feat: add "Stützende molekulare Alterationen"

README.md

@@ -51,7 +51,7 @@ var jsonResult = Converter.toJsonString(
 | IHC-Berichte                     |        |                                                                                |
 | MSI-Befunde                      |        |                                                                                |
 | NGS-Berichte                     | ⌛      | Aktuell in Arbeit                                                              |
-| MTB-Beschlüsse                   | ⛅      | Best effort: Stützende molekulare Alteration(en) aktuell nicht möglich (2)     |
+| MTB-Beschlüsse                   | ✅      | Stützende molekulare Alteration(en) für einfache Variante und CNV              |
 | Follow-Up Verlauf                |        |                                                                                |
 | Antrag Kostenübernahme           |        |                                                                                |
 | Antwort Kostenübernahme          |        |                                                                                |
@@ -63,3 +63,12 @@ var jsonResult = Converter.toJsonString(
 1. Nicht alle möglichen Ausprägungen in `OS.Molekulargenetik` vorhanden.
 2. Nach Implementierung Mapping von HGNC-Symbol (Gen-Name) zu HGNC-ID ist die Angabe der optionalen stützenden
    molekularen Alteration(en) möglich.
+
+## Enthaltene Liste mit Genen
+
+Es ist eine Liste mit über 43000 Genen
+von [https://genenames.org](https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_pub_chrom_map&col=md_ensembl_id&status=Approved&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit)
+enthalten.
+
+Diese Liste der Gene unterliegt der folgenden Lizenz und ist frei
+verfügbar: [Creative Commons Public Domain (CC0) License](https://creativecommons.org/public-domain/cc0/).

build.gradle.kts

@@ -8,6 +8,7 @@ version = "0.1.0-SNAPSHOT"
 
 var versions = mapOf(
     "mtb-dto" to "0.1.0-SNAPSHOT",
+    "commons-csv" to "1.14.0",
     "slf4j" to "2.0.17",
     "junit" to "5.13.1",
     "assertj" to "3.27.3",
@@ -48,6 +49,7 @@ dependencies {
             prefer("4.3.8.RELEASE")
         }
     }
+    implementation("org.apache.commons:commons-csv:${versions["commons-csv"]}")
     implementation("org.slf4j:slf4j-api:${versions["slf4j"]}")
 
     testImplementation(platform("org.junit:junit-bom:${versions["junit"]}"))

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

@@ -0,0 +1,160 @@
+/*
+ * 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.genes;
+
+import dev.pcvolkmer.mv64e.mtb.Chromosome;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+
+/**
+ * Represents a gene
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1.0
+ */
+// Originally taken from https://github.com/pcvolkmer/onkostar-plugin-genes/blob/master/api/src/main/java/dev/pcvolkmer/onkostar/genes/Gene.java
+public class Gene {
+
+    private final String hgncId;
+
+    private final String ensembleId;
+
+    private final String symbol;
+
+    private final String name;
+
+    private final String chromosome;
+
+    Gene(
+            String hgncId,
+            String ensembleId,
+            String symbol,
+            String name,
+            String chromosome
+    ) {
+        this.hgncId = hgncId;
+        this.ensembleId = ensembleId;
+        this.symbol = symbol;
+        this.name = name;
+        this.chromosome = chromosome;
+    }
+
+    /**
+     * Returns the HGNC ID of this gene
+     *
+     * @return the HGNC ID
+     */
+    public String getHgncId() {
+        return hgncId;
+    }
+
+    /**
+     * Returns the EnsemblID of this gene
+     *
+     * @return the EnsemblID
+     */
+    public String getEnsemblId() {
+        return ensembleId;
+    }
+
+    /**
+     * Returns the Symbol of this gene
+     *
+     * @return the Symbol
+     */
+    public String getSymbol() {
+        return symbol;
+    }
+
+    /**
+     * Returns the name of this gene
+     *
+     * @return the name
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Returns the chromosome(s) the gene is located at
+     *
+     * @return the chromosome(s)
+     */
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    /**
+     * Returns a list of chromosomes using form 'chr?'
+     *
+     * @return a list of chromosomes
+     */
+    public List<Chromosome> getChromosomesInPropertyForm() {
+        return Arrays.stream(this.chromosome.split(" "))
+                .map(value -> {
+                    try {
+                        var pattern = Pattern.compile("^(\\d+|X|Y)");
+                        var matcher = pattern.matcher(value);
+                        if (matcher.find()) {
+                            return Chromosome.forValue(String.format("chr%s", matcher.group(0)));
+                        }
+                    } catch (Exception e) {
+                        // Nop
+                    }
+                    return null;
+                })
+                .filter(Objects::nonNull)
+                .collect(Collectors.toList());
+    }
+
+    /**
+     * Returns a chromosome using form 'chr...?' if one (single) chromosome listed
+     *
+     * @return an <code>Optional</code> containing the chromosome
+     */
+    public Optional<Chromosome> getSingleChromosomeInPropertyForm() {
+        var fixedChromosomes = this.getChromosomesInPropertyForm();
+
+        if (fixedChromosomes.size() == 1) {
+            return Optional.of(fixedChromosomes.get(0));
+        }
+
+        return Optional.empty();
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Gene gene = (Gene) o;
+        return Objects.equals(hgncId, gene.hgncId) && Objects.equals(ensembleId, gene.ensembleId) && Objects.equals(symbol, gene.symbol) && Objects.equals(name, gene.name) && Objects.equals(chromosome, gene.chromosome);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(hgncId, ensembleId, symbol, name, chromosome);
+    }
+}

