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https://github.com/pcvolkmer/mv64e-onkostar-data.git
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feat: add basic mapping for dk_dnpm_therapielinie
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@ -0,0 +1,185 @@
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package dev.pcvolkmer.onco.datamapper.mapper;
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import dev.pcvolkmer.mv64e.mtb.*;
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import dev.pcvolkmer.onco.datamapper.ResultSet;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.TherapielinieCatalogue;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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/**
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* Mapper class to load and map prozedur data from database table 'dk_dnpm_therapielinie'
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*
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* @author Paul-Christian Volkmer
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* @since 0.1
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*/
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public class KpaTherapielinieDataMapper implements SubformDataMapper<MtbSystemicTherapy> {
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private final TherapielinieCatalogue catalogue;
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public KpaTherapielinieDataMapper(final TherapielinieCatalogue catalogue) {
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this.catalogue = catalogue;
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}
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/**
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* Loads and maps Prozedur related by database id
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*
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* @param id The database id of the procedure data set
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* @return The loaded MtbDiagnosis file
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*/
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@Override
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public MtbSystemicTherapy getById(final int id) {
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var data = catalogue.getById(id);
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return this.map(data);
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}
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@Override
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public List<MtbSystemicTherapy> getByParentId(final int parentId) {
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return catalogue.getAllByParentId(parentId)
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.stream()
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.map(this::map)
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.collect(Collectors.toList());
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}
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private MtbSystemicTherapy map(final ResultSet resultSet) {
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var diseases = catalogue.getDiseases(resultSet.getProcedureId());
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if (diseases.size() != 1) {
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throw new IllegalStateException(String.format("No unique disease for procedure %s", resultSet.getProcedureId()));
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}
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var builder = MtbSystemicTherapy.builder();
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builder
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.id(resultSet.getString("id"))
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.patient(Reference.builder().id(resultSet.getString("patient_id")).build())
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.basedOn(Reference.builder().id(diseases.get(0).getDiseaseId().toString()).build())
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.recordedOn(resultSet.getDate("erfassungsdatum"))
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.therapyLine(resultSet.getLong("therapielinie"))
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.intent(getMtbTherapyIntentCoding(resultSet.getString("intention")))
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.status(getTherapyStatusCoding(resultSet.getString("status")))
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.statusReason(getMtbTherapyStatusReasonCoding(resultSet.getString("statusgrund")))
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.period(PeriodDate.builder().start(resultSet.getDate("beginn")).end(resultSet.getDate("ende")).build())
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/* TODO JSON deserialisation */
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//.medication()
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/* TODO Yet missing form fields */
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//.category(getMtbSystemicTherapyCategoryCoding())
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//.dosage(getMtbSystemicTherapyDosageDensityCoding())
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//.recommendationFulfillmentStatus(getMtbSystemicTherapyRecommendationFulfillmentStatusCoding()
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;
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return builder.build();
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}
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private MtbTherapyIntentCoding getMtbTherapyIntentCoding(String value) {
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if (value == null || !Arrays.stream(MtbTherapyIntentCodingCode.values()).map(MtbTherapyIntentCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = MtbTherapyIntentCoding.builder();
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switch (value) {
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case "X":
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resultBuilder.code(MtbTherapyIntentCodingCode.X);
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break;
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case "K":
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resultBuilder.code(MtbTherapyIntentCodingCode.K);
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break;
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case "P":
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resultBuilder.code(MtbTherapyIntentCodingCode.P);
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break;
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case "S":
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resultBuilder.code(MtbTherapyIntentCodingCode.S);
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break;
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}
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return resultBuilder.build();
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}
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private TherapyStatusCoding getTherapyStatusCoding(String value) {
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if (value == null || !Arrays.stream(TherapyStatusCodingCode.values()).map(TherapyStatusCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = TherapyStatusCoding.builder();
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switch (value) {
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case "not-done":
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resultBuilder.code(TherapyStatusCodingCode.NOT_DONE);
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break;
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case "on-going":
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resultBuilder.code(TherapyStatusCodingCode.ON_GOING);
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break;
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case "stopped":
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resultBuilder.code(TherapyStatusCodingCode.STOPPED);
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break;
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case "completed":
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resultBuilder.code(TherapyStatusCodingCode.COMPLETED);
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break;
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}
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return resultBuilder.build();
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}
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private MtbTherapyStatusReasonCoding getMtbTherapyStatusReasonCoding(String value) {
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if (value == null || !Arrays.stream(MtbTherapyStatusReasonCodingCode.values()).map(MtbTherapyStatusReasonCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = MtbTherapyStatusReasonCoding.builder();
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try {
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resultBuilder.code(MtbTherapyStatusReasonCodingCode.forValue(value));
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} catch (IOException e) {
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return null;
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}
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return resultBuilder.build();
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}
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private MtbSystemicTherapyRecommendationFulfillmentStatusCoding getMtbSystemicTherapyRecommendationFulfillmentStatusCoding(String value) {
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if (value == null || !Arrays.stream(MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.values()).map(MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = MtbSystemicTherapyRecommendationFulfillmentStatusCoding.builder();
