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Posted to commits@ctakes.apache.org by se...@apache.org on 2020/04/24 20:06:58 UTC
svn commit: r1876941 [1/3] - in /ctakes/trunk:
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/
ctakes-asserti...
Author: seanfinan
Date: Fri Apr 24 20:06:57 2020
New Revision: 1876941
URL: http://svn.apache.org/viewvc?rev=1876941&view=rev
Log:
Refactoring :
DocumentIDAnnotationUtil - renamed to DocIdUtil and moved to core.util.doc
WordTokenUtil - moved to core.util.annotation
DotLogger - moved to core.util.log
OntologyConceptUtil - moved to core.util.annotation
SourceMetadataUtil - moved to core.util.doc
EssentialAnnotationUtil - moved to core.util.annotation
ListParagraphFixer - Splits paragraphs by list entries
MrsDrSentenceJoiner - Removes Sentence breaks cause by Mrs. Mr. Dr. a.m. p.m.
IdentifiedAnnotationUtil - convenience methods for common identifiedAnnotation inquiries
CalendarUtil - Can create normalized calendar from text snippets, can create TimeMentions
SystemUtil - commented cmd output
ctakes-gui pom - removed ctakes-coreference dependency
Added:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CalendarUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
- copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java
- copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java
- copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java
- copied, changed from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
Removed:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/IdentifiedAnnotationUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java
Modified:
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/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/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.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-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.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/MaxentParserWrapper.java
ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
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/DocumentIdPrinterAnalysisEngine.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.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/SimpleSegmentWithTagsAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.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/cc/html/HtmlTextWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/note/NoteSpecs.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DateParser.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/EssentialAnnotationUtil.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java
ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.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-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
ctakes/trunk/ctakes-gui/pom.xml
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java
ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java
ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java
ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java
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/DocTimeApproximator.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/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/SimpleMedDatesFinder.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.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/EventTimeRelationFeatureExtractor.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java
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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -37,20 +37,9 @@ package org.apache.ctakes.assertion.cc;
* under the License.
*/
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-
import org.apache.ctakes.assertion.eval.AssertionEvaluation.Options;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.relation.Relation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -64,7 +53,6 @@ import org.apache.uima.cas.impl.XCASSeri
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;
@@ -72,6 +60,13 @@ import org.apache.uima.resource.Resource
import org.apache.uima.util.XMLSerializer;
import org.xml.sax.SAXException;
+import java.io.*;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
/**
*
* A simple CAS consumer that generates XCAS (XML representation of the CAS) files in the
@@ -178,7 +173,7 @@ public class JudgeAttributeInstances ext
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
- String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String sourceFileName = DocIdUtil.getDocumentID( jCas );
System.out.println("==================\nFile: "+sourceFileName);
deletableMentions = new ArrayList<IdentifiedAnnotation>();
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=1876941&r1=1876940&r2=1876941&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 Fri Apr 24 20:06:57 2020
@@ -18,32 +18,30 @@
*/
