feat: add patient mapper

src/main/java/dev/pcvolkmer/onco/datamapper/PatientDataMapper.java

@@ -0,0 +1,100 @@
+package dev.pcvolkmer.onco.datamapper;
+
+import dev.pcvolkmer.mv64e.mtb.Address;
+import dev.pcvolkmer.mv64e.mtb.GenderCoding;
+import dev.pcvolkmer.mv64e.mtb.GenderCodingCode;
+import dev.pcvolkmer.mv64e.mtb.Patient;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.PatientCatalogue;
+import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Date;
+
+/**
+ * Mapper class to load and map diagnosis data from database table 'dk_dnpm_kpa'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class PatientDataMapper implements DataMapper<Patient> {
+
+    private final JdbcTemplate jdbcTemplate;
+
+    private PatientDataMapper(final JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+    }
+
+    /**
+     * Create instance of the mapper class
+     *
+     * @param jdbcTemplate The Spring JdbcTemplate to be used
+     * @return The initialized mapper
+     */
+    public static PatientDataMapper create(final JdbcTemplate jdbcTemplate) {
+        return new PatientDataMapper(jdbcTemplate);
+    }
+
+    /**
+     * Loads and maps a patient using the patient database id
+     *
+     * @param id The database id of the procedure data set
+     * @return The loaded MtbDiagnosis file
+     */
+    @Override
+    public Patient getById(int id) {
+        var patientCatalogue = PatientCatalogue.create(this.jdbcTemplate);
+        var patientData = patientCatalogue.getById(id);
+
+        var builder = Patient.builder();
+        try {
+            builder
+                    .id(patientData.getString("id"))
+                    .gender(getGenderCoding(patientData))
+                    .birthDate(mapDate(patientData.getDate("geburtsdatum")))
+                    .dateOfDeath(mapDate(patientData.getDate("sterbedatum")))
+                    .address(Address.builder().municipalityCode(getMunicipalityCode(patientData)).build())
+            ;
+
+        } catch (SQLException e) {
+            throw new DataAccessException(e.getMessage());
+        }
+        return builder.build();
+    }
+
+    private GenderCoding getGenderCoding(ResultSet data) throws SQLException {
+        var genderCodingBuilder = GenderCoding.builder();
+        String geschlecht = data.getString("geschlecht");
+        switch (geschlecht) {
+            case "M":
+                genderCodingBuilder.code(GenderCodingCode.MALE);
+                break;
+            case "F":
+                genderCodingBuilder.code(GenderCodingCode.FEMALE);
+                break;
+            case "X":
+                genderCodingBuilder.code(GenderCodingCode.OTHER);
+                break;
+            default:
+                genderCodingBuilder.code(GenderCodingCode.UNKNOWN);
+        }
+        return genderCodingBuilder.build();
+    }
+
+    private String getMunicipalityCode(ResultSet data) throws SQLException {
+        var gkz = data.getString("GKZ");
+        if (gkz == null || gkz.trim().length() != 8) {
+            throw new DataAccessException("Municipality code not found");
+        }
+        return gkz.substring(0, 5);
+    }
+
+    private Date mapDate(java.sql.Date date) {
+        if (date == null) {
+            return null;
+        }
+        return new Date(date.getTime());
+    }
+
+}

src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/PatientCatalogue.java

@@ -0,0 +1,46 @@
+package dev.pcvolkmer.onco.datamapper.datacatalogues;
+
+import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.sql.ResultSet;
+
+/**
+ * Load raw result sets from database table 'patient'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class PatientCatalogue {
+
+    private final JdbcTemplate jdbcTemplate;
+
+    private PatientCatalogue(JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+    }
+
+    public static PatientCatalogue create(JdbcTemplate jdbcTemplate) {
+        return new PatientCatalogue(jdbcTemplate);
+    }
+
+    /**
+     * Get patient result set by procedure id
+     * @param id The procedure id
+     * @return The procedure id
+     */
+    public ResultSet getById(int id) {
+        var result = this.jdbcTemplate.query(
+                "SELECT * FROM patient WHERE id = ?",
+                (resultSet, i) -> resultSet,
+                id);
+
+        if (result.isEmpty()) {
+            throw new DataAccessException("No patient record found for id: " + id);
+        } else if (result.size() > 1) {
+            throw new DataAccessException("Multiple patient records found for id: " + id);
+        }
+
+        return result.get(0);
+    }
+
+}

src/test/java/dev/pcvolkmer/onco/datamapper/PatientDataMapperTest.java

@@ -0,0 +1,109 @@
+package dev.pcvolkmer.onco.datamapper;
+
+import dev.pcvolkmer.mv64e.mtb.Address;
+import dev.pcvolkmer.mv64e.mtb.GenderCodingCode;
+import dev.pcvolkmer.mv64e.mtb.Patient;
+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 org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.RowMapper;
+
+import javax.sql.DataSource;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+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.*;
+import static org.mockito.Mockito.doAnswer;
+
+@ExtendWith(MockitoExtension.class)
+class PatientDataMapperTest {
+
+    JdbcTemplate jdbcTemplate;
+
+    PatientDataMapper dataMapper;
+
+    @BeforeEach
+    void setUp(@Mock JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+        this.dataMapper = PatientDataMapper.create(jdbcTemplate);
+    }
+
+    @Test
+    void shouldCreateDataMapper(@Mock DataSource dataSource) {
+        assertThat(MtbDataMapper.create(dataSource)).isNotNull();
+    }
+
+    @Test
+    void shouldCreatePatientAlive(@Mock ResultSet resultSet) throws SQLException {
+        var testData = Map.of(
+                "id", "1",
+                "geschlecht", "M",
+                "geburtsdatum", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
+                "sterbedatum", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
+                "GKZ", "06634022"
+        );
+
+        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());
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .query(anyString(), any(RowMapper.class), anyInt());
+
+        var actual = this.dataMapper.getById(1);
+        assertThat(actual).isInstanceOf(Patient.class);
+        assertThat(actual.getId()).isEqualTo("1");
+        assertThat(actual.getGender().getCode()).isEqualTo(GenderCodingCode.MALE);
+        assertThat(actual.getBirthDate()).isEqualTo(Date.from(Instant.parse("2000-01-01T12:00:00Z")));
+        assertThat(actual.getDateOfDeath()).isEqualTo(Date.from(Instant.parse("2024-06-19T12:00:00Z")));
+        assertThat(actual.getAddress()).isEqualTo(Address.builder().municipalityCode("06634").build());
+    }
+
+    @Test
+    void shouldCreatePatientDead(@Mock ResultSet resultSet) throws SQLException {
+        var testData = Map.of(
+                "id", "1",
+                "geschlecht", "M",
+                "geburtsdatum", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
+                "GKZ", "06634022"
+        );
+
+        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());
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .query(anyString(), any(RowMapper.class), anyInt());
+
+        var actual = this.dataMapper.getById(1);
+        assertThat(actual).isInstanceOf(Patient.class);
+        assertThat(actual.getId()).isEqualTo("1");
+        assertThat(actual.getGender().getCode()).isEqualTo(GenderCodingCode.MALE);
+        assertThat(actual.getBirthDate()).isEqualTo(Date.from(Instant.parse("2000-01-01T12:00:00Z")));
+        assertThat(actual.getDateOfDeath()).isNull();
+        assertThat(actual.getAddress()).isEqualTo(Address.builder().municipalityCode("06634").build());
+    }
+
+}