diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java index 1a678ce..460af8c 100644 --- a/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java @@ -103,6 +103,8 @@ public class DataCatalogueFactory { return ConsentMvCatalogue.create(jdbcTemplate); } else if (c == ConsentMvVerlaufCatalogue.class) { return ConsentMvVerlaufCatalogue.create(jdbcTemplate); + } else if (c == KeimbahndiagnoseCatalogue.class) { + return KeimbahndiagnoseCatalogue.create(jdbcTemplate); } throw new DataCatalogueCreationException(clazz); }); diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogue.java b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogue.java new file mode 100644 index 0000000..135ffd5 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogue.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 . + * + */ + +package dev.pcvolkmer.onco.datamapper.datacatalogues; + +import org.springframework.jdbc.core.JdbcTemplate; + +/** + * Load raw result sets from database table 'dk_dnpm_uf_keimbahndiagnose' + * + * @author Paul-Christian Volkmer + * @since 0.1 + */ +public class KeimbahndiagnoseCatalogue extends AbstractSubformDataCatalogue { + + private KeimbahndiagnoseCatalogue(JdbcTemplate jdbcTemplate) { + super(jdbcTemplate); + } + + @Override + protected String getTableName() { + return "dk_dnpm_uf_keimbahndiagnose"; + } + + public static KeimbahndiagnoseCatalogue create(JdbcTemplate jdbcTemplate) { + return new KeimbahndiagnoseCatalogue(jdbcTemplate); + } + +} diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java b/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java index fd391d1..dd511b8 100644 --- a/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java @@ -23,6 +23,7 @@ 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.KeimbahndiagnoseCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue; @@ -44,17 +45,20 @@ public class KpaDiagnosisDataMapper implements DataMapper { private final KpaCatalogue kpaCatalogue; private final TumorausbreitungCatalogue tumorausbreitungCatalogue; private final TumorgradingCatalogue tumorgradingCatalogue; + private final KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue; private final PropertyCatalogue propertyCatalogue; public KpaDiagnosisDataMapper( final KpaCatalogue kpaCatalogue, final TumorausbreitungCatalogue tumorausbreitungCatalogue, final TumorgradingCatalogue tumorgradingCatalogue, + final KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue, final PropertyCatalogue propertyCatalogue ) { this.kpaCatalogue = kpaCatalogue; this.tumorausbreitungCatalogue = tumorausbreitungCatalogue; this.tumorgradingCatalogue = tumorgradingCatalogue; + this.keimbahndiagnoseCatalogue = keimbahndiagnoseCatalogue; this.propertyCatalogue = propertyCatalogue; } @@ -83,13 +87,12 @@ public class KpaDiagnosisDataMapper implements DataMapper { .recordedOn(data.getDate("datumerstdiagnose")) .topography(Coding.builder().code(data.getString("icdo3lokalisation")).build()) .type(getType(data)) - // Nicht in Onkostar erfasst - //.germlineCodes() .guidelineTreatmentStatus( getMtbDiagnosisGuidelineTreatmentStatusCoding(data.getString("leitlinienstatus"), data.getInteger("leitlinienstatus_propcat_version")) ) .grading(getGrading(id)) .staging(getStaging(id)) + .germlineCodes(getGermlineCodes(id)) ; return builder.build(); } @@ -172,6 +175,19 @@ public class KpaDiagnosisDataMapper implements DataMapper { return Staging.builder().history(all).build(); } + private List getGermlineCodes(final int id) { + return keimbahndiagnoseCatalogue.getAllByParentId(id).stream() + .map(it -> + Coding.builder() + .code(it.getString("icd10")) + .system("http://fhir.de/CodeSystem/bfarm/icd-10-gm") + .display(propertyCatalogue.getByCodeAndVersion(it.getString("icd10"), it.getInteger("icd10_propcat_version")).getShortdesc()) + .version(propertyCatalogue.getByCodeAndVersion(it.getString("icd10"), it.getInteger("icd10_propcat_version")).getVersionDescription()) + .build() + ) + .collect(Collectors.toList()); + } + private Type getType(final ResultSet resultSet) { var diagnosisCoding = MtbDiagnosisCoding.builder(); var code = resultSet.getString("diagnosetyp"); diff --git a/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java b/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java index 40653f7..01b9120 100644 --- a/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java +++ b/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java @@ -85,6 +85,7 @@ public class MtbDataMapper implements DataMapper { kpaCatalogue, catalogueFactory.catalogue(TumorausbreitungCatalogue.class), catalogueFactory.catalogue(TumorgradingCatalogue.class), + catalogueFactory.catalogue(KeimbahndiagnoseCatalogue.class), propertyCatalogue ); var mtbEpisodeDataMapper = new MtbEpisodeDataMapper(kpaCatalogue, propertyCatalogue); diff --git a/src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogueTest.java b/src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogueTest.java new file mode 100644 index 0000000..72a1e71 --- /dev/null +++ b/src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogueTest.