feat: initial support for NGS reports

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

@@ -93,6 +93,8 @@ public class DataCatalogueFactory {
                 return EinzelempfehlungCatalogue.create(jdbcTemplate);
             } else if (c == MolekulargenetikCatalogue.class) {
                 return MolekulargenetikCatalogue.create(jdbcTemplate);
+            } else if (c == MolekulargenuntersuchungCatalogue.class) {
+                return MolekulargenuntersuchungCatalogue.create(jdbcTemplate);
             } else if (c == RebiopsieCatalogue.class) {
                 return RebiopsieCatalogue.create(jdbcTemplate);
             } else if (c == ReevaluationCatalogue.class) {

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

@@ -20,15 +20,19 @@
 
 package dev.pcvolkmer.onco.datamapper.datacatalogues;
 
+import dev.pcvolkmer.onco.datamapper.ResultSet;
 import org.springframework.jdbc.core.JdbcTemplate;
 
+import java.util.List;
+import java.util.stream.Collectors;
+
 /**
  * Load raw result sets from database table 'dk_molekulargenetik'
  *
  * @author Paul-Christian Volkmer
  * @since 0.1
  */
-public class MolekulargenetikCatalogue extends AbstractSubformDataCatalogue {
+public class MolekulargenetikCatalogue extends AbstractDataCatalogue {
 
     private MolekulargenetikCatalogue(JdbcTemplate jdbcTemplate) {
         super(jdbcTemplate);
@@ -43,4 +47,55 @@ public class MolekulargenetikCatalogue extends AbstractSubformDataCatalogue {
         return new MolekulargenetikCatalogue(jdbcTemplate);
     }
 
+    /**
+     * Get procedure IDs by related Therapieplan procedure id
+     * Related form references in Einzelempfehlung, Rebiopsie, Reevaluation
+     *
+     * @param therapieplanId The procedure id
+     * @return The procedure ids
+     */
+    public List<Integer> getByTherapieplanId(int therapieplanId) {
+        return this.jdbcTemplate.queryForList(
+                        "SELECT DISTINCT ref_molekulargenetik FROM dk_dnpm_uf_einzelempfehlung JOIN prozedur ON (prozedur.id = dk_dnpm_uf_einzelempfehlung.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ? "
+                                + " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ? "
+                                + " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ?;"
+                        ,
+                        therapieplanId,
+                        therapieplanId,
+                        therapieplanId)
+                .stream()
+                .map(ResultSet::from)
+                .map(rs -> rs.getInteger("ref_molekulargenetik"))
+                .collect(Collectors.toList());
+    }
+
+    /**
+     * Get procedure IDs used in related KPA/Therapieplan procedures
+     * Related form references in Einzelempfehlung, Rebiopsie, Reevaluation
+     *
+     * @param kpaId The procedure id
+     * @return The procedure ids
+     */
+    public List<Integer> getIdsByKpaId(int kpaId) {
+        return this.jdbcTemplate.queryForList(
+                        "SELECT DISTINCT ref_molekulargenetik FROM dk_dnpm_uf_einzelempfehlung JOIN prozedur ON (prozedur.id = dk_dnpm_uf_einzelempfehlung.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?) "
+                                + " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?) "
+                                + " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) "
+                                + " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?);"
+                        ,
+                        kpaId,
+                        kpaId,
+                        kpaId)
+                .stream()
+                .map(ResultSet::from)
+                .map(rs -> rs.getInteger("ref_molekulargenetik"))
+                .distinct()
+                .collect(Collectors.toList());
+    }
+
 }

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

@@ -0,0 +1,50 @@
+/*
+ * 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 dev.pcvolkmer.onco.datamapper.ResultSet;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Load raw result sets from database table 'dk_molekulargenuntersuchung'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class MolekulargenuntersuchungCatalogue extends AbstractSubformDataCatalogue {
+
+    private MolekulargenuntersuchungCatalogue(JdbcTemplate jdbcTemplate) {
+        super(jdbcTemplate);
+    }
+
+    @Override
+    protected String getTableName() {
+        return "dk_molekulargenuntersuchung";
+    }
+
+    public static MolekulargenuntersuchungCatalogue create(JdbcTemplate jdbcTemplate) {
+        return new MolekulargenuntersuchungCatalogue(jdbcTemplate);
+    }
+
+}

src/main/java/dev/pcvolkmer/onco/datamapper/genes/GeneUtils.java

@@ -20,6 +20,7 @@
 
 package dev.pcvolkmer.onco.datamapper.genes;
 
