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Merge pull request #10 from etiennenavarre/etiennenavarre-patch-1
Etiennenavarre patch 1 after pre review.
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src/main/groovy/projects/cxx/napkon/BER/observation.groovy
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| package projects.cxx | ||
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| 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 | ||
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| 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 | ||
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| /** | ||
| * 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 | ||
| } | ||
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| final def extSampleId = context.source[laborMapping().sample().idContainer()]?.find { final def entry -> | ||
| "NAPKONProbenID" == entry[SampleIdContainer.ID_CONTAINER_TYPE]?.getAt(IdContainerType.CODE) | ||
| } | ||
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| final SampleCategory category = context.source[sample().sampleCategory()] as SampleCategory | ||
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| // 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 | ||
| } | ||
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| String napkonId = extSampleId?.getAt(SampleIdContainer.PSN) as String | ||
| if (napkonId && napkonId.length() == 20) { | ||
| napkonId = napkonId.substring(0, 10) | ||
| } | ||
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| // Filter HEPFIX mastersample childs | ||
| if (context.source[sample().sampleType().code()] == "HEPARINFIXATED") { | ||
| return | ||
| } | ||
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| id = "Observation/" + context.source[laborMapping().id()] | ||
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| status = Observation.ObservationStatus.UNKNOWN | ||
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| code { | ||
| coding { | ||
| system = "urn:centraxx" | ||
| code = context.source[laborMapping().laborFinding().shortName()] as String | ||
| } | ||
| } | ||
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| final def patIdContainer = context.source[laborMapping().relatedPatient().idContainer()]?.find { | ||
| "NAPKONPATID" == it[IdContainer.ID_CONTAINER_TYPE]?.getAt(IdContainerType.CODE) | ||
| } | ||
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| 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 | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| 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 | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| effectiveDateTime = context.source[laborMapping().laborFinding().findingDate().date()] | ||
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| method { | ||
| coding { | ||
| system = "urn:centraxx" | ||
| version = context.source[laborMapping().laborFinding().laborMethod().version()] | ||
| code = context.source[laborMapping().laborFinding().laborMethod().code()] as String | ||
| } | ||
| } | ||
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| 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 | ||
| } | ||
| } | ||
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| if (labFinLabVal[STRING_VALUE]) { | ||
| valueString(labFinLabVal[STRING_VALUE] as String) | ||
| } | ||
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| if (labFinLabVal[STRING_VALUE]) { | ||
| valueQuantity { | ||
| value = labFinLabVal[STRING_VALUE] | ||
| } | ||
| } | ||
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| if (labFinLabVal[DATE_VALUE]) { | ||
| valueDateTime { | ||
| date = labFinLabVal[DATE_VALUE]?.getAt(PrecisionDate.DATE) | ||
| } | ||
| } | ||
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| if (labFinLabVal[TIME_VALUE]) { | ||
| valueTime(labFinLabVal[TIME_VALUE] as String) | ||
| } | ||
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| if (labFinLabVal[BOOLEAN_VALUE]) { | ||
| valueBoolean(labFinLabVal[BOOLEAN_VALUE] as Boolean) | ||
| } | ||
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| 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 | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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