initial commit groovy files BER

src/main/groovy/projects/cxx/napkon/BER/observation.groovy

@@ -0,0 +1,194 @@
+package projects.cxx
+
+import de.kairos.fhir.centraxx.metamodel.CatalogEntry
+import de.kairos.fhir.centraxx.metamodel.IdContainer
+import de.kairos.fhir.centraxx.metamodel.IdContainerType
+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.SampleIdContainer
+import de.kairos.fhir.centraxx.metamodel.Unity
+import de.kairos.fhir.centraxx.metamodel.UsageEntry
+import de.kairos.fhir.centraxx.metamodel.enums.LaborMappingType
+import de.kairos.fhir.centraxx.metamodel.enums.SampleCategory
+import org.hl7.fhir.r4.model.Observation
+
+import static de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue.LABOR_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.BOOLEAN_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.DATE_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.NUMERIC_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.STRING_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.TIME_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RecordedValue.CATALOG_ENTRY_VALUE
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.laborMapping
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.sample
+
+/**
+ * Represented by a CXX LaborMapping
+ * @author Jonas Küttner, Mike Wähnert
+ * @since v.1.8.0, CXX.v.3.8.1.1
+ *
+ * Script to extract measurement results that contain only simple data types and single / multiple selections from value lists.
+ * Based on the assumption that the measurement profiles (LaborMethods), measurement parameters (LaborValues) and the associated value lists are
+ * defined with the same codes in both CXX instances. In this case, only one mapping to the oid of the value list in the target system is required
+ * for the import.
+ */
+observation {
+    if (!((LaborMappingType.SAMPLELABORMAPPING == context.source[laborMapping().mappingType()] as LaborMappingType) && (["DZHKFLAB"].contains(context.source[laborMapping().laborFinding().laborMethod().code()])))) {
+        return
+    }
+
+
+    final def extSampleId = context.source[laborMapping().sample().idContainer()]?.find { final def entry ->
+        "NAPKONProbenID" == entry[SampleIdContainer.ID_CONTAINER_TYPE]?.getAt(IdContainerType.CODE)
+    }
+
+
+    final SampleCategory category = context.source[sample().sampleCategory()] as SampleCategory
+
+
+    // Filter mastersamples of HEPFIX and its familly - in test was _BB
+    if ((category == SampleCategory.MASTER && !extSampleId) || (extSampleId && (extSampleId?.getAt(SampleIdContainer.PSN) as String).contains("_BB"))) {
+        return
+    }
+
+
+    String napkonId = extSampleId?.getAt(SampleIdContainer.PSN) as String
+    if (napkonId && napkonId.length() == 20) {
+        napkonId = napkonId.substring(0, 10)
+    }
+
+
+    // Filter HEPFIX mastersample childs
+    if (context.source[sample().sampleType().code()] == "HEPARINFIXATED") {
+        return
+    }
+
+
+    id = "Observation/" + context.source[laborMapping().id()]
+
+
+    status = Observation.ObservationStatus.UNKNOWN
+
+
+    code {
+        coding {
+            system = "urn:centraxx"
+            code = context.source[laborMapping().laborFinding().shortName()] as String
+        }
+    }
+
+
+    final def patIdContainer = context.source[laborMapping().relatedPatient().idContainer()]?.find {
+        "NAPKONPATID" == it[IdContainer.ID_CONTAINER_TYPE]?.getAt(IdContainerType.CODE)
+    }
+
+    if (patIdContainer) {
+        subject {
+            identifier {
+                value = patIdContainer[IdContainer.PSN]
+                type {
+                    coding {
+                        system = "urn:centraxx"
+                        code = "LIMSPSN"
+                        // patIdContainer[IdContainer.ID_CONTAINER_TYPE]?.getAt(IdContainerType.CODE) as String
+                    }
+                }
+            }
+        }
+    }
+
+    if (context.source[laborMapping().sample()] != null) {
+        // Reference by identifier SampleId, because parent MasterSample might already exists in the target system
+        // The napkon sample id of BB is provided as sample id to DZHK.
+        if (extSampleId) {
+            specimen {
+                identifier {
+                    type {
+                        coding {
+                            code = "SAMPLEID"
+                        }
+                    }
+                    value = napkonId
+                }
+            }
+        }
+    }
+
+
+    effectiveDateTime = context.source[laborMapping().laborFinding().findingDate().date()]
+
+
+    method {
+        coding {
+            system = "urn:centraxx"
+            version = context.source[laborMapping().laborFinding().laborMethod().version()]
+            code = context.source[laborMapping().laborFinding().laborMethod().code()] as String
+        }
+    }
+
+
+    context.source[laborMapping().laborFinding().laborFindingLaborValues()].each { final def labFinLabVal ->
+        component {
+            code {
+                coding {
+                    system = "urn:centraxx"
+                    code = labFinLabVal[LABOR_VALUE][LaborValue.CODE] as String
+                }
+            }
+            if (labFinLabVal[NUMERIC_VALUE]) {
+                valueQuantity {
+                    value = labFinLabVal[NUMERIC_VALUE]
+                    unit = labFinLabVal[LABOR_VALUE]?.getAt(LaborValueNumeric.UNIT)?.getAt(Unity.CODE) as String
+                }
+            }
+
+            if (labFinLabVal[STRING_VALUE]) {
+                valueString(labFinLabVal[STRING_VALUE] as String)
+            }
+
+            if (labFinLabVal[STRING_VALUE]) {
+                valueQuantity {
+                    value = labFinLabVal[STRING_VALUE]
+                }
+            }
+
+            if (labFinLabVal[DATE_VALUE]) {
+                valueDateTime {
+                    date = labFinLabVal[DATE_VALUE]?.getAt(PrecisionDate.DATE)
+                }
+            }
+
+            if (labFinLabVal[TIME_VALUE]) {
+                valueTime(labFinLabVal[TIME_VALUE] as String)
+            }
+
+            if (labFinLabVal[BOOLEAN_VALUE]) {
+                valueBoolean(labFinLabVal[BOOLEAN_VALUE] as Boolean)
+            }
+
+            if (labFinLabVal[CATALOG_ENTRY_VALUE]) {
+                valueCodeableConcept {
+                    labFinLabVal[LaborFindingLaborValue.CATALOG_ENTRY_VALUE].each { final def entry ->
+                        coding {
+                            system = "urn:centraxx:CodeSystem/UsageEntry-" + entry[CatalogEntry.ID]
+                            code = entry[CatalogEntry.CODE] as String
+                        }
+                    }
+                }
+            }
+            if (labFinLabVal[LaborFindingLaborValue.MULTI_VALUE]) {
+                valueCodeableConcept {
+                    labFinLabVal[LaborFindingLaborValue.MULTI_VALUE].each { final def entry ->
+                        coding {
+                            system = "urn:centraxx:CodeSystem/UsageEntry-" + entry[UsageEntry.ID]
+                            code = entry[UsageEntry.CODE] as String
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+