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Merge pull request #51 from kairos-fhir/custom-import-mii
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created first draft for Transformation of FHIR MII KDS -> CXX FHIR
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@kairosjonas
kairosjonas authored Mar 14, 2024
2 parents 33927d7 + 3e3985b commit f7de1e3
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0 ...in/groovy/customimport/ProjectConfig.json → ...y/customimport/example/ProjectConfig.json
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2 changes: 1 addition & 1 deletion src/main/groovy/customimport/patient.groovy → ...roovy/customimport/example/patient.groovy
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package customimport
package customimport.example

import de.kairos.centraxx.fhir.r4.utils.FhirUrls
import org.hl7.fhir.r4.model.Bundle
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102 changes: 102 additions & 0 deletions src/main/groovy/customimport/mii/modulperson/example-message-patient.json
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{
"resourceType": "Bundle",
"type": "transaction",
"entry": [
{
"fullUrl": "Patient/3365",
"resource":{
"resourceType": "Patient",
"id": "ExamplePatientPatientMinimal",
"meta": {
"profile": [
"https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
]
},
"identifier": [
{
"use": "usual",
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR"
}
]
},
"system": "https://www.example.org/fhir/sid/patienten",
"value": "42285243",
"assigner": {
"display": "Charité – Universitätsmedizin Berlin",
"identifier": {
"system": "http://fhir.de/NamingSystem/arge-ik/iknr",
"value": "261101015"
}
}
},
{
"use": "official",
"type": {
"coding": [
{
"system": "http://fhir.de/CodeSystem/identifier-type-de-basis",
"code": "GKV"
}
]
},
"system": "http://fhir.de/NamingSystem/gkv/kvid-10",
"value": "A999999999",
"assigner": {
"identifier": {
"use": "official",
"system": "http://fhir.de/NamingSystem/arge-ik/iknr",
"value": "260326822"
}
}
}
],
"name": [
{
"use": "official",
"family": "Van-der-Dussen",
"given": [
"Maja",
"Julia"
]
}
],
"address": [
{
"type": "both",
"line": [
"Teststraße 2"
],
"city": "Köln",
"postalCode": "50823",
"country": "DE"
}
],
"gender": "other",
"_gender": {
"extension": [
{
"url": "http://fhir.de/StructureDefinition/gender-amtlich-de",
"valueCoding": {
"system": "http://fhir.de/CodeSystem/gender-amtlich-de",
"code": "D",
"display": "divers"
}
}
]
},
"birthDate": "1998-09-19",
"managingOrganization": {
"reference": "Organization/Charite-Universitaetsmedizin-Berlin"
}
},
"request": {
"method": "POST",
"url": "Patient/575"
}
}
]
}
49 changes: 49 additions & 0 deletions src/main/groovy/customimport/mii/modulperson/masterdata_patient.xml
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<CentraXXDataExchange xmlns="http://www.kairos-med.de" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.kairos-med.de ../CentraXXExchange.xsd">
<Source>CENTRAXX</Source>
<SourceVersion>2024.2.0-SNAPSHOT</SourceVersion>
<ExportDate>2024-03-01T19:11:17.057+01:00</ExportDate>
<CatalogueData>
<IdType>
<Code>PATIENTID</Code>
<Name>Pat. ID</Name>
<Editable>true</Editable>
<Kind>PATIENT</Kind>
<Decisive>false</Decisive>
<Pseudonym>false</Pseudonym>
<Mandatory>false</Mandatory>
<SyncId>9AA837FD-89EB-41C3-8B32-1154C9F61536</SyncId>
<UserEntries assignStrict="true">
<Systemwide>true</Systemwide>
</UserEntries>
<Uniqueness>ORGANIZATION</Uniqueness>
</IdType>
<IdType>
<Code>GKV</Code>
<Name>Versichterten ID GKV</Name>
<Editable>true</Editable>
<Kind>PATIENT</Kind>
<Decisive>true</Decisive>
<Pseudonym>false</Pseudonym>
<Mandatory>false</Mandatory>
<SyncId>e8f9fb88-eed7-4f4e-a358-2fc49eb3277b</SyncId>
<UserEntries assignStrict="true">
<Systemwide>true</Systemwide>
</UserEntries>
<Uniqueness>SYSTEM</Uniqueness>
</IdType>
<IdType>
<Code>PKV</Code>
<Name>Versicherten ID PKV</Name>
<Editable>true</Editable>
<Kind>PATIENT</Kind>
<Decisive>true</Decisive>
<Pseudonym>false</Pseudonym>
<Mandatory>false</Mandatory>
<SyncId>9f9bf668-3802-4fb3-aa7a-329744283fb7</SyncId>
<UserEntries assignStrict="true">
<Systemwide>true</Systemwide>
</UserEntries>
<Uniqueness>SYSTEM</Uniqueness>
</IdType>
</CatalogueData>
</CentraXXDataExchange>
195 changes: 195 additions & 0 deletions src/main/groovy/customimport/mii/modulperson/patient.groovy
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package customimport.mii.modulperson

