From 84fb0d829832bf1628112376bba729422b169402 Mon Sep 17 00:00:00 2001
From: Paul-Christian Volkmer
Date: Thu, 23 Oct 2025 11:08:10 +0200
Subject: refactor: change package name

---
 src/main/java/dev/dnpm/dto/Variant.java | 134 --------------------------------
 1 file changed, 134 deletions(-)
 delete mode 100644 src/main/java/dev/dnpm/dto/Variant.java

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

diff --git a/src/main/java/dev/dnpm/dto/Variant.java b/src/main/java/dev/dnpm/dto/Variant.java
deleted file mode 100644
index 6fd646b..0000000
--- a/src/main/java/dev/dnpm/dto/Variant.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * 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.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();
-        }
-    }
-}
-- 
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