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

@@ -0,0 +1,80 @@
+/*
+ * 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.genes;
+
+import org.apache.commons.csv.CSVFormat;
+
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+/**
+ * Utility class for genes
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class GeneUtils {
+
+    private GeneUtils() {
+        // Empty
+    }
+
+    public static Optional<Gene> findByHgncId(String hgncId) {
+        return genes().stream().filter(gene -> gene.getHgncId().equalsIgnoreCase(hgncId)).findFirst();
+    }
+
+    public static Optional<Gene> findBySymbol(String symbol) {
+        return genes().stream().filter(gene -> gene.getSymbol().equalsIgnoreCase(symbol)).findFirst();
+    }
+
+    private static List<Gene> genes() {
+        var result = new ArrayList<Gene>();
+
+        try {
+            var inputStream = GeneUtils.class.getClassLoader().getResourceAsStream("genes.csv");
+            var parser = CSVFormat.RFC4180.builder()
+                    .setHeader()
+                    .setSkipHeaderRecord(true)
+                    .setDelimiter('\t')
+                    .get()
+                    .parse(new InputStreamReader(inputStream));
+            for (var row : parser) {
+                result.add(
+                        new Gene(
+                                row.get("HGNC ID"),
+                                row.get("Ensembl ID(supplied by Ensembl)"),
+                                row.get("Approved symbol"),
+                                row.get("Approved name"),
+                                row.get("Chromosome")
+                        )
+                );
+            }
+
+            return result;
+        } catch (IOException e) {
+            return List.of();
+        }
+    }
+
+}

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

@@ -72,6 +72,13 @@ public class EinzelempfehlungProzedurDataMapper extends AbstractEinzelempfehlung
             );
         }
 
+        // As of now: Simple variant and CSV only! - Not used but present for completeness
+        if (null != resultSet.getString("st_mol_alt_variante_json")) {
+            resultBuilder.supportingVariants(
+                    JsonToMolAltVarianteMapper.map(resultSet.getString("st_mol_alt_variante_json"))
+            );
+        }
+
         return resultBuilder.build();
     }
 

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

@@ -42,7 +42,7 @@ public class EinzelempfehlungStudieDataMapper extends AbstractEinzelempfehlungDa
 
     @Override
     protected MtbStudyEnrollmentRecommendation map(ResultSet resultSet) {
-        return MtbStudyEnrollmentRecommendation.builder()
+        var resultBuilder = MtbStudyEnrollmentRecommendation.builder()
                 .id(resultSet.getString("id"))
                 .patient(resultSet.getPatientReference())
                 // TODO Fix id?
@@ -56,8 +56,16 @@ public class EinzelempfehlungStudieDataMapper extends AbstractEinzelempfehlungDa
                 )
                 .medication(JsonToMedicationMapper.map(resultSet.getString("wirkstoffe_json")))
                 .levelOfEvidence(getLevelOfEvidence(resultSet))
-                .study(JsonToStudyMapper.map(resultSet.getString("studien_alle_json")))
+                .study(JsonToStudyMapper.map(resultSet.getString("studien_alle_json")));
-                .build();
+
+        // As of now: Simple variant and CSV only!
+        if (null != resultSet.getString("st_mol_alt_variante_json")) {
+            resultBuilder.supportingVariants(
+                    JsonToMolAltVarianteMapper.map(resultSet.getString("st_mol_alt_variante_json"))
+            );
+        }
+
+        return resultBuilder.build();
     }
 
     @Override

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

@@ -83,8 +83,11 @@ public class EinzelempfehlungWirkstoffDataMapper extends AbstractEinzelempfehlun
             );
         }
 
