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seanfinan pushed a commit to branch main
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The following commit(s) were added to refs/heads/main by this push:
new 6b760d2 CTAKES-503, patch from Sean Mullane
6b760d2 is described below
commit 6b760d2c7af6d17aa05dbd6abc314529dd128d80
Author: Sean Finan <[email protected]>
AuthorDate: Wed Dec 28 14:58:12 2022 -0500
CTAKES-503, patch from Sean Mullane
---
.../uima/mapper/DocumentMapperServiceImpl.java | 45 ++++++++++++++++++++--
1 file changed, 41 insertions(+), 4 deletions(-)
diff --git
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
index 4876b4a..093e7d2 100644
---
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
+++
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
@@ -1,4 +1,4 @@
-/**
+/*
* 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
@@ -48,6 +48,10 @@ import org.apache.commons.collections.map.CaseInsensitiveMap;
import org.apache.commons.jxpath.JXPathContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
+import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.ctakes.ytex.dao.DBUtil;
import org.apache.ctakes.ytex.uima.model.Document;
import org.apache.ctakes.ytex.uima.model.DocumentAnnotation;
@@ -589,8 +593,8 @@ public class DocumentMapperServiceImpl implements
DocumentMapperService,
/**
* load mapping info
*
- * @param type
- * @return
+ * @param fs -
+ * @return -
*/
private AnnoMappingInfo initMapInfo(final FeatureStructure fs) {
final Type type = fs.getType();
@@ -1153,7 +1157,7 @@ public class DocumentMapperServiceImpl implements
DocumentMapperService,
/**
* save the annotation properties for a given type
*
- * @param mapIdToAnno
+ * @param mapAnnoToId
* map of all annoIDs to Annotation
* @param annoIds
* annotation ids for a single type
@@ -1203,6 +1207,39 @@ public class DocumentMapperServiceImpl implements
DocumentMapperService,
Annotation anno =
mapIdToAnno.get(annoId);
saveAnnoBindVariables(type,
mapInfo, ps, annoId, anno,
mapAnnoToId);
+
+ // Pull out bodyLocation
relation (and severity relation?) for anno_link table
+ if(anno instanceof
DiseaseDisorderMention ) {
+ LocationOfTextRelation
blRel = ((DiseaseDisorderMention)anno).getBodyLocation();
+ //DegreeOfTextRelation
dtRel = ((DiseaseDisorderMention)anno).getSeverity();
+ if(blRel != null) {
+ Annotation site = blRel.getArg2().getArgument();
// get AnatomicalSiteLocation
+ Integer anatSiteAnnoId = mapAnnoToId.get(site);
+ if (anatSiteAnnoId != null) {
+ listAnnoLinks.add(new AnnoLink(annoId,
anatSiteAnnoId, "bodyLocation"));
+ }
+ }
+ } else if (anno instanceof
SignSymptomMention ){
+ LocationOfTextRelation
blRel = ((SignSymptomMention)anno).getBodyLocation();
+ //DegreeOfTextRelation
dtRel = ((SignSymptomMention)anno).getSeverity();
+ if(blRel != null) {
+ Annotation site = blRel.getArg2().getArgument();
// get AnatomicalSiteLocation
+ Integer anatSiteAnnoId = mapAnnoToId.get(site);
+ if (anatSiteAnnoId != null) {
+ listAnnoLinks.add(new AnnoLink(annoId,
anatSiteAnnoId, "bodyLocation"));
+ }
+ }
+ } else if (anno instanceof
ProcedureMention ){
+ LocationOfTextRelation blRel =
((ProcedureMention)anno).getBodyLocation();
+ if(blRel != null) {
+ Annotation site = blRel.getArg2().getArgument();
// get AnatomicalSiteLocation
+ Integer anatSiteAnnoId = mapAnnoToId.get(site);
+ if (anatSiteAnnoId != null) {
+ listAnnoLinks.add(new AnnoLink(annoId,
anatSiteAnnoId, "bodyLocation"));
+ }
+ }
+ }
+
// pull out the composite
fields for storage
for (String fieldName :
fsNames) {
Feature feat =
type.getFeatureByBaseName(fieldName);
