Merge pull request #3 from pcvolkmer/update_from_schema

Update model from schema and scala code

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

@@ -0,0 +1,36 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class BRCAness {
+    private ConfidenceRange confidenceRange;
+    private String id;
+    private Reference patient;
+    private Reference specimen;
+    private double value;
+
+    @JsonProperty("confidenceRange")
+    public ConfidenceRange getConfidenceRange() { return confidenceRange; }
+    @JsonProperty("confidenceRange")
+    public void setConfidenceRange(ConfidenceRange value) { this.confidenceRange = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("specimen")
+    public Reference getSpecimen() { return specimen; }
+    @JsonProperty("specimen")
+    public void setSpecimen(Reference value) { this.specimen = value; }
+
+    @JsonProperty("value")
+    public double getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(double value) { this.value = value; }
+}

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

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum CnvType {
+public enum CNVType {
     HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN;
 
     @JsonValue
@@ -17,7 +17,7 @@ public enum CnvType {
     }
 
     @JsonCreator
-    public static CnvType forValue(String value) throws IOException {
+    public static CNVType forValue(String value) throws IOException {
         switch (value) {
             case "high-level-gain":
                 return HIGH_LEVEL_GAIN;

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

@@ -1,94 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import java.io.IOException;
-import com.fasterxml.jackson.annotation.*;
-
-public enum Chromosome {
-    CHR1, CHR10, CHR11, CHR12, CHR13, CHR14, CHR15, CHR16, CHR17, CHR18, CHR19, CHR2, CHR20, CHR21, CHR22, CHR3, CHR4, CHR5, CHR6, CHR7, CHR8, CHR9, CHR_X, CHR_Y;
-
-    @JsonValue
-    public String toValue() {
-        switch (this) {
-            case CHR1: return "chr1";
-            case CHR10: return "chr10";
-            case CHR11: return "chr11";
-            case CHR12: return "chr12";
-            case CHR13: return "chr13";
-            case CHR14: return "chr14";
-            case CHR15: return "chr15";
-            case CHR16: return "chr16";
-            case CHR17: return "chr17";
-            case CHR18: return "chr18";
-            case CHR19: return "chr19";
-            case CHR2: return "chr2";
-            case CHR20: return "chr20";
-            case CHR21: return "chr21";
-            case CHR22: return "chr22";
-            case CHR3: return "chr3";
-            case CHR4: return "chr4";
-            case CHR5: return "chr5";
-            case CHR6: return "chr6";
-            case CHR7: return "chr7";
-            case CHR8: return "chr8";
-            case CHR9: return "chr9";
-            case CHR_X: return "chrX";
-            case CHR_Y: return "chrY";
-        }
-        return null;
-    }
-
-    @JsonCreator
-    public static Chromosome forValue(String value) throws IOException {
-        switch (value) {
-            case "chr1":
-                return CHR1;
-            case "chr10":
-                return CHR10;
-            case "chr11":
-                return CHR11;
-            case "chr12":
-                return CHR12;
-            case "chr13":
-                return CHR13;
-            case "chr14":
-                return CHR14;
-            case "chr15":
-                return CHR15;
-            case "chr16":
-                return CHR16;
-            case "chr17":
-                return CHR17;
-            case "chr18":
-                return CHR18;
-            case "chr19":
-                return CHR19;
-            case "chr2":
-                return CHR2;
-            case "chr20":
-                return CHR20;
-            case "chr21":
-                return CHR21;
-            case "chr22":
-                return CHR22;
-            case "chr3":
-                return CHR3;
-            case "chr4":
-                return CHR4;
-            case "chr5":
-                return CHR5;
-            case "chr6":
-                return CHR6;
-            case "chr7":
-                return CHR7;
-            case "chr8":
-                return CHR8;
-            case "chr9":
-                return CHR9;
-            case "chrX":
-                return CHR_X;
-            case "chrY":
-                return CHR_Y;
-        }
-        throw new IOException("Cannot deserialize Chromosome");
-    }
-}

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

@@ -0,0 +1,68 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum ChromosomeCode {
+    CHR1, CHR10, CHR11, CHR12, CHR13, CHR14, CHR15, CHR16, CHR17, CHR18, CHR19, CHR2, CHR20, CHR21, CHR22, CHR3, CHR4, CHR5, CHR6, CHR7, CHR8, CHR9, CHR_X, CHR_Y;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case CHR1: return "chr1";
+            case CHR10: return "chr10";
+            case CHR11: return "chr11";
+            case CHR12: return "chr12";
+            case CHR13: return "chr13";
+            case CHR14: return "chr14";
+            case CHR15: return "chr15";
+            case CHR16: return "chr16";
+            case CHR17: return "chr17";
+            case CHR18: return "chr18";
+            case CHR19: return "chr19";
+            case CHR2: return "chr2";
+            case CHR20: return "chr20";
+            case CHR21: return "chr21";
+            case CHR22: return "chr22";
+            case CHR3: return "chr3";
+            case CHR4: return "chr4";
+            case CHR5: return "chr5";
+            case CHR6: return "chr6";
+            case CHR7: return "chr7";
+            case CHR8: return "chr8";
+            case CHR9: return "chr9";
+            case CHR_X: return "chrX";
+            case CHR_Y: return "chrY";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static ChromosomeCode forValue(String value) throws IOException {
+        if (value.equals("chr1")) return CHR1;
+        if (value.equals("chr10")) return CHR10;
+        if (value.equals("chr11")) return CHR11;
+        if (value.equals("chr12")) return CHR12;
+        if (value.equals("chr13")) return CHR13;
+        if (value.equals("chr14")) return CHR14;
+        if (value.equals("chr15")) return CHR15;
+        if (value.equals("chr16")) return CHR16;
+        if (value.equals("chr17")) return CHR17;
+        if (value.equals("chr18")) return CHR18;
+        if (value.equals("chr19")) return CHR19;
+        if (value.equals("chr2")) return CHR2;
+        if (value.equals("chr20")) return CHR20;
+        if (value.equals("chr21")) return CHR21;
+        if (value.equals("chr22")) return CHR22;
+        if (value.equals("chr3")) return CHR3;
+        if (value.equals("chr4")) return CHR4;
+        if (value.equals("chr5")) return CHR5;
+        if (value.equals("chr6")) return CHR6;
+        if (value.equals("chr7")) return CHR7;
+        if (value.equals("chr8")) return CHR8;
+        if (value.equals("chr9")) return CHR9;
+        if (value.equals("chrX")) return CHR_X;
+        if (value.equals("chrY")) return CHR_Y;
+        throw new IOException("Cannot deserialize ChromosomeCode");
+    }
+}

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

@@ -0,0 +1,22 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum ChromosomeSystem {
+    CHROMOSOME;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case CHROMOSOME: return "chromosome";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static ChromosomeSystem forValue(String value) throws IOException {
+        if (value.equals("chromosome")) return CHROMOSOME;
+        throw new IOException("Cannot deserialize ChromosomeSystem");
+    }
+}

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

@@ -7,7 +7,8 @@ public class Claim {
     private String id;
     private Date issuedOn;
     private Patient patient;
-    private String therapy;
+    private Recommendation recommendation;
+    private Coding stage;
 
     @JsonProperty("id")
     public String getId() { return id; }
@@ -26,8 +27,13 @@ public class Claim {
     @JsonProperty("patient")
     public void setPatient(Patient value) { this.patient = value; }
 
-    @JsonProperty("therapy")
+    @JsonProperty("recommendation")
-    public String getTherapy() { return therapy; }
+    public Recommendation getRecommendation() { return recommendation; }
-    @JsonProperty("therapy")
+    @JsonProperty("recommendation")
-    public void setTherapy(String value) { this.therapy = value; }
+    public void setRecommendation(Recommendation value) { this.recommendation = value; }
+
+    @JsonProperty("stage")
+    public Coding getStage() { return stage; }
+    @JsonProperty("stage")
+    public void setStage(Coding value) { this.stage = value; }
 }

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

@@ -8,8 +8,8 @@ public class ClaimResponse {
     private String id;
     private Date issuedOn;
     private Patient patient;
-    private ClaimResponseStatusReason reason;
     private CodingClaimResponseStatus status;
+    private CodingClaimResponseStatusReason statusReason;
 
