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feat: add initial SystemischeTherapieMedicationStatementMapper (#170)
* feat: add initial SystemischeTherapieMedicationStatementMapper * add medication and bundle type * add missing subject, status and effective * change property "mii-pr-medication-statement" Co-authored-by: chgl <[email protected]> * set "partOf" * extract and change substance id generation from plain name * Revert "change property "mii-pr-medication-statement"" This reverts commit 71b87df. * use custom system for medical statement id --------- Co-authored-by: chgl <[email protected]>
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...racum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMedicationStatementMapper.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,121 @@ | ||
| package org.miracum.streams.ume.obdstofhir.mapper.mii; | ||
|
|
||
| import com.google.common.hash.Hashing; | ||
| import de.basisdatensatz.obds.v3.SYSTTyp; | ||
| import de.basisdatensatz.obds.v3.SYSTTyp.Meldeanlass; | ||
| import java.nio.charset.StandardCharsets; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
| import org.apache.commons.lang3.Validate; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.CodeableConcept; | ||
| import org.hl7.fhir.r4.model.Coding; | ||
| import org.hl7.fhir.r4.model.Enumerations.ResourceType; | ||
| import org.hl7.fhir.r4.model.Identifier; | ||
| import org.hl7.fhir.r4.model.MedicationStatement; | ||
| import org.hl7.fhir.r4.model.Period; | ||
| import org.hl7.fhir.r4.model.Reference; | ||
| import org.miracum.streams.ume.obdstofhir.FhirProperties; | ||
| import org.miracum.streams.ume.obdstofhir.mapper.ObdsToFhirMapper; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.stereotype.Service; | ||
| import org.springframework.util.StringUtils; | ||
|
|
||
| @Service | ||
| public class SystemischeTherapieMedicationStatementMapper extends ObdsToFhirMapper { | ||
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|
||
| private static final Logger LOG = | ||
| LoggerFactory.getLogger(SystemischeTherapieProcedureMapper.class); | ||
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| public SystemischeTherapieMedicationStatementMapper(FhirProperties fhirProperties) { | ||
| super(fhirProperties); | ||
| } | ||
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| public Bundle map(SYSTTyp syst, Reference patient, Reference procedure) { | ||
| Objects.requireNonNull(syst, "Systemtherapie must not be null"); | ||
| Objects.requireNonNull(patient, "Reference to Patient must not be null"); | ||
| Objects.requireNonNull(procedure, "Reference to Procedure must not be null"); | ||
|
|
||
| Validate.notBlank(syst.getSYSTID(), "Required SYST_ID is unset"); | ||
| Validate.isTrue( | ||
| Objects.equals( | ||
| patient.getReferenceElement().getResourceType(), ResourceType.PATIENT.toCode()), | ||
| "The subject reference should point to a Patient resource"); | ||
| Validate.isTrue( | ||
| Objects.equals( | ||
| procedure.getReferenceElement().getResourceType(), ResourceType.PROCEDURE.toCode()), | ||
| "The subject reference should point to a Procedure resource"); | ||
|
|
||
| var bundle = new Bundle(); | ||
| bundle.setType(Bundle.BundleType.TRANSACTION); | ||
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| for (var substanz : syst.getMengeSubstanz().getSubstanz()) { | ||
| var systMedicationStatement = new MedicationStatement(); | ||
| systMedicationStatement | ||
| .getMeta() | ||
| .addProfile(fhirProperties.getProfiles().getMiiPrMedicationStatement()); | ||
|
|
||
| if ((null != substanz.getATC() && StringUtils.hasText(substanz.getATC().getCode())) | ||
| || StringUtils.hasText(substanz.getBezeichnung())) { | ||
| var substanzId = ""; | ||
| if (null != substanz.getATC() && StringUtils.hasText(substanz.getATC().getCode())) { | ||
| substanzId = substanz.getATC().getCode(); | ||
| var atcCoding = | ||
| new Coding( | ||
| fhirProperties.getSystems().getAtcBfarm(), substanz.getATC().getCode(), ""); | ||
| systMedicationStatement.setMedication(new CodeableConcept(atcCoding)); | ||
| } else { | ||
| substanzId = createSubstanzIdFromPlain(substanz.getBezeichnung()); | ||
| systMedicationStatement.setMedication( | ||
| new CodeableConcept().setText(substanz.getBezeichnung())); | ||
| } | ||
|
|
||
| // TODO: can we be sure that this SYST-ID is globally unqiue across all SYSTs? | ||
| // if not we may instead need to construct the ID from the patient-id + others. | ||
| var identifier = | ||