import de.kairos.centraxx.fhir.r4.utils.FhirUrls
import org.hl7.fhir.r4.model.Address
import org.hl7.fhir.r4.model.Bundle
import org.hl7.fhir.r4.model.Extension
import org.hl7.fhir.r4.model.HumanName
import org.hl7.fhir.r4.model.Identifier
import org.hl7.fhir.r4.model.Patient
import org.hl7.fhir.r4.model.ResourceType
import org.hl7.fhir.r4.model.codesystems.NameUse

bundle {

// filter for patient entries
context.bundles.each { final def bundle ->
bundle.getEntry().findAll { it.getResource().getResourceType() == ResourceType.Patient }
.each {
final Patient sourcePatient = it.getResource() as Patient

// get bundle request to set to entries. Could also transform it here.
final Bundle.BundleEntryRequestComponent requestToSet = it.getRequest()


entry {
request = requestToSet
resource {
patient {
id = sourcePatient.getId()

final Identifier gkv = sourcePatient.identifier.find {
it.type?.codingFirstRep?.system == "http://fhir.de/CodeSystem/identifier-type-de-basis" && it.type?.codingFirstRep?.code == "GKV"
}

if (gkv) {
identifier {
type {
coding {
system = FhirUrls.System.IdContainerType.BASE_URL
code = "GKV"
}
}
value = gkv.value
}
}

final Identifier pid = sourcePatient.identifier.find {
it.type?.codingFirstRep?.system == "http://terminology.hl7.org/CodeSystem/v2-0203" && it.type?.codingFirstRep?.code == "MR"
}

if (pid) {
identifier {
type {
coding {
system = FhirUrls.System.IdContainerType.BASE_URL
code = "PATIENTID"
}
}
value = pid.value
}
}

final Identifier pkv = sourcePatient.identifier.find {
it.type?.codingFirstRep?.system == "http://fhir.de/CodeSystem/identifier-type-de-basis" && it.type?.codingFirstRep?.code == "PKV"
}

if (pkv) {
identifier {
type {
coding {
system = FhirUrls.System.IdContainerType.BASE_URL
code = "PKV"
}
}
value = pkv.value
}
}

/**
* For import the mandatory system Ids must be set.
* TODO: Figure something out here that makes sense.
*/
final Identifier notNull = [pkv, gkv, pid].find{it != null}

identifier {
type {
coding {
system = FhirUrls.System.IdContainerType.BASE_URL
code = "SID"
}
}
value = notNull.value
}

/**
* Names
* Currently we only import given and last name
* CXX supports title, affix, birthname
*/

final HumanName firstSourceName = sourcePatient.name.find {
it.use.toCode() == NameUse.OFFICIAL.toCode()
}

if (firstSourceName) {
humanName {
firstSourceName.given.each {
given.add(it.getValue())
}

family = firstSourceName.family
}
}

final HumanName firstSourceBirthName = sourcePatient.name.find {
it.use.toCode() == NameUse.MAIDEN.toCode()
}

if (firstSourceBirthName) {
/**
* not yet implemented in CXX importer
*/
}

/**
* CXX does only map the FHIR administrative Genders back to the CXX Genders
* MII uses and extension for the case UNKNOWN which specifies whether it is "unbestimmt" or "divers"
*/
gender = sourcePatient.gender

if (sourcePatient.birthDate) {
final Extension dataAbsentReasonExtension = sourcePatient.birthDateElement
.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/data-absent-reason")

birthDate {
date = sourcePatient.birthDate

if(dataAbsentReasonExtension){
extension.add(dataAbsentReasonExtension)
}
}

}

if (sourcePatient.deceasedDateTimeType) {
deceasedDateTime {
date = sourcePatient.deceasedDateTimeType.value
}
}

final Address firstAddress = sourcePatient.addressFirstRep

/**
* Importer currently considers first line item to be street and second to be HouseNo
*
* country, state, postfach is supported by CXX but not yet by the FHIR importer
*
*/

if (firstAddress) {
address {
city = firstAddress.city
postalCode = firstAddress.postalCode

if (firstAddress.line.size() == 1) {
line.add(firstAddress.line.get(0).getValue())
} else {
final String street = firstAddress.line.find {
it.hasExtension("http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-streetName")
}?.getValue()

final String houseNo = firstAddress.line.find {
it.hasExtension("http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-houseNumber")
}?.getValue()

/**
* not supported by importer yet
*/
final String postFach = firstAddress.line.find {
it.hasExtension("http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-postBox")
}?.getValue()

line.add(street)
line.add(houseNo)

}
}
}
}
}
}
}
}
}

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