package org.apache.ctakes.assertion.cr;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.Mapper;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+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.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.jdom.Document;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
-import org.apache.ctakes.typesystem.type.constants.CONST;
-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.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.Mapper;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
/**
* Read named entity annotations from knowtator xml files into the CAS
@@ -83,8 +81,8 @@ public class GoldEntityAndAttributeReade
initView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
} catch (CASException e) {
throw new AnalysisEngineProcessException(e);
- }
- String goldFilePath = inputDirectory + DocumentIDAnnotationUtil.getDocumentID(jCas) + ".knowtator.xml";
+ }
+ String goldFilePath = inputDirectory + DocIdUtil.getDocumentID( jCas ) + ".knowtator.xml";
SAXBuilder builder = new SAXBuilder();
Document document;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Fri Apr 24 20:06:57 2020
@@ -18,45 +18,19 @@
*/
package org.apache.ctakes.assertion.eval;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
+import com.google.common.base.Objects;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Sets;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator;
-import org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine;
+import org.apache.ctakes.assertion.medfacts.cleartk.*;
import org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.FEATURE_CONFIG;
-import org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine;
import org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus;
import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
-import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
-import org.apache.ctakes.typesystem.type.syntax.NumToken;
-import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
-import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
-import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.*;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -73,11 +47,7 @@ import org.apache.uima.cas.Feature;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.component.NoOpAnnotator;
-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.ConfigurationParameterFactory;
-import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.factory.*;
import org.apache.uima.fit.pipeline.JCasIterator;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.CasIOUtil;
@@ -103,10 +73,12 @@ import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
import org.kohsuke.args4j.spi.BooleanOptionHandler;
-import com.google.common.base.Objects;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.*;
public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatisticsCompact<String>>> {
@@ -916,7 +888,7 @@ public static void printScore(Map<String
// System.out.format("system entities: %d%nsystem events: %d%n%n", systemEntities.size(), systemEvents.size());
if (evaluationOutputDirectory != null){
- String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String sourceFileName = DocIdUtil.getDocumentID( jCas );
CasIOUtil.writeXmi(jCas, new File(evaluationOutputDirectory, sourceFileName + ".xmi"));
}
@@ -1065,7 +1037,7 @@ private static void printErrors(JCas jCa
Collection<IdentifiedAnnotation> goldEntitiesAndEvents,
Collection<IdentifiedAnnotation> systemEntitiesAndEvents, String classifierType, Object trueCategory, Class<? extends Object> categoryClass) throws ResourceProcessException {
- String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String documentId = DocIdUtil.getDocumentID( jCas );
Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
@@ -1142,7 +1114,7 @@ private static void printInstances(JCas
File outputfile)
throws ResourceProcessException, IOException {
- String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String documentId = DocIdUtil.getDocumentID( jCas );
Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
goldMap.put(new HashableAnnotation(mention), mention);
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java Fri Apr 24 20:06:57 2020
@@ -18,16 +18,9 @@
*/
package org.apache.ctakes.assertion.eval;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
-
import org.apache.ctakes.assertion.util.AssertionConst;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+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;
@@ -39,12 +32,6 @@ import org.apache.uima.analysis_engine.A
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.metadata.ResourceMetaData;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.apache.uima.util.CasCreationUtils;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.component.NoOpAnnotator;
import org.apache.uima.fit.component.ViewCreatorAnnotator;
@@ -53,10 +40,22 @@ import org.apache.uima.fit.factory.Analy
import org.apache.uima.fit.factory.CollectionReaderFactory;
