feat: add tumor staging mapping

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTumorausbreitungDataMapper.java

@@ -0,0 +1,118 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.*;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_tumorausbreitung'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaTumorausbreitungDataMapper implements SubformDataMapper<TumorStaging> {
+
+    private final TumorausbreitungCatalogue catalogue;
+
+    public KpaTumorausbreitungDataMapper(final TumorausbreitungCatalogue catalogue) {
+        this.catalogue = catalogue;
+    }
+
+    /**
+     * Loads and maps Prozedur related by database id
+     *
+     * @param id The database id of the procedure data set
+     * @return The loaded data set
+     */
+    @Override
+    public TumorStaging getById(final int id) {
+        var data = catalogue.getById(id);
+        return this.map(data);
+    }
+
+    @Override
+    public List<TumorStaging> getByParentId(final int parentId) {
+        return catalogue.getAllByParentId(parentId)
+                .stream()
+                .map(this::map)
+                .sorted(Comparator.comparing(TumorStaging::getDate))
+                .collect(Collectors.toList());
+    }
+
+    private TumorStaging map(final ResultSet resultSet) {
+        var diseases = catalogue.getDiseases(resultSet.getProcedureId());
+
+        if (diseases.size() != 1) {
+            throw new IllegalStateException(String.format("No unique disease for procedure %s", resultSet.getProcedureId()));
+        }
+
+        var builder = TumorStaging.builder();
+        builder
+                .date(resultSet.getDate("zeitpunkt"))
+                .method(getTumorStagingMethodCoding(resultSet.getString("typ")))
+                .otherClassifications(List.of(Coding.builder().code(resultSet.getString("wert")).build()))
+                .tnmClassification(getTnmClassification(resultSet))
+        ;
+
+
+        return builder.build();
+    }
+
+    private TumorStagingMethodCoding getTumorStagingMethodCoding(final String value) {
+        if (value == null || !Arrays.stream(TumorStagingMethodCodingCode.values()).map(TumorStagingMethodCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = TumorStagingMethodCoding.builder();
+        try {
+            resultBuilder.code(TumorStagingMethodCodingCode.forValue(value));
+        } catch (IOException e) {
+            throw new IllegalStateException("No valid code found");
+        }
+
+        return resultBuilder.build();
+    }
+
+    private TnmClassification getTnmClassification(final ResultSet resultSet) {
+        var tnpmClassificationBuilder = TnmClassification.builder();
+
+        var hasContent = false;
+
+        var tnmt = resultSet.getString("tnmt");
+        if (tnmt != null && !tnmt.isBlank()) {
+            tnpmClassificationBuilder.tumor(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmtprefix"), tnmt)).build()
+            );
+            hasContent = true;
+        }
+
+        var tnmn = resultSet.getString("tnmn");
+        if (tnmn != null && !tnmn.isBlank()) {
+            tnpmClassificationBuilder.nodes(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmnprefix"), tnmn)).build()
+            );
+            hasContent = true;
+        }
+
+        var tnmm = resultSet.getString("tnmm");
+        if (tnmm != null && !tnmm.isBlank()) {
+            tnpmClassificationBuilder.metastasis(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmmprefix"), tnmm)).build()
+            );
+            hasContent = true;
+        }
+
+        if (hasContent) {
+            return tnpmClassificationBuilder.build();
+        }
+
+        return null;
+    }
+
+}

src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTumorausbreitungDataMapperTest.java

@@ -0,0 +1,87 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.TumorStaging;
+import dev.pcvolkmer.mv64e.mtb.TumorStagingMethodCoding;
+import dev.pcvolkmer.mv64e.mtb.TumorStagingMethodCodingCode;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import java.time.Instant;
+import java.util.Date;
+import java.util.List;
+import java.util.Map;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.doAnswer;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class KpaTumorausbreitungDataMapperTest {
+
+    TumorausbreitungCatalogue catalogue;
+
+    KpaTumorausbreitungDataMapper dataMapper;
+
+    @BeforeEach
+    void setUp(@Mock TumorausbreitungCatalogue catalogue) {
+        this.catalogue = catalogue;
+        this.dataMapper = new KpaTumorausbreitungDataMapper(catalogue);
+    }
+
+    @Test
+    void shouldMapResultSet(@Mock ResultSet resultSet) {
+        var testData = Map.of(
+                "id", "1",
+                "zeitpunkt", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
+                "typ", "pathologic",
+                "wert", "tumor-free",
+                "tnmtprefix", "p",
+                "tnmt", "0",
+                "tnmnprefix", "p",
+                "tnmn", "0",
+                "tnmmprefix", "p",
+                "tnmm", "0"
+        );
+
+        doAnswer(invocationOnMock -> {
+            var columnName = invocationOnMock.getArgument(0, String.class);
+            return testData.get(columnName);
+        }).when(resultSet).getString(anyString());
+
+        doAnswer(invocationOnMock -> {
+            var columnName = invocationOnMock.getArgument(0, String.class);
+            return testData.get(columnName);
+        }).when(resultSet).getDate(anyString());
+
+        when(resultSet.getProcedureId()).thenReturn(1);
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(catalogue)
+                .getAllByParentId(anyInt());
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(catalogue)
+                .getDiseases(anyInt());
+
+        var actualList = this.dataMapper.getByParentId(1);
+        assertThat(actualList).hasSize(1);
+
+        var actual = actualList.get(0);
+        assertThat(actual).isInstanceOf(TumorStaging.class);
+        assertThat(actual.getDate()).isEqualTo(new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()));
+        assertThat(actual.getMethod()).isEqualTo(TumorStagingMethodCoding.builder().code(TumorStagingMethodCodingCode.PATHOLOGIC).build());
+        assertThat(actual.getOtherClassifications()).hasSize(1);
+        assertThat(actual.getOtherClassifications().get(0).getCode()).isEqualTo("tumor-free");
+        assertThat(actual.getTnmClassification().getTumor().getCode()).isEqualTo("p0");
+        assertThat(actual.getTnmClassification().getNodes().getCode()).isEqualTo("p0");
+        assertThat(actual.getTnmClassification().getMetastasis().getCode()).isEqualTo("p0");
+    }
+
+}