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From tm...@apache.org
Subject svn commit: r1625365 [1/10] - in /ctakes/trunk: ./ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.uimafit/ ctakes-assertion-zoner/ ctakes-assertion-zoner/src/main/j...
Date Tue, 16 Sep 2014 19:57:25 GMT
Author: tmill
Date: Tue Sep 16 19:57:19 2014
New Revision: 1625365

URL: http://svn.apache.org/r1625365
Log:
CTAKES-280: Touches many files to upgrade to uimafit 2.1, cleartk 2.0.

Added:
    ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/
    ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt
    ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.apache.uima.fit/
      - copied from r1625032, ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/
    ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/
    ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
Removed:
    ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.uimafit/
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/CtakesFileNamer.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/META-INF/org.uimafit/
    ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.uimafit/
Modified:
    ctakes/trunk/ctakes-assertion-zoner/pom.xml
    ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java
    ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java
    ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
    ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
    ctakes/trunk/ctakes-assertion/pom.xml
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/XMIReader.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java
    ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java
    ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java
    ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java
    ctakes/trunk/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/contexttokenizer/ae/ContextDependentTokenizerAnnotator.java
    ctakes/trunk/ctakes-core/pom.xml
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
    ctakes/trunk/ctakes-dependency-parser/pom.xml
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java
    ctakes/trunk/ctakes-dependency-parser/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
    ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java
    ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java
    ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ExampleHelloWorldAnnotator.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java
    ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
    ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java
    ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java
    ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java
    ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/model.jar
    ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/location_of/model.jar
    ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar
    ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml
    ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml
    ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml
    ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
    ctakes/trunk/ctakes-relation-extractor/pom.xml
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationViewer.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/TreeFeatureConsumer.java
    ctakes/trunk/ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java
    ctakes/trunk/ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotatorsTest.java
    ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/contextualmodality/model.jar
    ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/doctimerel/model.jar
    ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/model.jar
    ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/timeannotator/model.jar
    ctakes/trunk/ctakes-temporal/pom.xml
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocumentCreationTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelWithTreeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistSemFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistanceFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/StringMatchingFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/TokenFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/UMLSFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CoreferenceLinkDistanceAnalyzer.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventPropertiesTk.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/RemoveTreeAlignedMentions.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventPrintingPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
    ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
    ctakes/trunk/ctakes-type-system/pom.xml
    ctakes/trunk/ctakes-utils/pom.xml
    ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java
    ctakes/trunk/pom.xml

Added: ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt?rev=1625365&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt (added)
+++ ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt Tue Sep 16 19:57:19 2014
@@ -0,0 +1 @@
+classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml

Modified: ctakes/trunk/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner/pom.xml Tue Sep 16 19:57:19 2014
@@ -42,10 +42,6 @@
       <groupId>org.apache.uima</groupId>
       <artifactId>uimaj-core</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
 		<dependency>
 				<groupId>org.springframework</groupId>
@@ -55,6 +51,10 @@
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-core</artifactId>
     </dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+		</dependency>
 	</dependencies>
 	<build>
 		<plugins>

Modified: ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java (original)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import java.io.FileOutputStream;
 import java.net.URISyntaxException;
 
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
 
 public class CreateAssertionZonerDescriptors
 {
@@ -62,7 +62,7 @@ public class CreateAssertionZonerDescrip
     String generalSectionRegexFileUri =
       "org/mitre/medfacts/zoner/section_regex.xml";
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );
@@ -71,7 +71,7 @@ public class CreateAssertionZonerDescrip
     String mayoSectionRegexFileUri =
       "org/mitre/medfacts/uima/mayo_sections.xml";
     AnalysisEngineDescription mayoZonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             mayoSectionRegexFileUri
             );
@@ -96,7 +96,7 @@ public class CreateAssertionZonerDescrip
     String generalSectionRegexFileUri =
       "org/mitre/medfacts/zoner/section_regex.xml";
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );
@@ -117,7 +117,7 @@ public class CreateAssertionZonerDescrip
     String generalSectionRegexFileUri =
       "org/mitre/medfacts/uima/mayo_sections.xml";
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );

Modified: ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java (original)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java Tue Sep 16 19:57:19 2014
@@ -27,8 +27,8 @@ import java.net.URISyntaxException;
 import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.xml.sax.SAXException;
 
 public class CreateZonerDescriptor
@@ -53,7 +53,7 @@ public class CreateZonerDescriptor
     AggregateBuilder builder = new AggregateBuilder();
 
 //    AnalysisEngineDescription documentIdPrinter =
-//        AnalysisEngineFactory.createPrimitiveDescription(DocumentIdPrinterAnalysisEngine.class);
+//        AnalysisEngineFactory.createEngineDescription(DocumentIdPrinterAnalysisEngine.class);
 //    builder.add(documentIdPrinter);
   
     URI generalSectionRegexFileUri =
@@ -61,7 +61,7 @@ public class CreateZonerDescriptor
 //    ExternalResourceDescription generalSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
 //        SectionRegexConfigurationResource.class, new File(generalSectionRegexFileUri));
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );
@@ -72,7 +72,7 @@ public class CreateZonerDescriptor
 //      ExternalResourceDescription mayoSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
 //          SectionRegexConfigurationResource.class, new File(mayoSectionRegexFileUri));
     AnalysisEngineDescription mayoZonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             mayoSectionRegexFileUri
             );

Modified: ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java (original)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java Tue Sep 16 19:57:19 2014
@@ -21,34 +21,23 @@ package org.mitre.medfacts.uima;
 import java.io.File;
 import java.io.FilenameFilter;
 import java.io.IOException;
-import java.net.URI;
 import java.net.URISyntaxException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import org.apache.log4j.Logger;
 
-import org.apache.ctakes.core.util.CtakesFileNamer;
 import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.core.cr.TextReader;
-import org.apache.ctakes.core.cr.XMIReader;
+import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.resource.DataResource;
-import org.apache.uima.resource.ExternalResourceDescription;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.SharedResourceObject;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.ExternalResourceFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.factory.UimaContextFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 public class RunZoner
 {
@@ -110,14 +99,14 @@ public class RunZoner
     TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath();
     
 //    CollectionReader reader = 
-//        CollectionReaderFactory.createCollectionReader(
+//        CollectionReaderFactory.createReader(
 //          XMIReader.class,
 //          typeSystemDescription,
 //          XMIReader.PARAM_FILES,
 //          inputFiles);
 
     CollectionReader reader = 
-    CollectionReaderFactory.createCollectionReader(
+    CollectionReaderFactory.createReader(
       TextReader.class,
       typeSystemDescription,
       TextReader.PARAM_FILES,
@@ -125,7 +114,7 @@ public class RunZoner
 
     
       AnalysisEngineDescription documentIdPrinter =
-          AnalysisEngineFactory.createPrimitiveDescription(DocumentIdPrinterAnalysisEngine.class);
+          AnalysisEngineFactory.createEngineDescription(DocumentIdPrinterAnalysisEngine.class);
       builder.add(documentIdPrinter);
     
       String generalSectionRegexFileUri =
@@ -135,7 +124,7 @@ public class RunZoner
 //      ExternalResourceDescription generalSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
 //          SectionRegexConfigurationResource.class, new File(generalSectionRegexFileUri));
       AnalysisEngineDescription zonerAnnotator =
-          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+          AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
               ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
               generalSectionRegexFileUri
               );
@@ -148,19 +137,17 @@ public class RunZoner
 //        ExternalResourceDescription mayoSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
 //            SectionRegexConfigurationResource.class, new File(mayoSectionRegexFileUri));
       AnalysisEngineDescription mayoZonerAnnotator =
-          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+          AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
               ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
               mayoSectionRegexFileUri
               );
       builder.add(mayoZonerAnnotator);
 
