/**
* form and apply a parent organ to parts
*
* @param description:
* @param statement
* @param parentStructure element holding a candidate parent
* @param parentOfParentStructure string of the name of the parent organ of the parentstructure
* @return
*/
private String attachParentOrganToOtherBiologicalEntities(
Document document,
Element description,
Element statement,
Element parentStructure,
String parentOfParentStructure,
String nonSpecificParts) {
String parentOrgan =
getParentOrgan(document, description, parentStructure, parentOfParentStructure);
// parentorgan = parentorgan.trim();
// attach parentorgan to other 'structures' in this statement
List<Element> biologicalEntities =
statement.getChildren("biological_entity"); // could include 'relation' too
String parentStructureName = null;
for (Element biologicalEntity : biologicalEntities) {
if (!biologicalEntity.equals(parentStructure)) {
// skip the 1st structure which is parentstruct
if (!hasStructuralConstraint(biologicalEntity)) {
String partOfChain =
getPartOfChain(document, description, biologicalEntity, 3)
.replace(" of ", ",")
.trim(); // part of organ of organ
String part =
biologicalEntity.getAttributeValue("name")
+ (partOfChain.isEmpty() ? "" : "," + partOfChain);
if (part.matches("\\b(" + nonSpecificParts + ")\\b.*")
&& !part.contains(",")
&& parentOrgan.equals("whole_organism")) {
parentStructureName =
hasPart(
parentStructure,
biologicalEntity,
description,
parentOrgan,
part,
nonSpecificParts);
if (!parentStructureName.isEmpty()) {
log(
LogLevel.DEBUG,
"===>[part of 1] use '"
+ parentStructureName
+ "' as constraint to '"
+ biologicalEntity.getName()
+ "'");
appendConstraint(biologicalEntity, formatParentOrgan(parentStructureName));
} else if (possess(parentStructure, biologicalEntity, description)) {
parentStructureName = formatParentOrgan(parentOrgan);
log(
LogLevel.DEBUG,
"===>[possess] use '"
+ parentStructureName
+ "' as constraint to '"
+ biologicalEntity.getName()
+ "'");
appendConstraint(biologicalEntity, formatParentOrgan(parentStructureName));
}
}
}
}
}
return parentStructureName != null
? parentStructureName
: parentOrgan.replaceAll("(^,|,$)", "");
}