+import dev.pcvolkmer.mv64e.mtb.Coding;
 import org.apache.commons.csv.CSVFormat;
 
 import java.io.IOException;
@@ -48,6 +49,14 @@ public class GeneUtils {
         return genes().stream().filter(gene -> gene.getSymbol().equalsIgnoreCase(symbol)).findFirst();
     }
 
+    public static Coding toCoding(Gene gene) {
+        return Coding.builder()
+                .code(gene.getHgncId())
+                .display(gene.getSymbol())
+                .system("https://www.genenames.org/")
+                .build();
+    }
+
     private static List<Gene> genes() {
         var result = new ArrayList<Gene>();
 

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

@@ -23,7 +23,6 @@ package dev.pcvolkmer.onco.datamapper.mapper;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import dev.pcvolkmer.mv64e.mtb.Coding;
 import dev.pcvolkmer.mv64e.mtb.GeneAlterationReference;
 import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
@@ -53,19 +52,11 @@ public class JsonToMolAltVarianteMapper {
                     }).stream()
                     .map(variante -> {
                         var resultBuilder = GeneAlterationReference.builder();
-                        GeneUtils.findBySymbol(variante.getGen()).ifPresent(gene -> {
+                        GeneUtils.findBySymbol(variante.getGen()).ifPresent(gene -> resultBuilder
-                            resultBuilder
+                                .gene(GeneUtils.toCoding(gene))
-                                    .gene(
+                                .variant(
-                                            Coding.builder()
+                                        Reference.builder().id(variante.id).type("Variant").build()
-                                                    .code(gene.getHgncId())
+                                ));
-                                                    .display(gene.getSymbol())
-                                                    .system("https://www.genenames.org/")
-                                                    .build()
-                                    )
-                                    .variant(
-                                            Reference.builder().id(variante.id).type("Variant").build()
-                                    );
-                        });
                         return resultBuilder.build();
                     })
                     .collect(Collectors.toList());

