From 3afe109494e2b4a751874a027694c17f6cabc4cd Mon Sep 17 00:00:00 2001
From: Paul-Christian Volkmer
Date: Mon, 8 May 2023 16:23:52 +0200
Subject: Issue #28: Initiale Implementierung zur Ermittlung der
 NGS-Befund-Varianten

---
 src/main/java/DNPM/dto/Variant.java | 67 +++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 src/main/java/DNPM/dto/Variant.java

(limited to 'src/main/java/DNPM/dto/Variant.java')

diff --git a/src/main/java/DNPM/dto/Variant.java b/src/main/java/DNPM/dto/Variant.java
new file mode 100644
index 0000000..36788f2
--- /dev/null
+++ b/src/main/java/DNPM/dto/Variant.java
@@ -0,0 +1,67 @@
+package DNPM.dto;
+
+import de.itc.onkostar.api.Procedure;
+
+import java.util.Optional;
+
+public class Variant {
+    private final Integer id;
+
+    private final String shortDescription;
+
+    private Variant(
+            final int id,
+            final String shortDescription
+    ) {
+        this.id = id;
+        this.shortDescription = shortDescription.trim();
+    }
+
+    public Integer getId() {
+        return id;
+    }
+
+    public String getShortDescription() {
+        return shortDescription;
+    }
+
+    public static Optional<Variant> fromProcedure(Procedure procedure) {
+        if (! "OS.Molekulargenetische Untersuchung".equals(procedure.getFormName())) {
+            return Optional.empty();
+        }
+
+        var ergebnis = procedure.getValue("Ergebnis");
+        var gene = procedure.getValue("Untersucht");
+        var exon = procedure.getValue("ExonInt");
+        var pathogenitaetsklasse = procedure.getValue("Pathogenitaetsklasse");
+
+        if (null == gene) {
+            return Optional.empty();
+        }
+
+        if (ergebnis.getString().equals("P")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Einfache Variante: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else if (ergebnis.getString().equals("CNV")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Copy Number Variation: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else if (ergebnis.getString().equals("F")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Fusion: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else {
+            return Optional.empty();
+        }
+    }
+}
-- 
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