feat: add mapping for KPA prozeduren

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

@@ -1,5 +1,7 @@
 package dev.pcvolkmer.onco.datamapper;
 
+import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
+
 import java.sql.Date;
 import java.util.Map;
 
@@ -25,8 +27,35 @@ public class ResultSet {
         return rawData;
     }
 
+    /**
+     * Get the procedure id
+     *
+     * @return The procedure id if any
+     */
+    public Integer getProcedureId() {
+        var procedureId = this.getInteger("procedure.id");
+        if (procedureId == null) {
+            throw new DataAccessException("No procedure id found");
+        }
+        return procedureId;
+    }
+
+    /**
+     * Get the disease id
+     *
+     * @return The procedure id if any
+     */
+    public Integer getDiseaseId() {
+        var diseaseId = this.getInteger("erkrankung.id");
+        if (diseaseId == null) {
+            throw new DataAccessException("No disease id found");
+        }
+        return diseaseId;
+    }
+
     /**
      * Get column value as String and cast value if possible
+     *
      * @param columnName The name of the column
      * @return The column value as String
      */
@@ -46,6 +75,7 @@ public class ResultSet {
 
     /**
      * Get column value as Integer and cast value if possible
+     *
      * @param columnName The name of the column
      * @return The column value as Integer
      */
@@ -61,8 +91,29 @@ public class ResultSet {
         throw new IllegalArgumentException("Cannot convert " + raw.getClass() + " to Integer");
     }
 
+    /**
+     * Get column value as Long and cast value if possible
+     *
+     * @param columnName The name of the column
+     * @return The column value as Integer
+     */
+    public Long getLong(String columnName) {
+        var raw = this.rawData.get(columnName);
+
+        if (raw == null) {
+            return null;
+        } else if (raw instanceof Integer) {
+            return ((Integer) raw).longValue();
+        } else if (raw instanceof Long) {
+            return ((Long) raw);
+        }
+
+        throw new IllegalArgumentException("Cannot convert " + raw.getClass() + " to Integer");
+    }
+
     /**
      * Get column value as Date and cast value if possible
+     *
      * @param columnName The name of the column
      * @return The column value as Date
      */

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

@@ -4,6 +4,9 @@ import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
 import org.springframework.jdbc.core.JdbcTemplate;
 
+import java.util.List;
+import java.util.stream.Collectors;
+
 /**
  * Common implementations for all data catalogues
  *
@@ -45,4 +48,21 @@ public abstract class AbstractDataCatalogue implements DataCatalogue {
         return ResultSet.from(result.get(0));
     }
 
+    /**
+     * Returns related diseases
+     * @param procedureId The procedure id
+     * @return the diseases
+     */
+    public List<ResultSet> getDiseases(int procedureId) {
+        return this.jdbcTemplate.queryForList(
+                        String.format(
+                                "SELECT * FROM erkrankung_prozedur JOIN erkrankung ON (erkrankung.id = erkrankung_prozedur.erkrankung.id) WHERE erkrankung_prozedur.prozedur_id = ?",
+                                getTableName(),
+                                getTableName()
+                        ),
+                        procedureId)
+                .stream()
+                .map(ResultSet::from)
+                .collect(Collectors.toList());
+    }
 }

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

@@ -21,12 +21,12 @@ public abstract class AbstractSubformDataCatalogue extends AbstractDataCatalogue
     protected abstract String getTableName();
 
     /**
-     * Get procedure result sets by main procedure id
+     * Get procedure result sets by parent procedure id
      *
-     * @param id The procedure id
-     * @return The procedure id
+     * @param id The parents procedure id
+     * @return The sub procedures
      */
-    public List<ResultSet> getAllByMainId(int id) {
+    public List<ResultSet> getAllByParentId(int id) {
         return this.jdbcTemplate.queryForList(
                         String.format(
                                 "SELECT * FROM %s JOIN prozedur ON (prozedur.id = %s.id) WHERE geloescht = 0 AND hauptprozedur_id = ?",

