Update Mapping Tree

Fixes: #151

pom.xml

@@ -32,7 +32,7 @@
         <hapi-fhir.version>7.2.1</hapi-fhir.version>
         <testcontainers.version>1.20.0</testcontainers.version>
         <slf4j.version>2.0.13</slf4j.version>
-        <ontology.version>2.2.0</ontology.version>
+        <ontology.version>3.0.0-test.1</ontology.version>
     </properties>
 
     <dependencies>
@@ -177,7 +177,7 @@
                             <goal>download-single</goal>
                         </goals>
                         <configuration>
-                            <url>https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v${ontology.version}/example/mii_core_data_set/ontology/mapping.zip</url>
+                            <url>https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v${ontology.version}/example/fdpg-ontology/mapping.zip</url>
                             <toDir>${project.build.directory}</toDir>
                         </configuration>
                     </execution>

src/main/java/de/numcodex/sq2cql/model/MappingContext.java

@@ -21,10 +21,10 @@
 public class MappingContext {
 
     private final Map<ContextualTermCode, Mapping> mappings;
-    private final TermCodeNode conceptTree;
+    private final MappingTreeBase conceptTree;
     private final Map<String, CodeSystemDefinition> codeSystemDefinitions;
 
-    private MappingContext(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree,
+    private MappingContext(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree,
                            Map<String, CodeSystemDefinition> codeSystemDefinitions) {
         this.mappings = mappings;
         this.conceptTree = conceptTree;
@@ -48,7 +48,7 @@ public static MappingContext of() {
      * @param codeSystemAliases a map of code system URLs to their aliases
      * @return the mapping context
      */
-    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree,
+    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree,
                                     Map<String, String> codeSystemAliases) {
         return new MappingContext(Map.copyOf(mappings), conceptTree, codeSystemAliases.entrySet().stream()
                 .collect(Collectors.toConcurrentMap(Map.Entry::getKey,

src/main/java/de/numcodex/sq2cql/model/MappingTreeBase.java

@@ -0,0 +1,17 @@
+package de.numcodex.sq2cql.model;
+
+
+import de.numcodex.sq2cql.model.structured_query.ContextualTermCode;
+
+import java.util.List;
+import java.util.stream.Stream;
+
+public record MappingTreeBase(List<MappingTreeModuleRoot> moduleRoots) {
+
+    public Stream<ContextualTermCode> expand(ContextualTermCode termCode) {
+        var key = termCode.termCode().code();
+
+        return moduleRoots.stream().flatMap(moduleRoot ->
+                moduleRoot.isModuleMatching(termCode) ? moduleRoot.expand(key) : Stream.empty());
+    }
+}

src/main/java/de/numcodex/sq2cql/model/MappingTreeModuleEntry.java

@@ -0,0 +1,16 @@
+package de.numcodex.sq2cql.model;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.List;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public record MappingTreeModuleEntry(String key, List<String> children) {
+    @JsonCreator
+    static MappingTreeModuleEntry fromJson(@JsonProperty("key") String key,
+                                           @JsonProperty("children") List<String> children) {
+        return new MappingTreeModuleEntry(key, children);
+    }
+}

src/main/java/de/numcodex/sq2cql/model/MappingTreeModuleRoot.java

@@ -0,0 +1,40 @@
+package de.numcodex.sq2cql.model;
+
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.sq2cql.model.common.TermCode;
+import de.numcodex.sq2cql.model.structured_query.ContextualTermCode;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static java.util.function.Function.identity;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public record MappingTreeModuleRoot(TermCode context, String system, Map<String, MappingTreeModuleEntry> entries) {
+    @JsonCreator
+    static MappingTreeModuleRoot fromJson(@JsonProperty("context") TermCode context,
+                                          @JsonProperty("system") String system,
+                                          @JsonProperty("entries") List<MappingTreeModuleEntry> entries) {
+        return new MappingTreeModuleRoot(
+                context,
+                system,
+                entries.stream().collect(Collectors.toMap(MappingTreeModuleEntry::key, identity())));
+    }
+
+    public Stream<ContextualTermCode> expand(String key) {
+        var newTermCode = new ContextualTermCode(context, new TermCode(system, key, ""));
+
+        return Stream.concat(Stream.of(newTermCode), entries.get(key).children().stream().flatMap(this::expand));
+    }
+
+    boolean isModuleMatching(ContextualTermCode contextualTermCode) {
+        return context.equals(contextualTermCode.context()) &&
+                system.equals(contextualTermCode.termCode().system()) &&
+                entries.containsKey(contextualTermCode.termCode().code());
+    }
+}

src/test/java/de/numcodex/sq2cql/EvaluationIT.java

@@ -5,9 +5,7 @@
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import de.numcodex.sq2cql.model.Mapping;
-import de.numcodex.sq2cql.model.MappingContext;
-import de.numcodex.sq2cql.model.TermCodeNode;
+import de.numcodex.sq2cql.model.*;
 import de.numcodex.sq2cql.model.common.TermCode;
 import de.numcodex.sq2cql.model.structured_query.ContextualConcept;
 import de.numcodex.sq2cql.model.structured_query.ContextualTermCode;
@@ -31,6 +29,7 @@
 import java.util.Map;
 import java.util.UUID;
 
