connection _connection;
// final private String _tableName;
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/CuiCodeUtil.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/CuiCodeUtil.java
index 0b53f58..39df42d 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/CuiCodeUtil.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/CuiCodeUtil.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.dictionary.lookup2.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.Arrays;
@@ -19,7 +19,7 @@ public enum CuiCodeUtil {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "CuiCodeUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiCodeUtil" );
static private final long PREFIX_MULTIPLIER = 100000000;
final private List<PrefixerPair> _prefixerPairList = new ArrayList<>();
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java
index ba7c4ff..4062762 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.dictionary.lookup2.util;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.FileNotFoundException;
import java.lang.reflect.InvocationTargetException;
@@ -26,9 +26,9 @@ public enum JdbcConnectionFactory {
static public final String JDBC_USER = "jdbcUser";
static public final String JDBC_PASS = "jdbcPass";
- static final private Logger LOGGER = LogManager.getLogger( "JdbcConnectionFactory" );
- static final private Logger DOT_LOGGER = LogManager.getLogger( "ProgressAppender" );
- static final private Logger EOL_LOGGER = LogManager.getLogger( "ProgressDone" );
+ static final private Logger LOGGER = LoggerFactory.getLogger( "JdbcConnectionFactory" );
+ static final private Logger DOT_LOGGER = LoggerFactory.getLogger( "ProgressAppender" );
+ static final private Logger EOL_LOGGER = LoggerFactory.getLogger( "ProgressDone" );
static private final String HSQL_PREFIX = "jdbc:hsqldb:";
static private final String FILE_PREFIX = "file:";
diff --git a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
index cf03fce..ccc0147 100644
--- a/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
+++ b/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.dictionary.lookup2.util;
import org.apache.ctakes.core.pipeline.StandardCliOptions;
import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import java.io.BufferedReader;
@@ -66,7 +66,7 @@ public enum UmlsUserApprover {
public final static String API_KEY_LABEL = "umls_api_key";
public final static String OLDY_KEY_PROP = "ctakes.umls_apikey";
- static final private Logger LOGGER = LogManager.getLogger( "UmlsUserApprover" );
+ static final private Logger LOGGER = LoggerFactory.getLogger( "UmlsUserApprover" );
static final private String CHANGEME = "CHANGEME";
static final private String CHANGE_ME = "CHANGE_ME";
diff --git a/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/ae/TestDictionaryLoadResources.java b/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/ae/TestDictionaryLoadResources.java
index 6d78e7f..e96e1a1 100644
--- a/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/ae/TestDictionaryLoadResources.java
+++ b/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/ae/TestDictionaryLoadResources.java
@@ -1,8 +1,8 @@
//package org.apache.ctakes.dictionary.lookup2.ae;
//
//import org.apache.ctakes.dictionary.lookup2.util.UmlsUserTester;
-//import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
//import org.apache.uima.UIMAException;
//import org.apache.uima.analysis_engine.AnalysisEngineDescription;
//import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -18,7 +18,7 @@ import org.apache.logging.log4j.LogManager;
//
//final public class TestDictionaryLoadResources {
//
-// static private final Logger LOGGER = LogManager.getLogger( "TestDictionaryLoadResources" );
+// static private final Logger LOGGER = LoggerFactory.getLogger( "TestDictionaryLoadResources" );
//
//
// static private final String TEST_TEXT
diff --git a/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java b/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
index 9f4fcae..466e766 100644
--- a/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
+++ b/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.dictionary.lookup2.util;
import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -33,7 +33,7 @@ import java.util.Properties;
@Ignore // needed for successful maven build/test when no API key is supplied
final public class UmlsUserTest {
- static private final Logger LOGGER = LogManager.getLogger( "UmlsUserTester" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UmlsUserTester" );
static UimaContext _uimaContext = null;
private final String apiKeyForTesting = "CHANGE_ME";
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
index 90c18a4..35ee89b 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.dictionary.lookup.MetaDataHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.*;
import org.apache.uima.UimaContext;
@@ -51,7 +51,7 @@ public class AssertionCuePhraseConsumerImpl extends BaseLookupConsumerImpl
public static final String CUE_PHRASE_FIRST_WORD_FIELD_NAME = "cuePhraseFirstWord";
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
private final String CODE_MF_PRP_KEY = "codeMetaField";
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DebugConsumerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DebugConsumerImpl.java
index 67ce6ef..c01a932 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DebugConsumerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DebugConsumerImpl.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.dictionary.lookup.ae;
import org.apache.ctakes.dictionary.lookup.MetaDataHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
@@ -39,7 +39,7 @@ import java.util.Properties;
public class DebugConsumerImpl implements LookupConsumer
{
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
public DebugConsumerImpl(UimaContext aCtx, Properties props)
{
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DictionaryLookupAnnotator.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DictionaryLookupAnnotator.java
index 42b918c..634e90f 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DictionaryLookupAnnotator.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DictionaryLookupAnnotator.java
@@ -26,8 +26,8 @@ import org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
import org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -57,7 +57,7 @@ import java.util.*;
public class DictionaryLookupAnnotator extends JCasAnnotator_ImplBase
{
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
private UimaContext iv_context;
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java
index 5360a26..57b67b0 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation;
import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
import org.apache.ctakes.typesystem.type.syntax.*;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException;
import org.apache.uima.cas.text.AnnotationIndex;
@@ -46,7 +46,7 @@ public class DirectLookupInitializerImpl implements LookupInitializer {
private final String CANONICAL_VARIANT_ATTR = "canonicalATTR";
// LOG4J logger based on class name
- final private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ final private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
public DirectLookupInitializerImpl( final UimaContext uimaContext, final Properties props ) {
// TODO property validation could be done here
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java
index aeb1120..b943733 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImp
import org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation;
import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
import org.apache.ctakes.typesystem.type.syntax.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException;
import org.apache.uima.cas.text.AnnotationIndex;
@@ -47,7 +47,7 @@ public class FirstTokenPermLookupInitializerImpl implements LookupInitializer {
static private final String FALSE_STRING = Boolean.toString( false );
// LOG4J logger based on class name
- final private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ final private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
// properties for firstWordPermutation algorithm
static private final String TEXT_MFS_PRP_KEY = "textMetaFields";
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
index fdec05b..27c7e94 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
@@ -30,8 +30,8 @@ import org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl;
import org.apache.ctakes.dictionary.lookup.strtable.StringTable;
import org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl;
import org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.index.IndexReader;
import org.apache.lucene.search.IndexSearcher;
import org.apache.uima.UimaContext;
@@ -60,7 +60,7 @@ import java.util.*;
@SuppressWarnings( "unchecked" )
final public class LookupParseUtilitiesRefactor {
- static private final Logger CLASS_LOGGER = LogManager.getLogger( LookupParseUtilitiesRefactor.class );
+ static private final Logger CLASS_LOGGER = LoggerFactory.getLogger( LookupParseUtilitiesRefactor.class );
private LookupParseUtilitiesRefactor() {}
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java
index abe3fcc..890f3b6 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.*;
import org.apache.uima.UimaContext;
@@ -46,7 +46,7 @@ import java.util.*;
*/
public class OrangeBookFilterConsumerImpl extends BaseLookupConsumerImpl {
// LOG4J logger based on class name
- private final Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private final Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
static private final String CODE_MF_PRP_KEY = "codeMetaField";
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java
index f8128c6..1364362 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
import org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -48,7 +48,7 @@ import java.util.concurrent.*;
public class ThreadedDictionaryLookupAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "ThreadedDictionaryLookupAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadedDictionaryLookupAnnotator" );
// We need to start using types wrt generics
private Set<LookupSpec> _lookupSpecSet = new HashSet<>();
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
index 9524e28..0da0943 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.dictionary.lookup.ae;
import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.resource.ResourceInitializationException;
@@ -40,7 +40,7 @@ import java.net.URLEncoder;
public class ThreadedUmlsDictionaryLookupAnnotator extends ThreadedDictionaryLookupAnnotator {
// TODO: use consistent variable names (_logger vs LOGGER vs logger)
- static final private Logger _LOGGER = LogManager.getLogger( ThreadedUmlsDictionaryLookupAnnotator.class );
+ static final private Logger _LOGGER = LoggerFactory.getLogger( ThreadedUmlsDictionaryLookupAnnotator.class );
@Override
public void initialize( final UimaContext aContext ) throws ResourceInitializationException {
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
index 7722639..82bd12d 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileResourceImpl;
import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -59,7 +59,7 @@ public class UmlsDictionaryLookupAnnotator extends DictionaryLookupAnnotator {
* User's will need to configure their UMLS username/password in their config
*/
- private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
private String UMLSAddr;
private String UMLSVendor;
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedLuceneConsumerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedLuceneConsumerImpl.java
index a0a0a45..1f1a6d0 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedLuceneConsumerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedLuceneConsumerImpl.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.resource.FileResource;
import org.apache.ctakes.dictionary.lookup.DictionaryException;
import org.apache.ctakes.dictionary.lookup.MetaDataHit;
import org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.index.DirectoryReader;
import org.apache.lucene.index.IndexReader;
import org.apache.lucene.search.IndexSearcher;
@@ -50,7 +50,7 @@ import java.util.Set;
public class UmlsToSnomedLuceneConsumerImpl extends UmlsToSnomedConsumerImpl {
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
//ohnlp-Bugs-3296301 limits the search results to fixed 100 records.
// Added 'MaxListSize'
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
index 20902b4..2b0e38b 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
@@ -24,8 +24,8 @@ import org.apache.ctakes.dictionary.lookup.phrasebuilder.PhraseBuilder;
import org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.*;
@@ -48,7 +48,7 @@ import java.util.*;
*/
public class FirstTokenPermutationImpl implements LookupAlgorithm {
// LOG4J logger based on class name
- final private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ final private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
/**
* Key value for context map. Value is expected to be a List of
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java
index 25ac996..76bf937 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.dictionary.lookup.lucene;
import org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary;
import org.apache.ctakes.dictionary.lookup.DictionaryException;
import org.apache.ctakes.dictionary.lookup.MetaDataHit;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.lucene.analysis.core.KeywordAnalyzer;
import org.apache.lucene.document.Document;
import org.apache.lucene.index.Term;
@@ -48,7 +48,7 @@ public class LuceneDictionaryImpl extends AbstractBaseDictionary {
//ohnlp-Bugs-3296301 limits the search results to fixed 100 records.
private int iv_maxHits;
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
/**
* Constructor
diff --git a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
index 207b4de..4c58e04 100644
--- a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
+++ b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
@@ -40,8 +40,8 @@ import org.apache.ctakes.typesystem.type.syntax.*;
import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -72,7 +72,7 @@ import java.util.*;
public class DrugMentionAnnotator extends JCasAnnotator_ImplBase
{
// LOG4J logger based on class name
- public static Logger LOGGER = LogManager.getLogger(DrugMentionAnnotator.class);
+ public static Logger LOGGER = LoggerFactory.getLogger(DrugMentionAnnotator.class);
/**
* This identifies the section ids that will be considered in generating DrugMentionAnnotaitons
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
index 4949237..a7f0e40 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
@@ -12,8 +12,8 @@ import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
import org.apache.ctakes.typesystem.type.textsem.BodySideModifier;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -50,7 +50,7 @@ import java.util.stream.Collectors;
)
final public class BodySideFinder extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "BodySideFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BodySideFinder" );
/**
* Holds a umls CUI and some synonyms for body sides.
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ConfigParameterExample.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ConfigParameterExample.java
index ba60b19..899faa9 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ConfigParameterExample.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ConfigParameterExample.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.examples.ae;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -38,7 +38,7 @@ public class ConfigParameterExample extends JCasAnnotator_ImplBase {
public static final String PARAM_SAVE_ANN = "PARAM_SAVE_ANN";
public static final String PARAM_PRINT_ANN = "PARAM_PRINT_ANN";
- static private final Logger LOGGER = LogManager.getLogger( "ConfigParameterExample" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ConfigParameterExample" );
@ConfigurationParameter(name = PARAM_SAVE_ANN, mandatory = false,
description = "Example of Options/Parameters Save Annotation?")