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

@@ -0,0 +1,149 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.*;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_prozedur'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaProzedurDataMapper implements SubformDataMapper<OncoProcedure> {
+
+    private final ProzedurCatalogue catalogue;
+
+    public KpaProzedurDataMapper(final ProzedurCatalogue 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 MtbDiagnosis file
+     */
+    @Override
+    public OncoProcedure getById(final int id) {
+        var data = catalogue.getById(id);
+        return this.map(data);
+    }
+
+    @Override
+    public List<OncoProcedure> getByParentId(final int parentId) {
+        return catalogue.getAllByParentId(parentId)
+                .stream()
+                .map(this::map)
+                .collect(Collectors.toList());
+    }
+
+    private OncoProcedure 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 = OncoProcedure.builder();
+        builder
+                .id(resultSet.getString("id"))
+                .patient(Reference.builder().id(resultSet.getString("patient_id")).build())
+                .basedOn(Reference.builder().id(diseases.get(0).getDiseaseId().toString()).build())
+                .recordedOn(resultSet.getDate("erfassungsdatum"))
+                .therapyLine(resultSet.getLong("therapielinie"))
+                .intent(getMtbTherapyIntentCoding(resultSet.getString("intention")))
+                .status(getTherapyStatusCoding(resultSet.getString("status")))
+                .statusReason(getMtbTherapyStatusReasonCoding(resultSet.getString("statusgrund")))
+                .period(PeriodDate.builder().start(resultSet.getDate("beginn")).end(resultSet.getDate("ende")).build())
+                .code(getOncoProcedureCoding(resultSet.getString("typ")))
+        ;
+        return builder.build();
+    }
+
+    private MtbTherapyIntentCoding getMtbTherapyIntentCoding(String value) {
+        if (value == null || ! Arrays.stream(MtbTherapyIntentCodingCode.values()).map(MtbTherapyIntentCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = MtbTherapyIntentCoding.builder();
+
+        switch (value) {
+            case "X":
+                resultBuilder.code(MtbTherapyIntentCodingCode.X);
+                break;
+            case "K":
+                resultBuilder.code(MtbTherapyIntentCodingCode.K);
+                break;
+            case "P":
+                resultBuilder.code(MtbTherapyIntentCodingCode.P);
+                break;
+            case "S":
+                resultBuilder.code(MtbTherapyIntentCodingCode.S);
+                break;
+        }
+
+        return resultBuilder.build();
+    }
+
+    private TherapyStatusCoding getTherapyStatusCoding(String value) {
+        if (value == null || ! Arrays.stream(TherapyStatusCodingCode.values()).map(TherapyStatusCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = TherapyStatusCoding.builder();
+
+        switch (value) {
+            case "not-done":
+                resultBuilder.code(TherapyStatusCodingCode.NOT_DONE);
+                break;
+            case "on-going":
+                resultBuilder.code(TherapyStatusCodingCode.ON_GOING);
+                break;
+            case "stopped":
+                resultBuilder.code(TherapyStatusCodingCode.STOPPED);
+                break;
+            case "completed":
+                resultBuilder.code(TherapyStatusCodingCode.COMPLETED);
+                break;
+        }
+
+        return resultBuilder.build();
+    }
+
+    private MtbTherapyStatusReasonCoding getMtbTherapyStatusReasonCoding(String value) {
+        if (value == null || ! Arrays.stream(MtbTherapyStatusReasonCodingCode.values()).map(MtbTherapyStatusReasonCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = MtbTherapyStatusReasonCoding.builder();
+        try {
+            resultBuilder.code(MtbTherapyStatusReasonCodingCode.forValue(value));
+        } catch (IOException e) {
+            return null;
+        }
+
+        return resultBuilder.build();
+    }
+
+    private OncoProcedureCoding getOncoProcedureCoding(String value) {
+        if (value == null || ! Arrays.stream(OncoProcedureCodingCode.values()).map(OncoProcedureCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = OncoProcedureCoding.builder();
+        try {
+            resultBuilder.code(OncoProcedureCodingCode.forValue(value));
+        } catch (IOException e) {
+            throw new IllegalStateException("No valid code found");
+        }
+
+        return resultBuilder.build();
+    }
+
+}

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

@@ -4,6 +4,7 @@ import dev.pcvolkmer.mv64e.mtb.Mtb;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.DataCatalogueFactory;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.PatientCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
 import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -60,6 +61,7 @@ public class MtbDataMapper implements DataMapper<Mtb> {
         var patientDataMapper = new PatientDataMapper(catalogueFactory.catalogue(PatientCatalogue.class));
         var kpaPatientDataMapper = new KpaPatientDataMapper(kpaCatalogue);
         var diagnosisDataMapper = new KpaDiagnosisDataMapper(kpaCatalogue);
+        var prozedurMapper = new KpaProzedurDataMapper(catalogueFactory.catalogue(ProzedurCatalogue.class));
 
         var resultBuilder = Mtb.builder();
 
@@ -70,7 +72,9 @@ public class MtbDataMapper implements DataMapper<Mtb> {
 
             resultBuilder
                     .patient(kpaPatient)
-                    .diagnoses(List.of(diagnosisDataMapper.getById(kpaId)));
+                    .diagnoses(List.of(diagnosisDataMapper.getById(kpaId)))
+                    .guidelineProcedures(prozedurMapper.getByParentId(kpaId))
+            ;
         } catch (DataAccessException e) {
             logger.error("Error while getting Mtb.", e);
         }

