feat: add Histologie and related specimens

README.md

@@ -47,11 +47,11 @@ var jsonResult = Converter.toJsonString(
 | ECOG-Verlauf                     | ✅      |                                                                                |
 | Tumor-Proben                     | ⛅      | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (1) |
 | vorherige Molekular-Diagnostik   | ✅      |                                                                                |
-| Histologie-Berichte              | ⌛      | Aktuell in Arbeit                                                              |
+| Histologie-Berichte              | ✅      | Hinweis (2)                                                                    |
 | IHC-Berichte                     | ⌛      | Aktuell in Arbeit                                                              |
 | MSI-Befunde                      | ⌛      | Aktuell in Arbeit                                                              |
-| NGS-Berichte                     | ⛅      | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (2) |
+| NGS-Berichte                     | ⛅      | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (3) |
-| MTB-Beschlüsse                   | ✅      | Stützende molekulare Alteration(en) für einfache Variante und CNV (3)          |
+| MTB-Beschlüsse                   | ✅      | Stützende molekulare Alteration(en) für einfache Variante und CNV (4)          |
 | Follow-Up Verlauf                |        |                                                                                |
 | Antrag Kostenübernahme           |        |                                                                                |
 | Antwort Kostenübernahme          |        |                                                                                |
@@ -61,9 +61,10 @@ var jsonResult = Converter.toJsonString(
 ### Hinweise
 
 1. Nicht alle möglichen Ausprägungen in `OS.Molekulargenetik` vorhanden.
-2. Aktuell nicht alle Angaben effektiv im Formular `OS.Molekulargenetik` wie gefordert angebbar.
+2. Aktuell wird die Version der Morphologie nicht mit exportiert, nur der Wert.
+3. Aktuell nicht alle Angaben effektiv im Formular `OS.Molekulargenetik` wie gefordert angebbar.
    Hinweis: Tumorzellgehalt-Methode problematisch, wenn auch im NGS-Bericht histologisch festgestellt.
-3. Implementierung des Mappings von HGNC-Symbol (Gen-Name) zu HGNC-ID über enthaltene Gen-Liste.
+4. 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/mapper/KpaHistologieDataMapper.java

@@ -0,0 +1,118 @@
+/*
+ * 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.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.HistologieCatalogue;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.MolekulargenetikCatalogue;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_dnpm_vorbefunde'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaHistologieDataMapper extends AbstractSubformDataMapper<HistologyReport> {
+
+    private final MolekulargenetikCatalogue molekulargenetikCatalogue;
+    private final PropertyCatalogue propertyCatalogue;
+
+    public KpaHistologieDataMapper(
+            final HistologieCatalogue catalogue,
+            final MolekulargenetikCatalogue molekulargenetikCatalogue,
+            final PropertyCatalogue propertyCatalogue
+    ) {
+        super(catalogue);
+        this.molekulargenetikCatalogue = molekulargenetikCatalogue;
+        this.propertyCatalogue = propertyCatalogue;
+    }
+
+    /**
+     * Loads and maps Prozedur related by database id
+     *
+     * @param id The database id of the procedure data set
+     * @return The loaded data set
+     */
+    @Override
+    public HistologyReport getById(final int id) {
+        var data = catalogue.getById(id);
+        return this.map(data);
+    }
+
+    @Override
+    public List<HistologyReport> getByParentId(final int parentId) {
+        return catalogue.getAllByParentId(parentId)
+                .stream()
+                .map(this::map)
+                .filter(Objects::nonNull)
+                .distinct()
+                .collect(Collectors.toList());
+    }
+
+    @Override
+    protected HistologyReport map(final ResultSet resultSet) {
+        var builder = HistologyReport.builder();
+
+        var osMolGen = molekulargenetikCatalogue.getById(resultSet.getInteger("histologie"));
+
+        if (null != osMolGen) {
+            builder
+                    .id(resultSet.getId().toString())
+                    .patient(resultSet.getPatientReference())
+                    .issuedOn(resultSet.getDate("erstellungsdatum"))
+                    .specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
+                    .results(
+                            HistologyReportResults.builder()
+                                    .tumorCellContent(
+                                            TumorCellContent.builder()
+                                                    .id(resultSet.getId().toString())
+                                                    .patient(resultSet.getPatientReference())
+                                                    .specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
+                                                    .value(resultSet.getLong("tumorzellgehalt"))
+                                                    // Nicht in OS.Molekulargenetik
+                                                    //.method()
+                                                    .build()
+                                    )
+                                    .tumorMorphology(
+                                            TumorMorphology.builder()
+                                                    .id(resultSet.getId().toString())
+                                                    .patient(resultSet.getPatientReference())
+                                                    .specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
+                                                    .value(Coding.builder().code(resultSet.getString("morphologie")).build())
+                                                    .build()
+                                    )
+                                    .build()
+                    )
+            ;
+
+            return builder.build();
+        }
+
+        return null;
+    }
+
+}