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/RegexBpFinder.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/RegexBpFinder.java
index 8d66ffb..17783a5 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/RegexBpFinder.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/RegexBpFinder.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.core.util.regex.RegexSpanFinder;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -28,7 +28,7 @@ import java.util.stream.Collectors;
)
final public class RegexBpFinder extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "RegexBpFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RegexBpFinder" );
static private final Collection<String> BP_SECTIONS
= Arrays.asList( "Vital Signs", "General Exam", "Objective", "SIMPLE_SEGMENT" );
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/FileTreeViewXmiWriter.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/FileTreeViewXmiWriter.java
index 942f641..5b3805e 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/FileTreeViewXmiWriter.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/FileTreeViewXmiWriter.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.cc.XMISerializer;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.patient.PatientViewUtil;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.impl.XmiCasSerializer;
@@ -33,7 +33,7 @@ import java.util.Collection;
)
final public class FileTreeViewXmiWriter extends AbstractJCasFileWriter {
- static private final Logger LOGGER = LogManager.getLogger( "FileTreeViewXmiWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileTreeViewXmiWriter" );
/**
* {@inheritDoc}
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenPrinter.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenPrinter.java
index 3ab6624..7ed4363 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenPrinter.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenPrinter.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.examples.cc;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.util.JCasUtil;
@@ -16,7 +16,7 @@ import java.util.Collection;
*/
public final class TokenPrinter extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "TokenPrinter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TokenPrinter" );
/**
* Entry point for processing.
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenSpanWriter.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenSpanWriter.java
index 6041d60..417a69f 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenSpanWriter.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cc/TokenSpanWriter.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -27,7 +27,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.DOCUMENT_I
public class TokenSpanWriter extends AbstractJCasFileWriter {
// If you do not need to utilize the entire cas, or need more than the doc cas, consider AbstractFileWriter<T>.
- static private final Logger LOGGER = LogManager.getLogger( "TokenSpanWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TokenSpanWriter" );
// to add a configuration parameter, type "param" and hit tab.
/**
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cr/LetterColumnReader.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cr/LetterColumnReader.java
index ffac565..4ee71d7 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/cr/LetterColumnReader.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/cr/LetterColumnReader.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.core.util.StringUtil;
import org.apache.ctakes.core.util.doc.JCasBuilder;
import org.apache.ctakes.core.util.doc.TextBySectionBuilder;
import org.apache.ctakes.core.util.regex.RegexSpanFinder;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.collection.CollectionException;
import org.apache.uima.jcas.JCas;
import org.apache.uima.util.Progress;
@@ -29,7 +29,7 @@ import java.util.stream.Collectors;
)
public class LetterColumnReader extends AbstractFileTreeReader {
- static private final Logger LOGGER = LogManager.getLogger( "LetterColumnReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LetterColumnReader" );
static private final Pattern LETTER_PATTERN = Pattern.compile( "\\bLetter [0-9]+\\|" );
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
index 830b1ee..96cdc66 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.examples.ae.ConfigParameterExample;
import org.apache.ctakes.postagger.POSTagger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.IOException;
@@ -26,7 +26,7 @@ import java.io.IOException;
*/
final public class HelloWorldBuilderRunner {
- static private final Logger LOGGER = LogManager.getLogger( "HelloWorldBuilderRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HelloWorldBuilderRunner" );
static private final String DOC_TEXT = "Hello World!";
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
index 46f7a90..6b348c1 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.examples.pipeline;
import org.apache.ctakes.core.pipeline.CuiCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.IOException;
@@ -22,7 +22,7 @@ import java.io.IOException;
*/
final public class HelloWorldCuiPiperRunner {
- static private final Logger LOGGER = LogManager.getLogger( "HelloWorldCuiPiperRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HelloWorldCuiPiperRunner" );
static private final String PIPER_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldCui.piper";
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
index 332207c..68a6fc2 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.examples.pipeline;
import org.apache.ctakes.core.pipeline.EntityCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.IOException;
@@ -22,7 +22,7 @@ import java.io.IOException;
*/
final public class HelloWorldPropsPiperRunner {
- static private final Logger LOGGER = LogManager.getLogger( "HelloWorldPropsPiperRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HelloWorldPropsPiperRunner" );
static private final String PIPER_FILE_PATH
= "org/apache/ctakes/examples/pipeline/HelloWorldProps.piper";
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java
index 0e23c35..c866496 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java
@@ -9,8 +9,8 @@ import org.apache.ctakes.core.pipeline.EntityCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.postagger.POSTagger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.IOException;
@@ -22,7 +22,7 @@ import java.io.IOException;
*/
final public class ProcessDirBuilderRunner {
- static private final Logger LOGGER = LogManager.getLogger( "ProcessDirBuilderRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ProcessDirBuilderRunner" );
static private final String INPUT_DIR = "org/apache/ctakes/examples/notes/annotated";
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
index 2e8608d..fe3d0f6 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.examples.pipeline;
import org.apache.ctakes.core.pipeline.EntityCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.IOException;
@@ -22,7 +22,7 @@ import java.io.IOException;
*/
final public class ProcessDirPiperRunner {
- static private final Logger LOGGER = LogManager.getLogger( "ProcessDirPiperRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ProcessDirPiperRunner" );
static private final String PIPER_FILE_PATH = "org/apache/ctakes/examples/pipeline/ProcessDir.piper";
diff --git a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessLinesClinicalRunner.java b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessLinesClinicalRunner.java
index 1e24764..262eb94 100644
--- a/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessLinesClinicalRunner.java
+++ b/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessLinesClinicalRunner.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.core.pipeline.EntityCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import java.io.File;
@@ -25,7 +25,7 @@ import java.io.IOException;
*/
final public class ProcessLinesClinicalRunner {
- static private final Logger LOGGER = LogManager.getLogger( "ProcessLinesClinicalRunner" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ProcessLinesClinicalRunner" );
static private final String PIPER_FILE_PATH = "org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/backbone/CompositionSectionCreator.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/backbone/CompositionSectionCreator.java
index de300a5..ae12562 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/backbone/CompositionSectionCreator.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/backbone/CompositionSectionCreator.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.fhir.backbone;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
@@ -19,7 +19,7 @@ import static org.hl7.fhir.dstu3.model.Composition.SectionComponent;
*/
final public class CompositionSectionCreator {
- static private final Logger LOGGER = LogManager.getLogger( "CompositionSectionCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CompositionSectionCreator" );
private CompositionSectionCreator() {
}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
index cf625b6..a7f0a76 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
@@ -12,8 +12,8 @@ import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -30,7 +30,7 @@ import java.util.stream.Collectors;
*/
final public class FhirDocComposer {
- static private final Logger LOGGER = LogManager.getLogger( "FhirDocComposer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirDocComposer" );
static private final String SIMPLE_SECTION = "SIMPLE_SEGMENT";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java
index ba2245f..dc74bd2 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.fhir.cc;
import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -36,7 +36,7 @@ public class FhirJsonFileWriter extends AbstractJCasFileWriter {
)
private boolean _writeNlpFhir;
- static private final Logger LOGGER = LogManager.getLogger( "FhirJsonFileWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirJsonFileWriter" );
/**
* {@inheritDoc}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java
index a1d8427..aa2b306 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java
@@ -4,8 +4,8 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.fhir.resource.PractitionerCtakes;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -36,7 +36,7 @@ final public class FhirJsonWriter extends JCasAnnotator_ImplBase {
)
private boolean _writeNlpFhir;
- static private final Logger LOGGER = LogManager.getLogger( "FhirJsonWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirJsonWriter" );
/**
* {@inheritDoc}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleReader.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleReader.java
index 6cd4cbe..d1fdc78 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleReader.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleReader.java
@@ -8,8 +8,8 @@ import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.io.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -21,7 +21,7 @@ final public class BundleReader {
private BundleReader() {
}
- static private final Logger LOGGER = LogManager.getLogger( "BundleReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BundleReader" );
static public Bundle readJsonBundle( final File file ) throws IOException {
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirJsonFileReader.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirJsonFileReader.java
index c5f4eb2..2a1d3d7 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirJsonFileReader.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirJsonFileReader.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.fhir.cr;
import org.apache.ctakes.core.cr.AbstractFileTreeReader;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Bundle;
@@ -24,7 +24,7 @@ import java.io.IOException;
)
public class FhirJsonFileReader extends AbstractFileTreeReader {
- static private final Logger LOGGER = LogManager.getLogger( "FhirJsonFileReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirJsonFileReader" );
/**
* {@inheritDoc}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirXmlFileReader.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirXmlFileReader.java
index 99d023f..ca296dd 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirXmlFileReader.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirXmlFileReader.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.fhir.cr;
import org.apache.ctakes.core.cr.AbstractFileTreeReader;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Bundle;
@@ -24,7 +24,7 @@ import java.io.IOException;
)
public class FhirXmlFileReader extends AbstractFileTreeReader {
- static private final Logger LOGGER = LogManager.getLogger( "FhirXmlFileReader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirXmlFileReader" );
/**
* {@inheritDoc}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
index 92c373c..7506e8f 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
@@ -13,8 +13,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.utilities.xhtml.NodeType;
@@ -32,7 +32,7 @@ import static org.apache.ctakes.fhir.resource.SectionCreator.SECTION_EXT;
*/
final public class FhirElementFactory {
- static private final Logger LOGGER = LogManager.getLogger( "FhirElementFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirElementFactory" );
static public final String CTAKES_FHIR_URL = "http://org.apache.ctakes/fhir/";
static public final String SPAN_BEGIN_EXT = "span-begin";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java
index be2a5f4..b461808 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.fhir.element;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.core.util.StringUtil;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseExtension;
@@ -27,7 +27,7 @@ import static org.apache.ctakes.fhir.element.FhirElementFactory.*;
*/
final public class FhirElementParser {
- static private final Logger LOGGER = LogManager.getLogger( "FhirElementParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirElementParser" );
private FhirElementParser() {
}
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationParser.java
index ffb99cc..69cba55 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationParser.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.fhir.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.hl7.fhir.dstu3.model.Basic;
@@ -21,7 +21,7 @@ import static org.apache.ctakes.fhir.element.FhirElementFactory.CODING_TYPE_SYST
*/
final public class AnnotationParser implements FhirBasicParser<Annotation> {
- static private final Logger LOGGER = LogManager.getLogger( "AnnotationBasicParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AnnotationBasicParser" );
public Annotation parseResource( final JCas jCas, final Basic resource ) {
String className = "";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenParser.java
index 9f3b95b..c903f83 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenParser.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -22,7 +22,7 @@ import static org.apache.ctakes.fhir.element.FhirElementFactory.CODING_TYPE_SYST
*/
final public class BaseTokenParser implements FhirBasicParser<BaseToken> {
- static private final Logger LOGGER = LogManager.getLogger( "BaseTokenParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BaseTokenParser" );
public BaseToken parseResource( final JCas jCas, final Basic resource ) {
String className = "";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BundleCreator.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BundleCreator.java
index 5abaf7e..4b46777 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BundleCreator.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BundleCreator.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.fhir.util.FhirNoteSpecs;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.TOP;
import org.hl7.fhir.dstu3.model.Bundle;
@@ -20,7 +20,7 @@ import java.util.Date;
*/
final public class BundleCreator implements FhirResourceCreator<TOP, Bundle> {
- static private final Logger LOGGER = LogManager.getLogger( "BundleCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BundleCreator" );
static private final String CTAKES_BUNDLE_ID = "ctakes_bundle";
static private final DateFormat DATE_FORMAT = new SimpleDateFormat( "yyyyMMddhhmm" );
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java