-      AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-          XWriter.class,
+      AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
+          XmiWriterCasConsumerCtakes.class,
           typeSystemDescription,
-          XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-          outputDirectory.toString(),
-          XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-          CtakesFileNamer.class.getName()
+          XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+          outputDirectory.toString()
           );
       
       builder.add(xWriter);

Modified: ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java (original)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java Tue Sep 16 19:57:19 2014
@@ -46,10 +46,10 @@ import org.mitre.medfacts.zoner.ZonerCli
 //import org.mitre.medfacts.zoner.ZonerCliSimplified;
 //import org.mitre.medfacts.zoner.ZonerCliSimplified.HeadingRange;
 //import org.mitre.medfacts.zoner.ZonerCliSimplified.Range;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.descriptor.ExternalResource;
-import org.uimafit.descriptor.TypeCapability;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.descriptor.ExternalResource;
+import org.apache.uima.fit.descriptor.TypeCapability;
 
 @TypeCapability(outputs =
 {

Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Tue Sep 16 19:57:19 2014
@@ -155,10 +155,6 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
 		<dependency>
 			<groupId>org.springframework</groupId>

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -23,8 +23,8 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
 
 import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -23,8 +23,8 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
 
 import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -25,13 +25,12 @@ import java.util.HashSet;
 import java.util.List;
 
 import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
-import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 
 /** SubjectFeaturesExtractor
@@ -40,7 +39,7 @@ import org.cleartk.classifier.feature.ex
  * @author m081914
  *
  */
-public class GenericFeaturesExtractor implements SimpleFeatureExtractor {
+public class GenericFeaturesExtractor implements FeatureExtractor1 {
 	
 	
 	@Override

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,15 +24,13 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 
-import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
 import org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier;
-import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 
 /** HistoryFeaturesExtractor
@@ -41,7 +39,7 @@ import org.cleartk.classifier.feature.ex
  * @author shalgrim
  *
  */
-public class HistoryFeaturesExtractor implements SimpleFeatureExtractor {
+public class HistoryFeaturesExtractor implements FeatureExtractor1 {
 	
 	
 	@Override

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,11 +27,10 @@ import java.util.List;
 import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 
 /** SubjectFeaturesExtractor
@@ -40,7 +39,7 @@ import org.cleartk.classifier.feature.ex
  * @author m081914
  *
  */
-public class SubjectFeaturesExtractor implements SimpleFeatureExtractor {
+public class SubjectFeaturesExtractor implements FeatureExtractor1 {
 	
 	
 	@Override

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -26,9 +26,9 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.net.URI;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.collect.HashBasedTable;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -22,10 +22,10 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
-import org.cleartk.classifier.feature.transform.TrainableExtractor_ImplBase;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Predicate;
 import com.google.common.collect.Collections2;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -29,9 +29,9 @@ import java.util.Collection;
 import java.util.Map;
 import java.util.Set;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Joiner;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java Tue Sep 16 19:57:19 2014
@@ -29,7 +29,7 @@ import java.util.regex.Pattern;
 import org.apache.uima.UIMAException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java Tue Sep 16 19:57:19 2014
@@ -32,7 +32,7 @@ import org.apache.uima.UIMAException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.jcas.tcas.DocumentAnnotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java Tue Sep 16 19:57:19 2014
@@ -36,7 +36,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.log4j.Logger;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 
 /**

