refactor: use package name following Java guidelines

3 files changed, 228 insertions, 0 deletions

diff --git a/src/main/java/dev/dnpm/dto/EcogStatusWithDate.java b/src/main/java/dev/dnpm/dto/EcogStatusWithDate.java
new file mode 100644
index 0000000..8b3140d
--- /dev/null
+++ b/src/main/java/dev/dnpm/dto/EcogStatusWithDate.java
@@ -0,0 +1,44 @@
+package dev.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/dev/dnpm/dto/Studie.java b/src/main/java/dev/dnpm/dto/Studie.java
new file mode 100644
index 0000000..2461788
--- /dev/null
+++ b/src/main/java/dev/dnpm/dto/Studie.java
@@ -0,0 +1,74 @@
+package dev.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/dev/dnpm/dto/Variant.java b/src/main/java/dev/dnpm/dto/Variant.java
new file mode 100644
index 0000000..a7f75cd
--- /dev/null
+++ b/src/main/java/dev/dnpm/dto/Variant.java
@@ -0,0 +1,110 @@
+package dev.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();
+        }
+    }
+}