import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.ResourceMetaData;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.apache.uima.util.CasCreationUtils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.COREFERENCE_RELATION;
-import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.MARKABLE;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.DOCUMENT_ID;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION;
/**
*
@@ -99,8 +98,8 @@ public class MergeGoldViewFromOneCasInto
if (!goldViewDir.exists()) throw new AnalysisEngineProcessException(new RuntimeException("Directory with gold view annotations not found:" + dirWithGoldViews));
if (!goldViewDir.isDirectory()) throw new AnalysisEngineProcessException(new RuntimeException("What is supposed to be a directory with gold view annotations is not a directory:" + dirWithGoldViews));
-
- String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+
+ String docId = DocIdUtil.getDocumentID( jCas );
JCas correspondingCasThatHasGoldAnnotations = getCorrespondingCasThatHasGoldAnnotations(docId);
JCas viewWithPreexistingGoldAnnotations = null;
JCas newGoldView = null;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -21,7 +21,7 @@ package org.apache.ctakes.assertion.medf
import org.apache.commons.io.FilenameUtils;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -309,7 +309,7 @@ public abstract class AssertionCleartkAn
@Override
public void process( JCas jCas ) throws AnalysisEngineProcessException {
- String documentId = DocumentIDAnnotationUtil.getDocumentID( jCas );
+ String documentId = DocIdUtil.getDocumentID( jCas );
String domainId = "";
String domainFeature = null;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -26,7 +26,7 @@ import org.apache.ctakes.assertion.medfa
import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.LastCoveredContext;
import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.PrecedingContext;
import org.apache.ctakes.assertion.medfacts.cleartk.windowed.context.feature.extractor.AbstractWindowedFeatureExtractor1;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -273,7 +273,7 @@ public abstract class WindowedAssertionC
@Override
public void process( JCas jCas ) throws AnalysisEngineProcessException {
- String documentId = DocumentIDAnnotationUtil.getDocumentID( jCas );
+ String documentId = DocIdUtil.getDocumentID( jCas );
String domainId = "";
String domainFeature = null;
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java Fri Apr 24 20:06:57 2020
@@ -18,21 +18,13 @@
*/
package org.apache.ctakes.assertion.pipelines;
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
import org.apache.ctakes.assertion.eval.XMIReader;
import org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.ATTRIBUTE;
import org.apache.ctakes.assertion.util.AssertionDepUtils;
import org.apache.ctakes.assertion.util.AssertionTreeUtils;
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -51,6 +43,14 @@ import org.kohsuke.args4j.CmdLineExcepti
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
public class GenerateDependencyRepresentation {
public static class Options {
@@ -110,7 +110,7 @@ public class GenerateDependencyRepresent
}
public static void processDocument(JCas jcas) {
- log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
+ log.info( "Processing document: " + DocIdUtil.getDocumentID( jcas ) );
Collection<Sentence> sents = JCasUtil.select(jcas, Sentence.class);
Sentence lastSent=null;
for(Sentence sent : sents){
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java Fri Apr 24 20:06:57 2020
@@ -18,19 +18,10 @@
*/
package org.apache.ctakes.assertion.pipelines;
-import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
import org.apache.ctakes.assertion.eval.XMIReader;
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -47,6 +38,15 @@ import org.kohsuke.args4j.CmdLineExcepti
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
+
public class GenerateTreeRepresentation{
enum ATTRIBUTE {NEG, UNC}
@@ -112,7 +112,7 @@ public class GenerateTreeRepresentation{
}
private static void processDocument(JCas jcas) {
- log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
+ log.info( "Processing document: " + DocIdUtil.getDocumentID( jcas ) );
Collection<IdentifiedAnnotation> mentions = JCasUtil.select(jcas, IdentifiedAnnotation.class);
for(IdentifiedAnnotation mention : mentions){
if(mention instanceof EventMention || mention instanceof EntityMention){
Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java Fri Apr 24 20:06:57 2020
@@ -19,11 +19,8 @@ package org.apache.ctakes.clinicalpipeli
*/
-import java.io.File;
-import java.util.Date;
-
import org.apache.ctakes.assertion.util.AssertionConst;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.collection.CollectionReaderDescription;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
@@ -32,6 +29,9 @@ import org.apache.uima.fit.util.CasIOUti
import org.apache.uima.jcas.JCas;
import org.cleartk.util.cr.FilesCollectionReader;
+import java.io.File;
+import java.util.Date;
+
/**
* Run the plaintext clinical pipeline, using the dictionary of terms from UMLS.