     @JsonProperty("claim")
     public ClaimResponseClaim getClaim() { return claim; }
@@ -33,13 +33,13 @@ public class ClaimResponse {
     @JsonProperty("patient")
     public void setPatient(Patient value) { this.patient = value; }
 
-    @JsonProperty("reason")
-    public ClaimResponseStatusReason getReason() { return reason; }
-    @JsonProperty("reason")
-    public void setReason(ClaimResponseStatusReason value) { this.reason = value; }
-
     @JsonProperty("status")
     public CodingClaimResponseStatus getStatus() { return status; }
     @JsonProperty("status")
     public void setStatus(CodingClaimResponseStatus value) { this.status = value; }
+
+    @JsonProperty("statusReason")
+    public CodingClaimResponseStatusReason getStatusReason() { return statusReason; }
+    @JsonProperty("statusReason")
+    public void setStatusReason(CodingClaimResponseStatusReason value) { this.statusReason = value; }
 }

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

@@ -4,23 +4,25 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.List;
 
 public class Cnv {
-    private Chromosome chromosome;
+    private CodingChromosome chromosome;
     private Double cnA;
     private Double cnB;
-    private List<CopyNumberNeutralLoH> copyNumberNeutralLoH;
+    private List<CodingGene> copyNumberNeutralLoH;
     private EndRange endRange;
     private String id;
+    private Reference indication;
+    private Patient patient;
     private Double relativeCopyNumber;
-    private List<ReportedAffectedGene> reportedAffectedGenes;
+    private List<CodingGene> reportedAffectedGenes;
     private String reportedFocality;
     private StartRange startRange;
     private Long totalCopyNumber;
-    private CnvType type;
+    private CodingCnvType type;
 
     @JsonProperty("chromosome")
-    public Chromosome getChromosome() { return chromosome; }
+    public CodingChromosome getChromosome() { return chromosome; }
     @JsonProperty("chromosome")
-    public void setChromosome(Chromosome value) { this.chromosome = value; }
+    public void setChromosome(CodingChromosome value) { this.chromosome = value; }
 
     @JsonProperty("cnA")
     public Double getCnA() { return cnA; }
@@ -33,9 +35,9 @@ public class Cnv {
     public void setCnB(Double value) { this.cnB = value; }
 
     @JsonProperty("copyNumberNeutralLoH")
-    public List<CopyNumberNeutralLoH> getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; }
+    public List<CodingGene> getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; }
     @JsonProperty("copyNumberNeutralLoH")
-    public void setCopyNumberNeutralLoH(List<CopyNumberNeutralLoH> value) { this.copyNumberNeutralLoH = value; }
+    public void setCopyNumberNeutralLoH(List<CodingGene> value) { this.copyNumberNeutralLoH = value; }
 
     @JsonProperty("endRange")
     public EndRange getEndRange() { return endRange; }
@@ -47,15 +49,25 @@ public class Cnv {
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
+    @JsonProperty("indication")
+    public Reference getIndication() { return indication; }
+    @JsonProperty("indication")
+    public void setIndication(Reference value) { this.indication = value; }
+
+    @JsonProperty("patient")
+    public Patient getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Patient value) { this.patient = value; }
+
     @JsonProperty("relativeCopyNumber")
     public Double getRelativeCopyNumber() { return relativeCopyNumber; }
     @JsonProperty("relativeCopyNumber")
     public void setRelativeCopyNumber(Double value) { this.relativeCopyNumber = value; }
 
     @JsonProperty("reportedAffectedGenes")
-    public List<ReportedAffectedGene> getReportedAffectedGenes() { return reportedAffectedGenes; }
+    public List<CodingGene> getReportedAffectedGenes() { return reportedAffectedGenes; }
     @JsonProperty("reportedAffectedGenes")
-    public void setReportedAffectedGenes(List<ReportedAffectedGene> value) { this.reportedAffectedGenes = value; }
+    public void setReportedAffectedGenes(List<CodingGene> value) { this.reportedAffectedGenes = value; }
 
     @JsonProperty("reportedFocality")
     public String getReportedFocality() { return reportedFocality; }
@@ -73,7 +85,7 @@ public class Cnv {
     public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; }
 
     @JsonProperty("type")
-    public CnvType getType() { return type; }
+    public CodingCnvType getType() { return type; }
     @JsonProperty("type")
-    public void setType(CnvType value) { this.type = value; }
+    public void setType(CodingCnvType value) { this.type = value; }
 }

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingCarePlanStatusReason {
+    private String code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public String getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(String value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingChromosome {
+    private ChromosomeCode code;
+    private String display;
+    private ChromosomeSystem system;
+
+    @JsonProperty("code")
+    public ChromosomeCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(ChromosomeCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public ChromosomeSystem getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(ChromosomeSystem value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingClaimResponseStatusReason {
+    private ClaimResponseStatusReason code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public ClaimResponseStatusReason getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(ClaimResponseStatusReason value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingCnvType {
+    private CNVType code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public CNVType getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(CNVType value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingGene {
+    private String code;
+    private String display;
+    private GeneSystem system;
+
+    @JsonProperty("code")
+    public String getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(String value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public GeneSystem getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(GeneSystem value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingTherapyRecommendationPriority {
+    private TherapyRecommendationPriority code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public TherapyRecommendationPriority getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(TherapyRecommendationPriority value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingTherapyStatus {
+    private TherapyStatus code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public TherapyStatus getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(TherapyStatus value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class CodingTherapyStatusReason {
-    private NotDoneReasonCode code;
+    private StatusReasonCode code;
     private String display;
     private String system;
     private String version;
 
     @JsonProperty("code")
-    public NotDoneReasonCode getCode() { return code; }
+    public StatusReasonCode getCode() { return code; }
     @JsonProperty("code")
-    public void setCode(NotDoneReasonCode value) { this.code = value; }
+    public void setCode(StatusReasonCode value) { this.code = value; }
 
     @JsonProperty("display")
     public String getDisplay() { return display; }

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingTumorCellContentMethod {
+    private TumorCellContentMethod code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public TumorCellContentMethod getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(TumorCellContentMethod value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class Code {
+public class CodingTumorGrade {
-    private String code;
+    private TumorGradeCode code;
     private String display;
     private String system;
     private String version;
 
     @JsonProperty("code")
-    public String getCode() { return code; }
+    public TumorGradeCode getCode() { return code; }
     @JsonProperty("code")
-    public void setCode(String value) { this.code = value; }
+    public void setCode(TumorGradeCode value) { this.code = value; }
 
     @JsonProperty("display")
     public String getDisplay() { return display; }

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingTumorSpread {
+    private StageCode code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public StageCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(StageCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Components {
+    private double loh;
+    private double lst;
+    private double tai;
+
+    @JsonProperty("loh")
+    public double getLoh() { return loh; }
+    @JsonProperty("loh")
+    public void setLoh(double value) { this.loh = value; }
+
+    @JsonProperty("lst")
+    public double getLst() { return lst; }
+    @JsonProperty("lst")
+    public void setLst(double value) { this.lst = value; }
+
+    @JsonProperty("tai")
+    public double getTai() { return tai; }
+    @JsonProperty("tai")
+    public void setTai(double value) { this.tai = value; }
+}

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class ConfidenceRange {
+    private double max;
+    private double min;
+
+    @JsonProperty("max")
+    public double getMax() { return max; }
+    @JsonProperty("max")
+    public void setMax(double value) { this.max = value; }
+
+    @JsonProperty("min")
+    public double getMin() { return min; }
+    @JsonProperty("min")
+    public void setMin(double value) { this.min = value; }
+}

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

@@ -1,24 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class Consent {
-    private String id;
-    private Patient patient;
-    private ConsentStatus status;
-
-    @JsonProperty("id")
-    public String getId() { return id; }
-    @JsonProperty("id")
-    public void setId(String value) { this.id = value; }
-
-    @JsonProperty("patient")
-    public Patient getPatient() { return patient; }
-    @JsonProperty("patient")
-    public void setPatient(Patient value) { this.patient = value; }
-
-    @JsonProperty("status")
-    public ConsentStatus getStatus() { return status; }
-    @JsonProperty("status")
-    public void setStatus(ConsentStatus value) { this.status = value; }
-}

