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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 [3/3] - 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...
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,188 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.core.util.doc;
+
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
+import org.apache.log4j.Logger;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.cas.CASRuntimeException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+
+import java.util.Collection;
+import java.util.Objects;
+import java.util.regex.Pattern;
+
+/**
+ * Utility class for fetching document id
+ */
+final public class DocIdUtil {
+
+ // Added for CTAKES-365
+ static public final String NO_DOCUMENT_ID = "UnknownDocument";
+ static public final String NO_DOCUMENT_ID_PREFIX = "UnknownDocumentPrefix";
+
+ static private final Logger LOGGER = Logger.getLogger( "DocumentIDAnnotationUtil" );
+
+ static private final Pattern FILE_FIX_PATTERN = Pattern.compile( "[^A-Za-z0-9\\.]" );
+
+ static private long _noDocIdIndex = 1;
+
+ // Utility classes should be final and have only a private constructor
+ private DocIdUtil() {
+ }
+
+ /**
+ * Check the jcas for a document id. Unlike {@link #getDeepDocumentId(JCas)},
+ * this method does not progress into deeper jcas layers/views.
+ *
+ * @param jcas ye olde ...
+ * @return the document id contained in the type "DocumentID" or {@link #NO_DOCUMENT_ID}
+ */
+ public static String getDocumentID( final JCas jcas ) {
+ if ( jcas == null ) {
+ // could throw an IllegalArgumentException,
+ // but a caller might be providing a null view, so a graceful handling is better
+ LOGGER.debug( "NULL CAS" );
+ return NO_DOCUMENT_ID;
+ }
+ final Collection<DocumentID> idSet = JCasUtil.select( jcas, DocumentID.class );
+ final DocumentID id = idSet.stream().filter( Objects::nonNull ).findAny().orElse( null );
+ if ( id == null ) {
+ return createDocumentId( jcas );
+ }
+ try {
+ return id.getDocumentID();
+ } catch ( CASRuntimeException casRTE ) {
+ final String newId = NO_DOCUMENT_ID + _noDocIdIndex;
+ _noDocIdIndex++;
+ LOGGER.warn( "document Id Annotation does not have the id feature set, setting to " + newId, casRTE );
+ id.setDocumentID( newId );
+ return newId;
+ }
+ }
+
+
+ /**
+ * Gets the document Id by progressing through 3 layers until an Id is found: starting JCas, Initial View, Plaintext View
+ *
+ * @param startingJcas initial JCas to start the checking
+ * @return Document Id from the starting JCas, the Initial View, the Plaintext View, or {@link #NO_DOCUMENT_ID}
+ */
+ static public String getDeepDocumentId( final JCas startingJcas ) {
+ String documentID = getDocumentID( startingJcas );
+ if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+ LOGGER.debug( "Checking document Id for initial view" );
+ try {
+ final JCas viewJcas = startingJcas.getView( "_InitialView" );
+ documentID = getDocumentID( viewJcas );
+ } catch ( CASException | CASRuntimeException casE ) {
+ LOGGER.warn( casE.getMessage() );
+ documentID = NO_DOCUMENT_ID;
+ }
+ if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+ LOGGER.debug( "Checking document Id for plaintext view" );
+ try {
+ final JCas viewJcas = startingJcas.getView( "plaintext" );
+ documentID = getDocumentID( viewJcas );
+ } catch ( CASException | CASRuntimeException casE ) {
+ LOGGER.warn( casE.getMessage() );
+ documentID = NO_DOCUMENT_ID;
+ }
+ if ( documentID == null || documentID.equals( NO_DOCUMENT_ID ) ) {
+ LOGGER.warn( "Unable to find DocumentIDAnnotation" );
+ return createDocumentId( startingJcas );
+ }
+ }
+ }
+ return documentID;
+ }
+
+ /**
+ * Create a unique id for the document that can be used for an output filename or url.
+ * Will be the source document file name if possible,
+ * otherwise the first 10 characters of the text plus text hashcode,
+ * or "Unknown_" and the current millis if there is no text.
+ * Non-alphanumeric characters are replaced with '_'.
+ *
+ * @param jcas -
+ * @return an ok document id
+ */
+ static public String getDocumentIdForFile( final JCas jcas ) {
+ String docId = getDeepDocumentId( jcas );
+ if ( docId == null || docId.isEmpty() ) {
+ String casDocText = jcas.getDocumentText();
+ if ( casDocText != null ) {
+ casDocText = casDocText.trim();
+ if ( !casDocText.isEmpty() ) {
+ docId = casDocText.substring( 0, Math.min( casDocText.length(), 10 ) ) + "_" + casDocText.hashCode();
+ }
+ }
+ }
+ if ( docId == null || docId.isEmpty() ) {
+ docId = "Unknown_" + System.currentTimeMillis();
+ }
+ return FILE_FIX_PATTERN.matcher( docId ).replaceAll( "_" );
+ }
+
+ /**
+ * @param jCas -
+ * @return {@link #NO_DOCUMENT_ID} plus an index based upon the number of documents without IDs fetched with this class.
+ * This may lead to documents having ids indexed out of order with respect to the order in which they were run.
