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Posted to commits@ctakes.apache.org by se...@apache.org on 2020/04/27 15:05:41 UTC
svn commit: r1877084 - in
/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util:
DocumentIDAnnotationUtil.java DotLogger.java FinishedLogger.java
OntologyConceptUtil.java SourceMetadataUtil.java WordTokenUtil.java
Author: seanfinan
Date: Mon Apr 27 15:05:41 2020
New Revision: 1877084
URL: http://svn.apache.org/viewvc?rev=1877084&view=rev
Log:
My IDE didn't add the deprecated copies of the classes that I moved Friday. I didn't notice that they weren't checked in.
Apologies if anybody with dependency got a broken build. - though it should have made you aware of the refactor!
Added:
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/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
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,89 @@
+/**
+ * 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;
+
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.uima.jcas.JCas;
+
+/**
+ * Utility class for fetching document id
+ * @deprecated use DocIdUtil in (sub) package doc
+ */
+@Deprecated
+final public class DocumentIDAnnotationUtil {
+
+ // Added for CTAKES-365
+ static public final String NO_DOCUMENT_ID = DocIdUtil.NO_DOCUMENT_ID;
+ static public final String NO_DOCUMENT_ID_PREFIX = DocIdUtil.NO_DOCUMENT_ID_PREFIX;
+
+ private DocumentIDAnnotationUtil() {
+ }
+
+ /**
+ * 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}
+ */
+ @Deprecated
+ public static String getDocumentID( final JCas jcas ) {
+ return DocIdUtil.getDocumentID( jcas );
+ }
+
+
+ /**
+ * 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}
+ */
+ @Deprecated
+ static public String getDeepDocumentId( final JCas startingJcas ) {
+ return DocIdUtil.getDeepDocumentId( startingJcas );
+ }
+
+ /**
+ * 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
+ */
+ @Deprecated
+ static public String getDocumentIdForFile( final JCas jcas ) {
+ return DocIdUtil.getDocumentIdForFile( jcas );
+ }
+
+ /**
+ * 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}
+ */
+ @Deprecated
+ public static String getDocumentIdPrefix( final JCas jcas ) {
+ return DocIdUtil.getDocumentIdPrefix( jcas );
+ }
+
+}
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,36 @@
+package org.apache.ctakes.core.util;
+
+import java.io.Closeable;
+import java.io.IOException;
+
+/**
+ * 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
+ * @deprecated use DotLogger in (sub) package log
+ */
+@Deprecated
+final public class DotLogger implements Closeable {
+
+ final private org.apache.ctakes.core.util.log.DotLogger _delegate;
+
+ /**
+ * Starts the Dot Logging
+ */
+ @Deprecated
+ public DotLogger() {
+ _delegate = new org.apache.ctakes.core.util.log.DotLogger();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ @Deprecated
+ public void close() throws IOException {
+ _delegate.close();
+ }
+
+}
Added: 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/FinishedLogger.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,40 @@
+package org.apache.ctakes.core.util;
+
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 5/21/2018
+ * @deprecated use FinishedLogger in (sub) package log
+ */
+@PipeBitInfo(
+ name = "Deprecated Finished Logger",
+ description = "use FinishedLogger in (sub) package log.",
+ role = PipeBitInfo.Role.SPECIAL
+)
+final public class FinishedLogger extends JCasAnnotator_ImplBase {
+
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void initialize( final UimaContext context ) throws ResourceInitializationException {
+ throw new ResourceInitializationException( new Exception( "Deprecated use FinishedLogger in (sub) package log." ) );
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void process( final JCas jCas ) throws AnalysisEngineProcessException {
+ throw new AnalysisEngineProcessException( new Exception( "Deprecated use FinishedLogger in (sub) package log." ) );
+ }
+
+}
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,431 @@
+package org.apache.ctakes.core.util;
+
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.cas.FeatureStructure;
+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.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 1/8/2015
+ * @deprecated use OntologyConceptUtil in (sub) package annotation
+ */
+@Deprecated
+final public class OntologyConceptUtil {
+
+ private OntologyConceptUtil() {
+ }
+
+ /**
+ * @param annotation -
+ * @return array of FeatureStructure castable to array of OntologyConcept
+ */
+ @Deprecated
+ static public FeatureStructure[] getConceptFeatureStructures( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getConceptFeatureStructures( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return stream of OntologyConcept
+ */
+ @Deprecated
+ static public Stream<OntologyConcept> getOntologyConceptStream( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getOntologyConceptStream( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return stream of OntologyConcept
+ */
+ @Deprecated
+ static public Collection<OntologyConcept> getOntologyConcepts( final IdentifiedAnnotation annotation ) {
+ return getOntologyConceptStream( annotation ).collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotation -
