feat: add MSI mapping as far as possible

README.md

@@ -54,7 +54,7 @@ Um Mithilfe wird gebeten.
 | vorherige Molekular-Diagnostik   | ✅      |                                                                                |
 | Histologie-Berichte              | ✅      |                                                                                |
 | IHC-Berichte                     | -      | Aktuell nicht vorgesehen                                                       |
-| MSI-Befunde                      | ⌛      | Aktuell in Arbeit, https://github.com/dnpm-dip/mtb-model/issues/10 ist behoben |
+| MSI-Befunde                      | ⛅      | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (2) |
 | NGS-Berichte                     | ⛅      | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (2) |
 | MTB-Beschlüsse                   | ✅      | Stützende molekulare Alteration(en) für einfache Variante und CNV (3)          |
 | Follow-Up Verlauf                | -      | Späterer Zeitpunkt                                                             |
@@ -67,7 +67,10 @@ Um Mithilfe wird gebeten.
 
 1. Nicht alle möglichen Ausprägungen in `OS.Molekulargenetik` vorhanden.
 2. Aktuell nicht alle Angaben effektiv im Formular `OS.Molekulargenetik` wie gefordert angebbar.
-   Hinweis: Tumorzellgehalt-Methode problematisch, wenn auch im NGS-Bericht histologisch festgestellt.
+   Hinweise:
+   * Tumorzellgehalt-Methode problematisch, wenn auch im NGS-Bericht histologisch festgestellt.
+   * Angabe zu MSI-Interpretation fehlt in Formular, ist aber Pflichtangabe - Wird gefiltert.
+   * Datenbanktabelle für MSI lautet tatsächlich `dk_molekluargenmsi` [sic!]
 3. Implementierung des Mappings von HGNC-Symbol (Gen-Name) zu HGNC-ID über enthaltene Gen-Liste.
 
 ## Enthaltene Liste mit Genen

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

@@ -140,6 +140,28 @@ public class ResultSet {
         throw new IllegalArgumentException("Cannot convert " + raw.getClass() + " to Integer");
     }
 
+    /**
+     * Get column value as Double and cast value if possible
+     *
+     * @param columnName The name of the column
+     * @return The column value as Integer
+     */
+    public Double getDouble(String columnName) {
+        var raw = this.rawData.get(columnName);
+
+        if (raw == null) {
+            return null;
+        } else if (raw instanceof Integer) {
+            return ((Integer) raw).doubleValue();
+        } else if (raw instanceof Long) {
+            return ((Long) raw).doubleValue();
+        } else if (raw instanceof Double) {
+            return ((Double) raw);
+        }
+
+        throw new IllegalArgumentException("Cannot convert " + raw.getClass() + " to Integer");
+    }
+
     /**
      * Get column value as Date and cast value if possible
      *

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

@@ -95,6 +95,8 @@ public class DataCatalogueFactory {
                 return MolekulargenetikCatalogue.create(jdbcTemplate);
             } else if (c == MolekulargenuntersuchungCatalogue.class) {
                 return MolekulargenuntersuchungCatalogue.create(jdbcTemplate);
+            } else if (c == MolekulargenMsiCatalogue.class) {
+                return MolekulargenMsiCatalogue.create(jdbcTemplate);
             } else if (c == RebiopsieCatalogue.class) {
                 return RebiopsieCatalogue.create(jdbcTemplate);
             } else if (c == ReevaluationCatalogue.class) {

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

@@ -0,0 +1,46 @@
+/*
+ * This file is part of mv64e-onkostar-data
+ *
+ * Copyright (C) 2025  Paul-Christian Volkmer
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package dev.pcvolkmer.onco.datamapper.datacatalogues;
+
+import org.springframework.jdbc.core.JdbcTemplate;
+
+/**
+ * Load raw result sets from database table 'dk_molekluargenmsi'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class MolekulargenMsiCatalogue extends AbstractSubformDataCatalogue {
+
+    private MolekulargenMsiCatalogue(JdbcTemplate jdbcTemplate) {
+        super(jdbcTemplate);
+    }
+
+    @Override
+    protected String getTableName() {
+        return "dk_molekluargenmsi";
+    }
+
+    public static MolekulargenMsiCatalogue create(JdbcTemplate jdbcTemplate) {
+        return new MolekulargenMsiCatalogue(jdbcTemplate);
+    }
+
+}