+ */
+ static private String createDocumentId( final JCas jCas ) {
+ final String newId = NO_DOCUMENT_ID + _noDocIdIndex;
+ _noDocIdIndex++;
+ LOGGER.debug( "Creating document ID " + newId );
+ final DocumentID documentIDAnnotation = new DocumentID( jCas );
+ documentIDAnnotation.setDocumentID( newId );
+ documentIDAnnotation.addToIndexes();
+ return newId;
+ }
+
+ /**
+ * Check the jcas for a document id prefix. Unlike {@link #getDeepDocumentId(JCas)},
+ * this method does not progress into deeper jcas layers/views.
+ *
+ * @param jcas ye olde ...
+ * @return the document id prefix contained in the type "DocumentIdPrefix" or {@link #NO_DOCUMENT_ID}
+ */
+ public static String getDocumentIdPrefix( final JCas jcas ) {
+ if ( jcas == null ) {
+ // could throw an IllegalArgumentException,
+ // but a caller might be providing a null view, so a graceful handling is better
+ LOGGER.debug( "NULL CAS" );
+ return NO_DOCUMENT_ID_PREFIX;
+ }
+ final Collection<DocumentIdPrefix> prefices = JCasUtil.select( jcas, DocumentIdPrefix.class );
+ final DocumentIdPrefix prefix = prefices.stream().filter( Objects::nonNull ).findAny().orElse( null );
+ if ( prefix == null ) {
+ LOGGER.debug( "No document id prefix information for " + getDocumentID( jcas ) );
+ return NO_DOCUMENT_ID_PREFIX;
+ }
+ try {
+ return prefix.getDocumentIdPrefix();
+ } catch ( CASRuntimeException casRTE ) {
+ LOGGER.debug( "No document id prefix information for " + getDocumentID( jcas ) );
+ return NO_DOCUMENT_ID_PREFIX;
+ }
+ }
+
+}
Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java (from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java&r1=1876940&r2=1876941&rev=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java Fri Apr 24 20:06:57 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.util;
+package org.apache.ctakes.core.util.doc;
import org.apache.ctakes.typesystem.type.structured.Metadata;
import org.apache.ctakes.typesystem.type.structured.SourceData;
@@ -40,7 +40,7 @@ final public class SourceMetadataUtil {
return patientId;
}
}
- final String docPrefix = DocumentIDAnnotationUtil.getDocumentIdPrefix( jcas );
+ final String docPrefix = DocIdUtil.getDocumentIdPrefix( jcas );
if ( docPrefix != null && !docPrefix.isEmpty() ) {
return docPrefix;
}
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java?rev=1876941&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java Fri Apr 24 20:06:57 2020
@@ -0,0 +1,60 @@
+package org.apache.ctakes.core.util.log;
+
+import java.io.Closeable;
+import java.io.IOException;
+import java.util.TimerTask;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Dot Logger Usable in try as resource blocks. Logs a dot every 0.5 seconds until a process completes.
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 3/18/2016
+ */
+final public class DotLogger implements Closeable {
+
+ static private final org.apache.log4j.Logger DOT_LOGGER = org.apache.log4j.Logger.getLogger( "ProgressAppender" );
+ static private final org.apache.log4j.Logger EOL_LOGGER = org.apache.log4j.Logger.getLogger( "ProgressDone" );
+
+ private final ExecutorService _timer;
+
+ /**
+ * Starts the Dot Logging
+ */
+ public DotLogger() {
+ _timer = Executors.newScheduledThreadPool( 1 );
+ ((ScheduledExecutorService)_timer).scheduleAtFixedRate(
+ new DotPlotter(), 500, 500, TimeUnit.MILLISECONDS );
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void close() throws IOException {
+ _timer.shutdownNow();
+ EOL_LOGGER.info( "" );
+ }
+
+ private class DotPlotter extends TimerTask {
+ private int _count = 0;
+
+ @Override
+ public void run() {
+ DOT_LOGGER.info( "." );
+ _count++;
+ if ( _count % 60 == 0 ) {
+ if ( _count % 120 == 0 ) {
+ EOL_LOGGER.info( " " + (_count / 2) );
+ } else {
+ DOT_LOGGER.info( " " + (_count / 2) + " " );
+ }
+ }
+ }
+ }
+
+}
Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java (from r1876940, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java&r1=1876940&r2=1876941&rev=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java Fri Apr 24 20:06:57 2020
@@ -1,4 +1,4 @@
-package org.apache.ctakes.core.util;
+package org.apache.ctakes.core.util.log;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.pipeline.ProgressManager;
Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java Fri Apr 24 20:06:57 2020
@@ -1,5 +1,6 @@
package org.apache.ctakes.core.util;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java Fri Apr 24 20:06:57 2020
@@ -1,15 +1,11 @@
package org.apache.ctakes.coreference.ae;
-import java.io.*;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-
+import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multiset;
import org.apache.ctakes.constituency.parser.util.TreeUtils;
import org.apache.ctakes.core.config.ConfigParameterConstants;
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.relation.CollectionTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -31,8 +27,14 @@ import org.apache.uima.jcas.tcas.Annotat
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.util.ViewUriUtil;
-import com.google.common.collect.HashMultiset;
-import com.google.common.collect.Multiset;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
@PipeBitInfo(
name = "Coreference Score Writer",
@@ -105,7 +107,7 @@ public class CoreferenceChainScoringOutp
try{
filename = new File(ViewUriUtil.getURI(jCas));
}catch(Exception e){
- filename = new File(DocumentIDAnnotationUtil.getDocumentID(jCas));
+ filename = new File( DocIdUtil.getDocumentID( jCas ) );
}
JCas chainsCas = null;
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.coreference.ae
import org.apache.ctakes.core.ae.NamedEngine;
import org.apache.ctakes.core.patient.PatientViewUtil;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
