add export script for siop MetPredict

src/main/groovy/projects/dktk/v2/ExportResourceMappingConfig.json

@@ -115,6 +115,11 @@
       "selectFromCxxEntity": "OTHER_CLASSIFICATION",
       "transformByTemplate": "weitereKlassifikation",
       "exportToFhirResource": "Observation"
+    },
+  	{
+      "selectFromCxxEntity": "LABOR_MAPPING",
+      "transformByTemplate": "siopObservation",
+      "exportToFhirResource": "Observation"
     }
   ]
 }

src/main/groovy/projects/dktk/v2/siopObservation.groovy

@@ -0,0 +1,213 @@
+package projects.dktk.v2
+
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum
+import de.kairos.centraxx.fhir.r4.utils.FhirUrls
+import de.kairos.fhir.centraxx.metamodel.AbstractCatalog
+import de.kairos.fhir.centraxx.metamodel.CatalogEntry
+import de.kairos.fhir.centraxx.metamodel.CrfTemplateField
+import de.kairos.fhir.centraxx.metamodel.IcdEntry
+import de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue
+import de.kairos.fhir.centraxx.metamodel.LaborValue
+import de.kairos.fhir.centraxx.metamodel.LaborValueNumeric
+import de.kairos.fhir.centraxx.metamodel.PrecisionDate
+import de.kairos.fhir.centraxx.metamodel.ValueReference
+import de.kairos.fhir.centraxx.metamodel.enums.LaborValueDType
+import org.hl7.fhir.r4.model.Observation
+
+import static de.kairos.fhir.centraxx.metamodel.AbstractCode.CODE
+import static de.kairos.fhir.centraxx.metamodel.AbstractCodeName.NAME_MULTILINGUAL_ENTRIES
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.ID_CONTAINER_TYPE
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
+import static de.kairos.fhir.centraxx.metamodel.MultilingualEntry.LANG
+import static de.kairos.fhir.centraxx.metamodel.MultilingualEntry.VALUE
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.laborMapping
+
+/**
+ * Represented by a CXX LaborMapping
+ * @author Mike Wähnert (adapted by David Scholz)
+ * @since kairos-fhir-dsl.v.1.12.0, CXX.v.3.18.1.19, CXX.v.3.18.2
+ * The first code of each component represents the LaborValue.Code in CXX. Further codes could be representations in LOINC, SNOMED-CT etc.
+ * LaborValueIdContainer in CXX are just an export example, but not intended to be imported by CXX FHIR API yet.
+ */
+observation {
+
+  def laborMethodCode = context.source[laborMapping().laborFinding().laborMethod().code()]
+  if (laborMethodCode == null || !(laborMethodCode as String).startsWith("PROFILE_SIOP")) {
+      return
+  }
+
+  id = "Observation/" + context.source[laborMapping().laborFinding().id()]
+
+  status = Observation.ObservationStatus.UNKNOWN
+
+  code {
+    coding {
+      system = FhirUrls.System.Finding.LABOR_FINDING_SHORTNAME
+      code = context.source[laborMapping().laborFinding().shortName()] as String
+    }
+  }
+
+  effectiveDateTime {
+    date = context.source[laborMapping().laborFinding().findingDate().date()]
+    precision = TemporalPrecisionEnum.DAY.name()
+  }
+
+  subject {
+    reference = "Patient/" + context.source[laborMapping().relatedPatient().id()]
+  }
+
+  method {
+    coding {
+      system = FhirUrls.System.LaborMethod.BASE_URL
+      version = context.source[laborMapping().laborFinding().laborMethod().version()]
+      code = context.source[laborMapping().laborFinding().laborMethod().code()] as String
+    }
+  }
+
+  context.source[laborMapping().laborFinding().laborFindingLaborValues()].each { final lflv ->
+
+    final def laborValue = lflv[LaborFindingLaborValue.LABOR_VALUE] != null
+        ? lflv[LaborFindingLaborValue.LABOR_VALUE] // before CXX.v.2022.3.0
+        : lflv[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE] // from CXX.v.2022.3.0
+
+    final String laborValueCode = laborValue?.getAt(CODE) as String
+    final String laborValueDisplay = laborValue?.getAt(NAME_MULTILINGUAL_ENTRIES)?.find { final mle -> mle[LANG] == "en" }?.getAt(VALUE) as String
+
+    component {
+      code {
+        coding {
+          system = FhirUrls.System.LaborValue.BASE_URL
+          code = laborValueCode
+          display = laborValueDisplay
+        }
+        laborValue?.getAt(LaborValue.IDCONTAINERS)?.each { final idContainer ->
+          coding {
+            system = idContainer[ID_CONTAINER_TYPE]?.getAt(CODE)
+            code = idContainer[PSN] as String
+          }
+        }
+      }
+
+      if (isNumeric(laborValue)) {
+        valueQuantity {
+          value = lflv[LaborFindingLaborValue.NUMERIC_VALUE]