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java Tue Sep 16 19:57:19 2014
@@ -49,6 +49,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.Options;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.relation.Relation;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -60,16 +61,14 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.impl.XCASSerializer;
 import org.apache.uima.cas.impl.XmiCasSerializer;
+import org.apache.uima.fit.component.JCasConsumer_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.initializable.InitializableFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.XMLSerializer;
-import org.uimafit.component.JCasConsumer_ImplBase;
-import org.uimafit.component.xwriter.XWriterFileNamer;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.factory.initializable.InitializableFactory;
-import org.uimafit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
 /**
@@ -85,31 +84,20 @@ public class JudgeAttributeInstances ext
 	/**
 	 * The parameter name for the configuration parameter that specifies the output directory
 	 */
-	public static final String PARAM_OUTPUT_DIRECTORY_NAME = ConfigurationParameterFactory
-	.createConfigurationParameterName(JudgeAttributeInstances.class, "outputDirectoryName");
-	@ConfigurationParameter(mandatory = true, description = "takes a path to directory into which output files will be written.")
+	public static final String PARAM_OUTPUT_DIRECTORY_NAME = "outputDirectoryName";
+	@ConfigurationParameter(name = PARAM_OUTPUT_DIRECTORY_NAME, mandatory = true, description = "takes a path to directory into which output files will be written.")
 	private String outputDirectoryName;
 
 	/**
 	 * The parameter name for the configuration parameter that provides the name of the XML scheme
 	 * to use.
 	 */
-	public static final String PARAM_XML_SCHEME_NAME = ConfigurationParameterFactory
-	.createConfigurationParameterName(JudgeAttributeInstances.class, "xmlSchemeName");
-	@ConfigurationParameter(mandatory = true, defaultValue = "XMI", description = "specifies the UIMA XML serialization scheme that should be used. "
+	public static final String PARAM_XML_SCHEME_NAME = "xmlSchemeName";
+	@ConfigurationParameter(name = PARAM_XML_SCHEME_NAME, mandatory = true, defaultValue = "XMI", description = "specifies the UIMA XML serialization scheme that should be used. "
 		+ "Valid values for this parameter are 'XMI' (default) and 'XCAS'.")
 		private String xmlSchemeName;
 
 	/**
-	 * The parameter name for the configuration parameter that specifies the name of the class that
-	 * implements the file namer
-	 */
-	public static final String PARAM_FILE_NAMER_CLASS_NAME = ConfigurationParameterFactory
-	.createConfigurationParameterName(JudgeAttributeInstances.class, "fileNamerClassName");
-	@ConfigurationParameter(mandatory = true, description = "the class name of the XWriterFileNamer implementation to use", defaultValue = "org.uimafit.component.xwriter.IntegerFileNamer")
-	protected String fileNamerClassName;
-
-	/**
 	 * The parameter name which to ignore
 	 */
 //	public static final String PARAM_IGNORABLE_ATTR = ConfigurationParameterFactory
@@ -158,8 +146,6 @@ public class JudgeAttributeInstances ext
 
 	private boolean useXMI = true;
 
-	private XWriterFileNamer fileNamer;
-
 	@Override
 	public void initialize(UimaContext context) throws ResourceInitializationException {
 		super.initialize(context);
@@ -181,14 +167,12 @@ public class JudgeAttributeInstances ext
 					XMI, XCAS), null);
 		}
 
-		fileNamer = InitializableFactory
-		.create(context, fileNamerClassName, XWriterFileNamer.class);
 	}
 
 	@Override
 	public void process(JCas jCas) throws AnalysisEngineProcessException {
-		String fileName = fileNamer.nameFile(jCas);
-		System.out.println("==================\nFile: "+fileName);
+		String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+		System.out.println("==================\nFile: "+sourceFileName);
 		deletableMentions = new ArrayList<IdentifiedAnnotation>();
 
 //		JCas jCas = null;
@@ -206,10 +190,10 @@ public class JudgeAttributeInstances ext
 		