import org.apache.ctakes.core.util.ListFactory;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.coreference.ae.features.cluster.*;
import org.apache.ctakes.coreference.ae.pairing.cluster.*;
import org.apache.ctakes.coreference.util.ClusterMentionFetcher;
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java Fri Apr 24 20:06:57 2020
@@ -18,30 +18,11 @@
*/
package org.apache.ctakes.coreference.ae;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
+import libsvm.svm_node;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.coreference.type.BooleanLabeledFS;
-import org.apache.ctakes.coreference.type.DemMarkable;
-import org.apache.ctakes.coreference.type.Markable;
-import org.apache.ctakes.coreference.type.MarkablePairSet;
-import org.apache.ctakes.coreference.type.NEMarkable;
-import org.apache.ctakes.coreference.type.PronounMarkable;
-import org.apache.ctakes.coreference.util.AbstractClassifier;
-import org.apache.ctakes.coreference.util.CorefConsts;
-import org.apache.ctakes.coreference.util.FSIteratorToList;
-import org.apache.ctakes.coreference.util.FeatureVector;
-import org.apache.ctakes.coreference.util.MarkableTreeUtils;
-import org.apache.ctakes.coreference.util.SvmVectorCreator;
-import org.apache.ctakes.coreference.util.SyntaxAttributeCalculator;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.coreference.type.*;
+import org.apache.ctakes.coreference.util.*;
import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -59,7 +40,8 @@ import org.apache.uima.jcas.cas.NonEmpty
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
-import libsvm.svm_node;
+import java.io.File;
+import java.util.*;
@PipeBitInfo(
name = "SVM Chain Creator (MiPACQ)",
@@ -146,7 +128,7 @@ public class MipacqSvmChainCreator exten
LinkedList<Annotation> lm = FSIteratorToList.convert(
jcas.getJFSIndexRepository().getAnnotationIndex(Markable.type).iterator());
Map<Markable, NonEmptyFSList> collectionRas = new HashMap<>();
- String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String docName = DocIdUtil.getDocumentID( jcas );
logger.info("Classifying coreference in document: " + docName);
// ArrayList<CollectionTextRelation> chains = new ArrayList<CollectionTextRelation>();
int chainId = 0;
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java Fri Apr 24 20:06:57 2020
@@ -6,7 +6,7 @@ import org.apache.ctakes.core.patient.Pa
import org.apache.ctakes.core.patient.PatientNoteStore;
import org.apache.ctakes.core.patient.PatientViewUtil;
import org.apache.ctakes.core.util.ListFactory;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.coreference.eval.EvaluationOfEventCoreference;
import org.apache.ctakes.coreference.util.ThymeCasOrderer;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
@@ -46,8 +46,6 @@ import java.net.MalformedURLException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.IntStream;
/**
* Created by tmill on 2/22/18.
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java Fri Apr 24 20:06:57 2020
@@ -1,12 +1,6 @@
package org.apache.ctakes.coreference.ae.features;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
@@ -22,6 +16,8 @@ import org.apache.uima.jcas.cas.FSArray;
import org.cleartk.ml.Feature;
import org.cleartk.util.ViewUriUtil;
+import java.util.*;
+
public class UMLSFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
String docId = null;
@@ -140,9 +136,11 @@ public class UMLSFeatureExtractor implem
public static String getDocId(JCas jcas) {
String docId = null;
-
- docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
- if(docId != DocumentIDAnnotationUtil.NO_DOCUMENT_ID) return docId;
+
+ docId = DocIdUtil.getDocumentID( jcas );
+ if ( docId != DocIdUtil.NO_DOCUMENT_ID ) {
+ return docId;
+ }
try{
if(jcas.getView(ViewUriUtil.URI) != null){
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java Fri Apr 24 20:06:57 2020
@@ -18,34 +18,14 @@
*/
package org.apache.ctakes.coreference.cc;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Scanner;
-
import libsvm.svm_node;
-
import org.apache.ctakes.constituency.parser.treekernel.TreeExtractor;
import org.apache.ctakes.constituency.parser.util.TreeUtils;
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.coreference.type.BooleanLabeledFS;
-import org.apache.ctakes.coreference.type.DemMarkable;
-import org.apache.ctakes.coreference.type.Markable;
-import org.apache.ctakes.coreference.type.MarkablePairSet;
-import org.apache.ctakes.coreference.type.NEMarkable;
-import org.apache.ctakes.coreference.util.CorefConsts;
-import org.apache.ctakes.coreference.util.FSIteratorToList;
-import org.apache.ctakes.coreference.util.GoldStandardLabeler;
-import org.apache.ctakes.coreference.util.MarkableTreeUtils;
-import org.apache.ctakes.coreference.util.PairAttributeCalculator;
-import org.apache.ctakes.coreference.util.SvmVectorCreator;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.coreference.type.*;
+import org.apache.ctakes.coreference.util.*;
import org.apache.ctakes.relationextractor.eval.XMIReader;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.utils.tree.SimpleTree;
@@ -56,15 +36,19 @@ import org.apache.uima.analysis_engine.A
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.collection.CollectionReader;
+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.jcas.cas.FSList;
import org.apache.uima.jcas.cas.NonEmptyFSList;
import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-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 java.io.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.Scanner;
@PipeBitInfo(
name = "ODIE Vector File Writer",
@@ -211,7 +195,7 @@ public class ODIEVectorFileWriter extend
// return;
// }
- String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String docId = DocIdUtil.getDocumentID( jcas );
docId = docId.substring(docId.lastIndexOf('/')+1, docId.length());