* Note you must have the UMLS password supplied in some way - see the
@@ -63,7 +63,7 @@ public class ClinicalPipelineWithUmls {
"desc/analysis_engine/AggregatePlaintextUMLSProcessor");
for(JCas jCas : SimplePipeline.iteratePipeline(collectionReader, pipelineIncludingUmlsDictionaries)){
- CasIOUtil.writeXmi(jCas, new File(AssertionConst.evalOutputDir, DocumentIDAnnotationUtil.getDocumentID(jCas) + ".xmi"));
+ CasIOUtil.writeXmi( jCas, new File( AssertionConst.evalOutputDir, DocIdUtil.getDocumentID( jCas ) + ".xmi" ) );
}
System.out.println("Done at " + new Date());
Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.clinicalpipeline.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.clinicalpipeline.runtime;
import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
@@ -66,7 +66,7 @@ public abstract class BagOfAnnotationsGe
JCasIterator casIter = new JCasIterator(reader, ae);
while(casIter.hasNext()){
JCas jcas = casIter.next();
- String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String docId = DocIdUtil.getDocumentID( jcas );
// extract info from cas
processCas(jcas, outputDir + File.separator + docId);
Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java Fri Apr 24 20:06:57 2020
@@ -23,7 +23,7 @@ import opennlp.tools.parser.Parse;
import opennlp.tools.parser.ParserModel;
import opennlp.tools.parser.chunking.Parser;
import org.apache.ctakes.constituency.parser.util.TreeUtils;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+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;
@@ -72,7 +72,7 @@ public class MaxentParserWrapper impleme
*/
@Override
public void createAnnotations( final JCas jcas ) throws AnalysisEngineProcessException {
- final String docId = DocumentIDAnnotationUtil.getDocumentID( jcas );
+ final String docId = DocIdUtil.getDocumentID( jcas );
logger.info( "Started processing: " + docId );
// iterate over sentences
Parse parse = null;
Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java Fri Apr 24 20:06:57 2020
@@ -22,7 +22,7 @@ import org.apache.ctakes.constituency.pa
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.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -21,7 +21,7 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
@@ -137,7 +137,7 @@ public class CDASegmentAnnotator extends
public void process(JCas jCas) throws AnalysisEngineProcessException {
String text = jCas.getDocumentText();
if (text == null) {
- String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String docId = DocIdUtil.getDocumentID( jCas );
logger.info("text is null for docId=" + docId);
} else {
ArrayList<Segment> sorted_segments = new ArrayList<>();
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.log4j.Logger;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
@@ -39,7 +39,7 @@ public class DocumentIdPrinterAnalysisEn
@Override
public void process(JCas jcas) throws AnalysisEngineProcessException
{
- String documentId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String documentId = DocIdUtil.getDocumentID( jcas );
String logMessage = String.format("##### current file document id: \"%s\"", documentId);
logger.info(logMessage);
System.out.println(logMessage);
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.core.util.textspan.DefaultAspanComparator;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java Fri Apr 24 20:06:57 2020
@@ -41,7 +41,7 @@ public class ListEntryNegator extends JC
static private final Pattern NEGATIVE_PATTERN
= Pattern
- .compile( "(?:\\s?:\\s*)(?:NEGATIVE|(?:NO\\.?\\b)|NONE|(?:NOT (?:SEEN|PRESENT|INDICATED|FOUND|DISCOVERED)?)|DENIE(?:S|D))",
+ .compile( "(?:\\s?:\\s*)(?:NEGATIVE|(?:NO\\.?\\b)|NONE|(?:NOT (?:SEEN|PRESENT|INDICATED|FOUND|DISCOVERED)?)|DENIE[SD])",
Pattern.CASE_INSENSITIVE );
/**
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,96 @@
+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.log4j.Logger;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.*;
+import java.util.regex.Pattern;
+
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 9/28/2016
+ */
+@PipeBitInfo(
+ name = "List Paragraph Fixer",
+ description = "Re-annotates Paragraphs based upon existing Lists, preventing a Paragraph from spanning more than one List.",
+ dependencies = { PipeBitInfo.TypeProduct.LIST, PipeBitInfo.TypeProduct.SENTENCE }
+)
+final public class ListParagraphFixer extends JCasAnnotator_ImplBase {
+
+ static private final Logger LOGGER = Logger.getLogger( "ListSentenceFixer" );
+
+ static private final Pattern WHITESPACE = Pattern.compile( "\\s+" );
+
+ /**
+ * Where Sentence annotations and List entry annotation ends overlap, Sentences are abbreviated.
