feat: add specimens related to Vorbefunde

This also uses DB id as specimen id.

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

@@ -21,6 +21,7 @@
 package dev.pcvolkmer.onco.datamapper.datacatalogues;
 
 import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
 import org.springframework.jdbc.core.JdbcTemplate;
 
 import java.util.List;
@@ -98,4 +99,42 @@ public class MolekulargenetikCatalogue extends AbstractDataCatalogue {
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Get procedure result set by einsendenummer
+     *
+     * @param einsendenummer The case id related to this procedure
+     * @return The procedure id
+     */
+    public ResultSet getByEinsendenummer(String einsendenummer) {
+        var result = this.jdbcTemplate.queryForList(
+                String.format(
+                        "SELECT patient.patienten_id, %s.*, prozedur.* FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND %s.einsendenummer = ?",
+                        getTableName(),
+                        getTableName(),
+                        getTableName(),
+                        getTableName()
+                ),
+                einsendenummer);
+
+        if (result.isEmpty()) {
+            throw new DataAccessException("No record found for einsendenummer: " + einsendenummer);
+        } else if (result.size() > 1) {
+            throw new DataAccessException("Multiple records found for einsendenummer: " + einsendenummer);
+        }
+
+        var resultSet = ResultSet.from(result.get(0));
+
+        if (resultSet.getRawData().containsKey("id")) {
+            var merkmale = getMerkmaleById(resultSet.getId());
+            if (merkmale.isEmpty()) {
+                return resultSet;
+            }
+            merkmale.forEach((key, value) ->
+                    resultSet.getRawData().put(key, value)
+            );
+        }
+
+        return resultSet;
+    }
+
 }

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

@@ -20,15 +20,19 @@
 
 package dev.pcvolkmer.onco.datamapper.mapper;
 
-import dev.pcvolkmer.mv64e.mtb.*;
+import dev.pcvolkmer.mv64e.mtb.MolecularDiagnosticReportCoding;
+import dev.pcvolkmer.mv64e.mtb.MolecularDiagnosticReportCodingCode;
+import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
+import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
-import dev.pcvolkmer.onco.datamapper.datacatalogues.EcogCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.MolekulargenetikCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.VorbefundeCatalogue;
 
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Objects;
 import java.util.stream.Collectors;
 
 /**
@@ -39,10 +43,16 @@ import java.util.stream.Collectors;
  */
 public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiagnosticReport> {
 
+    private final MolekulargenetikCatalogue molekulargenetikCatalogue;
     private final PropertyCatalogue propertyCatalogue;
 
-    public KpaVorbefundeDataMapper(final VorbefundeCatalogue catalogue, PropertyCatalogue propertyCatalogue) {
+    public KpaVorbefundeDataMapper(
+            final VorbefundeCatalogue catalogue,
+            final MolekulargenetikCatalogue molekulargenetikCatalogue,
+            final PropertyCatalogue propertyCatalogue
+    ) {
         super(catalogue);
+        this.molekulargenetikCatalogue = molekulargenetikCatalogue;
         this.propertyCatalogue = propertyCatalogue;
     }
 
@@ -63,17 +73,24 @@ public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiag
         return catalogue.getAllByParentId(parentId)
                 .stream()
                 .map(this::map)
+                .filter(Objects::nonNull)
+                .distinct()
                 .collect(Collectors.toList());
     }
 
     @Override
     protected PriorDiagnosticReport map(final ResultSet resultSet) {
         var builder = PriorDiagnosticReport.builder();
+        var einsendenummer = resultSet.getString("befundnummer");
+
+        var osMolGen = molekulargenetikCatalogue.getByEinsendenummer(einsendenummer);
+
+        if (null != osMolGen) {
             builder
                     .id(resultSet.getId().toString())
                     .patient(resultSet.getPatientReference())
                     .issuedOn(resultSet.getDate("erstellungsdatum"))
-                .specimen(Reference.builder().id(resultSet.getString("befundnummer")).type("Specimen").build())
+                    .specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
                     .type(
                             getMolecularDiagnosticReportCoding(
                                     resultSet.getString("artderdiagnostik"),
@@ -88,6 +105,9 @@ public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiag
             return builder.build();
         }
 