// Hashtable<Integer, Integer> sysId2AlignId = new Hashtable<Integer, Integer>();
// Hashtable<Integer, Integer> goldId2AlignId = new Hashtable<Integer, Integer>();
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.coreference.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.uima.UIMAException;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -122,8 +122,8 @@ public class PreprocessAndWriteXmi {
// FIXME - not using this right now, just use default jcas
// JCas goldView = jCas.getView(RelationExtractorEvaluation.GOLD_VIEW_NAME);
JCas goldView = jCas;
- String documentID = DocumentIDAnnotationUtil.getDocumentID( goldView );
- if ( documentID == null || documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ String documentID = DocIdUtil.getDocumentID( goldView );
+ if ( documentID == null || documentID.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
throw new IllegalArgumentException( "No documentID for CAS:\n" + jCas );
}
File outFile = new File( this.outputDirectory, documentID + ".xmi" );
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java Fri Apr 24 20:06:57 2020
@@ -16,7 +16,7 @@ import org.apache.ctakes.core.patient.Pa
import org.apache.ctakes.core.patient.PatientViewUtil;
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.coreference.ae.*;
import org.apache.ctakes.coreference.factory.CoreferenceAnnotatorFactory;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
@@ -26,7 +26,10 @@ import org.apache.ctakes.temporal.ae.Doc
import org.apache.ctakes.temporal.ae.EventAnnotator;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase;
-import org.apache.ctakes.typesystem.type.relation.*;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
+import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -508,8 +511,8 @@ public class EvaluationOfEventCoreferenc
static Logger logger = Logger.getLogger(DocumentIDPrinter.class);
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
- String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
- if(docId.startsWith(DocumentIDAnnotationUtil.NO_DOCUMENT_ID)){
+ String docId = DocIdUtil.getDocumentID( jCas );
+ if ( docId.startsWith( DocIdUtil.NO_DOCUMENT_ID ) ) {
docId = new File(ViewUriUtil.getURI(jCas)).getName();
}
logger.info(String.format("Processing %s\n", docId));
Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java Fri Apr 24 20:06:57 2020
@@ -43,7 +43,7 @@ package org.apache.ctakes.dependency.par
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.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.log4j.Logger;
@@ -100,10 +100,10 @@ public class DependencyNodeWriter extend
private void processView( JCas jCas ) throws Exception {
// String docText = view.getDocumentText();
- String docName = DocumentIDAnnotationUtil.getDocumentID( jCas );
+ String docName = DocIdUtil.getDocumentID( jCas );
File outputFile;
- if ( docName == null || docName.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
+ if ( docName == null || docName.equals( DocIdUtil.NO_DOCUMENT_ID ) ) {
docName = "doc" + iv_procCount + "." + iv_outputFormat.toLowerCase();
} else {
docName = docName + "." + iv_outputFormat.toLowerCase();
Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.dictionary.lookup2.util;
import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.utils.env.EnvironmentVariable;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
Modified: ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java (original)
+++ ctakes/trunk/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java Fri Apr 24 20:06:57 2020
@@ -151,17 +151,17 @@ final public class SystemUtil {
processBuilder.command( "cmd.exe", "/c", command.replace( '/', '\\' ) );
final Process process = processBuilder.start();
- final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
- String line;
- while ( (line = reader.readLine()) != null ) {
- System.out.println( line );
- }
-
- final BufferedReader errors = new BufferedReader( new InputStreamReader( process.getErrorStream() ) );
- String error;
- while ( (error = errors.readLine()) != null ) {
- System.err.println( error );
- }
+// final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
+// String line;
+// while ( (line = reader.readLine()) != null ) {
+// System.out.println( line );
+// }
+//
+// final BufferedReader errors = new BufferedReader( new InputStreamReader( process.getErrorStream() ) );
+// String error;
+// while ( (error = errors.readLine()) != null ) {
+// System.err.println( error );
+// }
int exitCode = process.waitFor();
// System.out.println( "\nCMD Exited with error code : " + exitCode );
@@ -177,12 +177,12 @@ final public class SystemUtil {
processBuilder.command( "bash", "-c", command );
final Process process = processBuilder.start();
- final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
-
- String line;
- while ( (line = reader.readLine()) != null ) {
- System.out.println( line );
- }
+// final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
+//
+// String line;
+// while ( (line = reader.readLine()) != null ) {
+// System.out.println( line );
+// }
int exitCode = process.waitFor();
// System.out.println( "\nBASH Exited with error code : " + exitCode );
Modified: ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java (original)
+++ ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,99 +18,26 @@
*/
package org.apache.ctakes.drugner.ae;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
import org.apache.ctakes.core.ae.TokenizerAnnotator;
-import org.apache.ctakes.core.fsm.adapters.ContractionTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.NewlineTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.PunctuationTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.SymbolTokenAdapter;
-import org.apache.ctakes.core.fsm.adapters.WordTokenAdapter;