+ * For each List Entry with a boundary within a Sentence, a new Sentence is created
+ * {@inheritDoc}
+ */
+ @Override
+ public void process( final JCas jcas ) throws AnalysisEngineProcessException {
+ LOGGER.info( "Adjusting Sentences overlapping Lists ..." );
+ final Collection<List> lists = JCasUtil.select( jcas, List.class );
+ if ( lists == null || lists.isEmpty() ) {
+ LOGGER.info( "Finished Processing" );
+ return;
+ }
+ adjustListParagraphs( jcas );
+ LOGGER.info( "Finished Processing" );
+ }
+
+
+ static private void adjustListParagraphs( final JCas jCas ) {
+ final Collection<List> lists = JCasUtil.select( jCas, List.class );
+ final java.util.List<Paragraph> allParagraphs = new ArrayList<>( JCasUtil.select( jCas, Paragraph.class ) );
+ allParagraphs.sort( Comparator.comparingInt( Annotation::getBegin ) );
+ // gather map of paragraphs that cross boundaries of lists
+ final Map<Paragraph, Collection<Integer>> paragraphCrossBounds = new HashMap<>();
+ for ( List list : lists ) {
+ for ( Paragraph paragraph : allParagraphs ) {
+ if ( paragraph.getBegin() > list.getEnd() ) {
+ // past the list entry
+ break;
+ } else if ( paragraph.getEnd() < list.getBegin() ) {
+ // haven't reached the list entry
+ continue;
+ } else if ( paragraph.getBegin() >= list.getBegin() && paragraph.getEnd() <= list.getEnd() ) {
+ // within the list entry
+ continue;
+ }
+ // sentence overlaps but isn't contained
+ Collection<Integer> crossBounds = paragraphCrossBounds.get( paragraph );
+ if ( crossBounds == null ) {
+ crossBounds = new HashSet<>();
+ paragraphCrossBounds.put( paragraph, crossBounds );
+ crossBounds.add( paragraph.getBegin() );
+ crossBounds.add( paragraph.getEnd() );
+ }
+ crossBounds.add( Math.max( paragraph.getBegin(), list.getBegin() ) );
+ crossBounds.add( Math.min( paragraph.getEnd(), list.getEnd() ) );
+ }
+ }
+ for ( Map.Entry<Paragraph, Collection<Integer>> crossBounds : paragraphCrossBounds.entrySet() ) {
+ final java.util.List<Integer> sortedBounds = new ArrayList<>( crossBounds.getValue() );
+ Collections.sort( sortedBounds );
+ for ( int i = 0; i < sortedBounds.size() - 1; i++ ) {
+ final Paragraph paragraph = new Paragraph( jCas, sortedBounds.get( i ), sortedBounds.get( i + 1 ) );
+ if ( WHITESPACE.matcher( paragraph.getCoveredText() ).replaceAll( " " ).trim().length() > 0 ) {
+ paragraph.addToIndexes();
+ }
+ }
+ crossBounds.getKey().removeFromIndexes();
+ jCas.removeFsFromIndexes( crossBounds.getKey() );
+ }
+ }
+
+
+}
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,93 @@
+package org.apache.ctakes.core.ae;
+
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 4/15/2020
+ */
+@PipeBitInfo(
+ name = "MrsDrSentenceJoiner",
+ description = "Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.",
+ dependencies = PipeBitInfo.TypeProduct.SENTENCE,
+ role = PipeBitInfo.Role.SPECIAL
+)
+final public class MrsDrSentenceJoiner extends JCasAnnotator_ImplBase {
+
+ static private final Logger LOGGER = Logger.getLogger( "MrsDrSentenceJoiner" );
+
+ /**
+ * Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.
+ * Note : this does not take into account Sections or Paragraphs.
+ * {@inheritDoc}
+ */
+ @Override
+ public void process( final JCas jCas ) throws AnalysisEngineProcessException {
+ LOGGER.info( "Joining Sentences ending with person titles (Mr. Mrs. Dr.) ..." );
+ // Obtain a list of Sentences, sorted by character offset.
+ final List<Sentence> sentences
+ = JCasUtil.select( jCas, Sentence.class ).stream()
+ .sorted( Comparator.comparingInt( Annotation::getBegin ) )
+ .collect( Collectors.toList() );
+ // Account for (intentional?) EOL after person title.
