diff options
Diffstat (limited to 'src/main/java/DNPM/dto')
| -rw-r--r-- | src/main/java/DNPM/dto/EcogStatusWithDate.java | 44 | ||||
| -rw-r--r-- | src/main/java/DNPM/dto/Studie.java | 74 | ||||
| -rw-r--r-- | src/main/java/DNPM/dto/Variant.java | 110 |
3 files changed, 0 insertions, 228 deletions
diff --git a/src/main/java/DNPM/dto/EcogStatusWithDate.java b/src/main/java/DNPM/dto/EcogStatusWithDate.java deleted file mode 100644 index a1ec575..0000000 --- a/src/main/java/DNPM/dto/EcogStatusWithDate.java +++ /dev/null @@ -1,44 +0,0 @@ -package DNPM.dto; - -import org.springframework.util.Assert; - -import java.util.Date; - -/** - * Datenklasse zum Abbilden des ECOG-Status und Datum - */ -public class EcogStatusWithDate { - private final Date date; - private final String status; - - public EcogStatusWithDate(Date date, String status) { - Assert.notNull(date, "Date cannot be null"); - Assert.hasText(status, "Status cannot be empty String"); - Assert.isTrue(isValidEcogCode(status), "Not a valid ADT.LeistungszustandECOG code"); - this.date = date; - this.status = status; - } - - private boolean isValidEcogCode(String status) { - switch (status) { - case "0": - case "1": - case "2": - case "3": - case "4": - case "5": - case "U": - return true; - default: - return false; - } - } - - public Date getDate() { - return date; - } - - public String getStatus() { - return status; - } -} diff --git a/src/main/java/DNPM/dto/Studie.java b/src/main/java/DNPM/dto/Studie.java deleted file mode 100644 index 59d3cfe..0000000 --- a/src/main/java/DNPM/dto/Studie.java +++ /dev/null @@ -1,74 +0,0 @@ -package DNPM.dto; - -public class Studie { - private final String kategorieName; - private final String code; - private final String studiennummer; - private final String shortDesc; - private final String description; - private final int version; - - private final boolean active; - - public Studie(final String kategorieName, final int version, final String code, final String studiennummer, final String shortDesc, final String description, final boolean active) { - this.kategorieName = kategorieName; - this.version = version; - this.code = code; - this.studiennummer = studiennummer; - this.shortDesc = shortDesc; - this.description = description; - this.active = active; - } - - public String getKategorieName() { - return kategorieName; - } - - public int getVersion() { - return version; - } - - public String getCode() { - return code; - } - - public String getStudiennummer() { - return studiennummer; - } - - public String getShortDesc() { - return shortDesc; - } - - public String getDescription() { - return description; - } - - public boolean isActive() { - return active; - } - - public Type getType() { - if (this.hasNctNumber()) { - return Type.NCT; - } else if (this.hasEudraCtNumber()) { - return Type.EUDRA_CT; - } else { - return Type.UNKNOWN; - } - } - - private boolean hasNctNumber() { - return null != studiennummer && studiennummer.toLowerCase().startsWith("nct"); - } - - private boolean hasEudraCtNumber() { - return null != studiennummer && studiennummer.matches("\\d{4}-\\d{6}-\\d{2}"); - } - - public enum Type { - NCT, - EUDRA_CT, - UNKNOWN - } -} diff --git a/src/main/java/DNPM/dto/Variant.java b/src/main/java/DNPM/dto/Variant.java deleted file mode 100644 index d3fab9e..0000000 --- a/src/main/java/DNPM/dto/Variant.java +++ /dev/null @@ -1,110 +0,0 @@ -package 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(); - } - } -} |