+import org.apache.ctakes.core.fsm.adapters.*;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DateParser;
+import org.apache.ctakes.core.util.CalendarUtil;
import org.apache.ctakes.core.util.FSUtil;
import org.apache.ctakes.core.util.JCasUtil;
import org.apache.ctakes.core.util.ParamUtil;
import org.apache.ctakes.drugner.DrugMention;
import org.apache.ctakes.drugner.elements.DrugChangeStatusElement;
-import org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FormFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM;
-import org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM;
+import org.apache.ctakes.drugner.fsm.machines.elements.*;
import org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM;
import org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM;
-import org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl;
-import org.apache.ctakes.drugner.fsm.output.elements.DosageToken;
-import org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken;
-import org.apache.ctakes.drugner.fsm.output.elements.DurationToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FormToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FrequencyToken;
-import org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken;
-import org.apache.ctakes.drugner.fsm.output.elements.RouteToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitCombinedToken;
-import org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitToken;
+import org.apache.ctakes.drugner.fsm.output.elements.*;
import org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator;
import org.apache.ctakes.drugner.fsm.output.util.SuffixStrengthToken;
-import org.apache.ctakes.drugner.type.ChunkAnnotation;
-import org.apache.ctakes.drugner.type.DecimalStrengthAnnotation;
-import org.apache.ctakes.drugner.type.DosagesAnnotation;
-import org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation;
-import org.apache.ctakes.drugner.type.DrugMentionAnnotation;
-import org.apache.ctakes.drugner.type.DurationAnnotation;
-import org.apache.ctakes.drugner.type.FormAnnotation;
-import org.apache.ctakes.drugner.type.FractionStrengthAnnotation;
-import org.apache.ctakes.drugner.type.FrequencyAnnotation;
-import org.apache.ctakes.drugner.type.FrequencyUnitAnnotation;
-import org.apache.ctakes.drugner.type.RangeStrengthAnnotation;
-import org.apache.ctakes.drugner.type.RouteAnnotation;
-import org.apache.ctakes.drugner.type.StrengthAnnotation;
-import org.apache.ctakes.drugner.type.StrengthUnitAnnotation;
-import org.apache.ctakes.drugner.type.SubSectionAnnotation;
-import org.apache.ctakes.drugner.type.SuffixStrengthAnnotation;
+import org.apache.ctakes.drugner.type.*;
import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.refsem.Date;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDosage;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDuration;
-import org.apache.ctakes.typesystem.type.refsem.MedicationForm;
-import org.apache.ctakes.typesystem.type.refsem.MedicationFrequency;
-import org.apache.ctakes.typesystem.type.refsem.MedicationRoute;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStrength;
-import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
-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.textsem.DateAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-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.TimeMention;
+import org.apache.ctakes.typesystem.type.refsem.*;
+import org.apache.ctakes.typesystem.type.syntax.*;
+import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.log4j.Logger;
@@ -123,9 +50,10 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.jcas.cas.FSArray;
import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.resource.ResourceAccessException;
import org.apache.uima.resource.ResourceInitializationException;
+import java.util.*;
+
/**
* Finds tokens based on context. There are two major groupings or ranges that
@@ -404,13 +332,15 @@ public class DrugMentionAnnotator extend
medicationMention.setMedicationStrength(modifier);
}
- if (fromAnnotation.getStartDate()!=null) {
- Date d = DateParser.parse(jcas, fromAnnotation.getStartDate());
- TimeMention timeMention = new TimeMention(jcas);
- timeMention.setDate(d);
- timeMention.setTimeClass(CONST.TIME_CLASS_DATE);
+ if ( fromAnnotation.getStartDate() != null ) {
+// Date d = DateParser.parse(jcas, fromAnnotation.getStartDate());
+// TimeMention timeMention = new TimeMention(jcas);
+// timeMention.setDate(d);
+// timeMention.setTimeClass(CONST.TIME_CLASS_DATE);
// if (d!=null) d.addToIndexes(); // don't need to be able to get these directly from the AnnotationIndex
- if (d!=null) medicationMention.setStartDate(timeMention);
+// if (d!=null) medicationMention.setStartDate(timeMention);
+ final TimeMention timeMention = CalendarUtil.createTimeMention( jcas, fromAnnotation.getStartDate() );
+ medicationMention.setStartDate( timeMention );
}
// Add fix CTAKES-129 Populate the Drug NER named entity confidence attribute
if (fromAnnotation.getConfidence() != 0.0 ) {
Modified: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper (original)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/pipeline/FullPipeline.piper Fri Apr 24 20:06:57 2020
@@ -1,34 +1,48 @@
+//set InputFileName=C:/Spiffy/ctakes_data/alon_geva/temp/temp.txt
+//reader LinesFromFileCollectionReader
// Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), Paragraphs, Lists
-load FullTokenizerPipeline
+//load FullTokenizerPipeline
// OR use the standard tokenizer pipeline:
//load DefaultTokenizerPipeline
+add BsvRegexSectionizer SectionsBsv=org/apache/ctakes/core/sections/NaaccrXmlSections.bsv
+
+add SectionFilter ValidSectionList=org/apache/ctakes/core/sections/NaaccrXmlSections.bsv
+
+add SentenceDetector
+add TokenizerAnnotatorPTB
+
// Always need these ...