| new Identifier() | ||
| .setSystem( | ||
| fhirProperties.getSystems().getSystemischeTherapieMedicationStatementId()) | ||
| .setValue(String.format("%s_%s", syst.getSYSTID(), substanzId)); | ||
| systMedicationStatement.addIdentifier(identifier); | ||
| systMedicationStatement.setId(computeResourceIdFromIdentifier(identifier)); | ||
|
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||
| // Status / Effective | ||
| var meldeanlass = syst.getMeldeanlass(); | ||
| var period = new Period(); | ||
| if (meldeanlass == Meldeanlass.BEHANDLUNGSENDE) { | ||
| systMedicationStatement.setStatus( | ||
| MedicationStatement.MedicationStatementStatus.COMPLETED); | ||
| convertObdsDatumToDateTimeType(syst.getBeginn()) | ||
| .ifPresent(start -> period.setStart(start.getValue(), start.getPrecision())); | ||
| convertObdsDatumToDateTimeType(syst.getEnde()) | ||
| .ifPresent(end -> period.setEnd(end.getValue(), end.getPrecision())); | ||
| } else { | ||
| systMedicationStatement.setStatus(MedicationStatement.MedicationStatementStatus.ACTIVE); | ||
| convertObdsDatumToDateTimeType(syst.getBeginn()) | ||
| .ifPresent(start -> period.setStart(start.getValue(), start.getPrecision())); | ||
| } | ||
| systMedicationStatement.setEffective(period); | ||
|
|
||
| // Subject | ||
| systMedicationStatement.setSubject(patient); | ||
|
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| // Part of | ||
| systMedicationStatement.setPartOf(List.of(procedure)); | ||
|
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| bundle = addResourceAsEntryInBundle(bundle, systMedicationStatement); | ||
| } | ||
| } | ||
|
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| return bundle; | ||
| } | ||
|
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| private String createSubstanzIdFromPlain(String plainName) { | ||
| Validate.notBlank(plainName, "Required substance name is unset"); | ||
| return String.format( | ||
| "%s_%s", | ||
| plainName.replaceAll("[^A-Za-z0-9]+", ""), | ||
| Hashing.sha256().hashString(plainName, StandardCharsets.UTF_8).toString().substring(0, 4)); | ||
| } | ||
| } |
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66 changes: 66 additions & 0 deletions
66
...m/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMedicationStatementMapperTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| package org.miracum.streams.ume.obdstofhir.mapper.mii; | ||
|
|
||
| import static org.assertj.core.api.Assertions.assertThat; | ||
|
|
||
| import ca.uhn.fhir.context.FhirContext; | ||
| import com.fasterxml.jackson.databind.DeserializationFeature; | ||
| import com.fasterxml.jackson.dataformat.xml.XmlMapper; | ||
| import com.fasterxml.jackson.datatype.jdk8.Jdk8Module; | ||
| import com.fasterxml.jackson.module.jakarta.xmlbind.JakartaXmlBindAnnotationModule; | ||
| import de.basisdatensatz.obds.v3.OBDS; | ||
| import java.io.IOException; | ||
| import org.approvaltests.Approvals; | ||
| import org.hl7.fhir.r4.model.Reference; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.params.ParameterizedTest; | ||
| import org.junit.jupiter.params.provider.CsvSource; | ||
| import org.miracum.streams.ume.obdstofhir.FhirProperties; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.context.properties.EnableConfigurationProperties; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
|
|
||
| @SpringBootTest(classes = {FhirProperties.class}) | ||
| @EnableConfigurationProperties | ||
| class SystemischeTherapieMedicationStatementMapperTest { | ||
| private static SystemischeTherapieMedicationStatementMapper sut; | ||
|
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| @BeforeAll | ||
| static void beforeAll(@Autowired FhirProperties fhirProps) { | ||
| sut = new SystemischeTherapieMedicationStatementMapper(fhirProps); | ||
| } | ||
|
|
||
| @ParameterizedTest | ||
| @CsvSource({"Testpatient_1.xml", "Testpatient_2.xml", "Testpatient_3.xml"}) | ||
| void map_withGivenObds_shouldCreateValidMedicationStatement(String sourceFile) | ||
| throws IOException { | ||
| final var resource = this.getClass().getClassLoader().getResource("obds3/" + sourceFile); | ||
| assertThat(resource).isNotNull(); | ||
|
|
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| final var xmlMapper = | ||
| XmlMapper.builder() | ||
| .defaultUseWrapper(false) | ||
| .addModule(new JakartaXmlBindAnnotationModule()) | ||
| .addModule(new Jdk8Module()) | ||
| .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false) | ||
| .build(); | ||
|