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

@@ -1,24 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import java.io.IOException;
-import com.fasterxml.jackson.annotation.*;
-
-public enum ConsentStatus {
-    ACTIVE, REJECTED;
-
-    @JsonValue
-    public String toValue() {
-        switch (this) {
-            case ACTIVE: return "active";
-            case REJECTED: return "rejected";
-        }
-        return null;
-    }
-
-    @JsonCreator
-    public static ConsentStatus forValue(String value) throws IOException {
-        if (value.equals("active")) return ACTIVE;
-        if (value.equals("rejected")) return REJECTED;
-        throw new IOException("Cannot deserialize ConsentStatus");
-    }
-}

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class CopyNumberNeutralLoH {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class DnaFusion {
+public class DNAFusion {
     private DnaFusionFusionPartner3Prime fusionPartner3Prime;
     private DnaFusionFusionPartner5Prime fusionPartner5Prime;
     private String id;

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Diagnosis {
+    private String id;
+    private String type;
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("type")
+    public String getType() { return type; }
+    @JsonProperty("type")
+    public void setType(String value) { this.type = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java

@@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class DnaFusionFusionPartner3Prime {
-    private Chromosome chromosome;
+    private CodingChromosome chromosome;
-    private PurpleGene gene;
+    private CodingGene gene;
     private double position;
 
     @JsonProperty("chromosome")
-    public Chromosome getChromosome() { return chromosome; }
+    public CodingChromosome getChromosome() { return chromosome; }
     @JsonProperty("chromosome")
-    public void setChromosome(Chromosome value) { this.chromosome = value; }
+    public void setChromosome(CodingChromosome value) { this.chromosome = value; }
 
     @JsonProperty("gene")
-    public PurpleGene getGene() { return gene; }
+    public CodingGene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(PurpleGene value) { this.gene = value; }
+    public void setGene(CodingGene value) { this.gene = value; }
 
     @JsonProperty("position")
     public double getPosition() { return position; }

src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java

@@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class DnaFusionFusionPartner5Prime {
-    private Chromosome chromosome;
+    private CodingChromosome chromosome;
-    private FluffyGene gene;
+    private Gene gene;
     private double position;
 
     @JsonProperty("chromosome")
-    public Chromosome getChromosome() { return chromosome; }
+    public CodingChromosome getChromosome() { return chromosome; }
     @JsonProperty("chromosome")
-    public void setChromosome(Chromosome value) { this.chromosome = value; }
+    public void setChromosome(CodingChromosome value) { this.chromosome = value; }
 
     @JsonProperty("gene")
-    public FluffyGene getGene() { return gene; }
+    public Gene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(FluffyGene value) { this.gene = value; }
+    public void setGene(Gene value) { this.gene = value; }
 
     @JsonProperty("position")
     public double getPosition() { return position; }

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class EXTId {
+    private EXTIdSystem system;
+    private String value;
+
+    @JsonProperty("system")
+    public EXTIdSystem getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(EXTIdSystem value) { this.system = value; }
+
+    @JsonProperty("value")
+    public String getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(String value) { this.value = value; }
+}

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

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum SystemEnum {
+public enum EXTIdSystem {
     HTTPS_PUBMED_NCBI_NLM_NIH_GOV;
 
     @JsonValue
@@ -15,8 +15,8 @@ public enum SystemEnum {
     }
 
     @JsonCreator
-    public static SystemEnum forValue(String value) throws IOException {
+    public static EXTIdSystem forValue(String value) throws IOException {
         if (value.equals("https://pubmed.ncbi.nlm.nih.gov/")) return HTTPS_PUBMED_NCBI_NLM_NIH_GOV;
-        throw new IOException("Cannot deserialize SystemEnum");
+        throw new IOException("Cannot deserialize EXTIdSystem");
     }
 }

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

@@ -0,0 +1,31 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.List;
+
+public class EpisodeOfCare {
+    private List<Reference> diagnoses;
+    private String id;
+    private Reference patient;
+    private PeriodLocalDate period;
+
+    @JsonProperty("diagnoses")
+    public List<Reference> getDiagnoses() { return diagnoses; }
+    @JsonProperty("diagnoses")
+    public void setDiagnoses(List<Reference> value) { this.diagnoses = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("period")
+    public PeriodLocalDate getPeriod() { return period; }
+    @JsonProperty("period")
+    public void setPeriod(PeriodLocalDate value) { this.period = value; }
+}

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

@@ -2,14 +2,14 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class ExtId {
+public class ExternalId {
-    private SystemEnum system;
+    private String system;
     private String value;
 
     @JsonProperty("system")
-    public SystemEnum getSystem() { return system; }
+    public String getSystem() { return system; }
     @JsonProperty("system")
-    public void setSystem(SystemEnum value) { this.system = value; }
+    public void setSystem(String value) { this.system = value; }
 
     @JsonProperty("value")
     public String getValue() { return value; }

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class FluffyGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class PurpleGene {
+public class Gene {
     private String ensemblId;
     private String hgncId;
 

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

@@ -0,0 +1,22 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum GeneSystem {
+    HTTPS_Www_GENENAMES_ORG;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case HTTPS_Www_GENENAMES_ORG: return "https://www.genenames.org/";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static GeneSystem forValue(String value) throws IOException {
+        if (value.equals("https://www.genenames.org/")) return HTTPS_Www_GENENAMES_ORG;
+        throw new IOException("Cannot deserialize GeneSystem");
+    }
+}

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

@@ -7,7 +7,7 @@ public class GeneticCounselingRecommendation {
     private String id;
     private Date issuedOn;
     private Patient patient;
-    private String reason;
+    private Coding reason;
 
     @JsonProperty("id")
     public String getId() { return id; }
@@ -25,7 +25,7 @@ public class GeneticCounselingRecommendation {
     public void setPatient(Patient value) { this.patient = value; }
 
     @JsonProperty("reason")
-    public String getReason() { return reason; }
+    public Coding getReason() { return reason; }
     @JsonProperty("reason")
-    public void setReason(String value) { this.reason = value; }
+    public void setReason(Coding value) { this.reason = value; }
 }

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

@@ -1,37 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import java.io.IOException;
-import com.fasterxml.jackson.annotation.*;
-
-public enum GuidelineTreatmentStatus {
-    EXHAUSTED, IMPOSSIBLE, NON_EXHAUSTED, NO_GUIDELINES_AVAILABLE, UNKNOWN;
-
-    @JsonValue
-    public String toValue() {
-        switch (this) {
-            case EXHAUSTED: return "exhausted";
-            case IMPOSSIBLE: return "impossible";
-            case NON_EXHAUSTED: return "non-exhausted";
-            case NO_GUIDELINES_AVAILABLE: return "no-guidelines-available";
-            case UNKNOWN: return "unknown";
-        }
-        return null;
-    }
-
-    @JsonCreator
-    public static GuidelineTreatmentStatus forValue(String value) throws IOException {
-        switch (value) {
-            case "exhausted":
-                return EXHAUSTED;
-            case "impossible":
-                return IMPOSSIBLE;
-            case "non-exhausted":
-                return NON_EXHAUSTED;
-            case "no-guidelines-available":
-                return NO_GUIDELINES_AVAILABLE;
-            case "unknown":
-                return UNKNOWN;
-        }
-        throw new IOException("Cannot deserialize GuidelineTreatmentStatus");
-    }
-}

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

@@ -0,0 +1,42 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class HRDScore {
+    private Components components;
+    private String id;
+    private Coding interpretation;
+    private Reference patient;
+    private Reference specimen;
+    private double value;
+
+    @JsonProperty("components")
+    public Components getComponents() { return components; }
+    @JsonProperty("components")
+    public void setComponents(Components value) { this.components = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("interpretation")
+    public Coding getInterpretation() { return interpretation; }
+    @JsonProperty("interpretation")
+    public void setInterpretation(Coding value) { this.interpretation = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("specimen")
+    public Reference getSpecimen() { return specimen; }
+    @JsonProperty("specimen")
+    public void setSpecimen(Reference value) { this.specimen = value; }
+
+    @JsonProperty("value")
+    public double getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(double value) { this.value = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class HealthInsurance {
+    private String display;
+    private ExternalId extId;
+    private Type type;
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("extId")
+    public ExternalId getExtId() { return extId; }
+    @JsonProperty("extId")
+    public void setExtId(ExternalId value) { this.extId = value; }
+
+    @JsonProperty("type")
+    public Type getType() { return type; }
+    @JsonProperty("type")
+    public void setType(Type value) { this.type = value; }
+}