-add ContextDependentTokenizerAnnotator
+//add ContextDependentTokenizerAnnotator
add POSTagger
// Chunkers
-load ChunkerSubPipe
+//load ChunkerSubPipe
// Default fast dictionary lookup
-set minimumSpan=2
+//set minimumSpan=2
load DictionarySubPipe
// Cleartk Entity Attributes (negation, uncertainty, etc.)
-load AttributeCleartkSubPipe
+//load AttributeCleartkSubPipe
+
+//package org.apache.ctakes.examples.ae
+//add BodySideFinder
// Entity Relations (degree/severity, anatomical location)
-load RelationSubPipe
+//load RelationSubPipe
// Temporal (event, time, dtr, tlink)
-load TemporalSubPipe
+//load TemporalSubPipe
// Coreferences (e.g. patient = he)
-load CorefSubPipe
+//load CorefSubPipe
// Html output
add pretty.html.HtmlTextWriter
// XMI output
//writeXmis
+
+//add SentenceFirstCuiWriter
Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/MultiThreadedPipeline.java Fri Apr 24 20:06:57 2020
@@ -18,21 +18,14 @@
*/
package org.apache.ctakes.examples.pipeline;
-import java.io.IOException;
-
-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.SubjectCleartkAnalysisEngine;
-import org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine;
+import org.apache.ctakes.assertion.medfacts.cleartk.*;
import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
import org.apache.ctakes.core.ae.SentenceDetector;
import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
import org.apache.ctakes.lvg.ae.ThreadSafeLvg;
@@ -53,6 +46,8 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.util.ProcessTrace;
+import java.io.IOException;
+
public class MultiThreadedPipeline {
public static final int NUM_THREADS = 3;
@@ -152,7 +147,7 @@ public class MultiThreadedPipeline {
public void entityProcessComplete(CAS aCas, EntityProcessStatus aStatus) {
try {
JCas jcas = aCas.getJCas();
- String docId = DocumentIDAnnotationUtil.getDeepDocumentId(jcas);
+ String docId = DocIdUtil.getDeepDocumentId( jcas );
System.out.println("Doc id for entity process complete: " + docId);
System.out.println("Found " + JCasUtil.select(jcas, IdentifiedAnnotation.class).size() + " medical terms.");
// The following was a bit verbose, but here's how you'd print out the text of each discovered entity span:
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
package org.apache.ctakes.fhir.cc;
-import org.apache.ctakes.core.util.EssentialAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.EssentialAnnotationUtil;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.fhir.resource.*;
import org.apache.ctakes.fhir.util.FhirNoteSpecs;
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java Fri Apr 24 20:06:57 2020
@@ -3,8 +3,8 @@ package org.apache.ctakes.fhir.element;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import org.apache.ctakes.core.semantic.SemanticGroup;
-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.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
@@ -161,7 +161,7 @@ final public class FhirElementFactory {
* @return fhir id containing name and code.
*/
static public String createId( final JCas jCas, final String name, final String code ) {
- return DocumentIDAnnotationUtil.getDocumentID( jCas ) + DIVIDER_CHAR + name + DIVIDER_CHAR + code;
+ return DocIdUtil.getDocumentID( jCas ) + DIVIDER_CHAR + name + DIVIDER_CHAR + code;
}
// Identifiers are 0 .. 1 , so unnecessary
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java Fri Apr 24 20:06:57 2020
@@ -1,8 +1,8 @@
package org.apache.ctakes.fhir.resource;
import org.apache.ctakes.core.semantic.SemanticGroup;
-import org.apache.ctakes.core.util.EssentialAnnotationUtil;
-import org.apache.ctakes.core.util.IdentifiedAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.EssentialAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.IdentifiedAnnotationUtil;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.fhir.util.FhirNoteSpecs;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.fhir.util;
import org.apache.ctakes.core.note.NoteSpecs;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.fhir.element.FhirElementFactory;
import org.apache.ctakes.typesystem.type.structured.SourceData;
import org.apache.log4j.Logger;
Modified: ctakes/trunk/ctakes-gui/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/pom.xml?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/pom.xml (original)
+++ ctakes/trunk/ctakes-gui/pom.xml Fri Apr 24 20:06:57 2020
@@ -18,10 +18,6 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-gui-res</artifactId>
</dependency>
- <!-- <dependency>-->
- <!-- <groupId>org.apache.ctakes</groupId>-->
- <!-- <artifactId>ctakes-coreference</artifactId>-->
- <!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-core</artifactId>
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java Fri Apr 24 20:06:57 2020
@@ -5,7 +5,7 @@ import io.github.lukehutch.fastclasspath
import io.github.lukehutch.fastclasspathscanner.ScanInterruptedException;
import io.github.lukehutch.fastclasspathscanner.matchprocessor.SubclassMatchProcessor;
import io.github.lukehutch.fastclasspathscanner.scanner.ScanResult;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.log4j.Logger;
import org.apache.uima.analysis_component.Annotator_ImplBase;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java Fri Apr 24 20:06:57 2020
@@ -25,7 +25,7 @@ import com.google.common.collect.Orderin
import com.lexicalscope.jewel.cli.Option;
import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
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.structured.DocumentID;
import org.apache.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -183,7 +183,7 @@ public class SHARPXMI {
