refactor: rename catalogue classes

build.gradle.kts

@@ -8,6 +8,7 @@ version = "0.1.0-SNAPSHOT"
 
 var versions = mapOf(
     "mtb-dto" to "0.1.0-SNAPSHOT",
+    "slf4j" to "2.0.17",
     "junit" to "5.13.1",
     "assertj" to "3.27.3",
     "mockito" to "5.18.0"
@@ -46,6 +47,7 @@ dependencies {
             prefer("4.3.8.RELEASE")
         }
     }
+    implementation("org.slf4j:slf4j-api:${versions["slf4j"]}")
 
     testImplementation(platform("org.junit:junit-bom:${versions["junit"]}"))
     testImplementation("org.junit.jupiter:junit-jupiter")

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

@@ -1,13 +1,11 @@
 package dev.pcvolkmer.onco.datamapper;
 
 import dev.pcvolkmer.mv64e.mtb.Coding;
-import dev.pcvolkmer.mv64e.mtb.Mtb;
 import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis;
-import dev.pcvolkmer.onco.datamapper.datacatalogues.Kpa;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
 import org.springframework.jdbc.core.JdbcTemplate;
 
-import javax.sql.DataSource;
 import java.sql.SQLException;
 
 /**
@@ -20,18 +18,18 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
 
     private final JdbcTemplate jdbcTemplate;
 
-    KpaDiagnosisDataMapper(final JdbcTemplate jdbcTemplate) {
+    private KpaDiagnosisDataMapper(final JdbcTemplate jdbcTemplate) {
         this.jdbcTemplate = jdbcTemplate;
     }
 
     /**
      * Create instance of the mapper class
      *
-     * @param dataSource The datasource to be used
+     * @param jdbcTemplate The Spring JdbcTemplate to be used
      * @return The initialized mapper
      */
-    public static KpaDiagnosisDataMapper create(final DataSource dataSource) {
+    public static KpaDiagnosisDataMapper create(final JdbcTemplate jdbcTemplate) {
-        return new KpaDiagnosisDataMapper(new JdbcTemplate(dataSource));
+        return new KpaDiagnosisDataMapper(jdbcTemplate);
     }
 
     /**
@@ -42,7 +40,7 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
      */
     @Override
     public MtbDiagnosis getById(int id) {
-        var kpa = Kpa.create(this.jdbcTemplate);
+        var kpa = KpaCatalogue.create(this.jdbcTemplate);
         var data = kpa.getById(id);
 
         var builder =  MtbDiagnosis.builder();

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

@@ -1,10 +1,14 @@
 package dev.pcvolkmer.onco.datamapper;
 
 import dev.pcvolkmer.mv64e.mtb.Mtb;
-import dev.pcvolkmer.onco.datamapper.datacatalogues.Kpa;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
+import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.jdbc.core.JdbcTemplate;
 
 import javax.sql.DataSource;
+import java.util.List;
 
 /**
  * Mapper class to load and map Mtb files from database
@@ -14,6 +18,8 @@ import javax.sql.DataSource;
  */
 public class MtbDataMapper implements DataMapper<Mtb> {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     private final JdbcTemplate jdbcTemplate;
 
     MtbDataMapper(final JdbcTemplate jdbcTemplate) {
@@ -30,15 +36,35 @@ public class MtbDataMapper implements DataMapper<Mtb> {
         return new MtbDataMapper(new JdbcTemplate(dataSource));
     }
 
+    /**
+     * Create instance of the mapper class
+     *
+     * @param jdbcTemplate The Spring JdbcTemplate to be used
+     * @return The initialized mapper
+     */
+    public static MtbDataMapper create(final JdbcTemplate jdbcTemplate) {
+        return new MtbDataMapper(jdbcTemplate);
+    }
+
     /**
      * Loads and maps a Mtb file using the root procedures database id
      *
-     * @param id The database id of the root procedure data set
+     * @param kpaId The database id of the root procedure data set
      * @return The loaded Mtb file
      */
     @Override
-    public Mtb getById(int id) {
+    public Mtb getById(int kpaId) {
-        return Mtb.builder().build();
+        var diagnosisDataMapper = KpaDiagnosisDataMapper.create(jdbcTemplate);
+        var resultBuilder = Mtb.builder();
+
+        try {
+            resultBuilder
+                    .diagnoses(List.of(diagnosisDataMapper.getById(kpaId)));
+        } catch (DataAccessException e) {
+            logger.error("Error while getting Mtb.", e);
+        }
+
+        return resultBuilder.build();
     }
 
     /**
@@ -48,7 +74,7 @@ public class MtbDataMapper implements DataMapper<Mtb> {
      * @return The loaded Mtb file
      */
     public Mtb getByCaseId(String caseId) {
-        var kpa = Kpa.create(this.jdbcTemplate);
+        var kpa = KpaCatalogue.create(this.jdbcTemplate);
         return this.getById(
                 kpa.getProcedureIdByCaseId(caseId)
         );

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

@@ -11,16 +11,16 @@ import java.sql.ResultSet;
  * @author Paul-Christian Volkmer
  * @since 0.1
  */
-public class Kpa {
+public class KpaCatalogue {
 
     private final JdbcTemplate jdbcTemplate;
 
-    private Kpa(JdbcTemplate jdbcTemplate) {
+    private KpaCatalogue(JdbcTemplate jdbcTemplate) {
         this.jdbcTemplate = jdbcTemplate;
     }
 
-    public static Kpa create(JdbcTemplate jdbcTemplate) {
+    public static KpaCatalogue create(JdbcTemplate jdbcTemplate) {
-        return new Kpa(jdbcTemplate);
+        return new KpaCatalogue(jdbcTemplate);
     }
 
     /**

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

@@ -13,6 +13,7 @@ import javax.sql.DataSource;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.ArgumentMatchers.*;
@@ -28,7 +29,7 @@ class KpaDiagnosisDataMapperTest {
     @BeforeEach
     void setUp(@Mock JdbcTemplate jdbcTemplate) {
         this.jdbcTemplate = jdbcTemplate;
-        this.dataMapper = new KpaDiagnosisDataMapper(jdbcTemplate);
+        this.dataMapper = KpaDiagnosisDataMapper.create(jdbcTemplate);
     }
 
     @Test
@@ -37,17 +38,10 @@ class KpaDiagnosisDataMapperTest {
     }
 
     @Test
-    void shouldUseKpaProcedureId(@Mock ResultSet resultSet) throws SQLException {
+    void shouldCreateDiagnosis(@Mock ResultSet resultSet) throws SQLException {
         doAnswer(invocationOnMock -> {
             var columnName = invocationOnMock.getArgument(0, String.class);
-            switch (columnName) {
+            return testData().get(columnName);
-                case "id":
-                    return "1";
-                case "icd10":
-                    return "F79.9";
-                default:
-                    return null;
-            }
         }).when(resultSet).getString(anyString());
 
         doAnswer(invocationOnMock -> List.of(resultSet))
@@ -60,4 +54,11 @@ class KpaDiagnosisDataMapperTest {
         assertThat(actual.getCode().getCode()).isEqualTo("F79.9");
     }
 
+    private static Map<String, Object> testData() {
+        return Map.of(
+                "id", "1",
+                "icd10", "F79.9"
+        );
+    }
+
 }