🐛 Update ConceptMapContext to support multiple mappings per source key

srdc · Jan 20, 2025 · 7264ba3 · 7264ba3
1 parent e222e30
commit 7264ba3
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Showing 6 changed files with 74 additions and 35 deletions.
diff --git a/tofhir-engine/src/main/scala/io/tofhir/engine/mapping/context/MappingContextLoader.scala b/tofhir-engine/src/main/scala/io/tofhir/engine/mapping/context/MappingContextLoader.scala
@@ -62,16 +62,46 @@ class MappingContextLoader extends IMappingContextLoader {
 
   /**
    * Read concept mappings from the given CSV file.
+   * Example dataset to understand what this function does:
+   * Input CSV content (concept mappings), assumed to be at some file path specified:
+   * -----------------------------
+   * source_code,target_code,display_value
+   * 001,A1,Foo
+   * 001,A2,Bar
+   * 002,B1,Baz
+   * -----------------------------
+   *
+   * Explanation of this structure:
+   * - "source_code" is the key (the first column header), which will group the rows.
+   * - "target_code" and "display_value" are part of the data for each key grouping.
+   *
+   * Expected output of processing:
+   * Map(
+   *   "001" -> Seq(
+   *     Map("source_code" -> "001", "target_code" -> "A1", "display_value" -> "Foo"),
+   *     Map("source_code" -> "001", "target_code" -> "A2", "display_value" -> "Bar")
+   *   ),
+   *   "002" -> Seq(
+   *     Map("source_code" -> "002", "target_code" -> "B1", "display_value" -> "Baz")
+   *   )
+   * )
    *
    * @param filePath
    * @return
    */
-  private def readConceptMapContextFromCSV(filePath: String): Future[Map[String, Map[String, String]]] = {
+  private def readConceptMapContextFromCSV(filePath: String): Future[Map[String, Seq[Map[String, String]]]] = {
     readFromCSV(filePath) map {
       case (columns, records) =>
         //val (firstColumnName, _) = records.head.head // Get the first element in the records list and then get the first (k,v) pair to get the name of the first column.
-        records.foldLeft(Map[String, Map[String, String]]()) { (conceptMap, columnMap) =>
-          conceptMap + (columnMap(columns.head)-> columnMap)
+        val columnHeadKey = columns.head
+        records.foldLeft(Map[String, Seq[Map[String, String]]]()) { (conceptMap, columnMap) =>
+          val key = columnMap(columnHeadKey)
+          // If a source code has not been encountered before, add it as the first element.
+          // Otherwise, append the new target values to the existing sequence.
+          conceptMap.updatedWith(key) {
+            case Some(existingValues) => Some(existingValues :+ columnMap)
+            case None => Some(Seq(columnMap))
+          }
         }
     }
   }

diff --git a/...ir-engine/src/main/scala/io/tofhir/engine/mapping/fhirPath/FhirPathMappingFunctions.scala b/...ir-engine/src/main/scala/io/tofhir/engine/mapping/fhirPath/FhirPathMappingFunctions.scala
@@ -132,18 +132,13 @@ class FhirPathMappingFunctions(context: FhirPathEnvironment, current: Seq[FhirPa
     val evaluator = new FhirPathExpressionEvaluator(context, current)
     // Should return the code of the concept whose mapping is requested
     evaluator.visit(keyExpr) match {
-      case Nil =>
-        Nil
+      case Nil => Seq.empty
       case Seq(FhirPathString(conceptCode)) =>
         conceptMapContext
           .concepts
           .get(conceptCode)
-          .map {
-            case mws:Map[String, String] if mws.size == 1 => FhirPathString(mws.values.head)
-            case mws =>
-              FhirPathComplex(JObject(mws.toList.map(i => i._1 -> JString(i._2))))
-          }
-          .toSeq
+          .map(mws => mws.map(res => FhirPathComplex(JObject(res.toList.map(i => i._1 -> JString(i._2))))))
+          .getOrElse(Seq.empty)
       case _ =>
         throw new FhirPathException(s"Invalid function call 'getConcept', given expression for keyExpr:${keyExpr.getText} for the concept code should return a string value!")
     }
@@ -191,21 +186,18 @@ class FhirPathMappingFunctions(context: FhirPathEnvironment, current: Seq[FhirPa
       throw new FhirPathException(s"Invalid function call 'getConcept', given expression for keyExpr:${keyExpr.getText} for the concept code should return a string value!")
     }
     //If conceptCode returns empty, also return empty, if there is no such key or target column is null also return empty
-    val result =
+    val result: Seq[FhirPathResult] =
       conceptCodeResult
-      .headOption
-      .map(_.asInstanceOf[FhirPathString].s) match {
-        case None => Nil
-        case Some(conceptCode) =>
-          conceptMapContext
-            .concepts
-            .get(conceptCode)
-            .flatMap(codeEntry =>
-              codeEntry.get(targetField).filter(_ != "")
-            )
-            .map(mappedValue =>  FhirPathString(mappedValue))
-            .toSeq
-    }
+        .headOption
+        .map(_.asInstanceOf[FhirPathString].s)
+        .flatMap { conceptCode =>
+          conceptMapContext.concepts.get(conceptCode).map { conceptMapEntries =>
+            conceptMapEntries
+              .flatMap(_.get(targetField))
+              .filter(_.nonEmpty)
+              .map(mappedValue => FhirPathString(mappedValue))
+          }
+      }.getOrElse(Seq.empty)
     result
   }
 

