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Code Issues Activity

Issue #28: Verwende erforderliche Informationen ohne Zusammenfassung

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This commit is contained in:
Paul-Christian Volkmer
2023-05-09 08:50:47 +02:00
parent 3afe109494
commit c45dc8f5df
2 changed files with 144 additions and 8 deletions
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49
src/main/java/DNPM/dto/Variant.java
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@ -7,22 +7,46 @@ import java.util.Optional;
public class Variant {
private final Integer id;
private final String shortDescription;
private final String ergebnis;
private final String gen;
private final String exon;
private final String pathogenitaetsklasse;
private Variant(
final int id,
final String shortDescription
final String ergebnis,
final String gen,
final String exon,
final String pathogenitaetsklasse
) {
this.id = id;
this.shortDescription = shortDescription.trim();
this.ergebnis = ergebnis;
this.gen = gen;
this.exon = exon;
this.pathogenitaetsklasse = pathogenitaetsklasse;
}
public Integer getId() {
return id;
}
public String getShortDescription() {
return shortDescription;
public String getErgebnis() {
return ergebnis;
}
public String getGen() {
return gen;
}
public String getExon() {
return exon;
}
public String getPathogenitaetsklasse() {
return pathogenitaetsklasse;
}
public static Optional<Variant> fromProcedure(Procedure procedure) {
@ -43,21 +67,30 @@ public class Variant {
return Optional.of(
new Variant(
procedure.getId(),
String.format("Einfache Variante: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
"Einfache Variante",
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())
"Copy Number Variation",
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())
"Fusion",
gene.getString(),
exon.getString(),
pathogenitaetsklasse.getString()
)
);
} else {

103
src/test/java/DNPM/dto/VariantTest.java Normal file
View File

@ -0,0 +1,103 @@
package DNPM.dto;
import de.itc.onkostar.api.Item;
import de.itc.onkostar.api.Procedure;
import org.junit.jupiter.api.Test;
import static org.assertj.core.api.Assertions.assertThat;
public class VariantTest {
@Test
void testShouldMapVariantFromProcedureForSimpleVariant() {
var procedure = new Procedure(null);
procedure.setId(12345);
procedure.setFormName("OS.Molekulargenetische Untersuchung");
procedure.setValue("Ergebnis", new Item("Ergebnis", "P"));
procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
procedure.setValue("ExonInt", new Item("ExonInt", 123));
procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
var actual = Variant.fromProcedure(procedure);
assertThat(actual).isPresent();
assertThat(actual.get().getId()).isEqualTo(12345);
assertThat(actual.get().getErgebnis()).isEqualTo("Einfache Variante");
assertThat(actual.get().getGen()).isEqualTo("BRAF");
assertThat(actual.get().getExon()).isEqualTo("123");
assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
}
@Test
void testShouldMapVariantFromProcedureForCopyNumberVariation() {
var procedure = new Procedure(null);
procedure.setId(12345);
procedure.setFormName("OS.Molekulargenetische Untersuchung");
procedure.setValue("Ergebnis", new Item("Ergebnis", "CNV"));
procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
procedure.setValue("ExonInt", new Item("ExonInt", 123));
procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
var actual = Variant.fromProcedure(procedure);
assertThat(actual).isPresent();
assertThat(actual.get().getId()).isEqualTo(12345);
assertThat(actual.get().getErgebnis()).isEqualTo("Copy Number Variation");
assertThat(actual.get().getGen()).isEqualTo("BRAF");
assertThat(actual.get().getExon()).isEqualTo("123");
assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
}
@Test
void testShouldMapVariantFromProcedureForFusion() {
var procedure = new Procedure(null);
procedure.setId(12345);
procedure.setFormName("OS.Molekulargenetische Untersuchung");
procedure.setValue("Ergebnis", new Item("Ergebnis", "F"));
procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
procedure.setValue("ExonInt", new Item("ExonInt", 123));
procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
var actual = Variant.fromProcedure(procedure);
assertThat(actual).isPresent();
assertThat(actual.get().getId()).isEqualTo(12345);
assertThat(actual.get().getErgebnis()).isEqualTo("Fusion");
assertThat(actual.get().getGen()).isEqualTo("BRAF");
assertThat(actual.get().getExon()).isEqualTo("123");
assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
}
@Test
void testShouldNotMapVariantFromProcedureForUnknownVariant() {
var procedure = new Procedure(null);
procedure.setId(12345);
procedure.setFormName("OS.Molekulargenetische Untersuchung");
procedure.setValue("Ergebnis", new Item("Ergebnis", "X"));
procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
procedure.setValue("ExonInt", new Item("ExonInt", 123));
procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
var actual = Variant.fromProcedure(procedure);
assertThat(actual).isEmpty();
}
@Test
void testShouldNotMapVariantFromUnknownProcedureForm() {
var procedure = new Procedure(null);
procedure.setId(12345);
procedure.setFormName("ABC.Irgendwas");
procedure.setValue("Testfeld", new Item("Testfeld", "T"));
var actual = Variant.fromProcedure(procedure);
assertThat(actual).isEmpty();
}
}