index 58d6872..76e014a 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.fhir.util.FhirNoteSpecs;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.TOP;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -17,7 +17,7 @@ import org.hl7.fhir.dstu3.model.Composition;
*/
final public class CompositionCreator implements FhirResourceCreator<TOP, Composition> {
- static private final Logger LOGGER = LogManager.getLogger( "DpheCompositionCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DpheCompositionCreator" );
static public final String ID_NAME_COMPOSITION = "Composition";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionParser.java
index 6805811..b83f52a 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionParser.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.fhir.resource;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.Narrative;
@@ -15,7 +15,7 @@ import org.hl7.fhir.utilities.xhtml.XhtmlNode;
*/
public class CompositionParser {
- static private final Logger LOGGER = LogManager.getLogger( "CompositionParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CompositionParser" );
public void parseResource( final JCas jCas, final Basic resource ) {
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicParser.java
index ebe38ff..f49f3d5 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicParser.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.core.util.Pair;
import org.apache.ctakes.fhir.element.FhirElementParser;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.tcas.Annotation;
import org.hl7.fhir.dstu3.model.Basic;
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationCreator.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationCreator.java
index a09840f..5508b74 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationCreator.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationCreator.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.fhir.util.FhirNoteSpecs;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.Extension;
@@ -19,7 +19,7 @@ import org.hl7.fhir.dstu3.model.Extension;
*/
final public class IdentifiedAnnotationCreator implements FhirBasicCreator<IdentifiedAnnotation> {
- static private final Logger LOGGER = LogManager.getLogger( "IdentifiedAnnotationBasicCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IdentifiedAnnotationBasicCreator" );
static public final String ID_NAME_IDENTIFIED_ANNOTATION = "IdentifiedAnnotation";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java
index 7468133..767b1cc 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
import org.hl7.fhir.dstu3.model.Basic;
@@ -31,7 +31,7 @@ import static org.apache.ctakes.fhir.resource.IdentifiedAnnotationCreator.*;
*/
final public class IdentifiedAnnotationParser implements FhirBasicParser<IdentifiedAnnotation> {
- static private final Logger LOGGER = LogManager.getLogger( "IdentifiedAnnotationBasicParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IdentifiedAnnotationBasicParser" );
public IdentifiedAnnotation parseResource( final JCas jCas, final Basic resource ) {
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphParser.java
index 9ced40b..d6456bd 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphParser.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.typesystem.type.textspan.Paragraph;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
@@ -14,7 +14,7 @@ import org.hl7.fhir.dstu3.model.Basic;
*/
final public class ParagraphParser implements FhirBasicParser<Paragraph> {
- static private final Logger LOGGER = LogManager.getLogger( "ParagraphBasicParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParagraphBasicParser" );
public Paragraph parseResource( final JCas jCas, final Basic resource ) {
final Paragraph paragraph = new Paragraph( jCas );
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionCreator.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionCreator.java
index 1e6daa0..6849dd6 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionCreator.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionCreator.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.fhir.util.FhirNoteSpecs;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -18,7 +18,7 @@ import org.hl7.fhir.dstu3.model.Coding;
*/
final public class SectionCreator implements FhirBasicCreator<Segment> {
- static private final Logger LOGGER = LogManager.getLogger( "SectionBasicCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SectionBasicCreator" );
static public final String CODING_SECTION_NAME = "section-name";
static public final String CODING_SECTION_ID = "section-id";
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionParser.java
index 4780f31..68a424a 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionParser.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -21,7 +21,7 @@ import static org.apache.ctakes.fhir.resource.SectionCreator.CODING_SECTION_NAME
*/
final public class SectionParser implements FhirBasicParser<Segment> {
- static private final Logger LOGGER = LogManager.getLogger( "SectionBasicParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SectionBasicParser" );
public Segment parseResource( final JCas jCas, final Basic resource ) {
final CodeableConcept codeableConcept = resource.getCode();
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceParser.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceParser.java
index 13f4440..4d37e17 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceParser.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceParser.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.Basic;
@@ -14,7 +14,7 @@ import org.hl7.fhir.dstu3.model.Basic;
*/
final public class SentenceParser implements FhirBasicParser<Sentence> {
- static private final Logger LOGGER = LogManager.getLogger( "SentenceBasicParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SentenceBasicParser" );
public Sentence parseResource( final JCas jCas, final Basic resource ) {
final Sentence sentence = new Sentence( jCas );
diff --git a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
index 7917e9c..d669a8b 100644
--- a/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
+++ b/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.doc.NoteSpecs;
import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.typesystem.type.structured.SourceData;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.jcas.JCas;
import org.hl7.fhir.dstu3.model.*;
@@ -23,7 +23,7 @@ import java.util.stream.Collectors;
*/
final public class FhirNoteSpecs {
- static private final Logger LOGGER = LogManager.getLogger( "FhirNoteSpecs" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FhirNoteSpecs" );
// ClinicalNote is not yet a fhir resource, but it may be in the future and is the best fit.
// http://wiki.hl7.org/index.php?title=ClinicalNote_FHIR_Resource_Proposal
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/action/GlobalHotKeyManager.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/action/GlobalHotKeyManager.java
index 13c7ef8..1ecf003 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/action/GlobalHotKeyManager.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/action/GlobalHotKeyManager.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.action;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -31,7 +31,7 @@ final public class GlobalHotKeyManager extends EventQueue implements HotKeyManag
private GlobalHotKeyManager() {
}
- static private final Logger LOGGER = LogManager.getLogger( "HotKeyManager" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HotKeyManager" );
private final InputMap _keyStrokes = new InputMap();
private final ActionMap _actions = new ActionMap();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererLabel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererLabel.java
index c690aed..49549b3 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererLabel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererLabel.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -14,7 +14,7 @@ import java.awt.*;
*/
public class CellRendererLabel extends JLabel {
- static private final Logger LOGGER = LogManager.getLogger( "CellRendererLabel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CellRendererLabel" );
public CellRendererLabel() {
super();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererPanel.java
index 7dcd043..e137300 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererPanel.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -14,7 +14,7 @@ import java.awt.*;
*/
final public class CellRendererPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "CellRendererPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CellRendererPanel" );
public CellRendererPanel( final LayoutManager layoutManager ) {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/DisablerPane.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/DisablerPane.java
index 45a0513..f04438f 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/DisablerPane.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/DisablerPane.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -27,7 +27,7 @@ public final class DisablerPane extends JPanel implements MouseListener,
static private final DisablerPane INSTANCE = new DisablerPane();
}
- static private final Logger LOGGER = LogManager.getLogger( "DisablerPane" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DisablerPane" );
private JMenuBar _menuBar;
private Container _contentPane;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileChooserPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileChooserPanel.java
index bc0611a..cff5d6e 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileChooserPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileChooserPanel.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
@@ -25,7 +25,7 @@ import java.nio.file.Paths;
*/
final public class FileChooserPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "FileChooserPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileChooserPanel" );
public FileChooserPanel( final String name, final String defaultDirectory,
final ActionListener fileChangeListener ) {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileTableCellEditor.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileTableCellEditor.java
index f4ff19e..f599443 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileTableCellEditor.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileTableCellEditor.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.table.TableCellEditor;
@@ -21,7 +21,7 @@ import java.nio.file.Paths;
final public class FileTableCellEditor extends AbstractCellEditor
implements TableCellRenderer, TableCellEditor, ActionListener {
- static private final Logger LOGGER = LogManager.getLogger( "FileTableCellEditor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileTableCellEditor" );
final private JButton _button;
final private JFileChooser _chooser;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/PositionedSplitPane.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/PositionedSplitPane.java
index 6be4118..a28a701 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/PositionedSplitPane.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/PositionedSplitPane.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import javax.swing.*;
import java.awt.*;
@@ -13,7 +13,7 @@ import java.awt.*;
*/
final public class PositionedSplitPane extends JSplitPane {
- static private final Logger LOGGER = LogManager.getLogger( "PositionedSplitPane" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PositionedSplitPane" );
private final Object LOCKER = new Object();
private boolean _isLocationSet;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SystemOutPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SystemOutPanel.java
index 717dfe0..c939867 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SystemOutPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SystemOutPanel.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.component;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.annotation.concurrent.NotThreadSafe;
import javax.swing.*;
@@ -21,7 +21,7 @@ import java.io.PrintStream;
*/
final public class SystemOutPanel extends JScrollPane {
- static private final Logger LOGGER = LogManager.getLogger( "SystemOutPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SystemOutPanel" );
private final boolean _isStandardOutRedirect;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java
index ed23648..3255380 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java
@@ -12,8 +12,8 @@ import org.apache.ctakes.gui.dictionary.umls.UmlsTermUtil;
import org.apache.ctakes.gui.dictionary.util.HsqlUtil;
import org.apache.ctakes.gui.dictionary.util.JdbcUtil;
import org.apache.ctakes.gui.dictionary.util.RareWordDbWriter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
import java.sql.Connection;
@@ -27,7 +27,7 @@ import java.util.stream.Collectors;
*/
final class DictionaryBuilder {
- static private final Logger LOGGER = LogManager.getLogger( "DictionaryBuilder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DictionaryBuilder" );
static private final String DEFAULT_DATA_DIR = "org/apache/ctakes/gui/dictionary/data/tiny";
static public final String CTAKES_APP_DB_PATH = "resources/org/apache/ctakes/dictionary/lookup/fast";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryCreator.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryCreator.java
index 672f6c0..20334e8 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryCreator.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryCreator.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary;
import org.apache.ctakes.gui.component.DisablerPane;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -15,7 +15,7 @@ import java.awt.*;
*/
final public class DictionaryCreator {
- static private final Logger LOGGER = LogManager.getLogger( DictionaryCreator.class );
+ static private final Logger LOGGER = LoggerFactory.getLogger( DictionaryCreator.class );
private DictionaryCreator() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryDownloader.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryDownloader.java
index 24e6b9a..59877ea 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryDownloader.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryDownloader.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.gui.component.DisablerPane;
import org.apache.ctakes.gui.component.LoggerPanel;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -21,7 +21,7 @@ import java.util.concurrent.Executors;
*/
final public class DictionaryDownloader {
- static private final Logger LOGGER = LogManager.getLogger( "PiperRunnerGui" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperRunnerGui" );
static private final String DICTIONARY_NAME = "Fast UMLS Dictionary for Apache cTAKES";
static private final String DICTIONARY_URL
= "https://sourceforge.net/projects/ctakesresources/files/sno_rx_16ab.zip";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryXmlWriter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryXmlWriter.java
index 40e5c8e..8937778 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryXmlWriter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryXmlWriter.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary;
import org.apache.ctakes.gui.dictionary.umls.VocabularyStore;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.*;
@@ -14,7 +14,7 @@ import java.io.*;
*/
final class DictionaryXmlWriter {
- static private final Logger LOGGER = LogManager.getLogger( "DictionaryXmlWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DictionaryXmlWriter" );
private DictionaryXmlWriter() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/MainPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/MainPanel.java
index e8d2b20..0c5b3fa 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/MainPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/MainPanel.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.gui.component.LoggerPanel;
import org.apache.ctakes.gui.component.PositionedSplitPane;
import org.apache.ctakes.gui.dictionary.umls.*;
import org.apache.ctakes.gui.dictionary.util.FileUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
