Update Mapping Tree

.gitignore

@@ -1,4 +1,5 @@
 .mvn
+.idea/
 cache
 target
 /ontology/mapping.zip

pom.xml

@@ -21,7 +21,7 @@
  <properties>
  <java.version>17</java.version>
  <testcontainers.version>1.19.8</testcontainers.version>
- <ontology.version>2.2.0</ontology.version>
+ <ontology.version>3.0.0-test.1</ontology.version>
  </properties>
 
  <dependencies>
@@ -206,9 +206,10 @@
  <goal>wget</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>
  <outputFileName>mapping.zip</outputFileName>
  <outputDirectory>ontology/</outputDirectory>
+ <skipCache>true</skipCache>
  </configuration>
  </execution>
  </executions>

src/main/java/de/medizininformatikinitiative/flare/Util.java

@@ -3,7 +3,8 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.medizininformatikinitiative.flare.model.mapping.Mapping;
 import de.medizininformatikinitiative.flare.model.mapping.MappingContext;
-import de.medizininformatikinitiative.flare.model.mapping.TermCodeNode;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeBase;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeModuleRoot;
 import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
 
 import java.io.BufferedInputStream;
@@ -79,11 +80,11 @@ static double durationSecondsSince(long startNanoTime) {
  static MappingContext flareMappingContext(Clock clock) throws Exception {
  var mapper = new ObjectMapper();
  String ontologyZipFile = "ontology/mapping.zip";
- String mappingFile = "ontology/mapping/mapping_fhir.json";
- String conceptTreeFile = "ontology/mapping/mapping_tree.json";
+ String mappingFile = "mapping/fhir/mapping_fhir.json";
+ String conceptTreeFile = "mapping/mapping_tree.json";
 
  Map<ContextualTermCode, Mapping> mappings = null;
- TermCodeNode conceptTree = null;
+ MappingTreeBase conceptTree = null;
 
  try (FileInputStream fis = new FileInputStream(ontologyZipFile);
  BufferedInputStream bis = new BufferedInputStream(fis);
@@ -94,8 +95,8 @@ static MappingContext flareMappingContext(Clock clock) throws Exception {
  mappings = Arrays.stream(mapper.readValue(readZipEntryContent(zis), Mapping[].class))
  .collect(Collectors.toMap(Mapping::key, identity()));
  } else if (ze.getName().equals(conceptTreeFile)) {
- String treeString = readZipEntryContent(zis);
- conceptTree = mapper.readValue(treeString, TermCodeNode.class);
+ conceptTree = new MappingTreeBase(
+  Arrays.stream(mapper.readValue(readZipEntryContent(zis), MappingTreeModuleRoot[].class)).toList());
  }
  }
  }

src/main/java/de/medizininformatikinitiative/flare/model/mapping/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 Clock clock;
 
- private MappingContext(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree, Clock clock) {
+ private MappingContext(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree, Clock clock) {
  this.mappings = Map.copyOf(mappings);
  this.conceptTree = requireNonNull(conceptTree);
  this.clock = requireNonNull(clock);
@@ -37,7 +37,7 @@ private MappingContext(Map<ContextualTermCode, Mapping> mappings, TermCodeNode c
  * @param conceptTree a tree of concepts to expand (can be null)
  * @return the mapping context
  */
- public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree) {
+ public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree) {
  return new MappingContext(mappings, conceptTree, Clock.systemDefaultZone());
  }
 
@@ -49,7 +49,7 @@ public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermC
  * @param clock a clock that is used for time-related calculations
  * @return the mapping context
  */
- public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree, Clock clock) {
+ public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree, Clock clock) {
  return new MappingContext(mappings, conceptTree, clock);
  }
 

src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java

@@ -0,0 +1,22 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+import de.medizininformatikinitiative.flare.model.sq.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 ->
+ isModuleMatching(termCode, moduleRoot) ? moduleRoot.expand(key) : Stream.empty());
+ }
+
+ private boolean isModuleMatching(ContextualTermCode termCode, MappingTreeModuleRoot moduleRoot) {
+ return termCode.context().equals(moduleRoot.context()) &&
+ moduleRoot.system().equals(termCode.termCode().system()) &&
+ moduleRoot.entries().containsKey(termCode.termCode().code());
+ }
+}

src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleEntry.java

@@ -0,0 +1,16 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+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)
+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/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java

@@ -0,0 +1,34 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
+import de.medizininformatikinitiative.flare.model.sq.TermCode;
+
+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));
+ }
+}

src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java

@@ -15,8 +15,6 @@
 import reactor.core.publisher.Flux;
 import reactor.core.publisher.Mono;
 
-import java.util.Set;
-
 import static de.medizininformatikinitiative.flare.model.translate.Operator.Name.UNION;
 import static java.util.Objects.requireNonNull;
 

src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java

@@ -5,6 +5,7 @@
 import de.medizininformatikinitiative.flare.model.sq.TermCode;
 import org.junit.jupiter.api.Test;
 
+import java.util.List;
 import java.util.Map;
 
 import static de.medizininformatikinitiative.flare.Assertions.assertThat;
@@ -13,36 +14,45 @@
 class MappingContextTest {
 
  static final TermCode CONTEXT = TermCode.of("context", "context", "context");
+ static final String SYSTEM = "sys";
  static final ContextualTermCode ROOT = ContextualTermCode.of(CONTEXT, TermCode.of("root", "root", "root"));
- static final ContextualTermCode C1 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c1", "c1"));
- static final ContextualTermCode C11 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c11", "c11"));
- static final ContextualTermCode C12 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c12", "c12"));
+ static final String C1 = "c1";
+ static final String C2 = "c2";
+
+ private ContextualTermCode contextualTermCodeOf(String code) {
+ return new ContextualTermCode(MappingContextTest.CONTEXT, new TermCode(MappingContextTest.SYSTEM, code, "display"));
+ }
 
  @Test
  void expandConcept_ConceptNotExpandable() {
- var context = MappingContext.of(Map.of(), TermCodeNode.createNormal(ROOT));
+ var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of()))));
 
- var result = context.expandConcept(ContextualConcept.of(C1));
+ var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
  assertThat(result).isLeftInstanceOf(ContextualConceptNotExpandableException.class);
  }
 
  @Test
  void expandConcept_OneConcept() {
- var context = MappingContext.of(Map.of(), TermCodeNode.createNormal(ROOT, TermCodeNode.createNormal(C1)));
+ var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(
+ new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of(C1, new MappingTreeModuleEntry(C1, List.of()))))));
 
- var result = context.expandConcept(ContextualConcept.of(C1));
+ var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
- assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(C1));
+ assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(contextualTermCodeOf(C1)));
  }
 
  @Test
  void expandConcept_TwoConcepts() {
- var context = MappingContext.of(Map.of(), TermCodeNode.createAbstract(C1, TermCodeNode.createNormal(C11),
- TermCodeNode.createNormal(C12)));
+ var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(
+ new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2)),
+ C2, new MappingTreeModuleEntry(C2, List.of()))))));
 
- var result = context.expandConcept(ContextualConcept.of(C1));
+ var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
- assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(C11, C12));
+ assertThat(result).isRightSatisfying(r -> {
+ assertThat(r.get(0)).isEqualTo(contextualTermCodeOf(C1));
+ assertThat(r.get(1)).isEqualTo(contextualTermCodeOf(C2));
+ });
  }
 }