feat: add display and system to diagnosis data

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

@@ -43,8 +43,16 @@ public class PropertyCatalogue {
     public Entry getByCodeAndVersion(String code, int version) {
         try {
             return this.jdbcTemplate.queryForObject(
-                    "SELECT code, shortdesc, description FROM property_catalogue_version_entry WHERE code = ? AND property_version_id = ?",
+                    "SELECT code, shortdesc, e.description, v.oid AS version_oid, v.description AS version_description FROM property_catalogue_version_entry e" +
-                    (rs, rowNum) -> new Entry(rs.getString("code"), rs.getString("shortdesc"), rs.getString("description")),
+                            " JOIN property_catalogue_version v ON (e.property_version_id = v.id)" +
+                            " WHERE code = ? AND property_version_id = ?",
+                    (rs, rowNum) -> new Entry(
+                            rs.getString("code"),
+                            rs.getString("shortdesc"),
+                            rs.getString("description"),
+                            rs.getString("version_oid"),
+                            rs.getString("version_description")
+                    ),
                     code,
                     version);
         } catch (RuntimeException e) {
@@ -59,11 +67,19 @@ public class PropertyCatalogue {
         private final String code;
         private final String shortdesc;
         private final String description;
+        private final String versionOid;
+        private final String versionDescription;
 
         public Entry(String code, String shortdesc, String description) {
+            this(code, shortdesc, description, null, null);
+        }
+
+        public Entry(String code, String shortdesc, String description, String versionOid, String versionDescription) {
             this.code = code;
             this.shortdesc = shortdesc;
             this.description = description;
+            this.versionOid = versionOid;
+            this.versionDescription = versionDescription;
         }
 
         public String getCode() {
@@ -77,6 +93,14 @@ public class PropertyCatalogue {
         public String getShortdesc() {
             return shortdesc;
         }
+
+        public String getVersionOid() {
+            return versionOid;
+        }
+
+        public String getVersionDescription() {
+            return versionDescription;
+        }
     }
 
 }

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

@@ -1,8 +1,16 @@
 package dev.pcvolkmer.onco.datamapper.mapper;
 
-import dev.pcvolkmer.mv64e.mtb.Coding;
+import dev.pcvolkmer.mv64e.mtb.*;
-import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis;
+import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
 
 /**
  * Mapper class to load and map diagnosis data from database table 'dk_dnpm_kpa'
@@ -13,9 +21,20 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
 
     private final KpaCatalogue kpaCatalogue;
+    private final TumorausbreitungCatalogue tumorausbreitungCatalogue;
+    private final TumorgradingCatalogue tumorgradingCatalogue;
+    private final PropertyCatalogue propertyCatalogue;
 
-    public KpaDiagnosisDataMapper(final KpaCatalogue kpaCatalogue) {
+    public KpaDiagnosisDataMapper(
+            final KpaCatalogue kpaCatalogue,
+            final TumorausbreitungCatalogue tumorausbreitungCatalogue,
+            final TumorgradingCatalogue tumorgradingCatalogue,
+            final PropertyCatalogue propertyCatalogue
+    ) {
         this.kpaCatalogue = kpaCatalogue;
+        this.tumorausbreitungCatalogue = tumorausbreitungCatalogue;
+        this.tumorgradingCatalogue = tumorgradingCatalogue;
+        this.propertyCatalogue = propertyCatalogue;
     }
 
     /**
@@ -31,12 +50,102 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
         var builder = MtbDiagnosis.builder();
         builder
                 .id(data.getString("id"))
+                .patient(Reference.builder().id(data.getString("patient_id")).build())
                 .code(
                         Coding.builder()
                                 .code(data.getString("icd10"))
+                                .system("http://fhir.de/CodeSystem/bfarm/icd-10-gm")
+                                .display(propertyCatalogue.getByCodeAndVersion(data.getString("icd10"), data.getInteger("icd10_propcat_version")).getShortdesc())
+                                .version(propertyCatalogue.getByCodeAndVersion(data.getString("icd10"), data.getInteger("icd10_propcat_version")).getVersionDescription())
                                 .build()
-                );
+                )
+                .topography(Coding.builder().code(data.getString("icdo3localisation")).build())
+                // Nicht in Onkostar erfasst
+                //.germlineCodes()
+                .guidelineTreatmentStatus(
+                        getMtbDiagnosisGuidelineTreatmentStatusCoding(data.getString("leitlinienstatus"), data.getInteger("leitlinienstatus_propcat_version"))
+                )
+                .grading(getGrading(id))
+                .staging(getStaging(id))
+        ;
         return builder.build();
     }
 
