You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by se...@apache.org on 2023/02/04 20:11:49 UTC
[ctakes] branch main updated: Added get/set AnatomicalSite to Procedure Types. AnatomicalSite has slots for body side and laterality. So, this actually will replace 3 slots with 1, and the whole "circular argument" thing is unnecessary.
This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new a95a9aa Added get/set AnatomicalSite to Procedure Types. AnatomicalSite has slots for body side and laterality. So, this actually will replace 3 slots with 1, and the whole "circular argument" thing is unnecessary.
a95a9aa is described below
commit a95a9aa885f269e4e9075229897aa7ab6b81ac04
Author: Sean Finan <se...@childrens.harvard.edu>
AuthorDate: Sat Feb 4 15:11:35 2023 -0500
Added get/set AnatomicalSite to Procedure Types.
AnatomicalSite has slots for body side and laterality.
So, this actually will replace 3 slots with 1, and the whole "circular argument" thing is unnecessary.
---
.../src/main/java/org/mitre/medfacts/uima/RunZoner.java | 11 +++++++----
.../CreateAssertionLuceneIndexFromDelimitedFile.java | 4 ++--
.../lookup/ae/AssertionCuePhraseConsumerImpl.java | 1 +
.../dictionary/lookup/ae/LookupParseUtilitiesRefactor.java | 1 +
.../dictionary/lookup/strtable/FieldConstraintImpl.java | 1 +
.../java/org/apache/ctakes/temporal/ae/TimeAnnotator.java | 1 +
.../temporal/pipelines/EventAndTimeExtractionPipeline.java | 1 -
.../pipelines/TemporalExtractionPipeline_ImplBase.java | 3 ---
.../org/apache/ctakes/typesystem/types/TypeSystem.xml | 13 +++++++++++--
9 files changed, 24 insertions(+), 12 deletions(-)
diff --git a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
index ee00126..b5433db 100644
--- a/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
+++ b/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
@@ -26,7 +26,8 @@ import java.util.Arrays;
import java.util.List;
import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
+import org.apache.ctakes.core.cc.FileTreeXmiWriter;
+import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.cr.TextReader;
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
@@ -144,9 +145,11 @@ public class RunZoner
builder.add(mayoZonerAnnotator);
AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
- XmiWriterCasConsumerCtakes.class,
- typeSystemDescription,
- XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+// XmiWriterCasConsumerCtakes.class,
+// typeSystemDescription,
+// XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+ FileTreeXmiWriter.class,
+ ConfigParameterConstants.PARAM_OUTPUTDIR,
outputDirectory.toString()
);
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/CreateAssertionLuceneIndexFromDelimitedFile.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/CreateAssertionLuceneIndexFromDelimitedFile.java
index e199d86..26d382b 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/CreateAssertionLuceneIndexFromDelimitedFile.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/CreateAssertionLuceneIndexFromDelimitedFile.java
@@ -56,6 +56,7 @@ import org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB;
* hyphenated words so the dictionary entries are tokenized in the same way as
* the clinical text will be.
*/
+@SuppressWarnings( "unchecked" )
public class CreateAssertionLuceneIndexFromDelimitedFile {
private static TokenizerPTB tokenizer = new TokenizerPTB();
@@ -88,7 +89,7 @@ public class CreateAssertionLuceneIndexFromDelimitedFile {
/**
* Constructor
*
- * @param Tokenizer
+ * @param Tokenizer -
* Used to tokenize the dictionary entries
*/
public CreateAssertionLuceneIndexFromDelimitedFile(TokenizerPTB tokenizer)
@@ -367,7 +368,6 @@ public class CreateAssertionLuceneIndexFromDelimitedFile {
return "java LucenePopulateDriver <dir-containing-textfile(s)> [hyphenfile] [freqcutoff]";
}
- @SuppressWarnings( "unchecked" )
protected void writeToFormatLucene(String cuePhrase, String cuePhraseCategory, String cuePhraseFamily) {
Document doc = new Document();
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
index dfea503..6a6b244 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java
@@ -46,6 +46,7 @@ import org.apache.uima.jcas.cas.FSArray;
* Implementation that takes Rxnorm dictionary lookup hits and stores only the
* ones that are also present in the Orange Book.