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

@@ -7,9 +7,8 @@ public class HistologyReport {
     private String id;
     private Date issuedOn;
     private Patient patient;
+    private HistologyReportResults results;
     private HistologyReportSpecimen specimen;
-    private TumorCellContent tumorCellContent;
-    private TumorMorphology tumorMorphology;
 
     @JsonProperty("id")
     public String getId() { return id; }
@@ -28,18 +27,13 @@ public class HistologyReport {
     @JsonProperty("patient")
     public void setPatient(Patient value) { this.patient = value; }
 
+    @JsonProperty("results")
+    public HistologyReportResults getResults() { return results; }
+    @JsonProperty("results")
+    public void setResults(HistologyReportResults value) { this.results = value; }
+
     @JsonProperty("specimen")
     public HistologyReportSpecimen getSpecimen() { return specimen; }
     @JsonProperty("specimen")
     public void setSpecimen(HistologyReportSpecimen value) { this.specimen = value; }
-
-    @JsonProperty("tumorCellContent")
-    public TumorCellContent getTumorCellContent() { return tumorCellContent; }
-    @JsonProperty("tumorCellContent")
-    public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
-
-    @JsonProperty("tumorMorphology")
-    public TumorMorphology getTumorMorphology() { return tumorMorphology; }
-    @JsonProperty("tumorMorphology")
-    public void setTumorMorphology(TumorMorphology value) { this.tumorMorphology = value; }
 }

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class HistologyReportResults {
+    private TumorCellContent tumorCellContent;
+    private TumorMorphology tumorMorphology;
+
+    @JsonProperty("tumorCellContent")
+    public TumorCellContent getTumorCellContent() { return tumorCellContent; }
+    @JsonProperty("tumorCellContent")
+    public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
+
+    @JsonProperty("tumorMorphology")
+    public TumorMorphology getTumorMorphology() { return tumorMorphology; }
+    @JsonProperty("tumorMorphology")
+    public void setTumorMorphology(TumorMorphology value) { this.tumorMorphology = value; }
+}

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

@@ -0,0 +1,74 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.Date;
+import java.util.List;
+
+public class MTBCarePlan {
+    private String diagnosis;
+    private GeneticCounselingRecommendation geneticCounselingRecommendation;
+    private String id;
+    private Reference indication;
+    private Date issuedOn;
+    private List<MTBMedicationRecommendation> medicationRecommendations;
+    private NoTargetFinding noTargetFinding;
+    private String notes;
+    private Patient patient;
+    private CodingCarePlanStatusReason statusReason;
+    private List<StudyEnrollmentRecommendation> studyEnrollmentRecommendations;
+
+    @JsonProperty("diagnosis")
+    public String getDiagnosis() { return diagnosis; }
+    @JsonProperty("diagnosis")
+    public void setDiagnosis(String value) { this.diagnosis = value; }
+
+    @JsonProperty("geneticCounselingRecommendation")
+    public GeneticCounselingRecommendation getGeneticCounselingRecommendation() { return geneticCounselingRecommendation; }
+    @JsonProperty("geneticCounselingRecommendation")
+    public void setGeneticCounselingRecommendation(GeneticCounselingRecommendation value) { this.geneticCounselingRecommendation = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("indication")
+    public Reference getIndication() { return indication; }
+    @JsonProperty("indication")
+    public void setIndication(Reference value) { this.indication = value; }
+
+    @JsonProperty("issuedOn")
+    public Date getIssuedOn() { return issuedOn; }
+    @JsonProperty("issuedOn")
+    public void setIssuedOn(Date value) { this.issuedOn = value; }
+
+    @JsonProperty("medicationRecommendations")
+    public List<MTBMedicationRecommendation> getMedicationRecommendations() { return medicationRecommendations; }
+    @JsonProperty("medicationRecommendations")
+    public void setMedicationRecommendations(List<MTBMedicationRecommendation> value) { this.medicationRecommendations = value; }
+
+    @JsonProperty("noTargetFinding")
+    public NoTargetFinding getNoTargetFinding() { return noTargetFinding; }
+    @JsonProperty("noTargetFinding")
+    public void setNoTargetFinding(NoTargetFinding value) { this.noTargetFinding = value; }
+
+    @JsonProperty("notes")
+    public String getNotes() { return notes; }
+    @JsonProperty("notes")
+    public void setNotes(String value) { this.notes = value; }
+
+    @JsonProperty("patient")
+    public Patient getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Patient value) { this.patient = value; }
+
+    @JsonProperty("statusReason")
+    public CodingCarePlanStatusReason getStatusReason() { return statusReason; }
+    @JsonProperty("statusReason")
+    public void setStatusReason(CodingCarePlanStatusReason value) { this.statusReason = value; }
+
+    @JsonProperty("studyEnrollmentRecommendations")
+    public List<StudyEnrollmentRecommendation> getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; }
+    @JsonProperty("studyEnrollmentRecommendations")
+    public void setStudyEnrollmentRecommendations(List<StudyEnrollmentRecommendation> value) { this.studyEnrollmentRecommendations = value; }
+}

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

@@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.Date;
 import java.util.List;
 
-public class MtbDiagnosis {
+public class MTBDiagnosis {
     private Coding code;
     private Coding guidelineTreatmentStatus;
     private List<String> histologyResults;
@@ -12,8 +12,11 @@ public class MtbDiagnosis {
     private String id;
     private Patient patient;
     private Date recordedOn;
-    private List<StatusHistory> statusHistory;
+    private List<StageHistory> stageHistory;
+    private Coding topography;
+    private CodingTumorGrade tumorGrade;
     private Coding whoGrade;
+    private Coding whoGrading;
 
     @JsonProperty("code")
     public Coding getCode() { return code; }
@@ -50,13 +53,28 @@ public class MtbDiagnosis {
     @JsonProperty("recordedOn")
     public void setRecordedOn(Date value) { this.recordedOn = value; }
 
-    @JsonProperty("statusHistory")
+    @JsonProperty("stageHistory")
-    public List<StatusHistory> getStatusHistory() { return statusHistory; }
+    public List<StageHistory> getStageHistory() { return stageHistory; }
-    @JsonProperty("statusHistory")
+    @JsonProperty("stageHistory")
-    public void setStatusHistory(List<StatusHistory> value) { this.statusHistory = value; }
+    public void setStageHistory(List<StageHistory> value) { this.stageHistory = value; }
+
+    @JsonProperty("topography")
+    public Coding getTopography() { return topography; }
+    @JsonProperty("topography")
+    public void setTopography(Coding value) { this.topography = value; }
+
+    @JsonProperty("tumorGrade")
+    public CodingTumorGrade getTumorGrade() { return tumorGrade; }
+    @JsonProperty("tumorGrade")
+    public void setTumorGrade(CodingTumorGrade value) { this.tumorGrade = value; }
 
     @JsonProperty("whoGrade")
     public Coding getWhoGrade() { return whoGrade; }
     @JsonProperty("whoGrade")
     public void setWhoGrade(Coding value) { this.whoGrade = value; }
+
+    @JsonProperty("whoGrading")
+    public Coding getWhoGrading() { return whoGrading; }
+    @JsonProperty("whoGrading")
+    public void setWhoGrading(Coding value) { this.whoGrading = value; }
 }

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class MtbEpisode {
+public class MTBEpisode {
     private String id;
     private Patient patient;
     private PeriodLocalDate period;

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

@@ -4,27 +4,27 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.Date;
 import java.util.List;
 
-public class MtbMedicationRecommendation {
+public class MTBMedicationRecommendation {
-    private String diagnosis;
     private String id;
+    private Reference indication;
     private Date issuedOn;
     private LevelOfEvidence levelOfEvidence;
     private List<Coding> medication;
     private String ngsReport;
     private Patient patient;
-    private TherapyRecommendationPriority priority;
+    private CodingTherapyRecommendationPriority priority;
-    private List<String> supportingVariants;
+    private List<Reference> supportingVariants;
-
-    @JsonProperty("diagnosis")
-    public String getDiagnosis() { return diagnosis; }
-    @JsonProperty("diagnosis")
-    public void setDiagnosis(String value) { this.diagnosis = value; }
 