+          unit = laborValue?.getAt(LaborValueNumeric.UNIT)?.getAt(CODE) as String
+        }
+      } else if (isBoolean(laborValue)) {
+        valueBoolean(lflv[LaborFindingLaborValue.BOOLEAN_VALUE] as Boolean)
+      } else if (isDate(laborValue)) {
+        valueDateTime {
+          date = lflv[LaborFindingLaborValue.DATE_VALUE]?.getAt(PrecisionDate.DATE)
+        }
+      } else if (isTime(laborValue)) {
+        valueTime(lflv[LaborFindingLaborValue.TIME_VALUE] as String)
+      } else if (isString(laborValue)) {
+        valueString(lflv[LaborFindingLaborValue.STRING_VALUE] as String)
+      } else if (isEnumeration(laborValue)) {
+        valueCodeableConcept {
+          lflv[LaborFindingLaborValue.MULTI_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/UsageEntry"
+              code = entry[CODE] as String
+            }
+          }
+          lflv[LaborFindingLaborValue.CATALOG_ENTRY_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/ValueList-" + entry[CatalogEntry.CATALOG]?.getAt(AbstractCatalog.ID)
+              code = entry[CODE] as String
+            }
+          }
+        }
+      } else if (isOptionGroup(laborValue)) {
+        valueCodeableConcept {
+          lflv[LaborFindingLaborValue.MULTI_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/UsageEntry"
+              code = entry[CODE] as String
+            }
+          }
+          lflv[LaborFindingLaborValue.CATALOG_ENTRY_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/ValueList-" + entry[CatalogEntry.CATALOG]?.getAt(AbstractCatalog.ID)
+              code = entry[CODE] as String
+            }
+          }
+        }
+      } else if (isCatalog(laborValue)) {
+        valueCodeableConcept {
+          lflv[LaborFindingLaborValue.CATALOG_ENTRY_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/ValueList-" + entry[CatalogEntry.CATALOG]?.getAt(AbstractCatalog.ID)
+              code = entry[CODE] as String
+            }
+          }
+          lflv[LaborFindingLaborValue.ICD_ENTRY_VALUE].each { final entry ->
+            coding {
+              system = "urn:centraxx:CodeSystem/IcdCatalog-" + entry[IcdEntry.CATALOGUE]?.getAt(AbstractCatalog.ID)
+              code = entry[CODE] as String
+            }
+          }
+          // example for master data catalog entries of blood group
+          lflv[LaborFindingLaborValue.MULTI_VALUE_REFERENCES].each { final entry ->
+            final def bloodGroup = entry[ValueReference.BLOOD_GROUP_VALUE]
+            if (bloodGroup != null) {
+              coding {
+                system = FhirUrls.System.Patient.BloodGroup.BASE_URL
+                code = bloodGroup?.getAt(CODE) as String
+              }
+            }
+
+            // example for master data catalog entries of attending doctor
+            final def attendingDoctor = entry[ValueReference.ATTENDING_DOCTOR_VALUE]
+            if (attendingDoctor != null) {
+              coding {
+                system = FhirUrls.System.AttendingDoctor.BASE_URL
+                // CXX uses the reference embedded in a coding to support multi selects
+                code = "Practitioner/" + attendingDoctor?.getAt(AbstractCatalog.ID) as String
+              }
+            }
+          }
+        }
+      } else {
+        final String msg = laborValue?.getAt(LaborValue.D_TYPE) + " not implemented yet."
+        System.out.println(msg)
+      }
+    }
+  }
+}
+
+static boolean isDTypeOf(final Object laborValue, final List<LaborValueDType> types) {
+  return types.contains(laborValue?.getAt(LaborValue.D_TYPE) as LaborValueDType)
+}
+
+static boolean isBoolean(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.BOOLEAN])
+}
+
+static boolean isNumeric(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.INTEGER, LaborValueDType.DECIMAL, LaborValueDType.SLIDER])
+}
+
+static boolean isDate(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.DATE, LaborValueDType.LONGDATE])
+}
+
+static boolean isTime(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.TIME])
+}
+
+static boolean isEnumeration(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.ENUMERATION])
+}
+
+static boolean isString(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.STRING, LaborValueDType.LONGSTRING])
+}
+
+static boolean isCatalog(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.CATALOG])
+}
+
+static boolean isOptionGroup(final Object laborValue) {
+  return isDTypeOf(laborValue, [LaborValueDType.OPTIONGROUP])
+}