+ * @return stream of all Umls Concepts associated with the annotation
+ */
+ @Deprecated
+ static public Stream<UmlsConcept> getUmlsConceptStream( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getUmlsConceptStream( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return set of all Umls Concepts associated with the annotation
+ */
+ @Deprecated
+ static public Collection<UmlsConcept> getUmlsConcepts( final IdentifiedAnnotation annotation ) {
+ return getUmlsConceptStream( annotation ).collect( Collectors.toSet() );
+ }
+
+
+ //
+ // Get cuis, tuis, or codes for a single IdentifiedAnnotation
+ //
+
+ /**
+ * @param annotation -
+ * @return set of all Umls cuis associated with the annotation
+ */
+ @Deprecated
+ static public Collection<String> getCuis( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCuis( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return set of all Umls tuis associated with the annotation
+ */
+ @Deprecated
+ static public Collection<String> getTuis( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getTuis( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return map of ontology scheme names to a set of ontology codes associated each scheme
+ */
+ @Deprecated
+ static public Map<String, Collection<String>> getSchemeCodes( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getSchemeCodes( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @return set of ontology codes associated with all schemes
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final IdentifiedAnnotation annotation ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCodes( annotation );
+ }
+
+ /**
+ * @param annotation -
+ * @param schemeName name of the scheme of interest
+ * @return set of ontology codes associated the named scheme
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final IdentifiedAnnotation annotation,
+ final String schemeName ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCodes( annotation, schemeName );
+ }
+
+
+ //
+ // Get cuis, tuis, or codes for all IdentifiedAnnotations in a jcas
+ //
+
+ /**
+ * @param jcas -
+ * @return set of all cuis in jcas
+ */
+ @Deprecated
+ static public Collection<String> getCuis( final JCas jcas ) {
+ return getCuis( JCasUtil.select( jcas, IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @return map of all cuis in the jcas and their counts
+ */
+ @Deprecated
+ static public Map<String, Long> getCuiCounts( final JCas jcas ) {
+ return getCuiCounts( JCasUtil.select( jcas, IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @return set of all tuis in jcas
+ */
+ @Deprecated
+ static public Collection<String> getTuis( final JCas jcas ) {
+ return getTuis( JCasUtil.select( jcas, IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @return set of all ontology codes in jcas
+ */
+ @Deprecated
+ static public Map<String, Collection<String>> getSchemeCodes( final JCas jcas ) {
+ return getSchemeCodes( JCasUtil.select( jcas, IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @return set of all ontology codes in jcas
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final JCas jcas ) {
+ return getCodes( JCasUtil.select( jcas, IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @param schemeName name of the scheme of interest
+ * @return set of ontology codes associated the named scheme
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final JCas jcas,
+ final String schemeName ) {
+ return getCodes( JCasUtil.select( jcas, IdentifiedAnnotation.class ), schemeName );
+ }
+
+
+ //
+ // Get cuis, tuis, or codes for all IdentifiedAnnotations in a lookup window
+ //
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @return set of all cuis in lookupWindow
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<String> getCuis( final JCas jcas, final T lookupWindow ) {
+ return getCuis( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ) );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @return set of all tuis in lookupWindow
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<String> getTuis( final JCas jcas, final T lookupWindow ) {
+ return getTuis( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ) );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @return map of all schemes and their codes in lookupWindow
+ */
+ @Deprecated
+ static public <T extends Annotation> Map<String, Collection<String>> getSchemeCodes( final JCas jcas,
+ final T lookupWindow ) {
+ return getSchemeCodes( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ) );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @return set of all codes in lookupWindow
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<String> getCodes( final JCas jcas, final T lookupWindow ) {
+ return getCodes( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ) );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @param schemeName name of the scheme of interest
+ * @return set of ontology codes associated the named scheme
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<String> getCodes( final JCas jcas, final T lookupWindow,
+ final String schemeName ) {
+ return getCodes( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ), schemeName );
+ }
+
+