-        if (null != resultSet.getString("st_mol_alt_variante")) {
+        // As of now: Simple variant and CSV only!
-            // Empty for now
+        if (null != resultSet.getString("st_mol_alt_variante_json")) {
+            resultBuilder.supportingVariants(
+                    JsonToMolAltVarianteMapper.map(resultSet.getString("st_mol_alt_variante_json"))
+            );
         }
 
         return resultBuilder.build();

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

@@ -0,0 +1,91 @@
+/*
+ * 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 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;
+import dev.pcvolkmer.onco.datamapper.genes.GeneUtils;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Maps JSON strings used in Einzelempfehlung MolAltVariante
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class JsonToMolAltVarianteMapper {
+
+    private JsonToMolAltVarianteMapper() {
+        // intentionally left empty
+    }
+
+    public static List<GeneAlterationReference> map(String studyJson) {
+        if (studyJson == null) {
+            return List.of();
+        }
+        try {
+            return new ObjectMapper().readValue(studyJson, new TypeReference<List<MolAltVariante>>() {
+                    }).stream()
+                    .map(variante -> {
+                        var resultBuilder = GeneAlterationReference.builder();
+                        GeneUtils.findBySymbol(variante.getGen()).ifPresent(gene -> {
+                            resultBuilder
+                                    .gene(
+                                            Coding.builder()
+                                                    .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());
+        } catch (Exception e) {
+            throw new DataAccessException(String.format("Cannot map gene alteration for %s", studyJson));
+        }
+    }
+
+    @JsonIgnoreProperties(ignoreUnknown = true)
+    private static class MolAltVariante {
+        private String id;
+        private String gen;
+
+        public String getId() {
+            return id;
+        }
+
+        public String getGen() {
+            return gen;
+        }
+    }
+
+}

src/test/java/dev/pcvolkmer/onco/datamapper/genes/GeneUtilsTest.java

@@ -0,0 +1,57 @@
+/*
+ * 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.genes;
+
+import dev.pcvolkmer.mv64e.mtb.Chromosome;
+import org.junit.jupiter.api.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+class GeneUtilsTest {
+
+    @Test
+    void findByHgncId() {
+        var actual = GeneUtils.findByHgncId("HGNC:1097");
+
+        assertThat(actual).isPresent().hasValueSatisfying(gene -> {
+            assertThat(gene.getHgncId()).isEqualTo("HGNC:1097");
+            assertThat(gene.getEnsemblId()).isEqualTo("ENSG00000157764");
+            assertThat(gene.getSymbol()).isEqualTo("BRAF");
+            assertThat(gene.getName()).isEqualTo("B-Raf proto-oncogene, serine/threonine kinase");
+            assertThat(gene.getChromosome()).isEqualTo("7q34");
+            assertThat(gene.getSingleChromosomeInPropertyForm()).hasValue(Chromosome.CHR7);
+        });
+    }
+
+    @Test
+    void findByHgncSymbol() {
+        var actual = GeneUtils.findBySymbol("ABCD1");
+
+        assertThat(actual).isPresent().hasValueSatisfying(gene -> {
+            assertThat(gene.getHgncId()).isEqualTo("HGNC:61");
+            assertThat(gene.getEnsemblId()).isEqualTo("ENSG00000101986");
+            assertThat(gene.getSymbol()).isEqualTo("ABCD1");
+            assertThat(gene.getName()).isEqualTo("ATP binding cassette subfamily D member 1");
+            assertThat(gene.getChromosome()).isEqualTo("Xq28");
+            assertThat(gene.getSingleChromosomeInPropertyForm()).hasValue(Chromosome.CHR_X);
+        });
+    }
+}

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

@@ -0,0 +1,49 @@
+/*
+ * 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.Coding;
+import dev.pcvolkmer.mv64e.mtb.GeneAlterationReference;
+import dev.pcvolkmer.mv64e.mtb.Reference;
+import org.junit.jupiter.api.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+class JsonToMolAltVarianteMapperTest {
+
+    @Test
+    void shouldMapJson() {
+        var json = "[{\"id\":22641112,\"ergebnis\":\"Einfache Variante (Mutation)\",\"gen\":\"BRAF\",\"exon\":\"-\",\"pathogenitaetsklasse\":\"-\"}]";
+
+        var actual = JsonToMolAltVarianteMapper.map(json);
+
+        assertThat(actual).hasSize(1);
+
+        var variant = actual.get(0);
+        assertThat(variant).isEqualTo(
+                GeneAlterationReference.builder()
+                        .gene(Coding.builder().code("HGNC:1097").display("BRAF").system("https://www.genenames.org/").build())
+                        .variant(Reference.builder().id("22641112").type("Variant").build())
+                        .build()
+        );
+    }
+
+}