refactor: change package name

1 files changed, 134 insertions, 0 deletions

diff --git a/src/main/java/dev/dnpm/oshelper/dto/Variant.java b/src/main/java/dev/dnpm/oshelper/dto/Variant.java
new file mode 100644
index 0000000..6edee9b
--- /dev/null
+++ b/src/main/java/dev/dnpm/oshelper/dto/Variant.java
@@ -0,0 +1,134 @@
+/*
+ * This file is part of onkostar-plugin-dnpm
+ *
+ * Copyright (c) 2025 the original author or authors.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package dev.dnpm.oshelper.dto;
+
+import de.itc.onkostar.api.Procedure;
+
+import java.util.Optional;
+
+/**
+ * Ein Auszug der Variante aus dem NGS-Bericht zur Übertragung an das Frontend zur Auswahl der stützenden molekularen Alteration
+ *
+ * @since 0.2.0
+ */
+public class Variant {
+    private final Integer id;
+
+    private final String ergebnis;
+
+    private final String gen;
+
+    private final String exon;
+
+    private final String pathogenitaetsklasse;
+
+    private Variant(
+            final int id,
+            final String ergebnis,
+            final String gen,
+            final String exon,
+            final String pathogenitaetsklasse
+    ) {
+        this.id = id;
+        this.ergebnis = ergebnis;
+        this.gen = gen;
+        this.exon = exon;
+        this.pathogenitaetsklasse = pathogenitaetsklasse;
+    }
+
+    public Integer getId() {
+        return id;
+    }
+
+    public String getErgebnis() {
+        return ergebnis;
+    }
+
+    public String getGen() {
+        return gen;
+    }
+
+    public String getExon() {
+        return exon;
+    }
+
+    public String getPathogenitaetsklasse() {
+        return pathogenitaetsklasse;
+    }
+
+    /**
+     * Erstellt ein Optional einer Variante aus einer Prozedur
+     * @param procedure Die zu verwendende Prozedur
+     * @return Das Optional, wenn die Prozedur verwendet werden kann, ansonsten ein leeres Optional
+     */
+    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(),
+                            "Einfache Variante (Mutation)",
+                            gene.getString().isBlank() ? "-" : gene.getString(),
+                            null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
+                            null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
+                    )
+            );
+        } else if (ergebnis.getString().equals("CNV")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            "Copy Number Variation (CNV)",
+                            gene.getString().isBlank() ? "-" : gene.getString(),
+                            null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
+                            null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
+                    )
+            );
+        } else if (ergebnis.getString().equals("F")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            "Fusion (Translokation Inversion Insertion)",
+                            gene.getString().isBlank() ? "-" : gene.getString(),
+                            null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
+                            null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
+                    )
+            );
+        } else {
+            return Optional.empty();
+        }
+    }
+}