@@ -33,7 +33,7 @@ import static org.apache.ctakes.gui.dictionary.DictionaryBuilder.CTAKES_APP_DB_P
*/
final class MainPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "MainPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MainPanel" );
private String _umlsDirPath = System.getProperty( "user.dir" );
private String _ctakesPath = System.getProperty( "user.dir" );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedDictionaryCreator.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedDictionaryCreator.java
index ddb1bda..8cd4b8b 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedDictionaryCreator.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedDictionaryCreator.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary.cased;
import org.apache.ctakes.gui.component.DisablerPane;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -16,7 +16,7 @@ import java.awt.*;
*/
public class CasedDictionaryCreator {
- static private final Logger LOGGER = LogManager.getLogger( "CasedDictionaryCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasedDictionaryCreator" );
static private JFrame createFrame() {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedMainPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedMainPanel.java
index ef9d234..522f411 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedMainPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedMainPanel.java
@@ -15,8 +15,8 @@ import org.apache.ctakes.gui.dictionary.umls.MrconsoIndex;
import org.apache.ctakes.gui.dictionary.umls.MrsabIndex;
import org.apache.ctakes.gui.dictionary.umls.SourceTableModel;
import org.apache.ctakes.gui.dictionary.util.FileUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
@@ -40,7 +40,7 @@ import java.util.concurrent.Executors;
*/
final class CasedMainPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "CasedMainPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasedMainPanel" );
private String _umlsDirPath = System.getProperty( "user.dir" );
private String _ctakesPath = System.getProperty( "user.dir" );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedPiperWriter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedPiperWriter.java
index 8a25939..eaa8b80 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedPiperWriter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedPiperWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.dictionary.cased;
import org.apache.ctakes.gui.dictionary.umls.VocabularyStore;
import org.apache.ctakes.gui.dictionary.util.HsqlUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.*;
import java.util.ArrayList;
@@ -19,7 +19,7 @@ import java.util.List;
*/
final public class CasedPiperWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CasedPiperWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasedPiperWriter" );
private CasedPiperWriter() {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedReadmeWriter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedReadmeWriter.java
index 5577e06..18148a8 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedReadmeWriter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedReadmeWriter.java
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.util.annotation.SemanticGroup;
import org.apache.ctakes.core.util.annotation.SemanticTui;
import org.apache.ctakes.gui.dictionary.cased.umls.file.Tty;
import org.apache.ctakes.gui.dictionary.util.HsqlUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.*;
import java.util.Collection;
@@ -22,7 +22,7 @@ import java.util.stream.Collectors;
*/
final public class CasedReadmeWriter {
- static private final Logger LOGGER = LogManager.getLogger( "CasedReadmeWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CasedReadmeWriter" );
private CasedReadmeWriter() {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/HsqlWriter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/HsqlWriter.java
index c9d3268..c3a83af 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/HsqlWriter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/HsqlWriter.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.gui.dictionary.umls.VocabularyStore;
import org.apache.ctakes.gui.dictionary.util.HsqlUtil;
import org.apache.ctakes.gui.dictionary.util.JdbcUtil;
import org.apache.ctakes.gui.dictionary.util.RareWordUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.sql.Connection;
import java.sql.PreparedStatement;
@@ -28,7 +28,7 @@ import java.util.stream.Collectors;
*/
final public class HsqlWriter {
- static private final Logger LOGGER = LogManager.getLogger( "HsqlWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HsqlWriter" );
static public boolean writeHsql( final String hsqlPath,
final String dictionaryName,
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java
index 7deaf64..2c48ad2 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java
@@ -9,8 +9,8 @@ import org.apache.ctakes.gui.dictionary.cased.term.CuiTerm;
import org.apache.ctakes.gui.dictionary.cased.umls.file.MrConso;
import org.apache.ctakes.gui.dictionary.cased.umls.file.Tty;
import org.apache.ctakes.gui.dictionary.umls.CuiCodeUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.FileReader;
@@ -27,7 +27,7 @@ import static org.apache.ctakes.gui.dictionary.cased.umls.file.MrConso.*;
*/
public class UmlsParser {
- static private final Logger LOGGER = LogManager.getLogger( "UmlsParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UmlsParser" );
static public Collection<CuiTerm> createCuiTerms( final String consoPath,
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/AutoTermExtractor.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/AutoTermExtractor.java
index 8fa5457..cf7bd05 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/AutoTermExtractor.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/AutoTermExtractor.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -14,7 +14,7 @@ final public class AutoTermExtractor {
private AutoTermExtractor() {
}
- static private final Logger LOGGER = LogManager.getLogger( "AutoTermExtractor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AutoTermExtractor" );
// private Collection<String> autoExtractAcronyms( final String tokenizedText ) {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java
index 7a6016f..274a32b 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary.umls;
import org.apache.ctakes.core.util.annotation.SemanticTui;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Collection;
import java.util.Collections;
@@ -16,7 +16,7 @@ import java.util.Map;
*/
final public class ConceptMapFactory {
- static private final Logger LOGGER = LogManager.getLogger( "ConceptMapFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ConceptMapFactory" );
private ConceptMapFactory() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/CuiCodeUtil.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/CuiCodeUtil.java
index 0f6b7bb..9e0883c 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/CuiCodeUtil.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/CuiCodeUtil.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.Arrays;
@@ -20,7 +20,7 @@ public enum CuiCodeUtil {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "CuiCodeUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CuiCodeUtil" );
static private final long PREFIX_MULTIPLIER = 100000000;
final private List<PrefixerPair> _prefixerPairList = new ArrayList<>();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/DoseUtil.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/DoseUtil.java
index f89d56c..58dc4a9 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/DoseUtil.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/DoseUtil.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Arrays;
import java.util.Collection;
@@ -17,7 +17,7 @@ final public class DoseUtil {
private DoseUtil() {
}
- static private final Logger LOGGER = LogManager.getLogger( "DoseUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DoseUtil" );
// some of these are not strictly units, e.g. "ud" : "ut dictum" or "as directed"
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/LanguageTableModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/LanguageTableModel.java
index a4ca20a..d769eef 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/LanguageTableModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/LanguageTableModel.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.event.EventListenerList;
import javax.swing.event.TableModelEvent;
@@ -17,7 +17,7 @@ import java.util.*;
*/
final public class LanguageTableModel implements TableModel {
- static private final Logger LOGGER = LogManager.getLogger( "LanguageTableModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LanguageTableModel" );
static private final String[] COLUMN_NAMES = { "Use", "Language" };
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java
index 45caf4d..029a41c 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.dictionary.umls;
import org.apache.ctakes.gui.dictionary.util.FileUtil;
import org.apache.ctakes.gui.dictionary.util.TextTokenizer;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
@@ -20,7 +20,7 @@ import static org.apache.ctakes.gui.dictionary.umls.MrconsoIndex.*;
*/
final public class MrconsoParser {
- static private final Logger LOGGER = LogManager.getLogger( "MrConsoParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MrConsoParser" );
static private final String MR_CONSO_SUB_PATH = "/META/MRCONSO.RRF";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyParser.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyParser.java
index 3312a2d..c51f57f 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyParser.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyParser.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.dictionary.umls;
import org.apache.ctakes.core.util.annotation.SemanticTui;
import org.apache.ctakes.gui.dictionary.util.FileUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
@@ -22,7 +22,7 @@ import static org.apache.ctakes.gui.dictionary.umls.MrstyIndex.TUI;
*/
final public class MrstyParser {
- static private final Logger LOGGER = LogManager.getLogger( "MrStyParser" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MrStyParser" );
static private final String MRSTY_SUB_PATH = "/META/MRSTY.RRF";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java
index 231f8dc..8fe18fe 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.event.EventListenerList;
import javax.swing.event.TableModelEvent;
@@ -17,7 +17,7 @@ import java.util.*;
*/
final public class SourceTableModel implements TableModel {
- static private final Logger LOGGER = LogManager.getLogger( "SourceTableModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "SourceTableModel" );
static private final String[] COLUMN_NAMES = { "Read Synonyms", "Record Codes", "Code", "Vocabulary", "Version",
"CUIs" };
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiCellRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiCellRenderer.java
index a973256..3643d8e 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiCellRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiCellRenderer.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.table.TableCellRenderer;
@@ -15,7 +15,7 @@ import java.awt.*;
*/
final public class TuiCellRenderer implements TableCellRenderer {
- static private final Logger LOGGER = LogManager.getLogger( "TuiCellRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TuiCellRenderer" );
private final TuiTableModel _tuiModel;
private final TableCellRenderer _delegate;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiTableModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiTableModel.java
index afad5b2..62318ec 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiTableModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiTableModel.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary.umls;
import org.apache.ctakes.core.util.annotation.SemanticGroup;
import org.apache.ctakes.core.util.annotation.SemanticTui;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.event.EventListenerList;
import javax.swing.event.TableModelListener;
@@ -22,7 +22,7 @@ import static org.apache.ctakes.core.util.annotation.SemanticTui.*;
*/
final public class TuiTableModel implements TableModel {
- static private final Logger LOGGER = LogManager.getLogger( "TuiTableModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TuiTableModel" );
// static public final Tui[] CTAKES_ANAT = { T021, T022, T023, T024, T025, T026, T029, T030 };
// static public final Tui[] CTAKES_DRUG = { T109, T110, T114, T115, T116, T118, T119, T121, T122, T123, T124,
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java
index 9cb676b..f334568 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.dictionary.umls;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.Collection;
import java.util.HashMap;
@@ -19,7 +19,7 @@ public enum VocabularyStore {
return INSTANCE;
}
- private final Logger LOGGER = LogManager.getLogger( "Vocabulary" );
+ private final Logger LOGGER = LoggerFactory.getLogger( "Vocabulary" );
private final Map<String, Class<?>> _vocabularyClasses = new HashMap<>();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/FileUtil.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/FileUtil.java
index 525e631..306732c 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/FileUtil.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/FileUtil.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary.util;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.filechooser.FileSystemView;
import java.io.*;
@@ -19,7 +19,7 @@ final public class FileUtil {
private FileUtil() {
}
- static private final Logger LOGGER = LogManager.getLogger( "FileUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "FileUtil" );
static public String parseDirText( final String dirPath ) {
if ( dirPath == null || dirPath.isEmpty() ) {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/HsqlUtil.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/HsqlUtil.java
index f3ceb6a..2becd04 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/HsqlUtil.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/HsqlUtil.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.dictionary.util;
import org.apache.ctakes.gui.dictionary.umls.VocabularyStore;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.sql.Connection;
import java.sql.SQLException;
@@ -18,7 +18,7 @@ import java.util.stream.Collectors;
*/
final public class HsqlUtil {
- static private final Logger LOGGER = LogManager.getLogger( "HsqlUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "HsqlUtil" );
static public final String URL_PREFIX = "jdbc:hsqldb:file:";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java
index 43fd2af..261a89e 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.dictionary.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.sql.*;
@@ -12,7 +12,7 @@ import java.sql.*;
*/
final public class JdbcUtil {
- static private final Logger LOGGER = LogManager.getLogger( "JdbcUtil" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "JdbcUtil" );
private JdbcUtil() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordDbWriter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordDbWriter.java
index 76766f8..9e031e0 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordDbWriter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordDbWriter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.dictionary.util;
import org.apache.ctakes.core.util.annotation.SemanticTui;
import org.apache.ctakes.gui.dictionary.umls.Concept;
import org.apache.ctakes.gui.dictionary.umls.VocabularyStore;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.sql.Connection;
import java.sql.PreparedStatement;
@@ -24,7 +24,7 @@ import java.util.stream.Collectors;
*/
final public class RareWordDbWriter {
- static private final Logger LOGGER = LogManager.getLogger( "RareWordDbWriter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RareWordDbWriter" );
private RareWordDbWriter() {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/GenericRunnerGui.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/GenericRunnerGui.java
index af25309..38f8aec 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/GenericRunnerGui.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/GenericRunnerGui.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.generic;
