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Code Issues Activity

Issue #28: Initiale Implementierung zur Ermittlung der NGS-Befund-Varianten

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Paul-Christian Volkmer
2023-05-08 16:23:52 +02:00
parent 06b5381e88
commit 3afe109494
5 changed files with 224 additions and 0 deletions
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67
src/main/java/DNPM/dto/Variant.java Normal file
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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();
}
}
}