     @JsonProperty("id")
     public String getId() { return id; }
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
+    @JsonProperty("indication")
+    public Reference getIndication() { return indication; }
+    @JsonProperty("indication")
+    public void setIndication(Reference value) { this.indication = value; }
+
     @JsonProperty("issuedOn")
     public Date getIssuedOn() { return issuedOn; }
     @JsonProperty("issuedOn")
@@ -51,12 +51,12 @@ public class MtbMedicationRecommendation {
     public void setPatient(Patient value) { this.patient = value; }
 
     @JsonProperty("priority")
-    public TherapyRecommendationPriority getPriority() { return priority; }
+    public CodingTherapyRecommendationPriority getPriority() { return priority; }
     @JsonProperty("priority")
-    public void setPriority(TherapyRecommendationPriority value) { this.priority = value; }
+    public void setPriority(CodingTherapyRecommendationPriority value) { this.priority = value; }
 
     @JsonProperty("supportingVariants")
-    public List<String> getSupportingVariants() { return supportingVariants; }
+    public List<Reference> getSupportingVariants() { return supportingVariants; }
     @JsonProperty("supportingVariants")
-    public void setSupportingVariants(List<String> value) { this.supportingVariants = value; }
+    public void setSupportingVariants(List<Reference> value) { this.supportingVariants = value; }
 }

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

@@ -4,18 +4,18 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.Date;
 import java.util.List;
 
-public class MtbMedicationTherapy {
+public class MTBMedicationTherapy {
     private String basedOn;
     private String diagnosis;
     private String id;
+    private Reference indication;
     private List<Coding> medication;
-    private CodingTherapyStatusReason notDoneReason;
+    private String notes;
-    private String note;
     private Patient patient;
     private PeriodLocalDate period;
-    private CodingTherapyStatusReason reasonStopped;
     private Date recordedOn;
-    private TherapyStatus status;
+    private CodingTherapyStatus status;
+    private CodingTherapyStatusReason statusReason;
     private Long therapyLine;
 
     @JsonProperty("basedOn")
@@ -33,20 +33,20 @@ public class MtbMedicationTherapy {
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
+    @JsonProperty("indication")
+    public Reference getIndication() { return indication; }
+    @JsonProperty("indication")
+    public void setIndication(Reference value) { this.indication = value; }
+
     @JsonProperty("medication")
     public List<Coding> getMedication() { return medication; }
     @JsonProperty("medication")
     public void setMedication(List<Coding> value) { this.medication = value; }
 
-    @JsonProperty("notDoneReason")
+    @JsonProperty("notes")
-    public CodingTherapyStatusReason getNotDoneReason() { return notDoneReason; }
+    public String getNotes() { return notes; }
-    @JsonProperty("notDoneReason")
+    @JsonProperty("notes")
-    public void setNotDoneReason(CodingTherapyStatusReason value) { this.notDoneReason = value; }
+    public void setNotes(String value) { this.notes = value; }
-
-    @JsonProperty("note")
-    public String getNote() { return note; }
-    @JsonProperty("note")
-    public void setNote(String value) { this.note = value; }
 
     @JsonProperty("patient")
     public Patient getPatient() { return patient; }
@@ -58,20 +58,20 @@ public class MtbMedicationTherapy {
     @JsonProperty("period")
     public void setPeriod(PeriodLocalDate value) { this.period = value; }
 
-    @JsonProperty("reasonStopped")
-    public CodingTherapyStatusReason getReasonStopped() { return reasonStopped; }
-    @JsonProperty("reasonStopped")
-    public void setReasonStopped(CodingTherapyStatusReason value) { this.reasonStopped = value; }
-
     @JsonProperty("recordedOn")
     public Date getRecordedOn() { return recordedOn; }
     @JsonProperty("recordedOn")
     public void setRecordedOn(Date value) { this.recordedOn = value; }
 
     @JsonProperty("status")
-    public TherapyStatus getStatus() { return status; }
+    public CodingTherapyStatus getStatus() { return status; }
     @JsonProperty("status")
-    public void setStatus(TherapyStatus value) { this.status = value; }
+    public void setStatus(CodingTherapyStatus value) { this.status = value; }
+
+    @JsonProperty("statusReason")
+    public CodingTherapyStatusReason getStatusReason() { return statusReason; }
+    @JsonProperty("statusReason")
+    public void setStatusReason(CodingTherapyStatusReason value) { this.statusReason = value; }
 
     @JsonProperty("therapyLine")
     public Long getTherapyLine() { return therapyLine; }

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

@@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.List;
 
 public class MolecularTherapy {
-    private List<MtbMedicationTherapy> history;
+    private List<MTBMedicationTherapy> history;
 
     @JsonProperty("history")
-    public List<MtbMedicationTherapy> getHistory() { return history; }
+    public List<MTBMedicationTherapy> getHistory() { return history; }
     @JsonProperty("history")
-    public void setHistory(List<MtbMedicationTherapy> value) { this.history = value; }
+    public void setHistory(List<MTBMedicationTherapy> value) { this.history = value; }
 }

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

@@ -4,28 +4,29 @@ import com.fasterxml.jackson.annotation.*;
 import java.util.List;
 
 public class Mtb {
-    private List<MtbCarePlan> carePlans;
+    private List<MTBCarePlan> carePlans;
     private List<ClaimResponse> claimResponses;
     private List<Claim> claims;
-    private List<MtbDiagnosis> diagnoses;
+    private List<MTBDiagnosis> diagnoses;
-    private List<PerformanceStatus> ecogStatus;
+    private MTBEpisode episode;
-    private MtbEpisode episode;
+    private List<EpisodeOfCare> episodesOfCare;
     private List<GeneticCounselingRecommendation> geneticCounsellingRequests;
+    private List<OncoProdecure> guidelineProcedures;
+    private List<MTBMedicationTherapy> guidelineTherapies;
     private List<HistologyReport> histologyReports;
-    private List<MtbMedicationTherapy> lastGuidelineTherapies;
     private List<MolecularTherapy> molecularTherapies;
     private List<SomaticNgsReport> ngsReports;
     private MtbPatient patient;
-    private List<MtbMedicationTherapy> previousGuidelineTherapies;
+    private List<PerformanceStatus> performanceStatus;
-    private List<MtbMedicationRecommendation> recommendations;
+    private List<MTBMedicationRecommendation> recommendations;
     private List<Response> responses;
     private List<TumorSpecimen> specimens;
     private List<StudyEnrollmentRecommendation> studyInclusionRequests;
 
     @JsonProperty("carePlans")
-    public List<MtbCarePlan> getCarePlans() { return carePlans; }
+    public List<MTBCarePlan> getCarePlans() { return carePlans; }
     @JsonProperty("carePlans")
-    public void setCarePlans(List<MtbCarePlan> value) { this.carePlans = value; }
+    public void setCarePlans(List<MTBCarePlan> value) { this.carePlans = value; }
 
     @JsonProperty("claimResponses")
     public List<ClaimResponse> getClaimResponses() { return claimResponses; }
@@ -38,35 +39,40 @@ public class Mtb {
     public void setClaims(List<Claim> value) { this.claims = value; }
 
     @JsonProperty("diagnoses")
-    public List<MtbDiagnosis> getDiagnoses() { return diagnoses; }
+    public List<MTBDiagnosis> getDiagnoses() { return diagnoses; }
     @JsonProperty("diagnoses")
-    public void setDiagnoses(List<MtbDiagnosis> value) { this.diagnoses = value; }
+    public void setDiagnoses(List<MTBDiagnosis> value) { this.diagnoses = value; }
-
-    @JsonProperty("ecogStatus")
-    public List<PerformanceStatus> getEcogStatus() { return ecogStatus; }
-    @JsonProperty("ecogStatus")
-    public void setEcogStatus(List<PerformanceStatus> value) { this.ecogStatus = value; }
 
     @JsonProperty("episode")
-    public MtbEpisode getEpisode() { return episode; }
+    public MTBEpisode getEpisode() { return episode; }
     @JsonProperty("episode")
-    public void setEpisode(MtbEpisode value) { this.episode = value; }
+    public void setEpisode(MTBEpisode value) { this.episode = value; }
+
+    @JsonProperty("episodesOfCare")
+    public List<EpisodeOfCare> getEpisodesOfCare() { return episodesOfCare; }
+    @JsonProperty("episodesOfCare")
+    public void setEpisodesOfCare(List<EpisodeOfCare> value) { this.episodesOfCare = value; }
 
