feat: add tumor staging mapping

2025-07-04 19:32:55 +00:00 · 2025-06-21 15:08:15 +02:00
parent 6b95539982
commit 4450c01a17
2 changed files with 205 additions and 0 deletions
--- a/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTumorausbreitungDataMapper.java
+++ b/src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTumorausbreitungDataMapper.java
@ -0,0 +1,118 @@
+package dev.pcvolkmer.onco.datamapper.mapper;
+
+import dev.pcvolkmer.mv64e.mtb.*;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_tumorausbreitung'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KpaTumorausbreitungDataMapper implements SubformDataMapper<TumorStaging> {
+
+    private final TumorausbreitungCatalogue catalogue;
+
+    public KpaTumorausbreitungDataMapper(final TumorausbreitungCatalogue catalogue) {
+        this.catalogue = catalogue;
+    }
+
+    /**
+     * 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 TumorStaging getById(final int id) {
+        var data = catalogue.getById(id);
+        return this.map(data);
+    }
+
+    @Override
+    public List<TumorStaging> getByParentId(final int parentId) {
+        return catalogue.getAllByParentId(parentId)
+                .stream()
+                .map(this::map)
+                .sorted(Comparator.comparing(TumorStaging::getDate))
+                .collect(Collectors.toList());
+    }
+
+    private TumorStaging map(final ResultSet resultSet) {
+        var diseases = catalogue.getDiseases(resultSet.getProcedureId());
+
+        if (diseases.size() != 1) {
+            throw new IllegalStateException(String.format("No unique disease for procedure %s", resultSet.getProcedureId()));
+        }
+
+        var builder = TumorStaging.builder();
+        builder
+                .date(resultSet.getDate("zeitpunkt"))
+                .method(getTumorStagingMethodCoding(resultSet.getString("typ")))
+                .otherClassifications(List.of(Coding.builder().code(resultSet.getString("wert")).build()))
+                .tnmClassification(getTnmClassification(resultSet))
+        ;
+
+
+        return builder.build();
+    }
+
+    private TumorStagingMethodCoding getTumorStagingMethodCoding(final String value) {
+        if (value == null || !Arrays.stream(TumorStagingMethodCodingCode.values()).map(TumorStagingMethodCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
+            return null;
+        }
+
+        var resultBuilder = TumorStagingMethodCoding.builder();
+        try {
+            resultBuilder.code(TumorStagingMethodCodingCode.forValue(value));
+        } catch (IOException e) {
+            throw new IllegalStateException("No valid code found");
+        }
+
+        return resultBuilder.build();
+    }
+
+    private TnmClassification getTnmClassification(final ResultSet resultSet) {
+        var tnpmClassificationBuilder = TnmClassification.builder();
+
+        var hasContent = false;
+
+        var tnmt = resultSet.getString("tnmt");
+        if (tnmt != null && !tnmt.isBlank()) {
+            tnpmClassificationBuilder.tumor(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmtprefix"), tnmt)).build()
+            );
+            hasContent = true;
+        }
+
+        var tnmn = resultSet.getString("tnmn");
+        if (tnmn != null && !tnmn.isBlank()) {
+            tnpmClassificationBuilder.nodes(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmnprefix"), tnmn)).build()
+            );
+            hasContent = true;
+        }
+
+        var tnmm = resultSet.getString("tnmm");
+        if (tnmm != null && !tnmm.isBlank()) {
+            tnpmClassificationBuilder.metastasis(
+                    Coding.builder().code(String.format("%s%s", resultSet.getString("tnmmprefix"), tnmm)).build()
+            );
+            hasContent = true;
+        }
+
+        if (hasContent) {
+            return tnpmClassificationBuilder.build();
+        }
+
+        return null;
+    }
+
+}