+        return null;
+    }
+
     private MolecularDiagnosticReportCoding getMolecularDiagnosticReportCoding(String value, int version) {
         if (value == null || !Arrays.stream(MolecularDiagnosticReportCodingCode.values()).map(MolecularDiagnosticReportCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
             return null;

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

@@ -42,7 +42,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
     private final RebiopsieCatalogue rebiopsieCatalogue;
     private final ReevaluationCatalogue reevaluationCatalogue;
     private final EinzelempfehlungCatalogue einzelempfehlungCatalogue;
-    private final PropertyCatalogue propertyCatalogue;
+    private final VorbefundeCatalogue vorbefundeCatalogue;
 
     public MolekulargenetikToSpecimenDataMapper(
             final MolekulargenetikCatalogue molekulargenetikCatalogue,
@@ -50,19 +50,19 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
             final RebiopsieCatalogue rebiopsieCatalogue,
             final ReevaluationCatalogue reevaluationCatalogue,
             final EinzelempfehlungCatalogue einzelempfehlungCatalogue,
-            final PropertyCatalogue propertyCatalogue
+            final VorbefundeCatalogue vorbefundeCatalogue
     ) {
         this.molekulargenetikCatalogue = molekulargenetikCatalogue;
         this.therapieplanCatalogue = therapieplanCatalogue;
         this.rebiopsieCatalogue = rebiopsieCatalogue;
         this.reevaluationCatalogue = reevaluationCatalogue;
         this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
-        this.propertyCatalogue = propertyCatalogue;
+        this.vorbefundeCatalogue = vorbefundeCatalogue;
     }
 
     /**
      * Loads and maps a specimen using the database id
-     * The result does not include a diagnosis reference!
+     * Not intended for direct use! The result does not include a diagnosis reference!
      *
      * @param id The database id of the procedure data set
      * @return The loaded Patient data
@@ -77,7 +77,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
                 .patient(data.getPatientReference())
                 .type(getTumorSpecimenCoding(data.getString("materialfixierung")))
                 .collection(getCollection(data))
-        // TODO add diagnosis later
+                // diagnosis is added in getAllByKpaId()
         ;
 
 
@@ -127,8 +127,18 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
                         .collect(Collectors.toSet())
         );
 
+        // Vorbefunde anhand Einsendenummer
+        osMolGen.addAll(
+                vorbefundeCatalogue.getAllByParentId(kpaId).stream()
+                        .map(rs -> rs.getString("befundnummer"))
+                        .map(molekulargenetikCatalogue::getByEinsendenummer)
+                        .map(ResultSet::getId)
+                        .collect(Collectors.toList())
+        );
+
         return osMolGen.stream()
                 .filter(Objects::nonNull)
+                .distinct()
                 .map(this::getById)
                 .peek(it -> it.setDiagnosis(diagnoseReferenz))
                 .collect(Collectors.toList());

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

@@ -121,12 +121,16 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 catalogueFactory.catalogue(RebiopsieCatalogue.class),
                 catalogueFactory.catalogue(ReevaluationCatalogue.class),
                 einzelempfehlungCatalogue,
-                propertyCatalogue
+                catalogueFactory.catalogue(VorbefundeCatalogue.class)
         );
 
         var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
 
-        var kpaVorbefundeDataMapper = new KpaVorbefundeDataMapper(catalogueFactory.catalogue(VorbefundeCatalogue.class), propertyCatalogue);
+        var kpaVorbefundeDataMapper = new KpaVorbefundeDataMapper(
+                catalogueFactory.catalogue(VorbefundeCatalogue.class),
+                molekulargenetikCatalogue,
+                propertyCatalogue
+        );
 
         var resultBuilder = Mtb.builder();
 

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

@@ -26,6 +26,7 @@ import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
 import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.MolekulargenetikCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.VorbefundeCatalogue;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -48,6 +49,7 @@ import static org.mockito.Mockito.when;
 class KpaVorbefundeDataMapperTest {
 
