Feature/ikm 20260529 decimal interval

elk-snomed/src/main/java/dev/ikm/elk/snomed/ConceptComparer.java

@@ -4,7 +4,7 @@
  * #%L
  * ELK Integration with SNOMED
  * %%
- * Copyright (C) 2023 - 2025 Integrated Knowledge Management
+ * Copyright (C) 2023 - 2026 Integrated Knowledge Management
  * %%
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,13 +20,11 @@
  * #L%
  */
 
-import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
 import org.eclipse.collections.api.factory.primitive.LongSets;
 import org.eclipse.collections.api.set.primitive.MutableLongSet;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -37,7 +35,7 @@
 import dev.ikm.elk.snomed.model.RoleGroup;
 
 public class ConceptComparer {
-    private MutableLongSet mis_match_cons = LongSets.mutable.empty();
+	private MutableLongSet mis_match_cons = LongSets.mutable.empty();
 
 	private static final Logger LOG = LoggerFactory.getLogger(ConceptComparer.class);
 
@@ -53,22 +51,24 @@ public ConceptComparer(SnomedOntology inferredOntology) {
 		this.inferredOntology = inferredOntology;
 	}
 
-    /**
-     * Check if a concept ID has mismatches.
-     * @param conceptId the concept ID to check
-     * @return true if this concept has recorded mismatches
-     */
-    public boolean hasMismatch(long conceptId) {
-        return mis_match_cons.contains(conceptId);  // Primitive contains - no boxing!
-    }
+	/**
+	 * Check if a concept ID has mismatches.
+	 * 
+	 * @param conceptId the concept ID to check
+	 * @return true if this concept has recorded mismatches
+	 */
+	public boolean hasMismatch(long conceptId) {
+		return mis_match_cons.contains(conceptId); // Primitive contains - no boxing!
+	}
 
-    /**
-     * Get all concept IDs with mismatches.
-     * @return array of concept IDs (no boxing in array)
-     */
-    public long[] getMismatchConceptIds() {
-        return mis_match_cons.toArray();  // Primitive array - efficient!
-    }
+	/**
+	 * Get all concept IDs with mismatches.
+	 * 
+	 * @return array of concept IDs (no boxing in array)
+	 */
+	public long[] getMismatchConceptIds() {
+		return mis_match_cons.toArray(); // Primitive array - efficient!
+	}
 
 	public int getMisMatchCount() {
 		return mis_match_cnt;
@@ -96,7 +96,7 @@ public boolean compare(Concept concept1, Concept concept2) {
 		}
 		if (!match) {
 			mis_match_cnt++;
-			mis_match_cons.add(concept1.getId());  // No boxing - primitive add!
+			mis_match_cons.add(concept1.getId()); // No boxing - primitive add!
 			if (log_mis_match_detail) {
 				LOG.info("Concept: " + concept1);
 				LOG.info("Concept1 parents:");

elk-snomed/src/main/java/dev/ikm/elk/snomed/NecessaryNormalFormBuilder.java

@@ -21,7 +21,6 @@
  */
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -36,7 +35,6 @@
 import org.eclipse.collections.api.map.primitive.MutableLongObjectMap;
 import org.eclipse.collections.api.set.MutableSet;
 import org.eclipse.collections.api.set.primitive.MutableLongSet;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -107,17 +105,16 @@ protected NecessaryNormalFormBuilder(SnomedOntology snomedOntology, long root, P
 	}
 
 	public static NecessaryNormalFormBuilder create(SnomedOntology snomedOntology,
-			MutableLongObjectMap<MutableLongSet> superConcepts,  // ← Primitive map!
-			MutableLongObjectMap<MutableLongSet> superRoleTypes,  // ← Primitive map!
+			MutableLongObjectMap<MutableLongSet> superConcepts, // ← Primitive map!
+			MutableLongObjectMap<MutableLongSet> superRoleTypes, // ← Primitive map!
 			ProgressUpdater progressUpdater) {
 		return create(snomedOntology, superConcepts, superRoleTypes, SnomedIds.root, progressUpdater);
 	}
 