+ //
+ // Get cuis, tuis, or codes for a collections of IdentifiedAnnotations
+ //
+
+ /**
+ * @param annotations -
+ * @return set of all Umls cuis associated with the annotations
+ */
+ @Deprecated
+ static public Collection<String> getCuis( final Collection<IdentifiedAnnotation> annotations ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCuis( annotations );
+ }
+
+ /**
+ * @param annotations -
+ * @return map of all Umls cuis associated with the annotations and the counts of those cuis
+ */
+ @Deprecated
+ static public Map<String, Long> getCuiCounts( final Collection<IdentifiedAnnotation> annotations ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCuiCounts( annotations );
+ }
+
+ /**
+ * @param annotations -
+ * @return set of all Umls tuis associated with the annotation
+ */
+ @Deprecated
+ static public Collection<String> getTuis( final Collection<IdentifiedAnnotation> annotations ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getTuis( annotations );
+
+ }
+
+ /**
+ * @param annotations -
+ * @return map of ontology scheme names to a set of ontology codes associated each scheme
+ */
+ @Deprecated
+ static public Map<String, Collection<String>> getSchemeCodes( final Collection<IdentifiedAnnotation> annotations ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getSchemeCodes( annotations );
+ }
+
+ /**
+ * @param annotations -
+ * @return set of ontology codes associated with all schemes
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final Collection<IdentifiedAnnotation> annotations ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCodes( annotations );
+ }
+
+ /**
+ * @param annotations -
+ * @param schemeName name of the scheme of interest
+ * @return set of ontology codes associated the named scheme
+ */
+ @Deprecated
+ static public Collection<String> getCodes( final Collection<IdentifiedAnnotation> annotations,
+ final String schemeName ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getCodes( annotations, schemeName );
+ }
+
+
+ //
+ // Get all IdentifiedAnnotations in jcas with given cui, tui, or code
+ //
+
+ /**
+ * @param jcas -
+ * @param cui cui of interest
+ * @return all IdentifiedAnnotations that have the given cui
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCui( final JCas jcas,
+ final String cui ) {
+ return getAnnotationsByCui( JCasUtil.select( jcas, IdentifiedAnnotation.class ), cui );
+ }
+
+ /**
+ * @param jcas -
+ * @param tui tui of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByTui( final JCas jcas,
+ final String tui ) {
+ return getAnnotationsByTui( JCasUtil.select( jcas, IdentifiedAnnotation.class ), tui );
+ }
+
+ /**
+ * @param jcas -
+ * @param code code of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCode( final JCas jcas,
+ final String code ) {
+ return getAnnotationsByCode( JCasUtil.select( jcas, IdentifiedAnnotation.class ), code );
+ }
+
+
+ //
+ // Get all IdentifiedAnnotations in lookup window with given cui, tui, or code
+ //
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @param cui cui of interest
+ * @return all IdentifiedAnnotations that have the given cui
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCui( final JCas jcas,
+ final T lookupWindow,
+ final String cui ) {
+ return getAnnotationsByCui( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ), cui );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @param tui tui of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByTui( final JCas jcas,
+ final T lookupWindow,
+ final String tui ) {
+ return getAnnotationsByTui( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ), tui );
+ }
+
+ /**
+ * @param jcas -
+ * @param lookupWindow -
+ * @param code code of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ @Deprecated
+ static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCode( final JCas jcas,
+ final T lookupWindow,
+ final String code ) {
+ return getAnnotationsByCode( JCasUtil.selectCovered( jcas, IdentifiedAnnotation.class, lookupWindow ), code );
+ }
+
+
+ //
+ // Get all IdentifiedAnnotations in a collection of annotations with given cui, tui, or code
+ //
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param cui cui of interest
+ * @return all IdentifiedAnnotations that have the given cui
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCui(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String cui ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getAnnotationsByCui( annotations, cui );
+ }
+
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param tui tui of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByTui(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String tui ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getAnnotationsByTui( annotations, tui );
+ }
+
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param code code of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ @Deprecated
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCode(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String code ) {
+ return org.apache.ctakes.core.util.annotation.OntologyConceptUtil.getAnnotationsByCode( annotations, code );
+ }
+
+}
Added: 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/SourceMetadataUtil.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,133 @@