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

@@ -0,0 +1,113 @@
+/*
+ * This file is part of mv64e-onkostar-data
+ *
+ * Copyright (C) 2025  Paul-Christian Volkmer
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.Msi;
+import dev.pcvolkmer.mv64e.mtb.MsiMethodCoding;
+import dev.pcvolkmer.mv64e.mtb.MsiMethodCodingCode;
+import dev.pcvolkmer.mv64e.mtb.Reference;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.MolekulargenMsiCatalogue;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_molekluargenetik'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaMolekulargenetikMsiDataMapper extends AbstractSubformDataMapper<Msi> {
+
+    public KpaMolekulargenetikMsiDataMapper(
+            final MolekulargenMsiCatalogue molekulargenMsiCatalogue
+    ) {
+        super(molekulargenMsiCatalogue);
+    }
+
+    /**
+     * Loads and maps Prozedur related by database id
+     *
+     * @param id The database id of the procedure data set
+     * @return The loaded Procedure
+     */
+    @Override
+    public Msi getById(final int id) {
+        return this.map(catalogue.getById(id));
+    }
+
+    @Override
+    protected Msi map(ResultSet resultSet) {
+        var builder = Msi.builder();
+
+        if (!resultSet.getString("komplexerbiomarker").equals("MSI")) {
+            return null;
+        }
+
+        builder
+                .id(resultSet.getString("id"))
+                .patient(resultSet.getPatientReference())
+                .method(getMethodCode(resultSet))
+                .specimen(Reference.builder().id(resultSet.getString("hauptprozedur_id")).type("Specimen").build())
+                // Aktuell nicht in Onkostar vorhanden!
+                //.interpretation()
+                // In Onkostar nur für "Sequenzierung" bzw "BIOINFORMATIC" als Prozentwert angegeben => "0" als Fallback?
+                .value(getSeqProzentwert(resultSet))
+        ;
+
+
+        return builder.build();
+    }
+
+    private MsiMethodCoding getMethodCode(final ResultSet resultSet) {
+        var builder = MsiMethodCoding.builder()
+                .system("dnpm-dip/mtb/msi/method");
+
+        var analysemethoden = resultSet.getMerkmalList("analysemethoden");
+
+        // Achtung: Immer nur eine Methode wird betrachtet! In Onkostar sind gleichzeitig mehrere Angaben möglich!
+        if  (analysemethoden == null) {
+            return null;
+        } else if  (analysemethoden.contains("S")) {
+            builder.code(MsiMethodCodingCode.BIOINFORMATIC);
+            builder.display(MsiMethodCodingCode.BIOINFORMATIC.toString());
+        } else if  (analysemethoden.contains("P")) {
+            builder.code(MsiMethodCodingCode.PCR);
+            builder.display(MsiMethodCodingCode.PCR.toString());
+        } else if  (analysemethoden.contains("I")) {
+            builder.code(MsiMethodCodingCode.IHC);
+            builder.display(MsiMethodCodingCode.IHC.toString());
+        } else {
+            return null;
+        }
+
+        return builder.build();
+    }
+
+    private double getSeqProzentwert(final ResultSet resultSet) {
+        var analysemethoden = resultSet.getMerkmalList("analysemethoden");
+
+        // Achtung: Immer nur eine Methode wird betrachtet! In Onkostar sind gleichzeitig mehrere Angaben möglich!
+        if  (analysemethoden != null && analysemethoden.contains("S")) {
+            return resultSet.getDouble("seqprozentwert");
+        }
+
+        return 0;
+    }
+}

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

@@ -38,12 +38,12 @@ import java.util.stream.Collectors;
  * @author Paul-Christian Volkmer
  * @since 0.1
  */
-public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsReport> {
+public class KpaMolekulargenetikNgsDataMapper implements DataMapper<SomaticNgsReport> {
 
     private final MolekulargenetikCatalogue catalogue;
     private final MolekulargenuntersuchungCatalogue untersuchungCatalogue;
 
-    public KpaMolekulargenetikDataMapper(
+    public KpaMolekulargenetikNgsDataMapper(
             final MolekulargenetikCatalogue catalogue,
             final MolekulargenuntersuchungCatalogue untersuchungCatalogue,
             final PropertyCatalogue propertyCatalogue