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 . + * + */ + +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 KeimbahndiagnoseCatalogueTest { + + JdbcTemplate jdbcTemplate; + KeimbahndiagnoseCatalogue catalogue; + + @BeforeEach + void setUp(@Mock JdbcTemplate jdbcTemplate) { + this.jdbcTemplate = jdbcTemplate; + this.catalogue = KeimbahndiagnoseCatalogue.create(jdbcTemplate); + } + + @Test + void shouldUseCorrectQuery(@Mock Map 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_dnpm_uf_keimbahndiagnose.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_keimbahndiagnose JOIN prozedur ON (prozedur.id = dk_dnpm_uf_keimbahndiagnose.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?"); + } + + @Test + void shouldUseCorrectSubformQuery(@Mock Map 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_dnpm_uf_keimbahndiagnose.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_keimbahndiagnose JOIN prozedur ON (prozedur.id = dk_dnpm_uf_keimbahndiagnose.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?"); + } + + @Test + void shouldUseCorrectMerkmalQuery(@Mock Map 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_dnpm_uf_keimbahndiagnose_merkmale WHERE eintrag_id = ?"); + } + + @Test + void shouldUseMerkmalList() { + doAnswer(invocationOnMock -> { + var sql = invocationOnMock.getArgument(0, String.class); + ArrayList> 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(); + 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")); + } + +} diff --git a/src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java b/src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java index d292614..ec9406a 100644 --- a/src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java +++ b/src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java @@ -24,6 +24,7 @@ import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis; import dev.pcvolkmer.mv64e.mtb.Reference; import dev.pcvolkmer.onco.datamapper.PropertyCatalogue; import dev.pcvolkmer.onco.datamapper.ResultSet; +import dev.pcvolkmer.onco.datamapper.datacatalogues.KeimbahndiagnoseCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue; import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue; @@ -34,6 +35,7 @@ import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; import javax.sql.DataSource; +import java.util.List; import java.util.Map; import static org.assertj.core.api.Assertions.assertThat; @@ -47,6 +49,7 @@ class KpaDiagnosisDataMapperTest { KpaCatalogue kpaCatalogue; TumorausbreitungCatalogue tumorausbreitungCatalogue; TumorgradingCatalogue tumorgradingCatalogue; + KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue; PropertyCatalogue propertyCatalogue; KpaDiagnosisDataMapper dataMapper; @@ -56,13 +59,21 @@ class KpaDiagnosisDataMapperTest { @Mock KpaCatalogue kpaCatalogue, @Mock TumorausbreitungCatalogue tumorausbreitungCatalogue, @Mock TumorgradingCatalogue tumorgradingCatalogue, + @Mock KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue, @Mock PropertyCatalogue propertyCatalogue ) { this.kpaCatalogue = kpaCatalogue; this.tumorausbreitungCatalogue = tumorausbreitungCatalogue; this.tumorgradingCatalogue = tumorgradingCatalogue; + this.keimbahndiagnoseCatalogue = keimbahndiagnoseCatalogue; this.propertyCatalogue = propertyCatalogue; - this.dataMapper = new KpaDiagnosisDataMapper(kpaCatalogue, tumorausbreitungCatalogue, tumorgradingCatalogue, propertyCatalogue); + this.dataMapper = new KpaDiagnosisDataMapper( + kpaCatalogue, + tumorausbreitungCatalogue, + tumorgradingCatalogue, + keimbahndiagnoseCatalogue, + propertyCatalogue + ); } @Test @@ -88,12 +99,27 @@ class KpaDiagnosisDataMapperTest { new PropertyCatalogue.Entry("C00.0", "Bösartige Neubildung: Äußere Oberlippe", "Bösartige Neubildung: Äußere Oberlippe") ).when(propertyCatalogue).getByCodeAndVersion(anyString(), anyInt()); + doAnswer(invocationOnMock -> + List.of( + ResultSet.from( + Map.of( + "id", 1, + "icd10", "C00.0", + "icd10_propcat_version", 42 + ) + ) + ) + ).when(keimbahndiagnoseCatalogue).getAllByParentId(anyInt()); + var actual = this.dataMapper.getById(1); assertThat(actual).isInstanceOf(MtbDiagnosis.class); assertThat(actual.getId()).isEqualTo("1"); assertThat(actual.getPatient()) .isEqualTo(Reference.builder().id("42").type("Patient").build()); assertThat(actual.getCode().getCode()).isEqualTo("F79.9"); + + assertThat(actual.getGermlineCodes()).hasSize(1); + assertThat(actual.getGermlineCodes().get(0).getCode()).isEqualTo("C00.0"); } private static Map testData() {