     VorbefundeCatalogue catalogue;
+    MolekulargenetikCatalogue molekulargenetikCatalogue;
     PropertyCatalogue propertyCatalogue;
 
     KpaVorbefundeDataMapper dataMapper;
@@ -55,11 +57,13 @@ class KpaVorbefundeDataMapperTest {
     @BeforeEach
     void setUp(
             @Mock VorbefundeCatalogue catalogue,
+            @Mock MolekulargenetikCatalogue molekulargenetikCatalogue,
             @Mock PropertyCatalogue propertyCatalogue
     ) {
         this.catalogue = catalogue;
+        this.molekulargenetikCatalogue = molekulargenetikCatalogue;
         this.propertyCatalogue = propertyCatalogue;
-        this.dataMapper = new KpaVorbefundeDataMapper(catalogue, propertyCatalogue);
+        this.dataMapper = new KpaVorbefundeDataMapper(catalogue, molekulargenetikCatalogue, propertyCatalogue);
     }
 
     @Test
@@ -93,6 +97,10 @@ class KpaVorbefundeDataMapperTest {
                 .when(catalogue)
                 .getAllByParentId(anyInt());
 
+        doAnswer(invocationOnMock -> ResultSet.from(Map.of("id", 1, "einsendenummer", "X/2025/1234")))
+                .when(molekulargenetikCatalogue)
+                .getByEinsendenummer(anyString());
+
         doAnswer(invocationOnMock -> {
                     var testPropertyData = Map.of(
                             "panel", new PropertyCatalogue.Entry("panel", "Panel", "Panel")
@@ -119,7 +127,7 @@ class KpaVorbefundeDataMapperTest {
                 .isEqualTo(new java.sql.Date(Date.from(Instant.parse("2000-07-06T12:00:00Z")).getTime()));
         assertThat(actual.getSpecimen())
                 .isEqualTo(Reference.builder()
-                        .id("X/2025/1234")
+                        .id("1")
                         .type("Specimen")
                         .build()
                 );

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

@@ -21,7 +21,6 @@
 package dev.pcvolkmer.onco.datamapper.mapper;
 
 import dev.pcvolkmer.mv64e.mtb.*;
-import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
 import org.junit.jupiter.api.BeforeEach;
@@ -50,7 +49,7 @@ class MolekulargenetikToSpecimenDataMapperTest {
     RebiopsieCatalogue rebiopsieCatalogue;
     ReevaluationCatalogue reevaluationCatalogue;
     EinzelempfehlungCatalogue einzelempfehlungCatalogue;
-    PropertyCatalogue propertyCatalogue;
+    VorbefundeCatalogue vorbefundeCatalogue;
 
     MolekulargenetikToSpecimenDataMapper mapper;
 
@@ -61,14 +60,14 @@ class MolekulargenetikToSpecimenDataMapperTest {
             @Mock RebiopsieCatalogue rebiopsieCatalogue,
             @Mock ReevaluationCatalogue reevaluationCatalogue,
             @Mock EinzelempfehlungCatalogue einzelempfehlungCatalogue,
-            @Mock PropertyCatalogue propertyCatalogue
+            @Mock VorbefundeCatalogue vorbefundeCatalogue
     ) {
         this.molekulargenetikCatalogue = molekulargenetikCatalogue;
         this.therapieplanCatalogue = therapieplanCatalogue;
         this.rebiopsieCatalogue = rebiopsieCatalogue;
         this.reevaluationCatalogue = reevaluationCatalogue;
         this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
-        this.propertyCatalogue = propertyCatalogue;
+        this.vorbefundeCatalogue = vorbefundeCatalogue;
 
         this.mapper = new MolekulargenetikToSpecimenDataMapper(
                 molekulargenetikCatalogue,
@@ -76,7 +75,7 @@ class MolekulargenetikToSpecimenDataMapperTest {
                 rebiopsieCatalogue,
                 reevaluationCatalogue,
                 einzelempfehlungCatalogue,
-                propertyCatalogue
+                vorbefundeCatalogue
         );
     }