+ final Collection<Integer> newlines = new HashSet<>();
+ final char[] chars = jCas.getDocumentText().toCharArray();
+ for ( int i = 0; i < chars.length; i++ ) {
+ if ( chars[ i ] == '\r' || chars[ i ] == '\n' ) {
+ newlines.add( i );
+ }
+ }
+ final int sentenceCount = sentences.size();
+ final Collection<Sentence> removalSentences = new HashSet<>();
+ boolean appendNextSentence = false;
+ int appendSentenceBegin = 0;
+ for ( int i = 0; i < sentenceCount; i++ ) {
+ final Sentence sentence = sentences.get( i );
+ final String text = sentence.getCoveredText();
+ if ( (text.endsWith( " Mr." ) || text.endsWith( " Mrs." ) || text.endsWith( " Dr." )
+ || text.endsWith( " a.m." ) || text.endsWith( " p.m." )
+ || text.equals( "Mr." ) || text.equals( "Mrs." ) || text.equals( "Dr." ))
+ && i < sentenceCount - 1
+ && !newlines.contains( sentence.getEnd() ) ) {
+ // Sentence ends with a person title AND is not the last sentence in the document.
+ if ( !appendNextSentence ) {
+ appendSentenceBegin = sentence.getBegin();
+ }
+ removalSentences.add( sentence );
+ appendNextSentence = true;
+ continue;
+ }
+ if ( appendNextSentence ) {
+ // Create a new sentence that spans this sentence plus the preceding sentence(s) ending with a title.
+ final Sentence newSentence = new Sentence( jCas, appendSentenceBegin, sentence.getEnd() );
+ newSentence.addToIndexes();
+ removalSentences.add( sentence );
+ appendNextSentence = false;
+ }
+ }
+ // Get rid of all of the original sentences that are now covered by new sentences.
+ removalSentences.forEach( Sentence::removeFromIndexes );
+ // Just in case, set sentence numbers.
+ final AtomicInteger index = new AtomicInteger( 0 );
+ JCasUtil.select( jCas, Sentence.class ).stream()
+ .sorted( Comparator.comparingInt( Annotation::getBegin ) )
+ .forEach( s -> s.setSentenceNumber( index.incrementAndGet() ) );
+ }
+
+
+}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -22,8 +22,8 @@ import findstruct.Section;
import findstruct.StructFinder;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileResource;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
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.log4j.Logger;
import org.apache.uima.UimaContext;
@@ -85,7 +85,7 @@ public class SectionSegmentAnnotator ext
String text = jCas.getDocumentText();
if (text == null) {
- String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String docId = DocIdUtil.getDocumentID( jCas );
throw new AnalysisEngineProcessException("text is null for docId="
+ docId, null);
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -61,7 +61,7 @@ public class SimpleSegmentAnnotator exte
segment.setBegin(0);
String text = jCas.getDocumentText();
if (text == null) {
- String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ String docId = DocIdUtil.getDocumentID( jCas );
throw new AnalysisEngineProcessException("text is null for docId="
+ docId, null);
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
@@ -69,7 +69,7 @@ public class SimpleSegmentWithTagsAnnota
String text = jcas.getDocumentText();
if (text == null) {
System.out.println("text == null in Segmentannotator");
- String docID = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String docID = DocIdUtil.getDocumentID( jcas );
System.out.println(" \t\tdocID=" + docID);
}
if (segmentId.compareTo("parseSectionTag") != 0) {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.config.ConfigParameterConstants;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+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.log4j.Logger;
@@ -68,7 +68,7 @@ abstract public class AbstractFileWriter
*/
@Override
public void process( final JCas jcas ) throws AnalysisEngineProcessException {
- final String documentId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+ final String documentId = DocIdUtil.getDocumentIdForFile( jcas );
final String outputDir = getOutputDirectory( jcas, getRootDirectory(), documentId );
final String fileName = getSourceFileName( jcas, documentId );
try {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.resource.JdbcConnectionResource;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.typesystem.type.structured.SourceData;
import org.apache.log4j.Logger;
import org.apache.uima.cas.CAS;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.log4j.Logger;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.impl.XCASSerializer;
@@ -73,10 +73,10 @@ public class CasConsumer extends CasCons
