Merge pull request #93 from kairos-fhir/patientfinder-medications

Patientfinder medications

pom.xml

@@ -16,7 +16,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <java.compiler.level>1.8</java.compiler.level>
     <maven-compiler-plugin.version>3.11.0</maven-compiler-plugin.version>
-    <kairos-fhir-dsl.version>1.40.0</kairos-fhir-dsl.version>
+    <kairos-fhir-dsl.version>1.41.0</kairos-fhir-dsl.version>
     <junit-jupiter.version>5.8.2</junit-jupiter.version>
     <maven-surefire-plugin.version>3.1.2</maven-surefire-plugin.version>
     <gmavenplus-plugin.version>1.9.1</gmavenplus-plugin.version>

src/main/groovy/projects/patientfinder/README.md

@@ -15,6 +15,8 @@ The following imported data sets are supported/tested:
 
 ## 2024-11-06
 * moved telecom information from Patient.contact.telecom to Patient.telecom
+* Removed unused fields from the MedicationRequest and MedicationAdministration scripts
+* added Medication script
 
 ## 2024-10-17
 * Added the export of MedicationRequest requester from LaborMapping

src/main/groovy/projects/patientfinder/medication.groovy

@@ -0,0 +1,149 @@
+package projects.patientfinder
+
+import de.kairos.centraxx.fhir.r4.utils.FhirUrls
+import de.kairos.fhir.centraxx.metamodel.CrfTemplateField
+import de.kairos.fhir.centraxx.metamodel.Episode
+import de.kairos.fhir.centraxx.metamodel.LaborFinding
+import de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue
+import de.kairos.fhir.centraxx.metamodel.LaborMapping
+import de.kairos.fhir.centraxx.metamodel.LaborMethod
+import de.kairos.fhir.centraxx.metamodel.LaborValue
+import de.kairos.fhir.centraxx.metamodel.enums.MedicationServiceType
+import de.kairos.fhir.dsl.r4.context.Context
+
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.medication
+
+final String DOSAGE_SITE = "dosage.site"
+final String DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT = "dosage.doseAndRate.rateQuantity.unit"
+final String VOLUMEINFUSED = "volumeinfused"
+final String VOLUMEINFUSED_UOM = "volumeinfused_uom"
+final String CONCENTRATION_STRENGTH = "concentration_strength"
+final String CONCENTRATION_STRENGTH_UNIT = "concentration_strength_unit"
+
+final Map PROFILE_TYPES = [
+    DOSAGE_SITE                         : LaborFindingLaborValue.STRING_VALUE,
+    DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT: LaborFindingLaborValue.STRING_VALUE,
+    VOLUMEINFUSED                       : LaborFindingLaborValue.NUMERIC_VALUE,
+    VOLUMEINFUSED_UOM                   : LaborFindingLaborValue.STRING_VALUE,
+    CONCENTRATION_STRENGTH              : LaborFindingLaborValue.NUMERIC_VALUE,
+    CONCENTRATION_STRENGTH_UNIT         : LaborFindingLaborValue.STRING_VALUE
+]
+
+
+/**
+ * Represents a CXX MedicationAdministration -> extracts the Medication data
+ *
+ * @author Jonas Küttner
+ * v.1.41.0, CXX.v.2024.4.2
+ */
+medication {
+
+  if (context.source[medication().entitySource()] != "SACT") {
+    return
+  }
+
+  final def mapping = getLaborMapping(context)
+
+  final Map<String, Map> lflvMap = getLflvMap(mapping, PROFILE_TYPES)
+
+  id = "Medication/" + context.source[medication().id()]
+
+  code {
+    coding {
+      system = FhirUrls.System.Medication.BASE_URL
+      code = context.source[medication().code()] as String
+      display = context.source[medication().name()] as String
+    }
+  }
+
+  if (medication().applicationMedium()){
+    form {
+      coding {
+        code = context.source[medication().applicationMedium()] as String
+      }
+    }
+  }
+
+  ingredient {
+    itemCodeableConcept {
+      if (context.source[medication().agent()]) {
+        coding {
+          system = FhirUrls.System.Medication.AGENT
+          code = context.source[medication().agent()] as String
+        }
+      }
+      if (context.source[medication().agentGroup()]) {
+        coding {
+          system = FhirUrls.System.Medication.AGENT_GROUP
+          code = context.source[medication().agentGroup()] as String
+        }
+      }
+    }
+
+    strength {
+      if (lflvMap.containsKey(CONCENTRATION_STRENGTH)) {
+        numerator {
+          value = lflvMap[CONCENTRATION_STRENGTH][LaborFindingLaborValue.NUMERIC_VALUE]
+          unit = lflvMap[CONCENTRATION_STRENGTH_UNIT][LaborFindingLaborValue.STRING_VALUE]
+        }
+      }
+    }
+  }
+}
+
+/**
+ * removes milli seconds and time zone.
+ * @param dateTimeString the date time string
+ * @return the result might be something like "1989-01-15T00:00:00"
+ */
+static String normalizeDate(final String dateTimeString) {
+  return dateTimeString != null ? dateTimeString.substring(0, 19) : null
+}
+
+static boolean isFakeEpisode(final def episode) {
+  if (episode == null) {
+    return true
+  }
+
+  if (["SACT", "COSD"].contains(episode[Episode.ENTITY_SOURCE])) {
+    return true
+  }
+
+  final def fakeId = episode[Episode.ID_CONTAINER]?.find { (it[PSN] as String).toUpperCase().startsWith("FAKE") }
+  return fakeId != null
+}
+
+static Map<String, Map> getLflvMap(final def mapping, final Map<String, String> types) {
+  final Map<String, Map> lflvMap = [:]
+  if (!mapping) {
+    return lflvMap
+  }
+
+  types.each { final String lvCode, final String lvType ->
+    final def lflv = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find { final def lflv ->
+      lflv[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][LaborValue.CODE] == lvCode
+    }
+    if (lflv && lflv[lvType]) {
+      lflvMap[lvCode] = [key: lflv[lvType]]
+    }
+  }
+  return lflvMap
+}
+
+static def getLaborMapping(final Context context){
+  if (context.source[medication().serviceType()] as MedicationServiceType == MedicationServiceType.GAB) {
+    return context.source[medication().laborMappings()].find { final def lm ->
+      lm[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_METHOD][LaborMethod.CODE] == "MedicationAdministration_profile"
+    }
+  }
+
+  if (context.source[medication().serviceType()] as MedicationServiceType == MedicationServiceType.VER) {
+    return context.source[medication().laborMappings()].find { final def lm ->
+      lm[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_METHOD][LaborMethod.CODE] == "MedicationRequest_profile"
+    }
+  }
+
+  return null
+}
+