import org.apache.ctakes.gui.component.DisablerPane;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -15,7 +15,7 @@ import java.awt.*;
*/
final public class GenericRunnerGui {
- static private final Logger LOGGER = LogManager.getLogger( "GenericRunnerGui" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "GenericRunnerGui" );
static private JFrame createFrame() {
final JFrame frame = new JFrame( "cTAKES Simple Program Frame" );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/MainPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/MainPanel.java
index 55f36f3..f9efd2c 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/MainPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/MainPanel.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.generic;
import org.apache.ctakes.core.util.external.SystemUtil;
import org.apache.ctakes.gui.component.LoggerPanel;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
@@ -22,7 +22,7 @@ import java.io.IOException;
*/
public class MainPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "MainPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MainPanel" );
private JButton _runButton;
private JButton _stopButton;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java
index d0d180a..9a47ab0 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java
@@ -11,8 +11,8 @@ import org.apache.ctakes.gui.pipeline.bit.available.AvailablesListModel;
import org.apache.ctakes.gui.pipeline.bit.available.AvailablesRenderer;
import org.apache.ctakes.gui.pipeline.bit.info.PipeBitInfoPanel;
import org.apache.ctakes.gui.pipeline.bit.user.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -31,7 +31,7 @@ import java.util.concurrent.Executors;
*/
final class MainPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "MainPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MainPanel" );
private final AvailablesListModel _availablesListModel = new AvailablesListModel();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java
index 821357a..89c50cc 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java
@@ -11,8 +11,8 @@ import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterTableModel;
import org.apache.ctakes.gui.pipeline.piper.PiperFileView;
import org.apache.ctakes.gui.pipeline.piper.PiperTextFilter;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.event.TableModelEvent;
@@ -45,7 +45,7 @@ import static javax.swing.JOptionPane.PLAIN_MESSAGE;
*/
final class MainPanel2 extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "MainPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "MainPanel" );
private final JFileChooser _chooser = new JFileChooser();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperCreator.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperCreator.java
index 5ef1371..09d2b1b 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperCreator.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperCreator.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline;
import org.apache.ctakes.gui.component.DisablerPane;
import org.apache.ctakes.gui.pipeline.bit.PipeBitPainter;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -16,7 +16,7 @@ import java.awt.*;
*/
final public class PiperCreator {
- static private final Logger LOGGER = LogManager.getLogger( "PiperCreator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperCreator" );
private PiperCreator() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperDisplayModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperDisplayModel.java
index dc9bccd..3110007 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperDisplayModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperDisplayModel.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.pipeline;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -10,5 +10,5 @@ import org.apache.logging.log4j.LogManager;
*/
public class PiperDisplayModel {
- static private final Logger LOGGER = LogManager.getLogger( "PiperDisplayModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperDisplayModel" );
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java
index 6d18ff0..8ea68af 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.gui.pipeline;
import com.lexicalscope.jewel.cli.CliFactory;
import org.apache.ctakes.core.pipeline.CliOptionals;
import org.apache.ctakes.gui.component.DisablerPane;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -17,7 +17,7 @@ import java.awt.*;
*/
final public class PiperRunnerGui {
- static private final Logger LOGGER = LogManager.getLogger( "PiperRunnerGui" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperRunnerGui" );
static private JFrame createFrame() {
final JFrame frame = new JFrame( "cTAKES Piper File Submitter" );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java
index 6f29bc2..e67597d 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java
@@ -12,8 +12,8 @@ import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterCellRenderer;
import org.apache.ctakes.gui.pipeline.piper.PiperFileView;
import org.apache.ctakes.gui.pipeline.piper.PiperTextFilter;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.swing.*;
@@ -46,7 +46,7 @@ import java.util.stream.Collectors;
*/
final public class PiperRunnerPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "PiperRunnerPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperRunnerPanel" );
static private final String CLI_EXTENSION = "piper_cli";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitCellRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitCellRenderer.java
index 114430a..314706d 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitCellRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitCellRenderer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit;
import javax.swing.*;
import java.awt.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -13,7 +13,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class BitCellRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "BitCellRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BitCellRenderer" );
private final ListCellRenderer<Object> _delegate = new DefaultListCellRenderer();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitInfoPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitInfoPanel.java
index ac06a65..798bad1 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitInfoPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitInfoPanel.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.gui.component.SmoothTipTable;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterCellRenderer;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterInfoPanel;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterTableModel;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.swing.*;
@@ -26,7 +26,7 @@ import java.io.File;
*/
abstract public class BitInfoPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "BitInfoPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BitInfoPanel" );
protected PipeBitInfo _pipeBitInfo;
protected Class<?> _pipeBitClass;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
index e4b2afd..f1bd162 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
@@ -4,8 +4,8 @@ import io.github.classgraph.*;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.log.DotLogger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_component.Annotator_ImplBase;
import org.apache.uima.analysis_component.CasAnnotator_ImplBase;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
@@ -33,7 +33,7 @@ public enum PipeBitFinder {
return INSTANCE;
}
- private final Logger LOGGER = LogManager.getLogger("PipeBitFinder");
+ private final Logger LOGGER = LoggerFactory.getLogger("PipeBitFinder");
private final Collection<Class<?>> _pipeBits = new ArrayList<>();
private boolean _didScan = false;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitPainter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitPainter.java
index 15b70da..3e434e2 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitPainter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitPainter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.Border;
@@ -23,7 +23,7 @@ public enum PipeBitPainter {
return INSTANCE;
}
- static private final Logger LOGGER = LogManager.getLogger( "PipeBitPainter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipeBitPainter" );
static private final Color READER_COLOR = Color.GREEN.darker().darker();
static private final Color ANNOTATOR_COLOR = Color.CYAN.darker().darker();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesListModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesListModel.java
index 68fc817..c3d9b58 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesListModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesListModel.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit.available;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.PipeBitInfoUtil;
import org.apache.ctakes.gui.pipeline.bit.info.PipeBitInfoComparator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.util.*;
@@ -16,7 +16,7 @@ import java.util.*;
*/
final public class AvailablesListModel extends AbstractListModel<PipeBitInfo> {
- static private final Logger LOGGER = LogManager.getLogger( "AvailablesListModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AvailablesListModel" );
private final List<PipeBitInfo> _pipeBitInfos = new ArrayList<>();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesRenderer.java
index c689347..4379328 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesRenderer.java
@@ -9,8 +9,8 @@ import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
import javax.swing.border.LineBorder;
import java.awt.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -19,7 +19,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class AvailablesRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "AvailablesRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "AvailablesRenderer" );
static private final Border SELECTED_BORDER = new LineBorder( Color.DARK_GRAY, 1, true );
static private final Border UNSELECTED_BORDER = new EmptyBorder( 0, 0, 0, 5 );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoPanel.java
index 4616cb5..b681e35 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoPanel.java
@@ -7,8 +7,8 @@ import org.apache.ctakes.gui.pipeline.bit.available.AvailablesListModel;
import org.apache.ctakes.gui.pipeline.bit.parameter.DefaultParameterHolder;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterHolder;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterInfoPanel;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.event.ListSelectionEvent;
@@ -23,7 +23,7 @@ import java.util.stream.Collectors;
*/
final public class PipeBitInfoPanel extends BitInfoPanel {
- static private final Logger LOGGER = LogManager.getLogger( "PipeBitInfoPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipeBitInfoPanel" );
public void setPipeBitInfoList( final JList<PipeBitInfo> pipeBitList ) {
pipeBitList.getSelectionModel().addListSelectionListener( new PipeBitListListener( pipeBitList ) );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoRenderer.java
index a0f8e53..bc767b4 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoRenderer.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.PipeBitInfoUtil;
import org.apache.ctakes.gui.component.CellRendererLabel;
import org.apache.ctakes.gui.component.CellRendererPanel;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -21,7 +21,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct;
*/
final public class PipeBitInfoRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "PipeBitInfoRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PipeBitInfoRenderer" );
static private final Color READER_COLOR = Color.GREEN.darker().darker();
static private final Color ANNOTATOR_COLOR = Color.CYAN.darker().darker();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/RoleRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/RoleRenderer.java
index 92cddfc..ca505e4 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/RoleRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/RoleRenderer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit.info;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.gui.component.CellRendererLabel;
import org.apache.ctakes.gui.util.IconLoader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
@@ -17,7 +17,7 @@ import java.awt.*;
*/
final public class RoleRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "RoleRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RoleRenderer" );
static private final String READER_ICON_FILE = "GreenArrowIn.png";
static private final String ANNOTATOR_ICON_FILE = "BlueGear.png";
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductListModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductListModel.java
index 967a6eb..e106714 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductListModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductListModel.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.gui.pipeline.bit.info;
import javax.swing.*;
import javax.swing.event.ListDataListener;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct;
@@ -14,7 +14,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct;
*/
final public class TypeProductListModel implements ListModel<TypeProduct> {
- static private final Logger LOGGER = LogManager.getLogger( "TypeProductListModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TypeProductListModel" );
private final TypeProduct[] _typeProducts;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductRenderer.java
index 9d5ebac..e49a9b6 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductRenderer.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit.info;
import org.apache.ctakes.gui.component.CellRendererLabel;
import org.apache.ctakes.gui.util.ColorFactory;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
@@ -18,7 +18,7 @@ import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct;
*/
final public class TypeProductRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "TypeProductRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TypeProductRenderer" );
private final JLabel _delegate = new CellRendererLabel();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/DefaultParameterHolder.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/DefaultParameterHolder.java
index cf00c37..2105e43 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/DefaultParameterHolder.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/DefaultParameterHolder.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.bit.parameter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.annotation.concurrent.Immutable;
@@ -19,7 +19,7 @@ import java.util.Map;
@Immutable
final public class DefaultParameterHolder implements ParameterHolder {
- static private final Logger LOGGER = LogManager.getLogger( "DefaultParameterHolder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DefaultParameterHolder" );
private final List<ConfigurationParameter> _parameters;
private final Map<ConfigurationParameter, String> _typeMap;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterCellRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterCellRenderer.java
index 014aa37..db553fa 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterCellRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterCellRenderer.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.pipeline.bit.parameter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.swing.*;
@@ -16,7 +16,7 @@ import java.awt.*;
*/
final public class ParameterCellRenderer implements TableCellRenderer {
- static private final Logger LOGGER = LogManager.getLogger( "ParameterCellRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParameterCellRenderer" );
private final TableCellRenderer _delegate = new DefaultTableCellRenderer();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterInfoPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterInfoPanel.java
index d6974c4..6ca27ba 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterInfoPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterInfoPanel.java
@@ -1,7 +1,7 @@
package org.apache.ctakes.gui.pipeline.bit.parameter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.swing.*;