*/
+@SuppressWarnings( "unchecked" )
public class AssertionCuePhraseConsumerImpl extends BaseLookupConsumerImpl
implements LookupConsumer
{
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
index b7c069e..a2dff90 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java
@@ -56,6 +56,7 @@ import java.util.*;
/**
* @author Mayo Clinic
*/
+@SuppressWarnings( "unchecked" )
final public class LookupParseUtilitiesRefactor {
static private final Logger CLASS_LOGGER = Logger.getLogger( LookupParseUtilitiesRefactor.class );
diff --git a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java
index 4a2f482..7c3522e 100644
--- a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java
+++ b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java
@@ -26,6 +26,7 @@ package org.apache.ctakes.dictionary.lookup.strtable;
* @author Mayo Clinic
*
*/
+@SuppressWarnings( "unchecked" )
public class FieldConstraintImpl implements FieldConstraint
{
public static final int EQ_OP = 0;
diff --git a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
index 236d434..5b7f599 100644
--- a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
+++ b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
@@ -68,6 +68,7 @@ import org.cleartk.ml.jar.GenericJarClassifierFactory;
PipeBitInfo.TypeProduct.BASE_TOKEN },
products = { PipeBitInfo.TypeProduct.TIMEX }
)
+@SuppressWarnings( "unchecked" )
public class TimeAnnotator extends TemporalEntityAnnotator_ImplBase {
public static final String PARAM_FEATURE_SELECTION_THRESHOLD = "WhetherToDoFeatureSelection";
diff --git a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
index 619bb61..de1aaee 100644
--- a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
+++ b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
@@ -21,7 +21,6 @@ package org.apache.ctakes.temporal.pipelines;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
import org.apache.ctakes.core.cc.FileTreeXmiWriter;
-import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator;
import org.apache.ctakes.temporal.ae.EventAnnotator;
diff --git a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
index 25fe771..239427c 100644
--- a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
+++ b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
@@ -27,7 +27,6 @@ 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.cc.FileTreeXmiWriter;
-import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
@@ -39,8 +38,6 @@ import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.util.ViewUriUtil;
-import org.cleartk.util.ae.UriToDocumentTextAnnotator;
import com.lexicalscope.jewel.cli.Option;
diff --git a/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml b/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
index edf4a5d..b3fc587 100644
--- a/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
+++ b/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
@@ -779,7 +779,6 @@ More qualifying information on how the procedure was done.</description>
<rangeTypeName>org.apache.ctakes.typesystem.type.refsem.BodySide</rangeTypeName>
</featureDescription>
<featureDescription>
- <!-- Why is this a relation? This procedure will be an argument in the relation! Why not just the Anatomic Site? -->
<name>bodyLocation</name>
<description/>
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.LocationOf</rangeTypeName>
@@ -816,6 +815,11 @@ More qualifying information on how the procedure was done.</description>
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalRelation</rangeTypeName>
</featureDescription>
<!-- New in ctakes 5 -->
+ <featureDescription>
+ <name>anatomicalSite</name>
+ <description>Anatomical site replaces the circular bodyLocation relation plus bodyLaterality and bodySide.</description>
+ <rangeTypeName>org.apache.ctakes.typesystem.type.refsem.AnatomicalSite</rangeTypeName>
+ </featureDescription>
<featureDescription>
<name>dosageCount</name>
<description/>
@@ -2447,7 +2451,7 @@ More qualifying information on how the procedure was done.</description>
<description/>
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation</rangeTypeName>
</featureDescription>
- <featureDescription>
+ <featureDescription>
<name>procedureDevice</name>
<description/>
<rangeTypeName>org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier</rangeTypeName>
@@ -2479,6 +2483,11 @@ More qualifying information on how the procedure was done.</description>
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalTextRelation</rangeTypeName>
</featureDescription>
<!-- New in ctakes 5 -->
+ <featureDescription>
+ <name>anatomicalSite</name>
+ <description>Anatomical site mention replaces the circular bodyLocation relation plus bodyLaterality and bodySide.</description>
+ <rangeTypeName>org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention</rangeTypeName>
+ </featureDescription>
<featureDescription>
<name>dosageCount</name>
<description/>