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

@@ -0,0 +1,166 @@
+/*
+ * 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.*;
+import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
+import dev.pcvolkmer.onco.datamapper.genes.GeneUtils;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_molekulargenetik'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsReport> {
+
+    private final MolekulargenetikCatalogue catalogue;
+    private final MolekulargenuntersuchungCatalogue untersuchungCatalogue;
+
+    public KpaMolekulargenetikDataMapper(
+            final MolekulargenetikCatalogue catalogue,
+            final MolekulargenuntersuchungCatalogue untersuchungCatalogue,
+            final PropertyCatalogue propertyCatalogue
+    ) {
+        this.catalogue = catalogue;
+        this.untersuchungCatalogue = untersuchungCatalogue;
+    }
+
+    /**
+     * Loads and maps Prozedur related by database id
+     *
+     * @param id The database id of the procedure data set
+     * @return The loaded Procedure
+     */
+    @Override
+    public SomaticNgsReport getById(final int id) {
+        var data = catalogue.getById(id);
+
+        var builder = SomaticNgsReport.builder();
+        builder
+                .id(data.getString("id"))
+                .patient(data.getPatientReference())
+                .issuedOn(data.getDate("datum"))
+                .specimen(Reference.builder().id(data.getString("einsendenummer")).type("Specimen").build())
+                .results(this.getNgsReportResults(id))
+        ;
+
+        return builder.build();
+
+    }
+
+    /**
+     * Loads and maps all Prozedur related by KPA database id
+     *
+     * @param kpaId The database id of the KPA procedure data set
+     * @return The loaded Procedures
+     */
+    public List<SomaticNgsReport> getAllByKpaId(final int kpaId) {
+        return this.catalogue.getIdsByKpaId(kpaId).stream()
+                .distinct()
+                .map(this::getById)
+                .collect(Collectors.toList());
+    }
+
+    private NgsReportResults getNgsReportResults(int id) {
+        var subforms = this.untersuchungCatalogue.getAllByParentId(id);
+
+        var resultBuilder = NgsReportResults.builder();
+        resultBuilder.simpleVariants(
+                subforms.stream()
+                        // P => Einfache Variante
+                        .filter(subform -> "P".equals(subform.getString("ergebnis")))
+                        .map(subform -> {
+                            final var geneOptional = GeneUtils.findBySymbol(subform.getString("untersucht"));
+                            if (geneOptional.isEmpty()) {
+                                return null;
+                            }
+
+                            final var snvBuilder = Snv.builder()
+                                    .id(subform.getString("id"))
+                                    .patient(subform.getPatientReference())
+                                    .gene(GeneUtils.toCoding(geneOptional.get()))
+                                    .exonId(subform.getString("exon"))
+                                    .dnaChange(subform.getString("cdnanomenklatur"))
+                                    .proteinChange(subform.getString("proteinebenenomenklatur"));
+
+                            if (null != subform.getLong("allelfrequenz")) {
+                                snvBuilder.allelicFrequency(subform.getLong("allelfrequenz"));
+                            }
+                            if (null != subform.getLong("evreaddepth")) {
+                                snvBuilder.readDepth(subform.getLong("evreaddepth"));
+                            }
+                            geneOptional.get().getSingleChromosomeInPropertyForm().ifPresent(snvBuilder::chromosome);
+
+                            return snvBuilder.build();
+                        })
+                        .collect(Collectors.toList())
+        );
+
+        resultBuilder.copyNumberVariants(
+                subforms.stream()
+                        .filter(subform -> "CNV".equals(subform.getString("ergebnis")))
+                        .map(subform -> {
+                            final var geneOptional = GeneUtils.findBySymbol(subform.getString("untersucht"));
+                            if (geneOptional.isEmpty()) {
+                                return null;
+                            }
+
+                            final var reportedAffectedGenes = new ArrayList<String>();
+                            reportedAffectedGenes.add(subform.getString("untersucht"));
+
+                            // Weitere betroffene Gene aus Freitextfeld?
+                            if (null != subform.getString("cnvbetroffenegene")) {
+                                reportedAffectedGenes.addAll(
+                                        Arrays.stream(subform.getString("cnvbetroffenegene").split("\\s")).collect(Collectors.toList())
+                                );
+                            }
+
+                            final var cnvBuilder = Cnv.builder()
+                                    .id(subform.getString("id"))
+                                    .patient(subform.getPatientReference())
+                                    .reportedAffectedGenes(
+                                            reportedAffectedGenes.stream()
+                                                    .distinct()
+                                                    .map(GeneUtils::findBySymbol)
+                                                    .filter(Optional::isPresent)
+                                                    .map(gene -> GeneUtils.toCoding(gene.get()))
+                                                    .collect(Collectors.toList())
+                                    )
+                                    .totalCopyNumber(subform.getLong("cnvtotalcn"));
+
+                            geneOptional.get().getSingleChromosomeInPropertyForm().ifPresent(cnvBuilder::chromosome);
+
+                            return cnvBuilder.build();
+                        })
+                        .collect(Collectors.toList())
+        );
+        return resultBuilder.build();
+    }
+
+}

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

@@ -124,6 +124,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 propertyCatalogue
         );
 
+        var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
+
         var resultBuilder = Mtb.builder();
 
         try {
@@ -156,6 +158,11 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                                 Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
                         )
                     )
+                    // NGS Berichte
+                    .ngsReports(
+                        kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
+                    )
+
             ;
         } catch (DataAccessException e) {
             logger.error("Error while getting Mtb.", e);

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

@@ -64,19 +64,4 @@ class MolekulargenetikCatalogueTest {
                 .isEqualTo("SELECT patient.patienten_id, dk_molekulargenetik.*, prozedur.* FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.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_molekulargenetik.*, prozedur.* FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
-    }
-
 }

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

@@ -0,0 +1,82 @@
+/*
+ * 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.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.verify;
+
+@ExtendWith(MockitoExtension.class)
+class MolekulargenuntersuchungCatalogueTest {
+
+    JdbcTemplate jdbcTemplate;
+    MolekulargenuntersuchungCatalogue catalogue;
+
+    @BeforeEach
+    void setUp(@Mock JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+        this.catalogue = MolekulargenuntersuchungCatalogue.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_molekulargenuntersuchung.*, prozedur.* FROM dk_molekulargenuntersuchung JOIN prozedur ON (prozedur.id = dk_molekulargenuntersuchung.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_molekulargenuntersuchung.*, prozedur.* FROM dk_molekulargenuntersuchung JOIN prozedur ON (prozedur.id = dk_molekulargenuntersuchung.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
+    }
+
+}