 		try {
 			if (useXMI) {
-				writeXmi(jCas.getCas(), fileName);
+				writeXmi(jCas.getCas(), sourceFileName);
 			}
 			else {
-				writeXCas(jCas.getCas(), fileName);
+				writeXCas(jCas.getCas(), sourceFileName);
 			}
 		}
 		catch (IOException e) {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java Tue Sep 16 19:57:19 2014
@@ -35,7 +35,7 @@ import org.apache.uima.resource.Resource
 import org.jdom.Document;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
-import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java Tue Sep 16 19:57:19 2014
@@ -26,12 +26,12 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
 import org.apache.ctakes.assertion.util.AssertionConst;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.core.knowtator.KnowtatorAnnotation;
 import org.apache.ctakes.core.knowtator.KnowtatorXMLParser;
 import org.apache.ctakes.core.util.CtakesFileNamer;
@@ -57,17 +57,13 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.refsem.ProcedureMethod;
 import org.apache.ctakes.typesystem.type.refsem.Severity;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
-import org.apache.ctakes.typesystem.type.relation.AffectsTextRelation;
-import org.apache.ctakes.typesystem.type.relation.AspectualTextRelation;
 import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 import org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation;
 import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
 import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
 import org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation;
 import org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.RelationArgument;
 import org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
 import org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier;
@@ -94,7 +90,6 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier;
 import org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier;
 import org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier;
-import org.apache.ctakes.typesystem.type.textsem.Modifier;
 import org.apache.ctakes.typesystem.type.textsem.PolarityModifier;
 import org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier;
 import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
@@ -108,16 +103,15 @@ import org.apache.log4j.Logger;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.Feature;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.jdom2.JDOMException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Maps;
@@ -1399,15 +1393,12 @@ public class MiPACQKnowtatorXMLReader ex
 		  dirs[0] = AssertionConst.MiPACQ_CORPUS;
 	  }
 
-	  AnalysisEngine mipacqReader = AnalysisEngineFactory.createPrimitive(MiPACQKnowtatorXMLReader.class);
+	  AnalysisEngine mipacqReader = AnalysisEngineFactory.createEngine(MiPACQKnowtatorXMLReader.class);
 
-	  AnalysisEngine xWriter = AnalysisEngineFactory.createPrimitive(
-			  XWriter.class,
-			  XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-			  "/usr/data/MiPACQ/cTAKES-xmi/",
-			  XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-			  CtakesFileNamer.class.getName()
-			  );
+	  AnalysisEngine xWriter = AnalysisEngineFactory.createEngine(
+			  XmiWriterCasConsumerCtakes.class,
+			  XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+			  "/usr/data/MiPACQ/cTAKES-xmi/");
 
 	  int n = dirs.length;
 	  LOGGER.info("Processing " + n + " directories of knowtator xml files.");

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java Tue Sep 16 19:57:19 2014
@@ -26,10 +26,9 @@ import java.util.List;
 
 import org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents;
 import org.apache.ctakes.assertion.util.AssertionConst;
-import org.apache.ctakes.core.util.CtakesFileNamer;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.log4j.Logger;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.cas.CAS;
@@ -37,15 +36,14 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionException;
 import org.apache.uima.collection.CollectionReaderDescription;
 import org.apache.uima.collection.CollectionReader_ImplBase;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 /**
  * Reads lines from file named by AssertionConst.NEGEX_CORPUS
@@ -126,19 +124,16 @@ public class NegExCorpusReader extends C
 	  
 	  //CollectionReader negexReader = new NegExCorpusReader(false);
 	  //List<NegExAnnotation> list = readAndParseAllLines(filename);
-	  CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+	  CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 			  NegExCorpusReader.class,
 				typeSystemDescription
 		);
 
 	  //TypeSystemDescription typeSystemDescription = AssertionComponents.TYPE_SYSTEM_DESCRIPTION; // TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath();//.createTypeSystemDescription();
-	  AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-			  XWriter.class,
-			  typeSystemDescription,
-			  XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-			  AssertionConst.NEGEX_CORPUS_PREPROCESSED,
-			  XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-			  CtakesFileNamer.class.getName()
+	  AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
+			  XmiWriterCasConsumerCtakes.class,
+			  XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+			  AssertionConst.NEGEX_CORPUS_PREPROCESSED
 			  );
 
 	  AggregateBuilder aggregate = new AggregateBuilder();



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