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

@@ -21,7 +21,6 @@
 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.*;
 
@@ -43,6 +42,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
     private final ReevaluationCatalogue reevaluationCatalogue;
     private final EinzelempfehlungCatalogue einzelempfehlungCatalogue;
     private final VorbefundeCatalogue vorbefundeCatalogue;
+    private final HistologieCatalogue histologieCatalogue;
 
     public MolekulargenetikToSpecimenDataMapper(
             final MolekulargenetikCatalogue molekulargenetikCatalogue,
@@ -50,7 +50,8 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
             final RebiopsieCatalogue rebiopsieCatalogue,
             final ReevaluationCatalogue reevaluationCatalogue,
             final EinzelempfehlungCatalogue einzelempfehlungCatalogue,
-            final VorbefundeCatalogue vorbefundeCatalogue
+            final VorbefundeCatalogue vorbefundeCatalogue,
+            final HistologieCatalogue histologieCatalogue
     ) {
         this.molekulargenetikCatalogue = molekulargenetikCatalogue;
         this.therapieplanCatalogue = therapieplanCatalogue;
@@ -58,6 +59,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
         this.reevaluationCatalogue = reevaluationCatalogue;
         this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
         this.vorbefundeCatalogue = vorbefundeCatalogue;
+        this.histologieCatalogue = histologieCatalogue;
     }
 
     /**
@@ -136,6 +138,15 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
                         .collect(Collectors.toList())
         );
 
+        // Histologie
+        osMolGen.addAll(
+                histologieCatalogue.getAllByParentId(kpaId).stream()
+                        .map(rs -> rs.getInteger("histologie"))
+                        .map(molekulargenetikCatalogue::getById)
+                        .map(ResultSet::getId)
+                        .collect(Collectors.toList())
+        );
+
         return osMolGen.stream()
                 .filter(Objects::nonNull)
                 .distinct()

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

@@ -21,7 +21,6 @@
 package dev.pcvolkmer.onco.datamapper.mapper;
 
 import dev.pcvolkmer.mv64e.mtb.Mtb;
-import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
 import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
@@ -121,7 +120,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 catalogueFactory.catalogue(RebiopsieCatalogue.class),
                 catalogueFactory.catalogue(ReevaluationCatalogue.class),
                 einzelempfehlungCatalogue,
-                catalogueFactory.catalogue(VorbefundeCatalogue.class)
+                catalogueFactory.catalogue(VorbefundeCatalogue.class),
+                catalogueFactory.catalogue(HistologieCatalogue.class)
         );
 
         var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
@@ -132,6 +132,12 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 propertyCatalogue
         );
 
+        var kpaHistologieDataMapper = new KpaHistologieDataMapper(
+                catalogueFactory.catalogue(HistologieCatalogue.class),
+                molekulargenetikCatalogue,
+                propertyCatalogue
+        );
+
         var resultBuilder = Mtb.builder();
 
         try {
@@ -152,6 +158,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                     .familyMemberHistories(verwandteDataMapper.getByParentId(kpaId))
                     // Vorbefunde
                     .priorDiagnosticReports(kpaVorbefundeDataMapper.getByParentId(kpaId))
+                    // Histologie-Berichte
+                    .histologyReports(kpaHistologieDataMapper.getByParentId(kpaId))
                     // DNPM Therapieplan
                     .carePlans(
                             therapieplanCatalogue
@@ -161,14 +169,14 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                     )
                     // Tumorproben
                     .specimens(
-                        molekulargenetikToSpecimenDataMapper.getAllByKpaId(
+                            molekulargenetikToSpecimenDataMapper.getAllByKpaId(
-                                kpaId,
+                                    kpaId,
-                                Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
+                                    Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
-                        )
+                            )
                     )
                     // NGS Berichte
                     .ngsReports(
-                        kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
+                            kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
                     )
 
             ;
@@ -195,7 +203,7 @@ public class MtbDataMapper implements DataMapper<Mtb> {
      * Loads and maps a Mtb file using the patient id and tumor id
      *
      * @param patientId The patients id (not database id)
-     * @param tumorId The tumor identification
+     * @param tumorId   The tumor identification
      * @return The loaded Mtb file
      */
     public Mtb getLatestByPatientIdAndTumorId(String patientId, int tumorId) {