+    private MtbDiagnosisGuidelineTreatmentStatusCoding getMtbDiagnosisGuidelineTreatmentStatusCoding(final String code, final int version) {
+        if (code == null || !Arrays.stream(MtbDiagnosisGuidelineTreatmentStatusCodingCode.values()).map(MtbDiagnosisGuidelineTreatmentStatusCodingCode::toValue).collect(Collectors.toSet()).contains(code)) {
+            return null;
+        }
+
+        var resultBuilder = MtbDiagnosisGuidelineTreatmentStatusCoding.builder()
+                .display(propertyCatalogue.getByCodeAndVersion(code, version).getShortdesc())
+                .system("dnpm-dip/mtb/diagnosis/guideline-treatment-status");
+        try {
+            resultBuilder.code(MtbDiagnosisGuidelineTreatmentStatusCodingCode.forValue(code));
+        } catch (IOException e) {
+            throw new IllegalStateException("No valid code found");
+        }
+
+        return resultBuilder.build();
+    }
+
+    private Grading getGrading(final int id) {
+        var all = tumorgradingCatalogue.getAllByParentId(id).stream()
+                .map(resultSet -> {
+                            var builder = TumorGrading.builder()
+                                    .date(resultSet.getDate("zeitpunkt"));
+
+                            if (null != resultSet.getString("tumorgrading") && !resultSet.getString("tumorgrading").isBlank()) {
+                                var propertyEntry = propertyCatalogue
+                                        .getByCodeAndVersion(resultSet.getString("tumorgrading"), resultSet.getInteger("tumorgrading_propcat_version"));
+                                builder.codes(
+                                        List.of(
+                                                Coding.builder()
+                                                        .code(resultSet.getString("tumorgrading"))
+                                                        .system("https://www.basisdatensatz.de/feld/161/grading")
+                                                        // TODO Annahme: "v1" ist Version 2025
+                                                        .version(propertyEntry.getVersionDescription().equals("v1") ? "2025" : null)
+                                                        .display(propertyEntry.getShortdesc())
+                                                        .build()
+                                        )
+                                );
+                                return builder.build();
+                            } else if (null != resultSet.getString("whograd") && !resultSet.getString("whograd").isBlank()) {
+                                var propertyEntry = propertyCatalogue
+                                        .getByCodeAndVersion(resultSet.getString("whograd"), resultSet.getInteger("whograd_propcat_version"));
+                                builder.codes(
+                                        List.of(
+                                                Coding.builder()
+                                                        .code(resultSet.getString("whograd"))
+                                                        .system("dnpm-dip/mtb/who-grading-cns-tumors")
+                                                        .version(propertyEntry.getVersionDescription())
+                                                        .display(propertyEntry.getShortdesc())
+                                                        .build()
+                                        )
+                                );
+                                return builder.build();
+                            }
+
+                            return null;
+                        }
+                ).filter(Objects::nonNull).collect(Collectors.toList());
+
+        if (all.isEmpty()) {
+            return null;
+        }
+
+        return Grading.builder().history(all).build();
+    }
+
+    private Staging getStaging(final int id) {
+        var subMapper = new KpaTumorausbreitungDataMapper(tumorausbreitungCatalogue);
+
+        var all = tumorausbreitungCatalogue.getAllByParentId(id).stream()
+                .map(it -> subMapper.getById(it.getInteger("id")))
+                .collect(Collectors.toList());
+        if (all.isEmpty()) {
+            return null;
+        }
+
+        return Staging.builder().history(all).build();
+    }
 }

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

@@ -39,7 +39,14 @@ public class KpaTumorausbreitungDataMapper extends AbstractSubformDataMapper<Tum
         builder
                 .date(resultSet.getDate("zeitpunkt"))
                 .method(getTumorStagingMethodCoding(resultSet.getString("typ")))
-                .otherClassifications(List.of(Coding.builder().code(resultSet.getString("wert")).build()))
+                .otherClassifications(
+                        List.of(
+                                Coding.builder()
+                                        .code(resultSet.getString("wert"))
+                                        .system("dnpm-dip/mtb/diagnosis/kds-tumor-spread")
+                                        .build()
+                        )
+                )
                 .tnmClassification(getTnmClassification(resultSet))
         ;
 
@@ -51,7 +58,8 @@ public class KpaTumorausbreitungDataMapper extends AbstractSubformDataMapper<Tum
             return null;
         }
 