@@ -21,7 +21,7 @@ import java.util.stream.Collectors;
*/
public class ParameterInfoPanel extends JPanel {
- static private final Logger LOGGER = LogManager.getLogger( "ParameterInfoPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParameterInfoPanel" );
private JLabel _name;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterMapper.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterMapper.java
index 67db69f..4e94a87 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterMapper.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterMapper.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.bit.parameter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import java.lang.reflect.Field;
@@ -15,7 +15,7 @@ import java.util.*;
*/
final public class ParameterMapper {
- static private final Logger LOGGER = LogManager.getLogger( "ParameterMapper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParameterMapper" );
private ParameterMapper() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterTableModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterTableModel.java
index b88ea9c..d57045e 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterTableModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterTableModel.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.bit.parameter;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import javax.swing.event.EventListenerList;
@@ -23,7 +23,7 @@ import java.util.stream.Collectors;
*/
final public class ParameterTableModel implements TableModel {
- static private final Logger LOGGER = LogManager.getLogger( "ParameterTableModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ParameterTableModel" );
static private final String[] COLUMN_NAMES = { "Parameter Name", "Value", "" };
static private final Class<?>[] COLUMN_CLASSES = { ConfigurationParameter.class, String.class, File.class };
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/DefaultUserBit.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/DefaultUserBit.java
index 466f156..cd33ec6 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/DefaultUserBit.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/DefaultUserBit.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.gui.pipeline.bit.user;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterMapper;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import java.util.ArrayList;
@@ -18,7 +18,7 @@ import java.util.Map;
*/
final public class DefaultUserBit implements UserBit {
- static private final Logger LOGGER = LogManager.getLogger( "DefaultUserBit" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DefaultUserBit" );
private final PipeBitInfo _pipeBitInfo;
private final Class<?> _pipeBitClass;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitInfoPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitInfoPanel.java
index f15b6b2..7a5d731 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitInfoPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitInfoPanel.java
@@ -4,8 +4,8 @@ package org.apache.ctakes.gui.pipeline.bit.user;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.gui.pipeline.bit.BitInfoPanel;
import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterInfoPanel;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.swing.*;
import javax.swing.event.ListSelectionEvent;
@@ -23,7 +23,7 @@ import java.util.stream.Collectors;
*/
final public class UserBitInfoPanel extends BitInfoPanel {
- static private final Logger LOGGER = LogManager.getLogger( "UserBitInfoPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UserBitInfoPanel" );
private BitNameListener _bitNameListener = new BitNameListener();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitListModel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitListModel.java
index 31380b7..b480525 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitListModel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitListModel.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.bit.user;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
import javax.swing.*;
import java.util.ArrayList;
@@ -15,7 +15,7 @@ import java.util.List;
*/
final public class UserBitListModel extends AbstractListModel<UserBit> {
- static private final Logger LOGGER = LogManager.getLogger( "UserBitListModel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UserBitListModel" );
private UserBit _readerBit = null;
private final List<UserBit> _userBits = new ArrayList<>();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitRenderer.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitRenderer.java
index ac144b5..1fc8afe 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitRenderer.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitRenderer.java
@@ -10,8 +10,8 @@ import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
import javax.swing.border.LineBorder;
import java.awt.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -20,7 +20,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class UserBitRenderer implements ListCellRenderer<Object> {
- static private final Logger LOGGER = LogManager.getLogger( "UsersRenderer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UsersRenderer" );
static private final Border SELECTED_BORDER = new LineBorder( Color.DARK_GRAY, 1, true );
static private final Border UNSELECTED_BORDER = new EmptyBorder( 0, 0, 0, 5 );
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserParameterInfoPanel.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserParameterInfoPanel.java
index c68753e..2d5367f 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserParameterInfoPanel.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserParameterInfoPanel.java
@@ -4,8 +4,8 @@ import org.apache.ctakes.gui.pipeline.bit.parameter.ParameterInfoPanel;
import javax.swing.*;
import javax.swing.text.JTextComponent;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -14,7 +14,7 @@ import org.apache.logging.log4j.LogManager;
*/
public class UserParameterInfoPanel extends ParameterInfoPanel {
- static private final Logger LOGGER = LogManager.getLogger( "UserParameterInfoPanel" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "UserParameterInfoPanel" );
@Override
protected String getValueLabelPrefix() {
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFinder.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFinder.java
index 0db6606..0e4d913 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFinder.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFinder.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.piper;
import io.github.classgraph.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
@@ -20,7 +20,7 @@ import java.util.function.Consumer;
*/
public class PiperFinder {
- static private final Logger LOGGER = LogManager.getLogger( "PiperFinder" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperFinder" );
private final Collection<PiperInfo> _piperFiles = new ArrayList<>();
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperInfo.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperInfo.java
index a84739b..ac6181e 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperInfo.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperInfo.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.piper;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @author SPF , chip-nlp
@@ -11,7 +11,7 @@ import org.apache.logging.log4j.LogManager;
*/
final public class PiperInfo {
- static private final Logger LOGGER = LogManager.getLogger( "PiperInfo" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperInfo" );
private final String _urlPath;
private final String _filePath;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperTextFilter.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperTextFilter.java
index 176b69a..9320a38 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperTextFilter.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperTextFilter.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.pipeline.piper;
import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import javax.swing.*;
@@ -20,7 +20,7 @@ import java.util.concurrent.*;
*/
final public class PiperTextFilter extends DocumentFilter {
- static private final Logger LOGGER = LogManager.getLogger( "PiperTextFilter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PiperTextFilter" );
final private TextValidator _textValidator;
final private TextFormatter _textFormatter;
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/ColorFactory.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/ColorFactory.java
index 1e57511..02619e5 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/ColorFactory.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/ColorFactory.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.util;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.awt.*;
@@ -13,7 +13,7 @@ import java.awt.*;
*/
final public class ColorFactory {
- static private final Logger LOGGER = LogManager.getLogger( "ColorFactory" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ColorFactory" );
private ColorFactory() {
}
diff --git a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/IconLoader.java b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/IconLoader.java
index 905b1d3..08d4dbe 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/IconLoader.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/IconLoader.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.gui.util;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import javax.imageio.ImageIO;
import javax.swing.*;
@@ -18,7 +18,7 @@ import java.io.InputStream;
*/
final public class IconLoader {
- static private final Logger LOGGER = LogManager.getLogger( "IconLoader" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "IconLoader" );
private IconLoader() {
}
diff --git a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
index b1302a9..38bff0c 100644
--- a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
+++ b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
@@ -30,8 +30,8 @@ import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
import org.apache.ctakes.typesystem.type.syntax.Lemma;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -187,7 +187,7 @@ public class LvgAnnotator extends JCasAnnotator_ImplBase {
private Set<String> exclusionSet;
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "LvgAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LvgAnnotator" );
public static final String PARAM_LVGCMDAPI_RESRC_KEY = "LvgCmdApi";
@ExternalResource(
@@ -597,7 +597,7 @@ public class LvgAnnotator extends JCasAnnotator_ImplBase {
InputStream stream = LvgAnnotator.class.getClassLoader().getResourceAsStream(prefix+path);
File file = new File(absolutePath, path);
- Logger LOGGER = LogManager.getLogger(LvgAnnotator.class.getName());
+ Logger LOGGER = LoggerFactory.getLogger(LvgAnnotator.class.getName());
LOGGER.info("Copying lvg-related file to " + file.getAbsolutePath());
try {
@@ -621,7 +621,7 @@ public class LvgAnnotator extends JCasAnnotator_ImplBase {
// the lvg properties file or the lvg resources (plural.rul etc.)
// Instead we use getResource to find the URL for the lvg.properties file.
final String lvgProperties = "org/apache/ctakes/lvg/data/config/lvg.properties";
- Logger LOGGER = LogManager.getLogger(LvgAnnotator.class.getName());
+ Logger LOGGER = LoggerFactory.getLogger(LvgAnnotator.class.getName());
java.net.URL url = LvgAnnotator.class.getClassLoader().getResource(lvgProperties);
if (url!=null) {
LOGGER.info("URL for lvg.properties =" + url.getFile());
diff --git a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java
index 44d0e8e..bda89a2 100644
--- a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java
+++ b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java
@@ -28,8 +28,8 @@ import org.apache.ctakes.lvg.resource.LvgCmdApiResource;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.Lemma;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -83,7 +83,7 @@ public class LvgBaseTokenAnnotator extends JCasAnnotator_ImplBase {
public static final String PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF = "LemmaCacheFrequencyCutoff";
// LOG4J logger based on class name
- private final Logger LOGGER = LogManager.getLogger( getClass().getName() );
+ private final Logger LOGGER = LoggerFactory.getLogger( getClass().getName() );
private LvgCmdApi lvgCmd;
diff --git a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgSingleton.java b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgSingleton.java
index 60b8514..8327f77 100644
--- a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgSingleton.java
+++ b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgSingleton.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.lvg.ae;
import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.factory.ExternalResourceFactory;
@@ -32,7 +32,7 @@ enum LvgSingleton {
static public final String PROPERTIES_PATH = "org/apache/ctakes/lvg/data/config/lvg.properties";
- private final Logger LOGGER = LogManager.getLogger( "LvgSingleton" );
+ private final Logger LOGGER = LoggerFactory.getLogger( "LvgSingleton" );
private final Object LOCK = new Object();
private final LvgAnnotator _lvgAnnotator;
diff --git a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java
index e847653..0998ad9 100644
--- a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java
+++ b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.lvg.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -28,7 +28,7 @@ import java.io.IOException;
)
final public class ThreadSafeLvg extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeLvg" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeLvg" );
/**
diff --git a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResourceImpl.java b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResourceImpl.java
index e9df208..19e44b9 100644
--- a/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResourceImpl.java
+++ b/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResourceImpl.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.lvg.resource;
import gov.nih.nlm.nls.lvg.Api.LvgCmdApi;
import gov.nih.nlm.nls.lvg.Api.LvgLexItemApi;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.resource.DataResource;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.SharedResourceObject;
@@ -47,7 +47,7 @@ public class LvgCmdApiResourceImpl
implements LvgCmdApiResource, SharedResourceObject
{
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
private LvgCmdApi lvg;
private LvgLexItemApi lvgLexItem;
diff --git a/ctakes-mastif-zoner/pom.xml b/ctakes-mastif-zoner/pom.xml
index 3eacfdd..7984061 100644
--- a/ctakes-mastif-zoner/pom.xml
+++ b/ctakes-mastif-zoner/pom.xml
@@ -10,8 +10,9 @@
</parent>
<dependencies>
<dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-1.2-api</artifactId>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>${slf4j.version}</version>
</dependency>
</dependencies>
</project>
diff --git a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineTokenToCharacterOffsetConverter.java b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineTokenToCharacterOffsetConverter.java
index 2709bf3..1c8d37b 100644
--- a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineTokenToCharacterOffsetConverter.java
+++ b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineTokenToCharacterOffsetConverter.java
@@ -13,8 +13,8 @@ import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.logging.Level;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -24,7 +24,7 @@ import java.util.regex.Pattern;
*/
public class LineTokenToCharacterOffsetConverter
{
- public static final Logger LOGGER = LogManager.getLogger( "LineTokenToCharacterOffsetConverter" );
+ public static final Logger LOGGER = LoggerFactory.getLogger( "LineTokenToCharacterOffsetConverter" );
public static final Pattern endOfLinePattern = Pattern.compile("\\r?\\n");
public static final Pattern eolOrSpacePattern = Pattern.compile("( +)|(\\r?\\n)");
diff --git a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java
index 85c604e..e4b9fc8 100644
--- a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java
+++ b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java
@@ -24,7 +24,6 @@ import java.util.regex.Pattern;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