private void processView( JCas view ) throws Exception {
// String docText = view.getDocumentText();
- String docName = DocumentIDAnnotationUtil.getDocumentID( view );
+ String docName = DocIdUtil.getDocumentID( view );
File outputFile;
- if ( docName == null || docName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ if ( docName == null || docName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
docName = "doc" + iv_procCount + ".xml";
} else {
docName = docName + ".xml";
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+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.log4j.Logger;
@@ -124,7 +124,7 @@ public class CuiCountFileWriter extends
*/
public void process( final JCas jcas ) {
LOGGER.info( "Starting processing" );
- final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+ final String docId = DocIdUtil.getDocumentIdForFile( jcas );
File outputFile;
if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
outputFile = new File( docId + FILE_EXTENSION );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.semantic.SemanticTui;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
import org.apache.ctakes.core.util.RelationArgumentUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
package org.apache.ctakes.core.cc;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+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;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.log4j.Logger;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -76,8 +76,8 @@ public class FilesInDirectoryCasConsumer
String documentText = jcas.getDocumentText();
- String documentID = DocumentIDAnnotationUtil.getDeepDocumentId( jcas );
- if ( documentID == null || documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ String documentID = DocIdUtil.getDeepDocumentId( jcas );
+ if ( documentID == null || documentID.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
documentID = "doc_" + new java.util.Date().getTime() + ".xml"; // use timestamp in name: doc_TIMESTAMP.xml
LOGGER.warn( "Unable to find DocumentIDAnnotation, using " + documentID );
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+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.log4j.Logger;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,8 +19,8 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
@@ -83,7 +83,7 @@ public class NormalizedFilesInDirectoryC
normalizedText.append( " " );
}
}
- final String documentID = DocumentIDAnnotationUtil.getDocumentID( jcas );
+ final String documentID = DocIdUtil.getDocumentID( jcas );
writeToFile( documentID, normalizedText.toString() );
} catch ( CASException | IOException multE ) {
throw new ResourceProcessException( multE );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
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.log4j.Logger;
@@ -99,7 +99,7 @@ public class SentenceTokensPrinter exten
// JCasHashMap will throw this every once in a while. Assume the sentences are done and move on
LOGGER.warn( iobE.getMessage() );
}
- final String documentId = DocumentIDAnnotationUtil.getDocumentID( jcas );
+ final String documentId = DocIdUtil.getDocumentID( jcas );
outputSentenceTokens( documentId, tokenizedSentences );
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+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;
@@ -119,7 +119,7 @@ public class TextSpanWriter extends CasC
*/
public void process( final JCas jcas ) {
LOGGER.info( "Starting processing" );
- final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+ final String docId = DocIdUtil.getDocumentIdForFile( jcas );
File outputFile;
if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
outputFile = new File( docId + FILE_EXTENSION );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.core.cc;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -87,9 +87,9 @@ public class TokenOffsetsCasConsumer ext
BaseToken token = (BaseToken) tokenItr.next();
String offset = ""+token.getBegin()+"|"+token.getEnd();
offsets.add(offset);
- }
+ }
- String documentID = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String documentID = DocIdUtil.getDocumentID( jcas );
writeToFile(documentID, offsets);
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java Fri Apr 24 20:06:57 2020
@@ -38,7 +38,7 @@ package org.apache.ctakes.core.cc;
*/
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.log4j.Logger;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UimaContext;
@@ -125,11 +125,11 @@ public class XmiWriterCasConsumerCtakes