     @JsonProperty("geneticCounsellingRequests")
     public List<GeneticCounselingRecommendation> getGeneticCounsellingRequests() { return geneticCounsellingRequests; }
     @JsonProperty("geneticCounsellingRequests")
     public void setGeneticCounsellingRequests(List<GeneticCounselingRecommendation> value) { this.geneticCounsellingRequests = value; }
 
+    @JsonProperty("guidelineProcedures")
+    public List<OncoProdecure> getGuidelineProcedures() { return guidelineProcedures; }
+    @JsonProperty("guidelineProcedures")
+    public void setGuidelineProcedures(List<OncoProdecure> value) { this.guidelineProcedures = value; }
+
+    @JsonProperty("guidelineTherapies")
+    public List<MTBMedicationTherapy> getGuidelineTherapies() { return guidelineTherapies; }
+    @JsonProperty("guidelineTherapies")
+    public void setGuidelineTherapies(List<MTBMedicationTherapy> value) { this.guidelineTherapies = value; }
+
     @JsonProperty("histologyReports")
     public List<HistologyReport> getHistologyReports() { return histologyReports; }
     @JsonProperty("histologyReports")
     public void setHistologyReports(List<HistologyReport> value) { this.histologyReports = value; }
 
-    @JsonProperty("lastGuidelineTherapies")
-    public List<MtbMedicationTherapy> getLastGuidelineTherapies() { return lastGuidelineTherapies; }
-    @JsonProperty("lastGuidelineTherapies")
-    public void setLastGuidelineTherapies(List<MtbMedicationTherapy> value) { this.lastGuidelineTherapies = value; }
-
     @JsonProperty("molecularTherapies")
     public List<MolecularTherapy> getMolecularTherapies() { return molecularTherapies; }
     @JsonProperty("molecularTherapies")
@@ -82,15 +88,15 @@ public class Mtb {
     @JsonProperty("patient")
     public void setPatient(MtbPatient value) { this.patient = value; }
 
-    @JsonProperty("previousGuidelineTherapies")
+    @JsonProperty("performanceStatus")
-    public List<MtbMedicationTherapy> getPreviousGuidelineTherapies() { return previousGuidelineTherapies; }
+    public List<PerformanceStatus> getPerformanceStatus() { return performanceStatus; }
-    @JsonProperty("previousGuidelineTherapies")
+    @JsonProperty("performanceStatus")
-    public void setPreviousGuidelineTherapies(List<MtbMedicationTherapy> value) { this.previousGuidelineTherapies = value; }
+    public void setPerformanceStatus(List<PerformanceStatus> value) { this.performanceStatus = value; }
 
     @JsonProperty("recommendations")
-    public List<MtbMedicationRecommendation> getRecommendations() { return recommendations; }
+    public List<MTBMedicationRecommendation> getRecommendations() { return recommendations; }
     @JsonProperty("recommendations")
-    public void setRecommendations(List<MtbMedicationRecommendation> value) { this.recommendations = value; }
+    public void setRecommendations(List<MTBMedicationRecommendation> value) { this.recommendations = value; }
 
     @JsonProperty("responses")
     public List<Response> getResponses() { return responses; }

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

@@ -1,62 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-import java.util.Date;
-import java.util.List;
-
-public class MtbCarePlan {
-    private String description;
-    private String diagnosis;
-    private String geneticCounsellingRequest;
-    private String id;
-    private Date issuedOn;
-    private NoTargetFinding noTargetFinding;
-    private Patient patient;
-    private List<String> recommendations;
-    private List<String> studyInclusionRequests;
-
-    @JsonProperty("description")
-    public String getDescription() { return description; }
-    @JsonProperty("description")
-    public void setDescription(String value) { this.description = value; }
-
-    @JsonProperty("diagnosis")
-    public String getDiagnosis() { return diagnosis; }
-    @JsonProperty("diagnosis")
-    public void setDiagnosis(String value) { this.diagnosis = value; }
-
-    @JsonProperty("geneticCounsellingRequest")
-    public String getGeneticCounsellingRequest() { return geneticCounsellingRequest; }
-    @JsonProperty("geneticCounsellingRequest")
-    public void setGeneticCounsellingRequest(String value) { this.geneticCounsellingRequest = value; }
-
-    @JsonProperty("id")
-    public String getId() { return id; }
-    @JsonProperty("id")
-    public void setId(String value) { this.id = value; }
-
-    @JsonProperty("issuedOn")
-    public Date getIssuedOn() { return issuedOn; }
-    @JsonProperty("issuedOn")
-    public void setIssuedOn(Date value) { this.issuedOn = value; }
-
-    @JsonProperty("noTargetFinding")
-    public NoTargetFinding getNoTargetFinding() { return noTargetFinding; }
-    @JsonProperty("noTargetFinding")
-    public void setNoTargetFinding(NoTargetFinding value) { this.noTargetFinding = value; }
-
-    @JsonProperty("patient")
-    public Patient getPatient() { return patient; }
-    @JsonProperty("patient")
-    public void setPatient(Patient value) { this.patient = value; }
-
-    @JsonProperty("recommendations")
-    public List<String> getRecommendations() { return recommendations; }
-    @JsonProperty("recommendations")
-    public void setRecommendations(List<String> value) { this.recommendations = value; }
-
-    @JsonProperty("studyInclusionRequests")
-    public List<String> getStudyInclusionRequests() { return studyInclusionRequests; }
-    @JsonProperty("studyInclusionRequests")
-    public void setStudyInclusionRequests(List<String> value) { this.studyInclusionRequests = value; }
-}

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

@@ -5,17 +5,24 @@ import java.util.Date;
 
 public class MtbPatient {
     private Address address;
+    private ValueWithUnit age;
     private Date birthDate;
     private Date dateOfDeath;
     private CodingGender gender;
+    private HealthInsurance healthInsurance;
     private String id;
-    private String insurance;
+    private VitalStatus vitalStatus;
 
     @JsonProperty("address")
     public Address getAddress() { return address; }
     @JsonProperty("address")
     public void setAddress(Address value) { this.address = value; }
 
+    @JsonProperty("age")
+    public ValueWithUnit getAge() { return age; }
+    @JsonProperty("age")
+    public void setAge(ValueWithUnit value) { this.age = value; }
+
     @JsonProperty("birthDate")
     @JsonFormat(pattern = "yyyy-MM-dd")
     public Date getBirthDate() { return birthDate; }
@@ -33,13 +40,18 @@ public class MtbPatient {
     @JsonProperty("gender")
     public void setGender(CodingGender value) { this.gender = value; }
 
+    @JsonProperty("healthInsurance")
+    public HealthInsurance getHealthInsurance() { return healthInsurance; }
+    @JsonProperty("healthInsurance")
+    public void setHealthInsurance(HealthInsurance value) { this.healthInsurance = value; }
+
     @JsonProperty("id")
     public String getId() { return id; }
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
-    @JsonProperty("insurance")
+    @JsonProperty("vitalStatus")
-    public String getInsurance() { return insurance; }
+    public VitalStatus getVitalStatus() { return vitalStatus; }
-    @JsonProperty("insurance")
+    @JsonProperty("vitalStatus")
-    public void setInsurance(String value) { this.insurance = value; }
+    public void setVitalStatus(VitalStatus value) { this.vitalStatus = value; }
 }