@@ -35,8 +34,8 @@ import javax.xml.xpath.XPathExpression;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@@ -143,7 +142,7 @@ public class ZonerCli {
private boolean doSubsections;
private boolean convertOffsets;
private boolean includeGenerics = false;
- private static final Logger LOGGER = LogManager.getLogger("ZonerCli");;
+ private static final Logger LOGGER = LoggerFactory.getLogger("ZonerCli");;
public ZonerCli() {
@@ -438,10 +437,8 @@ public class ZonerCli {
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
transformer.transform(new DOMSource(node), new StreamResult(buffer));
str = buffer.toString();
- } catch (TransformerConfigurationException ex) {
- LOGGER.error(ex);
} catch (TransformerException ex) {
- LOGGER.error(ex);
+ LOGGER.error("Unable to convert node to string", ex);
}
return str;
}
@@ -537,8 +534,9 @@ public class ZonerCli {
int offset = 0;
for (HeadingRange r : this.getHeadings()) {
// gaps are only calculated around defined headings
- if (r.isGeneric())
- continue;
+ if (r.isGeneric()) {
+ continue;
+ }
if (gaps.size() == 0 && r.getHeadingBegin() != 0) {
int[] theGap = new int[]{offset, r.getHeadingBegin()};
gaps.add(theGap);
@@ -674,8 +672,9 @@ public class ZonerCli {
Collections.sort(headings);
for(Range r : genRangeList){
if (r.isGeneric()) {
- if(!headingsListHasRangeFuzzy(r))
- headingFromRange(r);
+ if(!headingsListHasRangeFuzzy(r)) {
+ headingFromRange(r);
+ }
}
}
}
@@ -684,10 +683,12 @@ public class ZonerCli {
int rmidpoint = (r.getBegin() + r.getEnd()) / 2;
for(HeadingRange hr : this.headings) {
int hmidpoint = (hr.getHeadingBegin() + hr.getHeadingEnd()) / 2;
- if (Math.abs(hmidpoint - rmidpoint) < 6)
- return true;
- if(hr.getHeadingBegin() > r.getEnd())
- break;
+ if (Math.abs(hmidpoint - rmidpoint) < 6) {
+ return true;
+ }
+ if(hr.getHeadingBegin() > r.getEnd()) {
+ break;
+ }
}
return false;
}
@@ -786,8 +787,9 @@ public class ZonerCli {
for (String fragName : fragList) {
LOGGER.debug(String.format("checking for match with fragment named %s", fragName));
// PA don't waste time on these two
- if (fragName.equals(EOH_FRAG) || fragName.equals(PROLOG_FRAG))
- continue;
+ if (fragName.equals(EOH_FRAG) || fragName.equals(PROLOG_FRAG)) {
+ continue;
+ }
try {
if (currentMatcher.group(fragName) != null) {
LOGGER.debug(String.format(">>> found match for fragment %s with attrs %s",
@@ -805,8 +807,9 @@ public class ZonerCli {
// key collection by the text that was captured as a generic
boolean isGeneric = false;
if (currentRange.getLabel().indexOf(GENERIC_TYPE) >= 0) {
- if (parentRange != null && parentRange.subsumes(currentRange))
- continue;
+ if (parentRange != null && parentRange.subsumes(currentRange)) {
+ continue;
+ }
String genkey = getEntireContents().substring(currentRange.getBegin(), currentRange.getEnd()).trim();
// allows us to remember the generic both as a potential section and subsection
@@ -997,7 +1000,8 @@ public class ZonerCli {
*/
public void trimFinalHeadingStarts() {
getHeadings().forEach(new Consumer<HeadingRange>() {
- public void accept(HeadingRange t) {
+ @Override
+ public void accept(HeadingRange t) {
String orig = t.getHeadingText();
String trimmed = orig.trim();
if (orig.equals(trimmed)) {
@@ -1177,8 +1181,9 @@ public class ZonerCli {
}
private String makeString(final String s) {
- if (s == null)
- return "null";
+ if (s == null) {
+ return "null";
+ }
return s;
}
@@ -1329,7 +1334,8 @@ public class ZonerCli {
this.truncated = truncated;
}
- public int compareTo(Range other) {
+ @Override
+ public int compareTo(Range other) {
if (this.begin < other.begin) {
return -1;
} else if (this.begin > other.begin) {
@@ -1441,7 +1447,8 @@ public class ZonerCli {
return String.format("HEADING \"%s\" (%s)", headingText, label);
}
- public int compareTo(HeadingRange other) {
+ @Override
+ public int compareTo(HeadingRange other) {
if (this.headingBegin < other.headingBegin) {
return -1;
} else if (this.headingBegin > other.headingBegin) {
diff --git a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerRunner.java b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerRunner.java
index 04d1485..8be7071 100644
--- a/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerRunner.java
+++ b/ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerRunner.java
@@ -4,8 +4,8 @@ import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
import java.util.List;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.mitre.medfacts.zoner.ZonerCli.Range;
/**
@@ -14,7 +14,7 @@ import org.mitre.medfacts.zoner.ZonerCli.Range;
*/
public class ZonerRunner
{
- public static final Logger LOGGER = LogManager.getLogger(ZonerRunner.class.getName());
+ public static final Logger LOGGER = LoggerFactory.getLogger(ZonerRunner.class.getName());
protected String inputDirectoryString;
diff --git a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java
index dbe9698..00658ca 100644
--- a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java
+++ b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.necontexts;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.JCasUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -62,7 +62,7 @@ import java.util.List;
)
public class ContextAnnotator extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- private Logger LOGGER = LogManager.getLogger(getClass().getName());
+ private Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
/**
* "MaxLeftScopeSize" is a required, single, integer parameter that
diff --git a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java
index 0a4e564..65401eb 100644
--- a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java
+++ b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.necontexts;
import org.apache.ctakes.core.fsm.adapters.TextTokenAdapter;
import org.apache.ctakes.core.fsm.token.TextToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.tcas.Annotation;
@@ -37,7 +37,7 @@ import java.util.*;
*/
public abstract class NamedEntityContextAnalyzer implements ContextAnalyzer {
- private static final Logger LOGGER = LogManager.getLogger(NamedEntityContextAnalyzer.class);
+ private static final Logger LOGGER = LoggerFactory.getLogger(NamedEntityContextAnalyzer.class);
private Set<String> _boundaryWordSet;
diff --git a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/concurrent/ThreadSafeContextAnnotator.java b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/concurrent/ThreadSafeContextAnnotator.java
index cf511df..6ef7a1b 100644
--- a/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/concurrent/ThreadSafeContextAnnotator.java
+++ b/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/concurrent/ThreadSafeContextAnnotator.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.necontexts.ContextAnnotator;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -40,7 +40,7 @@ import org.apache.uima.resource.ResourceInitializationException;
dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.BASE_TOKEN }
)
final public class ThreadSafeContextAnnotator extends ContextAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeContextAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeContextAnnotator" );
/**
* {@inheritDoc}
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStarter.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStarter.java
index 0c6b5e8..48f37cd 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStarter.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStarter.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
import org.apache.ctakes.pbj.util.ArtemisController;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -24,7 +24,7 @@ import java.io.IOException;
)
public class ArtemisStarter extends ArtemisController {
- static private final Logger LOGGER = LogManager.getLogger( "ArtemisStarter" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ArtemisStarter" );
/**
* {@inheritDoc}
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStopper.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStopper.java
index c679c1a..db0ed04 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStopper.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStopper.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
import org.apache.ctakes.pbj.util.ArtemisController;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -25,7 +25,7 @@ import java.io.IOException;
)
public class ArtemisStopper extends ArtemisController {
- static private final Logger LOGGER = LogManager.getLogger( "ArtemisStopper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ArtemisStopper" );
private boolean _stopped = false;
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjJmsSender.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjJmsSender.java
index f5307bd..e6302ae 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjJmsSender.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjJmsSender.java
@@ -22,8 +22,8 @@ import org.apache.activemq.artemis.jms.client.ActiveMQConnectionFactory;
import org.apache.activemq.artemis.jms.client.ActiveMQQueue;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.log.DotLogger;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.resource.ResourceInitializationException;
@@ -45,7 +45,7 @@ import java.util.Enumeration;
)
public class PbjJmsSender extends PbjSender {
- static private final Logger LOGGER = LogManager.getLogger( "PbjJmsSender" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjJmsSender" );
private MessageProducer _producer;
private Connection _connection;
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjPipper.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjPipper.java
index caa2d6f..921452c 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjPipper.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjPipper.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.ae.PythonRunner;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -23,7 +23,7 @@ import java.io.IOException;
)
public class PbjPipper extends PythonRunner {
- static private final Logger LOGGER = LogManager.getLogger( "PbjPipper" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjPipper" );
// to add a configuration parameter, type "param" and hit tab.
static public final String PIP_PBJ_PARAM = "PipPbj";
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
index 48a34ba..bb96b76 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
@@ -2,8 +2,8 @@ package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.pbj.cr.PbjReceiver;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.impl.CASImpl;
@@ -29,7 +29,7 @@ import static org.apache.ctakes.pbj.util.PbjConstants.*;
)
public class PbjReceiverAE extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PbjReceiverAE" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjReceiverAE" );
// Duplicates of all the PbjReceiver configuration parameters.
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java
index c09aad3..c60ed9f 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java
@@ -19,8 +19,8 @@
package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.cc.XMISerializer;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -44,7 +44,7 @@ import static org.apache.ctakes.pbj.util.PbjConstants.*;
*/
abstract public class PbjSender extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PbjSender" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjSender" );
static public final String PARAM_SENDER_NAME = "SendName";
static public final String PARAM_SENDER_PASS = "SendPass";
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjStompSender.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjStompSender.java
index e4731d8..aeab2e0 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjStompSender.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjStompSender.java
@@ -1,8 +1,8 @@
package org.apache.ctakes.pbj.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.resource.ResourceInitializationException;
@@ -24,7 +24,7 @@ import java.nio.charset.StandardCharsets;
)
public class PbjStompSender extends PbjSender {
- static private final Logger LOGGER = LogManager.getLogger( "PbjStompSender" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjStompSender" );
private static final String END_OF_FRAME = "\u0000";
static private final Object SOCKET_LOCK = new Object();
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
index 064a1be..a23be73 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
@@ -5,8 +5,8 @@ import org.apache.activemq.artemis.jms.client.ActiveMQConnectionFactory;
import org.apache.activemq.artemis.jms.client.ActiveMQQueue;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.doc.JCasBuilder;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.cas.impl.XmiCasDeserializer;
import org.apache.uima.collection.CollectionException;
@@ -52,7 +52,7 @@ final public class PbjReceiver extends JCasCollectionReader_ImplBase {
static public final String DESC_QUEUE = "The Artemis Queue from which this pipeline receives information.";
static public final String DESC_ACCEPT_STOP = "Yes to shut down when this pipeline receives a stop signal.";
- static private final Logger LOGGER = LogManager.getLogger( "PbjReceiver" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PbjReceiver" );
static private final String EMPTY_CAS = "BadMessageFormatReceivedCreateEmptyJCas";
@ConfigurationParameter(
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/ArtemisController.java b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/ArtemisController.java
index 302c2ea..5f4fc60 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/ArtemisController.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/ArtemisController.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.pbj.util;
import org.apache.ctakes.core.ae.PausableFileLoggerAE;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.external.SystemUtil;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -77,7 +77,7 @@ abstract public class ArtemisController extends PausableFileLoggerAE {
new IOException( "Cannot find Artemis Root Directory " + _artemisRoot ) );
}
if ( new File( _artemisRoot, "LICENSE" ).exists() && new File( _artemisRoot, "NOTICE" ).exists() ) {
- final Logger LOGGER = LogManager.getLogger( "ArtemisController" );
+ final Logger LOGGER = LoggerFactory.getLogger( "ArtemisController" );
LOGGER.error( "It looks like " + _artemisRoot + " might point to an Apache Artemis Source or binary "
+ "distribution." );
LOGGER.error( "You must point " + ARTEMIS_ROOT_PARAM + " to the root directory of an Artemis broker." );
diff --git a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java
index 02bbb99..6fcc481 100644
--- a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java
+++ b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java
@@ -27,8 +27,8 @@ import com.googlecode.clearnlp.reader.AbstractReader;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -67,7 +67,7 @@ import java.util.List;
public class ClearNLPPOSTaggerAE extends JCasAnnotator_ImplBase {
final String language = AbstractReader.LANG_EN;
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
// Default model values
public static final String DEFAULT_MODEL_FILE_NAME = "org/apache/ctakes/postagger/models/clearnlp/mayo-en-pos-1.3.0.jar";
diff --git a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java
index c2180cd..2fdf5f7 100644
--- a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java
+++ b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java
@@ -57,8 +57,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -85,7 +85,7 @@ import java.util.List;
public class POSTagger extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "POSTagger" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "POSTagger" );
/**
* "PosModelFile" is a required, single, string parameter that contains the
diff --git a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/concurrent/ThreadSafePosTagger.java b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/concurrent/ThreadSafePosTagger.java
index a017153..61b303d 100644
--- a/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/concurrent/ThreadSafePosTagger.java
+++ b/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/concurrent/ThreadSafePosTagger.java
