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/*
* This file is part of onkostar-plugin-dnpm
*
* Copyright (C) 2023-2026 the original author or authors.
*
* 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.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();
}
}
}
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