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| final var obds = xmlMapper.readValue(resource.openStream(), OBDS.class); | ||
|
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| var obdsPatient = obds.getMengePatient().getPatient().getFirst(); | ||
|
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| var patient = new Reference("Patient/any"); | ||
| var procedure = new Reference("Procedure/any"); | ||
| var systMeldung = | ||
| obdsPatient.getMengeMeldung().getMeldung().stream() | ||
| .filter(m -> m.getSYST() != null) | ||
| .findFirst() | ||
| .get(); | ||
| var bundle = sut.map(systMeldung.getSYST(), patient, procedure); | ||
|
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| var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true); | ||
| var fhirJson = fhirParser.encodeResourceToString(bundle); | ||
|
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| Approvals.verify( | ||
| fhirJson, Approvals.NAMES.withParameters(sourceFile).forFile().withExtension(".fhir.json")); | ||
| } | ||
| } |
39 changes: 39 additions & 0 deletions
39
...p_withGivenObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.approved.fhir.json
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|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| { | ||
| "resourceType": "Bundle", | ||
| "type": "transaction", | ||
| "entry": [ { | ||
| "fullUrl": "MedicationStatement/050a031e5a9043c28c565c6b60550c3d34cd059bc2f24c195cdb807f099cd978", | ||
| "resource": { | ||
| "resourceType": "MedicationStatement", | ||
| "id": "050a031e5a9043c28c565c6b60550c3d34cd059bc2f24c195cdb807f099cd978", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-medication-statement-id", | ||
| "value": "101_IN-1_L01FF05" | ||
| } ], | ||
| "partOf": [ { | ||
| "reference": "Procedure/any" | ||
| } ], | ||
| "status": "completed", | ||
| "medicationCodeableConcept": { | ||
| "coding": [ { | ||
| "system": "http://fhir.de/CodeSystem/bfarm/atc", | ||
| "code": "L01FF05" | ||
| } ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "effectivePeriod": { | ||
| "start": "2020-05", | ||
| "end": "2020-10-15" | ||
| } | ||
| }, | ||
| "request": { | ||
| "method": "PUT", | ||
| "url": "MedicationStatement/050a031e5a9043c28c565c6b60550c3d34cd059bc2f24c195cdb807f099cd978" | ||
| } | ||
| } ] | ||
| } |
35 changes: 35 additions & 0 deletions
35
...p_withGivenObds_shouldCreateValidMedicationStatement.Testpatient_2.xml.approved.fhir.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| { | ||
| "resourceType": "Bundle", | ||
| "type": "transaction", | ||
| "entry": [ { | ||
| "fullUrl": "MedicationStatement/e4b35c4756c9668e9c2b92f281667382020c401482e0a674566a695cd20a4cfa", | ||
| "resource": { | ||
| "resourceType": "MedicationStatement", | ||
| "id": "e4b35c4756c9668e9c2b92f281667382020c401482e0a674566a695cd20a4cfa", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-medication-statement-id", | ||
| "value": "11_1_Innere.1_Bicalutamid_fa96" | ||
| } ], | ||
| "partOf": [ { | ||
| "reference": "Procedure/any" | ||
| } ], | ||
| "status": "active", | ||
| "medicationCodeableConcept": { | ||
| "text": "Bicalutamid" | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "effectivePeriod": { | ||
| "start": "2021-11-08" | ||
| } | ||
| }, | ||
| "request": { | ||
| "method": "PUT", | ||
| "url": "MedicationStatement/e4b35c4756c9668e9c2b92f281667382020c401482e0a674566a695cd20a4cfa" | ||
| } | ||
| } ] | ||
| } |
35 changes: 35 additions & 0 deletions
35
...p_withGivenObds_shouldCreateValidMedicationStatement.Testpatient_3.xml.approved.fhir.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| { | ||
| "resourceType": "Bundle", | ||
| "type": "transaction", | ||
| "entry": [ { | ||
| "fullUrl": "MedicationStatement/da9d78a5d066bba6acd32a9a903c8663ecc1421cb373dcb51566b6d23dd30df7", | ||
| "resource": { | ||
| "resourceType": "MedicationStatement", | ||
| "id": "da9d78a5d066bba6acd32a9a903c8663ecc1421cb373dcb51566b6d23dd30df7", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-medication-statement-id", | ||
| "value": "12_1_Innere.1_Paclitaxel_a0a4" | ||
| } ], | ||
| "partOf": [ { | ||
| "reference": "Procedure/any" | ||
| } ], | ||
| "status": "active", | ||
| "medicationCodeableConcept": { | ||
| "text": "Paclitaxel" | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "effectivePeriod": { | ||
| "start": "2018-03-17" | ||
| } | ||
| }, | ||
| "request": { | ||
| "method": "PUT", | ||
| "url": "MedicationStatement/da9d78a5d066bba6acd32a9a903c8663ecc1421cb373dcb51566b6d23dd30df7" | ||
| } | ||
| } ] | ||
| } |