+import static de.numcodex.sq2cql.Util.createTreeWithoutChildren;
 import static de.numcodex.sq2cql.model.common.Comparator.LESS_THAN;
 import static java.lang.String.format;
 import static java.nio.charset.StandardCharsets.UTF_8;
@@ -42,8 +41,9 @@
 public class EvaluationIT {
 
     static final TermCode CONTEXT = TermCode.of("context", "context", "context");
-    static final ContextualTermCode ROOT = ContextualTermCode.of(CONTEXT, TermCode.of("", "", ""));
-    static final ContextualTermCode BLOOD_PRESSURE = ContextualTermCode.of(CONTEXT, TermCode.of("http://loinc.org", "85354-9",
+    static final String BLOOD_PRESSURE_CODE = "85354-9";
+    static final String BLOOD_PRESSURE_SYSTEM = "http://loinc.org";
+    static final ContextualTermCode BLOOD_PRESSURE = ContextualTermCode.of(CONTEXT, TermCode.of(BLOOD_PRESSURE_SYSTEM, BLOOD_PRESSURE_CODE,
             "Blood pressure panel with all children optional"));
     static final TermCode DIASTOLIC_BLOOD_PRESSURE = TermCode.of("http://loinc.org", "8462-4",
             "Diastolic blood pressure");
@@ -99,7 +99,7 @@ public void evaluateBloodPressure() throws Exception {
         var valueFhirPath = format("component.where(code.coding.exists(system = '%s' and code = '%s')).value.first()",
                 DIASTOLIC_BLOOD_PRESSURE.system(), DIASTOLIC_BLOOD_PRESSURE.code());
         var mappings = Map.of(BLOOD_PRESSURE, Mapping.of(BLOOD_PRESSURE, "Observation", valueFhirPath));
-        var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(BLOOD_PRESSURE));
+        var conceptTree = createTreeWithoutChildren(BLOOD_PRESSURE);
         var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
         var translator = Translator.of(mappingContext);
         var criterion = NumericCriterion.of(ContextualConcept.of(BLOOD_PRESSURE), LESS_THAN, BigDecimal.valueOf(80), "mm[Hg]");
@@ -157,7 +157,7 @@ public void evaluateBloodPressureAttribute() throws Exception {
                 }
                 """);
         var mappings = Map.of(BLOOD_PRESSURE, mapping);
-        var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(BLOOD_PRESSURE));
+        var conceptTree = createTreeWithoutChildren(BLOOD_PRESSURE);
         var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
         var translator = Translator.of(mappingContext);
         var structuredQuery = readStructuredQuery("""

src/test/java/de/numcodex/sq2cql/TranslatorTest.java

@@ -1,10 +1,7 @@
 package de.numcodex.sq2cql;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import de.numcodex.sq2cql.model.AttributeMapping;
-import de.numcodex.sq2cql.model.Mapping;
-import de.numcodex.sq2cql.model.MappingContext;
-import de.numcodex.sq2cql.model.TermCodeNode;
+import de.numcodex.sq2cql.model.*;
 import de.numcodex.sq2cql.model.common.TermCode;
 import de.numcodex.sq2cql.model.structured_query.*;
 import org.junit.jupiter.api.Nested;
@@ -15,6 +12,7 @@
 import java.util.Map;
 
 import static de.numcodex.sq2cql.Assertions.assertThat;
+import static de.numcodex.sq2cql.Util.*;
 import static de.numcodex.sq2cql.model.common.Comparator.LESS_THAN;
 import static org.assertj.core.api.Assertions.assertThatIllegalStateException;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -118,7 +116,7 @@ void nonExpandableConcept() {
 
         @Test
         void nonMappableConcept() {
-            var conceptTree = TermCodeNode.of(C71, TermCodeNode.of(C71_0), TermCodeNode.of(C71_1));
+            var conceptTree = createTreeWithChildren(C71, C71_0, C71_1);
             var mappingContext = MappingContext.of(Map.of(), conceptTree, CODE_SYSTEM_ALIASES);
 
             var message = assertThrows(TranslationException.class, () -> Translator.of(mappingContext)
@@ -136,7 +134,7 @@ void usage_Documentation() {
                     TermCode.of("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "C71.1",
                             "Malignant neoplasm of brain"));
             var mappings = Map.of(c71_1, Mapping.of(c71_1, "Condition"));
-            var conceptTree = TermCodeNode.of(c71_1);
+            var conceptTree = createTreeWithoutChildren(c71_1);
             var codeSystemAliases = Map.of("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "icd10");
             var mappingContext = MappingContext.of(mappings, conceptTree, codeSystemAliases);
 
@@ -167,7 +165,7 @@ void timeRestriction() {
                             "Malignant neoplasm of brain"));
             var mappings = Map.of(c71_1,
                     Mapping.of(c71_1, "Condition", null, null, List.of(), List.of(), "onset"));
-            var conceptTree = TermCodeNode.of(c71_1);
+            var conceptTree = createTreeWithoutChildren(c71_1);
             var codeSystemAliases = Map.of("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "icd10");
             var mappingContext = MappingContext.of(mappings, conceptTree, codeSystemAliases);
 