for ( Iterator<JCas> casIter = new JCasIterator( reader, builder.createAggregate() ); casIter.hasNext(); ) {
JCas jCas = casIter.next();
JCas goldView = jCas.getView( GOLD_VIEW_NAME );
- String documentID = DocumentIDAnnotationUtil.getDocumentID( goldView );
+ String documentID = DocIdUtil.getDocumentID( goldView );
if ( documentID == null ){//|| documentID.equals( DocumentIDAnnotationUtil.NO_DOCUMENT_ID ) ) {
throw new IllegalArgumentException( "No documentID for CAS:\n" + jCas );
}
Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,18 +18,11 @@
*/
package org.apache.ctakes.sideeffect.ae;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.PSESentence;
+import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -38,11 +31,11 @@ import org.apache.uima.jcas.JFSIndexRepo
import org.apache.uima.jcas.cas.StringArray;
import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.FSUtil;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.sideeffect.type.PSESentence;
-import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.*;
/**
* Extract SE sentence (from PSESentence) features and add them to
@@ -76,7 +69,7 @@ public class SESentenceFeatureAnnotator
public void process(JCas jcas)
throws AnalysisEngineProcessException {
- String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ String docName = DocIdUtil.getDocumentID( jcas );
System.out.println("---" + docName + "---");
// add features to cas
Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java Fri Apr 24 20:06:57 2020
@@ -18,17 +18,16 @@
*/
package org.apache.ctakes.sideeffect.ae;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.drugner.type.SubSectionAnnotation;
+import org.apache.ctakes.sideeffect.type.SESentence;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import org.apache.ctakes.sideeffect.util.PatternMatch;
+import org.apache.ctakes.sideeffect.util.SEUtil;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -36,16 +35,10 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.ctakes.core.resource.FileResource;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.core.util.FSUtil;
-import org.apache.ctakes.sideeffect.util.PatternMatch;
-import org.apache.ctakes.sideeffect.util.SEUtil;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.ctakes.drugner.type.SubSectionAnnotation;
-import org.apache.ctakes.sideeffect.type.SESentence;
-import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.util.*;
/**
* Rule-based side effect extraction.
@@ -157,8 +150,8 @@ public class SideEffectAnnotator extends
{
List<PotentialSideEffect> potentialSideEffectLst;
List<SideEffect> sideEffectLst;
-
- String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+
+ String docName = DocIdUtil.getDocumentID( jcas );
System.out.println("---"+docName+" processed---");
//remove duplicated named entities
Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
*/
package org.apache.ctakes.sideeffect.cc;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
import org.apache.ctakes.sideeffect.util.SEUtil;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -34,7 +29,11 @@ import org.apache.uima.resource.Resource
import org.apache.uima.resource.ResourceProcessException;
import org.apache.uima.util.ProcessTrace;
-import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
public class SideEffectCasConsumer extends CasConsumer_ImplBase {
public static final String PARAM_OUTPUT_FILE = "OutputFile";
@@ -73,10 +72,10 @@ public class SideEffectCasConsumer exten
if(jcas == null){
jcas = cas.getJCas();
}
-
- JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-
- String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+
+ JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+
+ String docName = DocIdUtil.getDocumentID( jcas );
Iterator seIter = indexes.getAnnotationIndex(SideEffectAnnotation.type).iterator();
while(seIter.hasNext()) {
Modified: ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java (original)
+++ ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
*/
package org.apache.ctakes.sideeffect.cc;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.sideeffect.type.SESentence;
import org.apache.ctakes.sideeffect.util.SEUtil;
import org.apache.uima.cas.CAS;
import org.apache.uima.collection.CasConsumer_ImplBase;
@@ -34,7 +29,11 @@ import org.apache.uima.resource.Resource
import org.apache.uima.resource.ResourceProcessException;
import org.apache.uima.util.ProcessTrace;
-import org.apache.ctakes.sideeffect.type.SESentence;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
public class SideEffectSentenceCasConsumer extends CasConsumer_ImplBase {
public static final String PARAM_OUTPUT_FILE = "OutputFile";
@@ -65,9 +64,9 @@ public class SideEffectSentenceCasConsum
try {
JCas jcas;
jcas = SEUtil.getJCasViewWithDefault(cas, "plaintext");
- JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-
- String docName = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+
+ String docName = DocIdUtil.getDocumentID( jcas );
Iterator ssIter = indexes.getAnnotationIndex(SESentence.type).iterator();
while(ssIter.hasNext()) {
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor;
import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java Fri Apr 24 20:06:57 2020
@@ -1,7 +1,7 @@
package org.apache.ctakes.temporal.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
import org.apache.ctakes.temporal.utils.CalendarUtil;
import org.apache.ctakes.typesystem.type.structured.SourceData;
import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java Fri Apr 24 20:06:57 2020
@@ -19,7 +19,7 @@