 	public static NecessaryNormalFormBuilder create(SnomedOntology snomedOntology,
-			MutableLongObjectMap<MutableLongSet> superConcepts,  // ← Primitive map!
-			MutableLongObjectMap<MutableLongSet> superRoleTypes,  // ← Primitive map!
-			long root,
-			ProgressUpdater progressUpdater) {
+			MutableLongObjectMap<MutableLongSet> superConcepts, // ← Primitive map!
+			MutableLongObjectMap<MutableLongSet> superRoleTypes, // ← Primitive map!
+			long root, ProgressUpdater progressUpdater) {
 		NecessaryNormalFormBuilder nnfb = new NecessaryNormalFormBuilder(snomedOntology, root, progressUpdater);
 		nnfb.initConcepts(superConcepts);
 		nnfb.initRoles(superRoleTypes);
@@ -131,16 +128,16 @@ protected void initSubsumption() {
 
 	protected void initConcepts(MutableLongObjectMap<MutableLongSet> superConcepts) {
 		isa = SnomedIsa.init(superConcepts, root);
-		MutableLongObjectMap<MutableLongSet> dependentOnConcepts = LongObjectMaps.mutable.ofInitialCapacity(
-				snomedOntology.getConcepts().size());
-		
+		MutableLongObjectMap<MutableLongSet> dependentOnConcepts = LongObjectMaps.mutable
+				.ofInitialCapacity(snomedOntology.getConcepts().size());
+
 		for (Concept concept : snomedOntology.getConcepts()) {
 			dependentOnConcepts.put(concept.getId(), getDependentOnConcepts(concept));
 		}
-		
+
 		SnomedIsa deps = SnomedIsa.init(dependentOnConcepts, root);
 		deps.getOrderedConcepts().forEach(id -> concepts.add(snomedOntology.getConcept(id)));
-		
+
 		LOG.info("Concepts: " + concepts.size());
 	}
 
@@ -151,14 +148,14 @@ protected void initRoles(MutableLongObjectMap<MutableLongSet> superRoles) {
 			MutableSet<RoleType> superTypes = Sets.mutable.empty();
 			superRolesTypes.put(rt, superTypes);
 			superTypes.add(rt);
-			
+
 			// Use primitive forEach - no boxing!
 			superRoles.get(rt.getId()).forEach(sup_id -> {
 				RoleType sup_rt = snomedOntology.getRoleType(sup_id);
 				superTypes.add(sup_rt);
 			});
 		}
-		
+
 		if (log_roles) {
 			for (Entry<RoleType, MutableSet<RoleType>> es : superRolesTypes.entrySet()) {
 				RoleType rt = es.getKey();
@@ -175,9 +172,9 @@ protected void initRoles(MutableLongObjectMap<MutableLongSet> superRoles) {
 	}
 
 	private MutableLongSet getDependentOnConcepts(Concept concept) {
-		MutableLongSet deps = LongSets.mutable.empty();  // ← Primitive set!
+		MutableLongSet deps = LongSets.mutable.empty(); // ← Primitive set!
 		long id = concept.getId();
-		deps.addAll(isa.getParents(id));  // Now returns primitive set
+		deps.addAll(isa.getParents(id)); // Now returns primitive set
 		deps.addAll(snomedOntology.getDependentOnConcepts(id, false, false));
 		return deps;
 	}
@@ -222,13 +219,9 @@ public Definition generateNNF(Concept con, boolean useDefining) {
 		}
 		MutableSet<Concept> sups;
 		if (useDefining) {
-			sups = con.getDefinitions()
-					.flatCollect(Definition::getSuperConcepts)
-					.toSet();
+			sups = con.getDefinitions().flatCollect(Definition::getSuperConcepts).toSet();
 		} else {
-			sups = isa.getParents(con.getId())
-					.collect(snomedOntology::getConcept)
-					.toSet();
+			sups = isa.getParents(con.getId()).collect(snomedOntology::getConcept).toSet();
 		}
 		sups.forEach(sup -> def.addSuperConcept(sup));
 		for (Concept sup : sups) {