@@ -201,7 +199,7 @@ void timeRestriction_missingPathInMapping() {
                             "Malignant neoplasm of brain"));
             var mappings = Map.of(c71_1,
                     Mapping.of(c71_1, "Condition", null, null, List.of(), List.of(), null));
-            var conceptTree = TermCodeNode.of(c71_1);
+            var conceptTree = createTreeWithoutChildren(c71_1);
             var codeSystemAliases = Map.of("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "icd10");
             var mappingContext = MappingContext.of(mappings, conceptTree, codeSystemAliases);
             var query = StructuredQuery.of(List.of(List.of(ConceptCriterion.of(ContextualConcept.of(c71_1),
@@ -220,8 +218,9 @@ void test_Task1() {
                     Mapping.of(C71_1, "Condition", null, null, List.of(),
                             List.of(VERIFICATION_STATUS_ATTR_MAPPING)), TMZ,
                     Mapping.of(TMZ, "MedicationStatement"));
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(TMZ),
-                    TermCodeNode.of(C71, TermCodeNode.of(C71_0), TermCodeNode.of(C71_1)));
+            var conceptTree = new MappingTreeBase(List.of(
+                    createTreeRootWithoutChildren(TMZ),
+                    createTreeRootWithChildren(C71, C71_0, C71_1)));
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
             var structuredQuery = StructuredQuery.of(List.of(List.of(
                             ConceptCriterion.of(ContextualConcept.of(C71))
@@ -270,8 +269,10 @@ void test_Task2() {
                     Mapping.of(HYPERTENSION, "Condition", null, null, List.of(),
                             List.of(VERIFICATION_STATUS_ATTR_MAPPING)), SERUM, Mapping.of(SERUM, "Specimen"), LIPID,
                     Mapping.of(LIPID, "MedicationStatement"));
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(HYPERTENSION), TermCodeNode.of(SERUM),
-                    TermCodeNode.of(LIPID));
+            var conceptTree = new MappingTreeBase(List.of(
+                    createTreeRootWithoutChildren(HYPERTENSION),
+                    createTreeRootWithoutChildren(SERUM),
+                    createTreeRootWithoutChildren(LIPID)));
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
             var structuredQuery = StructuredQuery.of(List.of(List.of(
                                     ConceptCriterion.of(ContextualConcept.of(HYPERTENSION))
@@ -324,7 +325,7 @@ void geccoTask2() {
                     Mapping.of(G47_31, "Condition", null, null,
                             List.of(CodingModifier.of("verificationStatus.coding", CONFIRMED)), List.of()),
                     TOBACCO_SMOKING_STATUS, Mapping.of(TOBACCO_SMOKING_STATUS, "Observation", "value"));
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(COPD), TermCodeNode.of(G47_31));
+            var conceptTree = new MappingTreeBase(List.of(createTreeRootWithoutChildren(COPD), createTreeRootWithoutChildren(G47_31)));
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
             var structuredQuery = StructuredQuery.of(
                     List.of(List.of(ValueSetCriterion.of(ContextualConcept.of(FRAILTY_SCORE), VERY_FIT, WELL))),
@@ -467,7 +468,7 @@ void onlyFixedCriteria() throws Exception {
                     }
                     """);
 
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(COMBINED_CONSENT));
+            var conceptTree = createTreeWithoutChildren(COMBINED_CONSENT);
             var mappings = Map.of(COMBINED_CONSENT, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -549,7 +550,7 @@ void numericAgeTranslation() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(AGE));
+            var conceptTree = createTreeWithoutChildren(AGE);
             var mappings = Map.of(AGE, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -625,7 +626,7 @@ void ageRangeTranslation() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(AGE));
+            var conceptTree = createTreeWithoutChildren(AGE);
             var mappings = Map.of(AGE, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -701,7 +702,7 @@ void numericAgeTranslationInHours() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(AGE));
+            var conceptTree = createTreeWithoutChildren(AGE);
             var mappings = Map.of(AGE, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -777,7 +778,7 @@ void patientGender() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(GENDER));
+            var conceptTree = createTreeWithoutChildren(GENDER);
             var mappings = Map.of(GENDER, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -844,7 +845,7 @@ void consent() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(CONSENT_MDAT));
+            var conceptTree = createTreeWithoutChildren(CONSENT_MDAT);
             var mappings = Map.of(CONSENT_MDAT, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);
 
@@ -938,7 +939,7 @@ void bloodPressure() throws Exception {
                       ]
                     }
                     """);
-            var conceptTree = TermCodeNode.of(ROOT, TermCodeNode.of(BLOOD_PRESSURE));
+            var conceptTree = createTreeWithoutChildren(BLOOD_PRESSURE);
             var mappings = Map.of(BLOOD_PRESSURE, mapping);
             var mappingContext = MappingContext.of(mappings, conceptTree, CODE_SYSTEM_ALIASES);