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

@@ -0,0 +1,61 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.List;
+
+public class NgsReportResults {
+    private BRCAness brcaness;
+    private List<Cnv> copyNumberVariants;
+    private List<DNAFusion> dnaFusions;
+    private HRDScore hrdScore;
+    private List<RNAFusion> rnaFusions;
+    private List<RNASeq> rnaSeqs;
+    private List<Snv> simpleVariants;
+    private Tmb tmb;
+    private TumorCellContent tumorCellContent;
+
+    @JsonProperty("brcaness")
+    public BRCAness getBrcaness() { return brcaness; }
+    @JsonProperty("brcaness")
+    public void setBrcaness(BRCAness value) { this.brcaness = value; }
+
+    @JsonProperty("copyNumberVariants")
+    public List<Cnv> getCopyNumberVariants() { return copyNumberVariants; }
+    @JsonProperty("copyNumberVariants")
+    public void setCopyNumberVariants(List<Cnv> value) { this.copyNumberVariants = value; }
+
+    @JsonProperty("dnaFusions")
+    public List<DNAFusion> getDnaFusions() { return dnaFusions; }
+    @JsonProperty("dnaFusions")
+    public void setDnaFusions(List<DNAFusion> value) { this.dnaFusions = value; }
+
+    @JsonProperty("hrdScore")
+    public HRDScore getHrdScore() { return hrdScore; }
+    @JsonProperty("hrdScore")
+    public void setHrdScore(HRDScore value) { this.hrdScore = value; }
+
+    @JsonProperty("rnaFusions")
+    public List<RNAFusion> getRnaFusions() { return rnaFusions; }
+    @JsonProperty("rnaFusions")
+    public void setRnaFusions(List<RNAFusion> value) { this.rnaFusions = value; }
+
+    @JsonProperty("rnaSeqs")
+    public List<RNASeq> getRnaSeqs() { return rnaSeqs; }
+    @JsonProperty("rnaSeqs")
+    public void setRnaSeqs(List<RNASeq> value) { this.rnaSeqs = value; }
+
+    @JsonProperty("simpleVariants")
+    public List<Snv> getSimpleVariants() { return simpleVariants; }
+    @JsonProperty("simpleVariants")
+    public void setSimpleVariants(List<Snv> value) { this.simpleVariants = value; }
+
+    @JsonProperty("tmb")
+    public Tmb getTmb() { return tmb; }
+    @JsonProperty("tmb")
+    public void setTmb(Tmb value) { this.tmb = value; }
+
+    @JsonProperty("tumorCellContent")
+    public TumorCellContent getTumorCellContent() { return tumorCellContent; }
+    @JsonProperty("tumorCellContent")
+    public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
+}

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

@@ -0,0 +1,79 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.Date;
+
+public class OncoProdecure {
+    private String basedOn;
+    private Coding code;
+    private String diagnosis;
+    private String id;
+    private Reference indication;
+    private String notes;
+    private Patient patient;
+    private PeriodLocalDate period;
+    private Date recordedOn;
+    private CodingTherapyStatus status;
+    private CodingTherapyStatusReason statusReason;
+    private Long therapyLine;
+
+    @JsonProperty("basedOn")
+    public String getBasedOn() { return basedOn; }
+    @JsonProperty("basedOn")
+    public void setBasedOn(String value) { this.basedOn = value; }
+
+    @JsonProperty("code")
+    public Coding getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(Coding value) { this.code = value; }
+
+    @JsonProperty("diagnosis")
+    public String getDiagnosis() { return diagnosis; }
+    @JsonProperty("diagnosis")
+    public void setDiagnosis(String value) { this.diagnosis = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("indication")
+    public Reference getIndication() { return indication; }
+    @JsonProperty("indication")
+    public void setIndication(Reference value) { this.indication = value; }
+
+    @JsonProperty("notes")
+    public String getNotes() { return notes; }
+    @JsonProperty("notes")
+    public void setNotes(String value) { this.notes = value; }
+
+    @JsonProperty("patient")
+    public Patient getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Patient value) { this.patient = value; }
+
+    @JsonProperty("period")
+    public PeriodLocalDate getPeriod() { return period; }
+    @JsonProperty("period")
+    public void setPeriod(PeriodLocalDate value) { this.period = value; }
+
+    @JsonProperty("recordedOn")
+    public Date getRecordedOn() { return recordedOn; }
+    @JsonProperty("recordedOn")
+    public void setRecordedOn(Date value) { this.recordedOn = value; }
+
+    @JsonProperty("status")
+    public CodingTherapyStatus getStatus() { return status; }
+    @JsonProperty("status")
+    public void setStatus(CodingTherapyStatus value) { this.status = value; }
+
+    @JsonProperty("statusReason")
+    public CodingTherapyStatusReason getStatusReason() { return statusReason; }
+    @JsonProperty("statusReason")
+    public void setStatusReason(CodingTherapyStatusReason value) { this.statusReason = value; }
+
+    @JsonProperty("therapyLine")
+    public Long getTherapyLine() { return therapyLine; }
+    @JsonProperty("therapyLine")
+    public void setTherapyLine(Long value) { this.therapyLine = value; }
+}

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class StartEnd {
+public class Position {
     private Double end;
     private double start;
 

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class RnaFusion {
+public class RNAFusion {
     private String cosmicId;
     private String effect;
     private RnaFusionFusionPartner3Prime fusionPartner3Prime;

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

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum RnaFusionStrand {
+public enum RNAFusionStrand {
     EMPTY, RNA_FUSION_STRAND;
 
     @JsonValue
@@ -16,7 +16,7 @@ public enum RnaFusionStrand {
     }
 
     @JsonCreator
-    public static RnaFusionStrand forValue(String value) throws IOException {
+    public static RNAFusionStrand forValue(String value) throws IOException {
         if (value.equals("+")) return EMPTY;
         if (value.equals("-")) return RNA_FUSION_STRAND;
         throw new IOException("Cannot deserialize RNAFusionStrand");

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

@@ -2,13 +2,13 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class RnaSeq {
+public class RNASeq {
     private Long cohortRanking;
     private String ensemblId;
     private String entrezId;
     private double fragmentsPerKilobaseMillion;
     private boolean fromNgs;
-    private RnaSeqGene gene;
+    private CodingGene gene;
     private String id;
     private long librarySize;
     private long rawCounts;
@@ -41,9 +41,9 @@ public class RnaSeq {
     public void setFromNgs(boolean value) { this.fromNgs = value; }
 
     @JsonProperty("gene")
-    public RnaSeqGene getGene() { return gene; }
+    public CodingGene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(RnaSeqGene value) { this.gene = value; }
+    public void setGene(CodingGene value) { this.gene = value; }
 
     @JsonProperty("id")
     public String getId() { return id; }

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Recommendation {
+    private String id;
+    private String type;
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("type")
+    public String getType() { return type; }
+    @JsonProperty("type")
+    public void setType(String value) { this.type = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Reference {
+    private String display;
+    private String id;
+    private String type;
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("type")
+    public String getType() { return type; }
+    @JsonProperty("type")
+    public void setType(String value) { this.type = value; }
+}

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

@@ -3,14 +3,14 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class ReferencePublication {
-    private ExtId extId;
+    private EXTId extId;
     private String type;
     private String uri;
 
     @JsonProperty("extId")
-    public ExtId getExtId() { return extId; }
+    public EXTId getExtId() { return extId; }
     @JsonProperty("extId")
-    public void setExtId(ExtId value) { this.extId = value; }
+    public void setExtId(EXTId value) { this.extId = value; }
 
     @JsonProperty("type")
     public String getType() { return type; }

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class ReportedAffectedGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java

@@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*;
 
 public class RnaFusionFusionPartner3Prime {
     private String exon;
-    private TentacledGene gene;
+    private CodingGene gene;
     private double position;
-    private RnaFusionStrand strand;
+    private RNAFusionStrand strand;
     private String transcriptId;
 
     @JsonProperty("exon")
@@ -15,9 +15,9 @@ public class RnaFusionFusionPartner3Prime {
     public void setExon(String value) { this.exon = value; }
 
     @JsonProperty("gene")
-    public TentacledGene getGene() { return gene; }
+    public CodingGene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(TentacledGene value) { this.gene = value; }
+    public void setGene(CodingGene value) { this.gene = value; }
 
     @JsonProperty("position")
     public double getPosition() { return position; }
@@ -25,9 +25,9 @@ public class RnaFusionFusionPartner3Prime {
     public void setPosition(double value) { this.position = value; }
 
     @JsonProperty("strand")
-    public RnaFusionStrand getStrand() { return strand; }
+    public RNAFusionStrand getStrand() { return strand; }
     @JsonProperty("strand")
-    public void setStrand(RnaFusionStrand value) { this.strand = value; }
+    public void setStrand(RNAFusionStrand value) { this.strand = value; }
 
     @JsonProperty("transcriptId")
     public String getTranscriptId() { return transcriptId; }

src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java

@@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*;
 
 public class RnaFusionFusionPartner5Prime {
     private String exon;
-    private StickyGene gene;
+    private CodingGene gene;
     private double position;
-    private RnaFusionStrand strand;
+    private RNAFusionStrand strand;
     private String transcriptId;
 
     @JsonProperty("exon")
@@ -15,9 +15,9 @@ public class RnaFusionFusionPartner5Prime {
     public void setExon(String value) { this.exon = value; }
 