diff --git a/tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingContext.scala b/tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMappingContext.scala
@@ -14,11 +14,15 @@ trait FhirMappingContext {
  *                 From a CSV who has a header like "source_code,source_system,source_display,unit,profile", and where
  *                 source_code is 9110-8, the concepts Map can be as in the following:
  *
- *                 Map[9110-8 -> Map[(source_system -> http://loinc.org,Bleeding (cumulative)),
- *                 (unit -> mL),
- *                 (profile -> https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation)]]
+ *                 Map[9110-8 -> Seq [
+ *                                    Map[(source_system -> http://loinc.org,Bleeding (cumulative)),
+ *                                        (unit -> mL),
+ *                                        (profile -> https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation)]
+ *                 ]]
+ *
+ *
  */
-case class ConceptMapContext(concepts: Map[String, Map[String, String]]) extends FhirMappingContext {
+case class ConceptMapContext(concepts: Map[String, Seq[Map[String, String]]]) extends FhirMappingContext {
   override def toContextObject: JObject = JObject()
 }
 

diff --git a/...r-engine/src/test/resources/test-mappings/some-folder-1/other-observation-concept-map.csv b/...r-engine/src/test/resources/test-mappings/some-folder-1/other-observation-concept-map.csv
@@ -9,6 +9,8 @@ source_code,source_system,source_display,unit,profile
 445619006,http://snomed.info/sct,NEWS score,{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-NEWSScore
 445597002,http://snomed.info/sct,PEWS score,{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-PEWSScore
 9269-2,http://loinc.org,Galscow Coma Scale (GCS),{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-GlascowComaScaleObservation
+1234-5,http://loinc.org,Hemogoblin,g/dL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
+1234-5,http://loinc.org,Hemogoblin X,g/cL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
 313002,http://www.nlm.nih.gov/research/umls/rxnorm,NaCl0.9% (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
 35629,http://www.nlm.nih.gov/research/umls/rxnorm,Ringer  (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
 33834,http://www.nlm.nih.gov/research/umls/rxnorm,Plasmalyte  (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
diff --git a/...r-engine/src/test/resources/test-mappings/some-folder-3/other-observation-concept-map.csv b/...r-engine/src/test/resources/test-mappings/some-folder-3/other-observation-concept-map.csv
@@ -9,6 +9,8 @@ source_code,source_system,source_display,unit,profile
 445619006,http://snomed.info/sct,NEWS score,{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-NEWSScore
 445597002,http://snomed.info/sct,PEWS score,{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-PEWSScore
 9269-2,http://loinc.org,Galscow Coma Scale (GCS),{score},https://aiccelerate.eu/fhir/StructureDefinition/AIC-GlascowComaScaleObservation
+1234-5,http://loinc.org,Hemogoblin,g/dL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
+1234-5,http://loinc.org,Hemogoblin X,g/cL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
 313002,http://www.nlm.nih.gov/research/umls/rxnorm,NaCl0.9% (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
 35629,http://www.nlm.nih.gov/research/umls/rxnorm,Ringer  (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
 33834,http://www.nlm.nih.gov/research/umls/rxnorm,Plasmalyte  (cumulative) given,mL,https://aiccelerate.eu/fhir/StructureDefinition/AIC-MedicationAdministration
diff --git a/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingFolderRepositoryTest.scala b/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingFolderRepositoryTest.scala
@@ -45,12 +45,21 @@ class FhirMappingFolderRepositoryTest extends AsyncFlatSpec with ToFhirTestSpec
     val mappingContextLoader = new MappingContextLoader
     mappingContextLoader.retrieveContext(contextDefinition) map { context =>
       val conceptMapContext = context.asInstanceOf[ConceptMapContext]
-      conceptMapContext.concepts.size shouldBe 13
+      conceptMapContext.concepts.size shouldBe 14
 
       // source_code,source_system,source_display,unit,profile
       // 9187-6,http://loinc.org,Urine Output,cm3,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
-      conceptMapContext.concepts("9187-6")("source_system") shouldBe "http://loinc.org"
-      conceptMapContext.concepts("9187-6")("unit") shouldBe "cm3"
+      conceptMapContext.concepts("9187-6").head("source_system") shouldBe "http://loinc.org"
+      conceptMapContext.concepts("9187-6").head("unit") shouldBe "cm3"
+
+      conceptMapContext.concepts("1234-5").length shouldBe 2
+      conceptMapContext.concepts("1234-5").head("source_system") shouldBe "http://loinc.org"
+      conceptMapContext.concepts("1234-5").head("source_display") shouldBe "Hemogoblin"
+      conceptMapContext.concepts("1234-5").head("unit") shouldBe "g/dL"
+
+      conceptMapContext.concepts("1234-5")(1)("source_system") shouldBe "http://loinc.org"
+      conceptMapContext.concepts("1234-5")(1)("source_display") shouldBe "Hemogoblin X"
+      conceptMapContext.concepts("1234-5")(1)("unit") shouldBe "g/cL"
     }
   }
 
@@ -60,12 +69,12 @@ class FhirMappingFolderRepositoryTest extends AsyncFlatSpec with ToFhirTestSpec
     val mappingContextLoader = new MappingContextLoader
     mappingContextLoader.retrieveContext(contextDefinition) map { context =>
       val conceptMapContext = context.asInstanceOf[ConceptMapContext]
-      conceptMapContext.concepts.size shouldBe 13
+      conceptMapContext.concepts.size shouldBe 14
 
       // source_code,source_system,source_display,unit,profile
       // 9187-6,http://loinc.org,Urine Output,cm3,https://aiccelerate.eu/fhir/StructureDefinition/AIC-IntraOperativeObservation
-      conceptMapContext.concepts("9187-6")("source_system") shouldBe "http://loinc.org"
-      conceptMapContext.concepts("9187-6")("unit") shouldBe "cm3"
+      conceptMapContext.concepts("9187-6").head("source_system") shouldBe "http://loinc.org"
+      conceptMapContext.concepts("9187-6").head("unit") shouldBe "cm3"
     }
   }