package org.apache.ctakes.temporal.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.temporal.ae.feature.*;
import org.apache.ctakes.temporal.utils.SoftMaxUtil;
import org.apache.ctakes.typesystem.type.refsem.Event;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java Fri Apr 24 20:06:57 2020
@@ -20,7 +20,7 @@ package org.apache.ctakes.temporal.ae;
import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java Fri Apr 24 20:06:57 2020
@@ -2,8 +2,8 @@ package org.apache.ctakes.temporal.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
import org.apache.ctakes.core.util.Pair;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.temporal.utils.CalendarUtil;
import org.apache.ctakes.typesystem.type.refsem.Date;
import org.apache.ctakes.typesystem.type.syntax.Chunk;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java Fri Apr 24 20:06:57 2020
@@ -2,7 +2,7 @@ package org.apache.ctakes.temporal.ae;
import com.google.common.collect.Lists;
-import org.apache.ctakes.core.util.WordTokenUtil;
+import org.apache.ctakes.core.util.annotation.WordTokenUtil;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,28 +18,22 @@
*/
package org.apache.ctakes.temporal.ae.feature;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-//import java.util.logging.Logger;
-import java.util.Set;
-
-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.NewlineToken;
-import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
import org.cleartk.ml.feature.extractor.CleartkExtractorException;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-import org.cleartk.util.ViewUriUtil;
+
+import java.util.*;
+
+//import java.util.logging.Logger;
public class EventPropertyExtractor implements FeatureExtractor1<Annotation> {
@@ -87,7 +81,7 @@ public class EventPropertyExtractor impl
//get Document ID:
String fname;
try {
- String docID = DocumentIDAnnotationUtil.getDocumentID(view);//ViewUriUtil.getURI(view).toString();
+ String docID = DocIdUtil.getDocumentID( view );//ViewUriUtil.getURI(view).toString();
int begin = docID.lastIndexOf("_");
fname = docID.substring(begin+1);
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,26 +18,24 @@
*/
package org.apache.ctakes.temporal.ae.feature;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Multimap;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
-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.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
import org.cleartk.util.ViewUriUtil;
-import org.apache.uima.fit.util.JCasUtil;
-import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Multimap;
+import java.util.ArrayList;
+import java.util.List;
/**
* Given a pair of arguments, if any one of them is an event, get the related event-sectiontime as features
* @author CH151862
@@ -58,7 +56,7 @@ RelationFeaturesExtractor<IdentifiedAnno
try{
docId = ViewUriUtil.getURI(jCas).toString();// get docID
}catch(Exception e){
- docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ docId = DocIdUtil.getDocumentID( jCas );
}
if(!docId.equals(cachedDocID)){
// rebuild cache
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java Fri Apr 24 20:06:57 2020
@@ -18,13 +18,8 @@
*/
package org.apache.ctakes.temporal.ae.feature;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.doc.DocIdUtil;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
@@ -36,21 +31,14 @@ import org.apache.uima.fit.util.JCasUtil
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.ml.Feature;
-import org.cleartk.ml.feature.extractor.CleartkExtractor;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
-import org.cleartk.ml.feature.extractor.CombinedExtractor1;
-import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
-import org.cleartk.ml.feature.extractor.DistanceExtractor;
-import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-import org.cleartk.ml.feature.extractor.NamingExtractor1;
+import org.cleartk.ml.feature.extractor.*;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.*;
import org.cleartk.util.ViewUriUtil;
-import com.google.common.collect.Multimap;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
/**
* for every UMLS entities covering the annotation, extracted related token features
@@ -114,7 +102,7 @@ public class MultiTokenFeaturesExtractor
try{
docId = ViewUriUtil.getURI(jCas).toString();// get docID
}catch(Exception e){
- docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ docId = DocIdUtil.getDocumentID( jCas );
}
if(!docId.equals(cachedDocID)){
// rebuild event-event map
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java Fri Apr 24 20:06:57 2020
@@ -1,24 +1,8 @@
package org.apache.ctakes.temporal.nn.ae;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
+import com.google.common.collect.Lists;
import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.ae.EventTimeTokenBasedAnnotator.OutputMode;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
@@ -39,7 +23,9 @@ import org.cleartk.ml.Feature;
import org.cleartk.ml.Instance;
import org.cleartk.util.ViewUriUtil;
-import com.google.common.collect.Lists;
+import java.io.*;
+import java.util.*;
+import java.util.Map.Entry;
/**
* a joint annotator for annotating both event-time and event-event relations using neural models.
* @author chenlin
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java?rev=1876941&r1=1876940&r2=1876941&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java Fri Apr 24 20:06:57 2020
@@ -26,6 +26,7 @@ import static java.util.Calendar.*;
* @author SPF , chip-nlp
* @version %I%
* @since 1/8/2019
+ * @deprecated use CalendarUtil in core.util
*/
final public class CalendarUtil {