@@ -6,8 +6,8 @@ import org.apache.ctakes.postagger.POSTagger;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -33,7 +33,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafePosTagger extends POSTagger {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafePosTagger" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafePosTagger" );
/**
* {@inheritDoc}
diff --git a/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java b/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java
index 36aff0e..2382b3a 100644
--- a/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java
+++ b/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java
@@ -18,8 +18,8 @@
*/
package org.apache.ctakes.preprocessor;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.xml.sax.*;
import org.xml.sax.helpers.DefaultHandler;
import org.xml.sax.helpers.XMLReaderFactory;
@@ -45,7 +45,7 @@ public class ClinicalNotePreProcessor extends DefaultHandler
implements PreProcessor
{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "ClinicalNotePreProcessor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ClinicalNotePreProcessor" );
// Jan 1, 1AM, 0001
// private final long DEFAULT_DATE_MILLIS = -62135571600l;
diff --git a/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java b/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java
index fb504f7..f6806b4 100644
--- a/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java
+++ b/ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java
@@ -31,8 +31,8 @@ import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.util.Pair;
import org.apache.ctakes.typesystem.type.util.Pairs;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -69,7 +69,7 @@ public class CdaCasInitializer extends JCasAnnotator_ImplBase
protected static final String DEFAULT_DTD_FILE = "org/apache/ctakes/preprocessor/cda/NotesIIST_RTF.DTD";
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "CdaCasInitializer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "CdaCasInitializer" );
private Boolean includeSectionMarkers;
private TextModifier tm;
diff --git a/ctakes-regression-test/src/test/java/org/apache/ctakes/core/ae/LabValueFinderTester.java b/ctakes-regression-test/src/test/java/org/apache/ctakes/core/ae/LabValueFinderTester.java
index 0259a82..2858a46 100644
--- a/ctakes-regression-test/src/test/java/org/apache/ctakes/core/ae/LabValueFinderTester.java
+++ b/ctakes-regression-test/src/test/java/org/apache/ctakes/core/ae/LabValueFinderTester.java
@@ -5,9 +5,8 @@ import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
import org.apache.ctakes.postagger.POSTagger;
import org.apache.ctakes.typesystem.type.textsem.LabMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.logging.log4j.Level;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.factory.AggregateBuilder;
@@ -39,7 +38,7 @@ import static org.apache.ctakes.core.ae.LabValueFinder.PARAM_ALL_SECTIONS;
*/
public class LabValueFinderTester {
- static private final Logger LOGGER = Logger
+ static private final Logger LOGGER = LoggerFactory
.getLogger("LabValueFinderTester");
static private final String LAB_RESULTS_OID = "2.16.840.1.113883.10.20.22.2.3.1";
@@ -89,8 +88,8 @@ public class LabValueFinderTester {
// LabValueFinder.PARAM_USE_DRUGS, "true",
LabValueFinder.PARAM_MAX_NEWLINES, 1,
PARAM_ALL_SECTIONS, "false");
- Logger LOGGER = LogManager.getLogger("LabValueFinder");
- LOGGER.setLevel(Level.INFO);
+// Logger LOGGER = LoggerFactory.getLogger("LabValueFinder");
+// LOGGER.setLevel(Level.INFO);
}
/**
diff --git a/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java b/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
index 523267e..0ea5e28 100644
--- a/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
+++ b/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.regression.test;
import org.apache.commons.io.FilenameUtils;
import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
import org.apache.ctakes.utils.env.EnvironmentVariable;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAFramework;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CollectionProcessingEngine;
@@ -69,7 +69,7 @@ import java.util.List;
*/
public class RegressionPipelineTest {
- static Logger LOGGER = LogManager.getLogger(RegressionPipelineTest.class.getName());
+ static Logger LOGGER = LoggerFactory.getLogger(RegressionPipelineTest.class.getName());
// MAX timeout for the CPE
private static final int MAX_TIMEOUT_MS = 60 * 60 * 1000; // 60 mins
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
index 15aacf0..c2ed5d5 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
@@ -26,8 +26,8 @@ import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.Modifier;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.util.JCasUtil;
@@ -50,7 +50,7 @@ import java.util.List;
products = { PipeBitInfo.TypeProduct.DEGREE_RELATION }
)
public class DegreeOfRelationExtractorAnnotator extends RelationExtractorAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "DegreeOfRelationExtractorAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "DegreeOfRelationExtractorAnnotator" );
@Override
public void initialize( UimaContext context ) throws ResourceInitializationException {
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
index 5e64a6e..9860e70 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.util.JCasUtil;
@@ -54,7 +54,7 @@ import java.util.Map;
)
public class LocationOfRelationExtractorAnnotator extends RelationExtractorAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "LocationOfRelationExtractorAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "LocationOfRelationExtractorAnnotator" );
@Override
public void initialize( UimaContext context ) throws ResourceInitializationException {
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
index b122a1e..d459477 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textsem.Modifier;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -49,7 +49,7 @@ import java.util.List;
products = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.CHUNK }
)
public class ModifierExtractorAnnotator extends CleartkAnnotator<String> {
- static private final Logger LOGGER = LogManager.getLogger( "ModifierExtractorAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ModifierExtractorAnnotator" );
public static AnalysisEngineDescription getDescription(Object... additionalConfiguration)
throws ResourceInitializationException {
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
index 0ad55b5..f8cfa25 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
@@ -23,8 +23,8 @@ import org.apache.ctakes.relationextractor.ae.features.*;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.UimaContextAdmin;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -69,7 +69,7 @@ private List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation
try {
featureExtractors = getFeatureExtractors();
} catch ( ResourceInitializationException riE ) {
- LogManager.getLogger( "RelationExtractorAnnotator" ).error( riE.getMessage() );
+ LoggerFactory.getLogger( "RelationExtractorAnnotator" ).error( riE.getMessage() );
}
}
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeDegreeExtractor.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeDegreeExtractor.java
index fb7107c..ec47e3b 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeDegreeExtractor.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeDegreeExtractor.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.relationextractor.concurrent;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -29,7 +29,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeDegreeExtractor extends DegreeOfRelationExtractorAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeDegreeExtractor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeDegreeExtractor" );
/**
* {@inheritDoc}
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeLocationExtractor.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeLocationExtractor.java
index cc6d236..9229f83 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeLocationExtractor.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeLocationExtractor.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.relationextractor.concurrent;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -29,7 +29,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeLocationExtractor extends LocationOfRelationExtractorAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeLocationExtractor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeLocationExtractor" );
/**
* {@inheritDoc}
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeModifierExtractor.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeModifierExtractor.java
index 6607fc3..60556e3 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeModifierExtractor.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeModifierExtractor.java
@@ -3,8 +3,8 @@ package org.apache.ctakes.relationextractor.concurrent;
import org.apache.ctakes.core.concurrent.ThreadSafeWrapper;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -28,7 +28,7 @@ import org.apache.uima.resource.ResourceInitializationException;
)
final public class ThreadSafeModifierExtractor extends ModifierExtractorAnnotator {
- static private final Logger LOGGER = LogManager.getLogger( "ThreadSafeModifierExtractor" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "ThreadSafeModifierExtractor" );
/**
* {@inheritDoc}
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/DeepPheXMI.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/DeepPheXMI.java
index 7238c03..26c4985 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/DeepPheXMI.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/DeepPheXMI.java
@@ -35,8 +35,8 @@ import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -185,7 +185,7 @@ public class DeepPheXMI extends CorpusXMI {
* Created by tmill on 2/7/17.
*/
public static class DeepPheAnaforaXMLReader extends JCasAnnotator_ImplBase {
- private static Logger LOGGER = LogManager.getLogger(DeepPheAnaforaXMLReader.class);
+ private static Logger LOGGER = LoggerFactory.getLogger(DeepPheAnaforaXMLReader.class);
public static final String PARAM_ANAFORA_DIRECTORY = "anaforaDirectory";
diff --git a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisAnaforaXMLReader.java b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisAnaforaXMLReader.java
index 8c8da4e..51f7df3 100644
--- a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisAnaforaXMLReader.java
+++ b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisAnaforaXMLReader.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -54,7 +54,7 @@ import java.util.Map;
)
public class MetastasisAnaforaXMLReader extends JCasAnnotator_ImplBase {
- private static Logger LOGGER = LogManager.getLogger(MetastasisAnaforaXMLReader.class);
+ private static Logger LOGGER = LoggerFactory.getLogger(MetastasisAnaforaXMLReader.class);
public static AnalysisEngineDescription getDescription() throws ResourceInitializationException {
return AnalysisEngineFactory.createEngineDescription(MetastasisAnaforaXMLReader.class);
diff --git a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java
index e23f787..ea3dc3d 100644
--- a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java
+++ b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java
@@ -31,8 +31,8 @@ import org.apache.ctakes.smokingstatus.util.TruthValue;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -629,7 +629,7 @@ public class ClassifiableEntries extends JCasAnnotator_ImplBase {
private ResourceSpecifier taeSpecifierStep2;
// LOG4J logger based on class name
- protected Logger LOGGER = LogManager.getLogger(getClass().getName());
+ protected Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
// counters to track sentence classification
private int iSmokerCtr;
diff --git a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java
index 80740c8..7d138ac 100644
--- a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java
+++ b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java
@@ -8,8 +8,8 @@ import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -41,7 +41,7 @@ import static org.apache.ctakes.smokingstatus.Const.*;
)
public class PcsClassifier extends JCasAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "PcsClassifier" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "PcsClassifier" );
static public final String CASED_PARAM = "CaseSensitive";
static public final String CASED_DESC = "yes/no for case sensitivity.";
diff --git a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java
index af06ba2..a94f4d0 100644
--- a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java
+++ b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation;
import org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorConfigurationException;
import org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException;
@@ -54,7 +54,7 @@ public class ResolutionAnnotator
{
Set<String> conWords; //contradiction words for negation -- if this word appears in sentence do not negate
// LOG4J logger based on class name
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
public void initialize(UimaContext aContext)
throws AnnotatorConfigurationException, AnnotatorInitializationException
diff --git a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java
index a3083db..c81d5ab 100644
--- a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java
+++ b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java
@@ -20,8 +20,8 @@ package org.apache.ctakes.smokingstatus.ae;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.analysis_engine.annotator.AnnotatorContextException;
@@ -55,7 +55,7 @@ public class SentenceAdjuster extends JCasAnnotator_ImplBase {
public static final String PARAM_WORDS_IN_PATTERN = "WordsInPattern";
// LOG4J logger based on class name
- public Logger LOGGER = LogManager.getLogger(getClass().getName());
+ public Logger LOGGER = LoggerFactory.getLogger(getClass().getName());
diff --git a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java
index e27efef..6ffaf3e 100644
--- a/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java
+++ b/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java
@@ -21,8 +21,8 @@ package org.apache.ctakes.smokingstatus.cc;
import org.apache.ctakes.core.cc.AbstractFileWriter;
import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CASException;
@@ -37,7 +37,7 @@ import java.util.Collection;
// TODO Rename. Also, extend AbstractTableFileWriter.
public class RecordResolutionCasConsumer extends AbstractFileWriter<String> {
- static private final Logger LOGGER = LogManager.getLogger( "RecordResolutionCasConsumer" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "RecordResolutionCasConsumer" );
@ConfigurationParameter(
name = "OutputFile",
diff --git a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java b/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
index d7d8ea1..0c0fea5 100644
--- a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
+++ b/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
@@ -25,8 +25,8 @@ import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.*;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -51,7 +51,7 @@ import java.util.Map;
public class TemplateFillerAnnotator extends JCasAnnotator_ImplBase{
// LOG4J logger based on class name
- static private final Logger LOGGER = LogManager.getLogger( "TemplateFillerAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "TemplateFillerAnnotator" );
private UimaContext uimaContext;
diff --git a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
index 931aa35..4fca8b2 100644
--- a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
+++ b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -69,7 +69,7 @@ import java.util.List;
)
public class BackwardsTimeAnnotator extends TemporalEntityAnnotator_ImplBase {
- static private final Logger LOGGER = LogManager.getLogger( "BackwardsTimeAnnotator" );
+ static private final Logger LOGGER = LoggerFactory.getLogger( "BackwardsTimeAnnotator" );
public static final String PARAM_TIMEX_VIEW = "TimexView";
@ConfigurationParameter(
diff --git a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
index a0478a7..5d63265 100644
--- a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
+++ b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
@@ -28,8 +28,8 @@ import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
... 2046 lines suppressed ...