diff options
Diffstat (limited to 'src/main/java/dev/dnpm/oshelper/dto')
| -rw-r--r-- | src/main/java/dev/dnpm/oshelper/dto/EcogStatusWithDate.java | 68 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/oshelper/dto/Studie.java | 98 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/oshelper/dto/Variant.java | 134 |
3 files changed, 300 insertions, 0 deletions
diff --git a/src/main/java/dev/dnpm/oshelper/dto/EcogStatusWithDate.java b/src/main/java/dev/dnpm/oshelper/dto/EcogStatusWithDate.java new file mode 100644 index 0000000..b09d9bf --- /dev/null +++ b/src/main/java/dev/dnpm/oshelper/dto/EcogStatusWithDate.java @@ -0,0 +1,68 @@ +/* + * 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 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/dev/dnpm/oshelper/dto/Studie.java b/src/main/java/dev/dnpm/oshelper/dto/Studie.java new file mode 100644 index 0000000..98b6fa5 --- /dev/null +++ b/src/main/java/dev/dnpm/oshelper/dto/Studie.java @@ -0,0 +1,98 @@ +/* + * 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; + +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/dev/dnpm/oshelper/dto/Variant.java b/src/main/java/dev/dnpm/oshelper/dto/Variant.java new file mode 100644 index 0000000..6edee9b --- /dev/null +++ b/src/main/java/dev/dnpm/oshelper/dto/Variant.java @@ -0,0 +1,134 @@ +/* + * 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(); + } + } +} |