Merge pull request #15 from pcvolkmer/update_datamodel

chore: update data model

src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReportResults.java

@@ -12,7 +12,7 @@ import java.util.List;
 public class IhcReportResults {
     @Getter(onMethod_ = {@JsonProperty("msiMmr")})
     @Setter(onMethod_ = {@JsonProperty("msiMmr")})
-    private List<MSIMmr> msiMmr;
+    private List<MsiMmr> msiMmr;
     @Getter(onMethod_ = {@JsonProperty("proteinExpression")})
     @Setter(onMethod_ = {@JsonProperty("proteinExpression")})
     private List<ProteinExpression> proteinExpression;

src/main/java/dev/pcvolkmer/mv64e/mtb/Msi.java

@@ -0,0 +1,29 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import lombok.*;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+@Builder
+public class Msi {
+    @Getter(onMethod_ = {@JsonProperty("id")})
+    @Setter(onMethod_ = {@JsonProperty("id")})
+    private String id;
+    @Getter(onMethod_ = {@JsonProperty("interpretation")})
+    @Setter(onMethod_ = {@JsonProperty("interpretation")})
+    private MsiInterpretationCoding interpretation;
+    @Getter(onMethod_ = {@JsonProperty("method")})
+    @Setter(onMethod_ = {@JsonProperty("method")})
+    private MsiMethodCoding method;
+    @Getter(onMethod_ = {@JsonProperty("patient")})
+    @Setter(onMethod_ = {@JsonProperty("patient")})
+    private Reference patient;
+    @Getter(onMethod_ = {@JsonProperty("specimen")})
+    @Setter(onMethod_ = {@JsonProperty("specimen")})
+    private Reference specimen;
+    @Getter(onMethod_ = {@JsonProperty("value")})
+    @Setter(onMethod_ = {@JsonProperty("value")})
+    private double value;
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MsiInterpretationCoding.java

@@ -0,0 +1,23 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import lombok.*;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+@Builder
+public class MsiInterpretationCoding {
+    @Getter(onMethod_ = {@JsonProperty("code")})
+    @Setter(onMethod_ = {@JsonProperty("code")})
+    private MsiInterpretationCodingCode code;
+    @Getter(onMethod_ = {@JsonProperty("display")})
+    @Setter(onMethod_ = {@JsonProperty("display")})
+    private String display;
+    @Getter(onMethod_ = {@JsonProperty("system")})
+    @Setter(onMethod_ = {@JsonProperty("system")})
+    private String system;
+    @Getter(onMethod_ = {@JsonProperty("version")})
+    @Setter(onMethod_ = {@JsonProperty("version")})
+    private String version;
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MsiInterpretationCodingCode.java

@@ -0,0 +1,32 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum MsiInterpretationCodingCode {
+    MMR_DEFICIENT, MMR_PROFICIENT, MSI_HIGH, MSI_LOW, STABLE, UNKNOWN;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case MMR_DEFICIENT: return "mmr-deficient";
+            case MMR_PROFICIENT: return "mmr-proficient";
+            case MSI_HIGH: return "msi-high";
+            case MSI_LOW: return "msi-low";
+            case STABLE: return "stable";
+            case UNKNOWN: return "unknown";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static MsiInterpretationCodingCode forValue(String value) throws IOException {
+        if (value.equals("mmr-deficient")) return MMR_DEFICIENT;
+        if (value.equals("mmr-proficient")) return MMR_PROFICIENT;
+        if (value.equals("msi-high")) return MSI_HIGH;
+        if (value.equals("msi-low")) return MSI_LOW;
+        if (value.equals("stable")) return STABLE;
+        if (value.equals("unknown")) return UNKNOWN;
+        throw new IOException("Cannot deserialize MSIInterpretationCodingCode");
+    }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MsiMethodCoding.java

@@ -0,0 +1,23 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import lombok.*;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+@Builder
+public class MsiMethodCoding {
+    @Getter(onMethod_ = {@JsonProperty("code")})
+    @Setter(onMethod_ = {@JsonProperty("code")})
+    private MsiMethodCodingCode code;
+    @Getter(onMethod_ = {@JsonProperty("display")})
+    @Setter(onMethod_ = {@JsonProperty("display")})
+    private String display;
+    @Getter(onMethod_ = {@JsonProperty("system")})
+    @Setter(onMethod_ = {@JsonProperty("system")})
+    private String system;
+    @Getter(onMethod_ = {@JsonProperty("version")})
+    @Setter(onMethod_ = {@JsonProperty("version")})
+    private String version;
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MsiMethodCodingCode.java

@@ -0,0 +1,26 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum MsiMethodCodingCode {
+    BIOINFORMATIC, IHC, PCR;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case BIOINFORMATIC: return "bioinformatic";
+            case IHC: return "IHC";
+            case PCR: return "PCR";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static MsiMethodCodingCode forValue(String value) throws IOException {
+        if (value.equals("bioinformatic")) return BIOINFORMATIC;
+        if (value.equals("IHC")) return IHC;
+        if (value.equals("PCR")) return PCR;
+        throw new IOException("Cannot deserialize MSIMethodCodingCode");
+    }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MsiMmr.java

@@ -7,7 +7,7 @@ import lombok.*;
 @AllArgsConstructor
 @NoArgsConstructor
 @Builder
-public class MSIMmr {
+public class MsiMmr {
     @Getter(onMethod_ = {@JsonProperty("icScore")})
     @Setter(onMethod_ = {@JsonProperty("icScore")})
     private ProteinExpressionIcScoreCoding icScore;

src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java

@@ -49,6 +49,9 @@ public class Mtb {
     @Getter(onMethod_ = {@JsonProperty("ngsReports")})
     @Setter(onMethod_ = {@JsonProperty("ngsReports")})
     private List<SomaticNgsReport> ngsReports;
+    @Getter(onMethod_ = {@JsonProperty("msiFindings")})
+    @Setter(onMethod_ = {@JsonProperty("msiFindings")})
+    private List<Msi> msiFindings;
     @Getter(onMethod_ = {@JsonProperty("patient")})
     @Setter(onMethod_ = {@JsonProperty("patient")})
     private Patient patient;