+package org.apache.ctakes.core.util;
+
+import org.apache.ctakes.typesystem.type.structured.Metadata;
+import org.apache.ctakes.typesystem.type.structured.SourceData;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceProcessException;
+
+import java.sql.Timestamp;
+
+/**
+ * Utility class with convenience methods for a few commonly-used JCas Metadata types that are begged of the source
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 1/8/2015
+ * @deprecated use SourceMetadataUtil in (sub) package doc
+ */
+@Deprecated
+final public class SourceMetadataUtil {
+
+ @Deprecated
+ static public final String UNKNOWN_PATIENT = org.apache.ctakes.core.util.doc.SourceMetadataUtil.UNKNOWN_PATIENT;
+ @Deprecated
+ static public final long UNKNOWN_PATIENT_NUM
+ = org.apache.ctakes.core.util.doc.SourceMetadataUtil.UNKNOWN_PATIENT_NUM;
+
+ private SourceMetadataUtil() {
+ }
+
+ /**
+ * @param jcas ye olde jay-cas
+ * @return the patient identifier for the source or {@link #UNKNOWN_PATIENT}
+ */
+ @Deprecated
+ static public String getPatientIdentifier( final JCas jcas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getPatientIdentifier( jcas );
+ }
+
+ /**
+ * @param jCas ye olde
+ * @param patientId the patient identifier for the source
+ */
+ @Deprecated
+ static public void setPatientIdentifier( final JCas jCas, final String patientId ) {
+ org.apache.ctakes.core.util.doc.SourceMetadataUtil.setPatientIdentifier( jCas, patientId );
+ }
+
+ /**
+ * @param jcas ye olde jay-cas
+ * @return the patient id for the source or {@link #UNKNOWN_PATIENT_NUM} if one is not found
+ */
+ @Deprecated
+ static public long getPatientNum( final JCas jcas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getPatientNum( jcas );
+ }
+
+ /**
+ * @param jcas ye olde jay-cas
+ * @return the Metadata for the given jcas or null if one is not found
+ */
+ @Deprecated
+ static public Metadata getMetadata( final JCas jcas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getMetadata( jcas );
+ }
+
+ /**
+ * @param jCas ye olde jay-cas
+ * @return the Metadata for the given jcas
+ */
+ @Deprecated
+ static public Metadata getOrCreateMetadata( final JCas jCas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getOrCreateMetadata( jCas );
+ }
+
+ /**
+ * The first step in utilizing SourceData is getting it!
+ *
+ * @param jcas ye olde jay-cas
+ * @return the metadata for the source associated with the jcas or null if one is not found
+ */
+ @Deprecated
+ static public SourceData getSourceData( final JCas jcas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getSourceData( jcas );
+ }
+
+ /**
+ * @param jCas ye olde jay-cas
+ * @return the metadata for the source associated with the jcas
+ */
+ @Deprecated
+ static public SourceData getOrCreateSourceData( final JCas jCas ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getOrCreateSourceData( jCas );
+ }
+
+ /**
+ * @param sourcedata -
+ * @return the instance id or -1 if there isn't one
+ * @throws ResourceProcessException if the internal value is not parseable as long
+ */
+ @Deprecated
+ static public long getInstanceNum( final SourceData sourcedata ) throws ResourceProcessException {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getInstanceNum( sourcedata );
+ }
+
+ /**
+ * @param sourcedata -
+ * @return the encounter id
+ * @throws ResourceProcessException if the encounter id does not exist or is not parseable as an int
+ */
+ @Deprecated
+ static public int getEncounterNum( final SourceData sourcedata ) throws ResourceProcessException {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getEncounterNum( sourcedata );
+ }
+
+ /**
+ * @param sourcedata -
+ * @return the author specialty
+ */
+ @Deprecated
+ static public String getProviderId( final SourceData sourcedata ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getProviderId( sourcedata );
+ }
+
+ /**
+ * @param sourcedata -
+ * @return the original date for the source
+ */
+ @Deprecated
+ static public Timestamp getStartDate( final SourceData sourcedata ) {
+ return org.apache.ctakes.core.util.doc.SourceMetadataUtil.getStartDate( sourcedata );
+ }
+
+}
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java?rev=1877084&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java Mon Apr 27 15:05:41 2020
@@ -0,0 +1,35 @@
+package org.apache.ctakes.core.util;
+
+
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+
+import javax.annotation.concurrent.Immutable;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 9/16/2015
+ * @deprecated use WordTokenUtil in (sub) package annotation.
+ */
+@Immutable
+@Deprecated
+final public class WordTokenUtil {
+
+ private WordTokenUtil() {
+ }
+
+
+ /**
+ * In some pipelines LVG is not run, hence a canonical form does not exist.
+ * In order to prevent NPEs, this method checks for null values of canonical form and covered text
+ *
+ * @param wordToken of interest
+ * @return The first non-null of the word token's canonical form, covered text .
+ */
+ @Deprecated
+ static public String getCanonicalForm( final WordToken wordToken ) {
+ return org.apache.ctakes.core.util.annotation.WordTokenUtil.getCanonicalForm( wordToken );
+ }
+
+
+}