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try {
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resultBuilder.code(MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.forValue(value));
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} catch (IOException e) {
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return null;
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}
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return resultBuilder.build();
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}
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private MtbSystemicTherapyCategoryCoding getMtbSystemicTherapyCategoryCoding(String value) {
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if (value == null || !Arrays.stream(MtbSystemicTherapyCategoryCodingCode.values()).map(MtbSystemicTherapyCategoryCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = MtbSystemicTherapyCategoryCoding.builder();
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try {
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resultBuilder.code(MtbSystemicTherapyCategoryCodingCode.forValue(value));
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} catch (IOException e) {
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return null;
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}
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return resultBuilder.build();
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}
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private MtbSystemicTherapyDosageDensityCoding getMtbSystemicTherapyDosageDensityCoding(String value) {
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if (value == null || !Arrays.stream(MtbSystemicTherapyDosageDensityCodingCode.values()).map(MtbSystemicTherapyDosageDensityCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
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return null;
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}
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var resultBuilder = MtbSystemicTherapyDosageDensityCoding.builder();
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try {
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resultBuilder.code(MtbSystemicTherapyDosageDensityCodingCode.forValue(value));
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} catch (IOException e) {
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return null;
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}
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return resultBuilder.build();
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}
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}
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@ -0,0 +1,101 @@
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package dev.pcvolkmer.onco.datamapper.mapper;
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import dev.pcvolkmer.mv64e.mtb.*;
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import dev.pcvolkmer.onco.datamapper.ResultSet;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.TherapielinieCatalogue;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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import org.mockito.junit.jupiter.MockitoExtension;
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import java.time.Instant;
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import java.util.Date;
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import java.util.List;
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import java.util.Map;
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import static org.assertj.core.api.Assertions.assertThat;
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import static org.mockito.ArgumentMatchers.anyInt;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.Mockito.doAnswer;
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import static org.mockito.Mockito.when;
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@ExtendWith(MockitoExtension.class)
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class KpaTherapielinieDataMapperTest {
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TherapielinieCatalogue catalogue;
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KpaTherapielinieDataMapper dataMapper;
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@BeforeEach
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void setUp(@Mock TherapielinieCatalogue catalogue) {
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this.catalogue = catalogue;
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this.dataMapper = new KpaTherapielinieDataMapper(catalogue);
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}
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@Test
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void shouldMapResultSet(@Mock ResultSet resultSet) {
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var testData = Map.of(
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"erkrankung.id", "1",
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"id", "1",
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"beginn", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
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"ende", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
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"erfassungsdatum", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
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"intention", "S",
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"status", "stopped",
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"statusgrund", "patient-death",
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"therapielinie", 1L
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);
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doAnswer(invocationOnMock -> {
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var columnName = invocationOnMock.getArgument(0, String.class);
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return testData.get(columnName);
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}).when(resultSet).getString(anyString());
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doAnswer(invocationOnMock -> {
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var columnName = invocationOnMock.getArgument(0, String.class);
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return testData.get(columnName);
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}).when(resultSet).getLong(anyString());
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doAnswer(invocationOnMock -> {
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var columnName = invocationOnMock.getArgument(0, String.class);
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return testData.get(columnName);
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}).when(resultSet).getDate(anyString());
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when(resultSet.getDiseaseId()).thenReturn(1);
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when(resultSet.getProcedureId()).thenReturn(1);
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doAnswer(invocationOnMock -> List.of(resultSet))
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.when(catalogue)
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.getAllByParentId(anyInt());
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doAnswer(invocationOnMock -> List.of(resultSet))
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.when(catalogue)
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.getDiseases(anyInt());
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var actualList = this.dataMapper.getByParentId(1);
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assertThat(actualList).hasSize(1);
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var actual = actualList.get(0);
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assertThat(actual).isInstanceOf(MtbSystemicTherapy.class);
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assertThat(actual.getId()).isEqualTo("1");
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assertThat(actual.getPeriod()).isEqualTo(
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PeriodDate.builder()
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.start(Date.from(Instant.parse("2000-01-01T12:00:00Z")))
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.end(Date.from(Instant.parse("2024-06-19T12:00:00Z")))
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.build()
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);
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assertThat(actual.getRecordedOn()).isEqualTo(Date.from(Instant.parse("2024-06-19T12:00:00Z")));
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assertThat(actual.getIntent()).isEqualTo(
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MtbTherapyIntentCoding.builder().code(MtbTherapyIntentCodingCode.S).build()
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);
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assertThat(actual.getStatus()).isEqualTo(
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TherapyStatusCoding.builder().code(TherapyStatusCodingCode.STOPPED).build()
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);
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assertThat(actual.getStatusReason()).isEqualTo(
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MtbTherapyStatusReasonCoding.builder().code(MtbTherapyStatusReasonCodingCode.PATIENT_DEATH).build()
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);
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assertThat(actual.getTherapyLine()).isEqualTo(1);
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}
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}
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