elk-snomed/src/main/java/dev/ikm/elk/snomed/SnomedIsa.java

@@ -25,7 +25,6 @@
 import java.nio.file.Path;
 import java.util.stream.Stream;
 
-import org.eclipse.collections.api.factory.Lists;
 import org.eclipse.collections.api.factory.primitive.LongLists;
 import org.eclipse.collections.api.factory.primitive.LongObjectMaps;
 import org.eclipse.collections.api.factory.primitive.LongSets;

elk-snomed/src/main/java/dev/ikm/elk/snomed/interval/Interval.java

@@ -1,5 +1,7 @@
 package dev.ikm.elk.snomed.interval;
 
+import java.math.BigDecimal;
+
 /*-
  * #%L
  * ELK Integration with SNOMED
@@ -27,28 +29,36 @@
 
 public class Interval {
 
-	private int lowerBound, upperBound;
+	private BigDecimal lowerBound, upperBound;
 
 	private boolean lowerOpen, upperOpen;
 
 	private Concept unitOfMeasure;
 
-	public int getLowerBound() {
+	public BigDecimal getLowerBound() {
 		return lowerBound;
 	}
 
-	public void setLowerBound(int lowerBound) {
+	public void setLowerBound(BigDecimal lowerBound) {
 		this.lowerBound = lowerBound;
 	}
 
-	public int getUpperBound() {
+	public void setLowerBound(int lowerBound) {
+		this.lowerBound = new BigDecimal(lowerBound);
+	}
+
+	public BigDecimal getUpperBound() {
 		return upperBound;
 	}
 
-	public void setUpperBound(int upperBound) {
+	public void setUpperBound(BigDecimal upperBound) {
 		this.upperBound = upperBound;
 	}
 
+	public void setUpperBound(int upperBound) {
+		this.upperBound = new BigDecimal(upperBound);
+	}
+
 	public boolean isLowerOpen() {
 		return lowerOpen;
 	}
@@ -73,7 +83,8 @@ public void setUnitOfMeasure(Concept unitOfMeasure) {
 		this.unitOfMeasure = unitOfMeasure;
 	}
 
-	public Interval(int lowerBound, boolean lowerOpen, int upperBound, boolean upperOpen, Concept unitOfMeasure) {
+	public Interval(BigDecimal lowerBound, boolean lowerOpen, BigDecimal upperBound, boolean upperOpen,
+			Concept unitOfMeasure) {
 		super();
 		this.lowerBound = lowerBound;
 		this.lowerOpen = lowerOpen;
@@ -87,17 +98,19 @@ private Interval() {
 
 	public static Interval fromString(String str) {
 		str = str.replace(" ", "");
-		String regex = "^(\\[|\\()(\\-?\\d+),(\\-?\\d+)(\\]|\\))(\\-?\\d+)$";
+		String integer = "(\\-?\\d+)";
+		String decimal = "(\\-?\\d+(\\.\\d+)?)";
+		String regex = "^(\\[|\\()" + decimal + "," + decimal + "(\\]|\\))" + integer + "$";
 		Pattern pat = Pattern.compile(regex);
 		Matcher mat = pat.matcher(str);
 		if (!mat.matches())
 			throw new IllegalArgumentException(str);
 		Interval ret = new Interval();
 		ret.lowerOpen = mat.group(1).equals("(");
-		ret.lowerBound = Integer.parseInt(mat.group(2));
-		ret.upperBound = Integer.parseInt(mat.group(3));
-		ret.upperOpen = mat.group(4).equals(")");
-		long uom = Long.parseLong(mat.group(5));
+		ret.lowerBound = new BigDecimal(mat.group(2));
+		ret.upperBound = new BigDecimal(mat.group(4));
+		ret.upperOpen = mat.group(6).equals(")");
+		long uom = Long.parseLong(mat.group(7));
 		ret.unitOfMeasure = new Concept(uom);
 		return ret;
 	}
@@ -112,22 +125,37 @@ public String toString(boolean includeUnitOfMeasure) {
 				+ (includeUnitOfMeasure ? unitOfMeasure.getId() : "");
 	}
 