throw new AnalysisEngineProcessException( e1 );
}
- String originalFileName = DocumentIDAnnotationUtil.getDocumentID( jcas );
+ String originalFileName = DocIdUtil.getDocumentID( jcas );
File outFile = null;
if ( originalFileName != null
- && !originalFileName.isEmpty()
- && !originalFileName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ && !originalFileName.isEmpty()
+ && !originalFileName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
File inFile;
try {
String outFileName = null;
@@ -153,8 +153,8 @@ public class XmiWriterCasConsumerCtakes
File inFile;
String outFileName = null;
if ( originalFileName != null
- && !originalFileName.isEmpty()
- && !originalFileName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ && !originalFileName.isEmpty()
+ && !originalFileName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
try {
if ( originalFileName.contains( "/" ) ) {
URI uri = UriUtils.quote( originalFileName );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java Fri Apr 24 20:06:57 2020
@@ -5,8 +5,8 @@ import org.apache.ctakes.core.cc.Abstrac
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.semantic.SemanticGroup;
import org.apache.ctakes.core.semantic.SemanticTui;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.core.util.textspan.DefaultTextSpan;
import org.apache.ctakes.core.util.textspan.TextSpan;
import org.apache.ctakes.typesystem.type.refsem.Event;
@@ -105,7 +105,7 @@ final public class HtmlTextWriter extend
final File htmlFile = new File( outputDir, fileName + FILE_EXTENSION );
LOGGER.info( "Writing HTML to " + htmlFile.getPath() + " ..." );
try ( final BufferedWriter writer = new BufferedWriter( new FileWriter( htmlFile ) ) ) {
- final String title = DocumentIDAnnotationUtil.getDocumentID( jCas );
+ final String title = DocIdUtil.getDocumentID( jCas );
writer.write( startBody() );
writer.write( getCssLink( CSS_FILENAME ) );
writer.write( getJsLink( JS_FILENAME ) );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc.jdbc.i
import org.apache.ctakes.core.cc.jdbc.field.*;
import org.apache.ctakes.core.cc.jdbc.row.JdbcRow;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.structured.SourceData;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.core.cc.jdbc.t
import org.apache.ctakes.core.cc.jdbc.row.JdbcRow;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+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.uima.fit.util.JCasUtil;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java Fri Apr 24 20:06:57 2020
@@ -1,6 +1,6 @@
package org.apache.ctakes.core.cc.pretty;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java Fri Apr 24 20:06:57 2020
@@ -4,8 +4,8 @@ package org.apache.ctakes.core.cc.pretty
import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
import org.apache.ctakes.core.cc.pretty.SemanticGroup;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.core.util.textspan.DefaultTextSpan;
import org.apache.ctakes.core.util.textspan.TextSpan;
import org.apache.ctakes.typesystem.type.refsem.Event;
@@ -105,7 +105,7 @@ final public class HtmlTextWriter extend
final File htmlFile = new File( outputDir, fileName + FILE_EXTENSION );
LOGGER.info( "Writing HTML to " + htmlFile.getPath() + " ..." );
try ( final BufferedWriter writer = new BufferedWriter( new FileWriter( htmlFile ) ) ) {
- final String title = DocumentIDAnnotationUtil.getDocumentID( jCas );
+ final String title = DocIdUtil.getDocumentID( jCas );
writer.write( startBody() );
writer.write( getCssLink( CSS_FILENAME ) );
writer.write( getJsLink( JS_FILENAME ) );
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java Fri Apr 24 20:06:57 2020
@@ -4,8 +4,8 @@ import org.apache.ctakes.core.cc.pretty.
import org.apache.ctakes.core.cc.pretty.cell.*;
import org.apache.ctakes.core.cc.pretty.row.DefaultItemRow;
import org.apache.ctakes.core.cc.pretty.row.ItemRow;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.core.util.textspan.DefaultTextSpan;
import org.apache.ctakes.core.util.textspan.TextSpan;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
@@ -78,7 +78,7 @@ final public class PrettyTextWriter {
*/
public void process( final JCas jcas ) {
LOGGER.info( "Starting processing" );
- final String docId = DocumentIDAnnotationUtil.getDocumentIdForFile( jcas );
+ final String docId = DocIdUtil.getDocumentIdForFile( jcas );
File outputFile;
if ( _outputDirPath == null || _outputDirPath.isEmpty() ) {
outputFile = new File( docId + FILE_EXTENSION );