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/*
* 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();
}
}
}
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