-        var resultBuilder = TumorStagingMethodCoding.builder();
+        var resultBuilder = TumorStagingMethodCoding.builder()
+                .system("dnpm-dip/mtb/tumor-staging/method");
         try {
             resultBuilder.code(TumorStagingMethodCodingCode.forValue(value));
         } catch (IOException e) {
@@ -69,7 +77,11 @@ public class KpaTumorausbreitungDataMapper extends AbstractSubformDataMapper<Tum
         var tnmt = resultSet.getString("tnmt");
         if (tnmt != null && !tnmt.isBlank()) {
             tnpmClassificationBuilder.tumor(
-                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmtprefix"), tnmt)).build()
+                    Coding.builder()
+                            // TODO With or withour prefix?
+                            .code(String.format("%s%s", resultSet.getString("tnmtprefix"), tnmt))
+                            .system("UICC")
+                            .build()
             );
             hasContent = true;
         }
@@ -77,7 +89,11 @@ public class KpaTumorausbreitungDataMapper extends AbstractSubformDataMapper<Tum
         var tnmn = resultSet.getString("tnmn");
         if (tnmn != null && !tnmn.isBlank()) {
             tnpmClassificationBuilder.nodes(
-                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmnprefix"), tnmn)).build()
+                    Coding.builder()
+                            // TODO With or withour prefix?
+                            .code(String.format("%s%s", resultSet.getString("tnmnprefix"), tnmn))
+                            .system("UICC")
+                            .build()
             );
             hasContent = true;
         }
@@ -85,7 +101,11 @@ public class KpaTumorausbreitungDataMapper extends AbstractSubformDataMapper<Tum
         var tnmm = resultSet.getString("tnmm");
         if (tnmm != null && !tnmm.isBlank()) {
             tnpmClassificationBuilder.metastasis(
-                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmmprefix"), tnmm)).build()
+                    Coding.builder()
+                            // TODO With or withour prefix?
+                            .code(String.format("%s%s", resultSet.getString("tnmmprefix"), tnmm))
+                            .system("UICC")
+                            .build()
             );
             hasContent = true;
         }

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

@@ -63,7 +63,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
         var diagnosisDataMapper = new KpaDiagnosisDataMapper(
                 kpaCatalogue,
                 catalogueFactory.catalogue(TumorausbreitungCatalogue.class),
-                catalogueFactory.catalogue(TumorgradingCatalogue.class)
+                catalogueFactory.catalogue(TumorgradingCatalogue.class),
+                propertyCatalogue
         );
         var prozedurMapper = new KpaProzedurDataMapper(catalogueFactory.catalogue(ProzedurCatalogue.class));
 

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

@@ -1,8 +1,11 @@
 package dev.pcvolkmer.onco.datamapper.mapper;
 
 import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis;
+import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -21,13 +24,24 @@ import static org.mockito.Mockito.doAnswer;
 class KpaDiagnosisDataMapperTest {
 
     KpaCatalogue kpaCatalogue;
+    TumorausbreitungCatalogue tumorausbreitungCatalogue;
+    TumorgradingCatalogue tumorgradingCatalogue;
+    PropertyCatalogue propertyCatalogue;
 
     KpaDiagnosisDataMapper dataMapper;
 
     @BeforeEach
-    void setUp(@Mock KpaCatalogue kpaCatalogue) {
+    void setUp(
+            @Mock KpaCatalogue kpaCatalogue,
+            @Mock TumorausbreitungCatalogue tumorausbreitungCatalogue,
+            @Mock TumorgradingCatalogue tumorgradingCatalogue,
+            @Mock PropertyCatalogue propertyCatalogue
+    ) {
         this.kpaCatalogue = kpaCatalogue;
-        this.dataMapper = new KpaDiagnosisDataMapper(kpaCatalogue);
+        this.tumorausbreitungCatalogue = tumorausbreitungCatalogue;
+        this.tumorgradingCatalogue = tumorgradingCatalogue;
+        this.propertyCatalogue = propertyCatalogue;
+        this.dataMapper = new KpaDiagnosisDataMapper(kpaCatalogue, tumorausbreitungCatalogue, tumorgradingCatalogue, propertyCatalogue);
     }
 
     @Test
@@ -46,6 +60,10 @@ class KpaDiagnosisDataMapperTest {
                 .when(kpaCatalogue)
                 .getById(anyInt());
 
+        doAnswer(invocationOnMock ->
+                new PropertyCatalogue.Entry("C00.0", "Bösartige Neubildung: Äußere Oberlippe", "Bösartige Neubildung: Äußere Oberlippe")
+        ).when(propertyCatalogue).getByCodeAndVersion(anyString(), anyInt());
+
         var actual = this.dataMapper.getById(1);
         assertThat(actual).isInstanceOf(MtbDiagnosis.class);
         assertThat(actual.getId()).isEqualTo("1");

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

@@ -69,7 +69,12 @@ class KpaTumorausbreitungDataMapperTest {
         var actual = actualList.get(0);
         assertThat(actual).isInstanceOf(TumorStaging.class);
         assertThat(actual.getDate()).isEqualTo(new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()));
-        assertThat(actual.getMethod()).isEqualTo(TumorStagingMethodCoding.builder().code(TumorStagingMethodCodingCode.PATHOLOGIC).build());
+        assertThat(actual.getMethod()).isEqualTo(
+                TumorStagingMethodCoding.builder()
+                        .code(TumorStagingMethodCodingCode.PATHOLOGIC)
+                        .system("dnpm-dip/mtb/tumor-staging/method")
+                        .build()
+        );
         assertThat(actual.getOtherClassifications()).hasSize(1);
         assertThat(actual.getOtherClassifications().get(0).getCode()).isEqualTo("tumor-free");
         assertThat(actual.getTnmClassification().getTumor().getCode()).isEqualTo("p0");