-	private int getLowerContainsValue() {
-		if (this.isLowerOpen())
-			return this.getLowerBound() + 1;
-		return this.getLowerBound();
+	private boolean lowerContains(Interval that) {
+		if (this.isLowerOpen() && !that.isLowerOpen())
+			return this.getLowerBound().compareTo(that.getLowerBound()) < 0;
+		return this.getLowerBound().compareTo(that.getLowerBound()) <= 0;
 	}
 
-	private int getUpperContainsValue() {
-		if (this.isUpperOpen())
-			return this.getUpperBound() - 1;
-		return this.getUpperBound();
+	private boolean upperContains(Interval that) {
+		if (this.isUpperOpen() && !that.isUpperOpen())
+			return this.getUpperBound().compareTo(that.getUpperBound()) > 0;
+		return this.getUpperBound().compareTo(that.getUpperBound()) >= 0;
 	}
 
+	// an open interval does not include endpoints
+	// (a, b) = { x | a < x < b }
+	// a closed interval includes endpoints
+	// [a, b] = { x | a <= x <= b }
+
+	// x contains y
+	//
+	// x.LO & y.LO -> x.LB <= y.LB
+	// x.LC & y.LC -> x.LB <= y.LB
+	// x.LC & y.LO -> x.LB <= y.LB
+	// x.LO & y.LC -> x.LB < y.LB
+	//
+	// x.UO & y.UO -> x.UB >= y.UB
+	// x.UC & y.UC -> x.UB >= y.UB
+	// x.UC & y.UO -> x.UB >= y.UB
+	// x.UO & y.UC -> x.UB > y.UB
+
 	public boolean contains(Interval that) {
-		return this.getLowerContainsValue() <= that.getLowerContainsValue()
-				&& this.getUpperContainsValue() >= that.getUpperContainsValue()
-				&& this.unitOfMeasure.equals(that.unitOfMeasure);
+		return lowerContains(that) && upperContains(that) && this.unitOfMeasure.equals(that.unitOfMeasure);
 	}
 
 }

elk-snomed/src/main/java/dev/ikm/elk/snomed/model/Concept.java

@@ -1,5 +1,11 @@
 package dev.ikm.elk.snomed.model;
 
+import java.util.List;
+import java.util.Objects;
+
+import org.eclipse.collections.api.factory.Lists;
+import org.eclipse.collections.api.list.MutableList;
+
 /*-
  * #%L
  * ELK Integration with SNOMED
@@ -20,13 +26,6 @@
  * #L%
  */
 
-import org.eclipse.collections.api.factory.Lists;
-import org.eclipse.collections.api.list.MutableList;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
 public class Concept extends SnomedEntity {
 
 	// Use Eclipse Collections adaptive lists
@@ -39,15 +38,15 @@ public Concept(long id) {
 	}
 
 	public MutableList<Definition> getDefinitions() {
-		return definitions;  // MutableList implements List
+		return definitions; // MutableList implements List
 	}
 
 	public void addDefinition(Definition definition) {
 		this.definitions.add(definition);
 	}
 
 	public void removeAllDefinitions() {
-		this.definitions.clear();  // More efficient than new allocation
+		this.definitions.clear(); // More efficient than new allocation
 	}
 
 	public List<Definition> getGciDefinitions() {