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

@@ -0,0 +1,21 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import java.util.List;
+
+/**
+ * General interface for subform data mappers
+ *
+ * @since 0.1
+ * @author Paul-Christian Volkmer
+ * @param <T> The destination type
+ */
+public interface SubformDataMapper<T> extends DataMapper<T> {
+
+    /**
+     * Loads a data set from database and maps it into destination data type
+     * @param parentId The database id of the parent procedure data set
+     * @return The data set to be loaded
+     */
+    List<T> getByParentId(int parentId);
+
+}

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

@@ -26,6 +26,13 @@ class ResultSetTest {
         assertThat(data.getInteger("int")).isEqualTo(42);
     }
 
+    @Test
+    void shouldReturnLongValues() {
+        var data = getTestData();
+
+        assertThat(data.getLong("int")).isEqualTo(42L);
+    }
+
     @Test
     void shouldReturnDateValues() {
         var data = getTestData();

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/EcogCatalogueTest.java

@@ -50,7 +50,7 @@ class EcogCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/HistologieCatalogueTest.java

@@ -50,7 +50,7 @@ class HistologieCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/ProzedurCatalogueTest.java

@@ -50,7 +50,7 @@ class ProzedurCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/TherapielinieCatalogueTest.java

@@ -50,7 +50,7 @@ class TherapielinieCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/TumorausbreitungCatalogueTest.java

@@ -50,7 +50,7 @@ class TumorausbreitungCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/TumorgradingCatalogueTest.java

@@ -50,7 +50,7 @@ class TumorgradingCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/VerwandteCatalogueTest.java

@@ -50,7 +50,7 @@ class VerwandteCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/VorbefundeCatalogueTest.java

@@ -50,7 +50,7 @@ class VorbefundeCatalogueTest {
                 .when(jdbcTemplate)
                 .queryForList(anyString(), anyInt());
 
-        this.catalogue.getAllByMainId(1);
+        this.catalogue.getAllByParentId(1);
 
         var captor = ArgumentCaptor.forClass(String.class);
         verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());

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

@@ -0,0 +1,105 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.*;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
+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 KpaProzedurDataMapperTest {
+
+    ProzedurCatalogue catalogue;
+
+    KpaProzedurDataMapper dataMapper;
+
+    @BeforeEach
+    void setUp(@Mock ProzedurCatalogue catalogue) {
+        this.catalogue = catalogue;
+        this.dataMapper = new KpaProzedurDataMapper(catalogue);
+    }
+
+    @Test
+    void shouldMapResultSet(@Mock ResultSet resultSet) {
+        var testData = Map.of(
+                "erkrankung.id", "1",
+                "id", "1",
+                "beginn", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
+                "ende", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
+                "erfassungsdatum", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
+                "intention", "S",
+                "status", "stopped",
+                "statusgrund", "patient-death",
+                "therapielinie", 1L,
+                "typ", "surgery"
+        );
+
+        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).getLong(anyString());
+
+        doAnswer(invocationOnMock -> {
+            var columnName = invocationOnMock.getArgument(0, String.class);
+            return testData.get(columnName);
+        }).when(resultSet).getDate(anyString());
+
+        when(resultSet.getDiseaseId()).thenReturn(1);
+        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(OncoProcedure.class);
+        assertThat(actual.getId()).isEqualTo("1");
+        assertThat(actual.getPeriod()).isEqualTo(
+                PeriodDate.builder()
+                        .start(Date.from(Instant.parse("2000-01-01T12:00:00Z")))
+                        .end(Date.from(Instant.parse("2024-06-19T12:00:00Z")))
+                        .build()
+        );
+        assertThat(actual.getRecordedOn()).isEqualTo(Date.from(Instant.parse("2024-06-19T12:00:00Z")));
+        assertThat(actual.getIntent()).isEqualTo(
+                MtbTherapyIntentCoding.builder().code(MtbTherapyIntentCodingCode.S).build()
+        );
+        assertThat(actual.getStatus()).isEqualTo(
+                TherapyStatusCoding.builder().code(TherapyStatusCodingCode.STOPPED).build()
+        );
+        assertThat(actual.getStatusReason()).isEqualTo(
+                MtbTherapyStatusReasonCoding.builder().code(MtbTherapyStatusReasonCodingCode.PATIENT_DEATH).build()
+        );
+        assertThat(actual.getTherapyLine()).isEqualTo(1);
+        assertThat(actual.getCode()).isEqualTo(
+                OncoProcedureCoding.builder().code(OncoProcedureCodingCode.SURGERY).build()
+        );
+    }
+
+}