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

@@ -124,7 +124,9 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 catalogueFactory.catalogue(HistologieCatalogue.class)
         );
 
-        var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
+        var kpaMolekulargenetikNgsDataMapper = new KpaMolekulargenetikNgsDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
+        var kpaMolekulargenetikMsiDataMapper = new KpaMolekulargenetikMsiDataMapper(catalogueFactory.catalogue(MolekulargenMsiCatalogue.class));
+
 
         var kpaVorbefundeDataMapper = new KpaVorbefundeDataMapper(
                 catalogueFactory.catalogue(VorbefundeCatalogue.class),
@@ -196,7 +198,16 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                     )
                     // NGS Berichte
                     .ngsReports(
-                            kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
+                            kpaMolekulargenetikNgsDataMapper.getAllByKpaId(kpaId)
+                    )
+                    // MSI Befunde
+                    .msiFindings(
+                            kpaMolekulargenetikNgsDataMapper.getAllByKpaId(kpaId).stream()
+                                    .map(ngs -> Integer.parseInt(ngs.getId()))
+                                    .flatMap(ngsId -> kpaMolekulargenetikMsiDataMapper.getByParentId(ngsId).stream())
+                                    // Filtere alle MSI: Nur mit Angabe Interpretation!
+                                    .filter(msi -> msi.getInterpretation() != null)
+                                    .collect(Collectors.toList())
                     )
             ;
 

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

@@ -55,6 +55,13 @@ class ResultSetTest {
         assertThat(data.getLong("int")).isEqualTo(42L);
     }
 
+    @Test
+    void shouldReturnDoubleValues() {
+        var data = getTestData();
+
+        assertThat(data.getDouble("int")).isEqualTo(42);
+    }
+
     @Test
     void shouldReturnDateValues() {
         var data = getTestData();

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

@@ -0,0 +1,126 @@
+/*
+ * This file is part of mv64e-onkostar-data
+ *
+ * Copyright (C) 2025  Paul-Christian Volkmer
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package dev.pcvolkmer.onco.datamapper.datacatalogues;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+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.*;
+
+@ExtendWith(MockitoExtension.class)
+class MolekulargenMsiCatalogueTest {
+
+    JdbcTemplate jdbcTemplate;
+    MolekulargenMsiCatalogue catalogue;
+
+    @BeforeEach
+    void setUp(@Mock JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+        this.catalogue = MolekulargenMsiCatalogue.create(jdbcTemplate);
+    }
+
+    @Test
+    void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getById(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT patient.patienten_id, dk_molekluargenmsi.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_molekluargenmsi JOIN prozedur ON (prozedur.id = dk_molekluargenmsi.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
+    }
+
+    @Test
+    void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getAllByParentId(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT patient.patienten_id, dk_molekluargenmsi.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_molekluargenmsi JOIN prozedur ON (prozedur.id = dk_molekluargenmsi.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
+    }
+
+    @Test
+    void shouldUseCorrectMerkmalQuery(@Mock Map<String, Object> resultSet) {
+        when(resultSet.get(anyString()))
+                .thenReturn(Map.of("feldname", "name", "feldwert", "wert"));
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getMerkmaleById(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT feldname, feldwert FROM dk_molekluargenmsi_merkmale WHERE eintrag_id = ?");
+    }
+
+    @Test
+    void shouldUseMerkmalList() {
+        doAnswer(invocationOnMock -> {
+            var sql = invocationOnMock.getArgument(0, String.class);
+            ArrayList<Map<String, Object>> result = new ArrayList<>();
+            if (sql.startsWith("SELECT feldname")) {
+                result.add(Map.of("feldname", "name", "feldwert", "wert1"));
+                result.add(Map.of("feldname", "name", "feldwert", "wert2"));
+            } else {
+                var map = new HashMap<String, Object>();
+                map.put("id", 1);
+                map.put("name", "x");
+                result.add(map);
+            }
+            return result;
+        })
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        var result = this.catalogue.getById(1);
+
+        assertThat(result.getInteger("id")).isEqualTo(1);
+        assertThat(result.getMerkmalList("name")).isEqualTo(List.of("wert1", "wert2"));
+    }
+
+}