     @JsonProperty("gene")
-    public StickyGene getGene() { return gene; }
+    public CodingGene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(StickyGene value) { this.gene = value; }
+    public void setGene(CodingGene value) { this.gene = value; }
 
     @JsonProperty("position")
     public double getPosition() { return position; }
@@ -25,9 +25,9 @@ public class RnaFusionFusionPartner5Prime {
     public void setPosition(double value) { this.position = value; }
 
     @JsonProperty("strand")
-    public RnaFusionStrand getStrand() { return strand; }
+    public RNAFusionStrand getStrand() { return strand; }
     @JsonProperty("strand")
-    public void setStrand(RnaFusionStrand value) { this.strand = value; }
+    public void setStrand(RNAFusionStrand value) { this.strand = value; }
 
     @JsonProperty("transcriptId")
     public String getTranscriptId() { return transcriptId; }

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class RnaSeqGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class SimpleVariantGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -1,21 +1,26 @@
 package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
+import java.util.List;
 
 public class Snv {
     private double allelicFrequency;
     private String altAllele;
     private Coding aminoAcidChange;
-    private Chromosome chromosome;
+    private CodingChromosome chromosome;
     private String cosmicId;
     private String dbSnpId;
     private Coding dnaChange;
-    private SimpleVariantGene gene;
+    private List<ExternalId> externalIds;
+    private CodingGene gene;
     private String id;
     private Coding interpretation;
+    private Patient patient;
+    private Position position;
+    private Coding proteinChange;
     private long readDepth;
     private String refAllele;
-    private StartEnd startEnd;
+    private ExternalId transcriptId;
 
     @JsonProperty("allelicFrequency")
     public double getAllelicFrequency() { return allelicFrequency; }
@@ -33,9 +38,9 @@ public class Snv {
     public void setAminoAcidChange(Coding value) { this.aminoAcidChange = value; }
 
     @JsonProperty("chromosome")
-    public Chromosome getChromosome() { return chromosome; }
+    public CodingChromosome getChromosome() { return chromosome; }
     @JsonProperty("chromosome")
-    public void setChromosome(Chromosome value) { this.chromosome = value; }
+    public void setChromosome(CodingChromosome value) { this.chromosome = value; }
 
     @JsonProperty("cosmicId")
     public String getCosmicId() { return cosmicId; }
@@ -52,10 +57,15 @@ public class Snv {
     @JsonProperty("dnaChange")
     public void setDnaChange(Coding value) { this.dnaChange = value; }
 
+    @JsonProperty("externalIds")
+    public List<ExternalId> getExternalIds() { return externalIds; }
+    @JsonProperty("externalIds")
+    public void setExternalIds(List<ExternalId> value) { this.externalIds = value; }
+
     @JsonProperty("gene")
-    public SimpleVariantGene getGene() { return gene; }
+    public CodingGene getGene() { return gene; }
     @JsonProperty("gene")
-    public void setGene(SimpleVariantGene value) { this.gene = value; }
+    public void setGene(CodingGene value) { this.gene = value; }
 
     @JsonProperty("id")
     public String getId() { return id; }
@@ -67,6 +77,21 @@ public class Snv {
     @JsonProperty("interpretation")
     public void setInterpretation(Coding value) { this.interpretation = value; }
 
+    @JsonProperty("patient")
+    public Patient getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Patient value) { this.patient = value; }
+
+    @JsonProperty("position")
+    public Position getPosition() { return position; }
+    @JsonProperty("position")
+    public void setPosition(Position value) { this.position = value; }
+
+    @JsonProperty("proteinChange")
+    public Coding getProteinChange() { return proteinChange; }
+    @JsonProperty("proteinChange")
+    public void setProteinChange(Coding value) { this.proteinChange = value; }
+
     @JsonProperty("readDepth")
     public long getReadDepth() { return readDepth; }
     @JsonProperty("readDepth")
@@ -77,8 +102,8 @@ public class Snv {
     @JsonProperty("refAllele")
     public void setRefAllele(String value) { this.refAllele = value; }
 
-    @JsonProperty("startEnd")
+    @JsonProperty("transcriptId")
-    public StartEnd getStartEnd() { return startEnd; }
+    public ExternalId getTranscriptId() { return transcriptId; }
-    @JsonProperty("startEnd")
+    @JsonProperty("transcriptId")
-    public void setStartEnd(StartEnd value) { this.startEnd = value; }
+    public void setTranscriptId(ExternalId value) { this.transcriptId = value; }
 }

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

@@ -5,46 +5,24 @@ import java.util.Date;
 import java.util.List;
 
 public class SomaticNgsReport {
-    private Double brcaness;
-    private List<Cnv> copyNumberVariants;
-    private List<DnaFusion> dnaFusions;
     private String id;
-    private Date issueDate;
+    private Date issuedOn;
     private List<Metadatum> metadata;
     private Double msi;
     private Patient patient;
-    private List<RnaFusion> rnaFusions;
+    private NgsReportResults results;
-    private List<RnaSeq> rnaSeqs;
     private Coding sequencingType;
-    private List<Snv> simpleVariants;
     private NgsReportSpecimen specimen;
-    private Double tmb;
-    private TumorCellContent tumorCellContent;
-
-    @JsonProperty("brcaness")
-    public Double getBrcaness() { return brcaness; }
-    @JsonProperty("brcaness")
-    public void setBrcaness(Double value) { this.brcaness = value; }
-
-    @JsonProperty("copyNumberVariants")
-    public List<Cnv> getCopyNumberVariants() { return copyNumberVariants; }
-    @JsonProperty("copyNumberVariants")
-    public void setCopyNumberVariants(List<Cnv> value) { this.copyNumberVariants = value; }
-
-    @JsonProperty("dnaFusions")
-    public List<DnaFusion> getDnaFusions() { return dnaFusions; }
-    @JsonProperty("dnaFusions")
-    public void setDnaFusions(List<DnaFusion> value) { this.dnaFusions = value; }
 
     @JsonProperty("id")
     public String getId() { return id; }
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
-    @JsonProperty("issueDate")
+    @JsonProperty("issuedOn")
-    public Date getIssueDate() { return issueDate; }
+    public Date getIssuedOn() { return issuedOn; }
-    @JsonProperty("issueDate")
+    @JsonProperty("issuedOn")
-    public void setIssueDate(Date value) { this.issueDate = value; }
+    public void setIssuedOn(Date value) { this.issuedOn = value; }
 
     @JsonProperty("metadata")
     public List<Metadatum> getMetadata() { return metadata; }
@@ -61,38 +39,18 @@ public class SomaticNgsReport {
     @JsonProperty("patient")
     public void setPatient(Patient value) { this.patient = value; }
 
-    @JsonProperty("rnaFusions")
+    @JsonProperty("results")
-    public List<RnaFusion> getRnaFusions() { return rnaFusions; }
+    public NgsReportResults getResults() { return results; }
-    @JsonProperty("rnaFusions")
+    @JsonProperty("results")
-    public void setRnaFusions(List<RnaFusion> value) { this.rnaFusions = value; }
+    public void setResults(NgsReportResults value) { this.results = value; }
-
-    @JsonProperty("rnaSeqs")
-    public List<RnaSeq> getRnaSeqs() { return rnaSeqs; }
-    @JsonProperty("rnaSeqs")
-    public void setRnaSeqs(List<RnaSeq> value) { this.rnaSeqs = value; }
 
     @JsonProperty("sequencingType")
     public Coding getSequencingType() { return sequencingType; }
     @JsonProperty("sequencingType")
     public void setSequencingType(Coding value) { this.sequencingType = value; }
 
-    @JsonProperty("simpleVariants")
-    public List<Snv> getSimpleVariants() { return simpleVariants; }
-    @JsonProperty("simpleVariants")
-    public void setSimpleVariants(List<Snv> value) { this.simpleVariants = value; }
-
     @JsonProperty("specimen")
     public NgsReportSpecimen getSpecimen() { return specimen; }
     @JsonProperty("specimen")
     public void setSpecimen(NgsReportSpecimen value) { this.specimen = value; }
-
-    @JsonProperty("tmb")
-    public Double getTmb() { return tmb; }
-    @JsonProperty("tmb")
-    public void setTmb(Double value) { this.tmb = value; }
-
-    @JsonProperty("tumorCellContent")
-    public TumorCellContent getTumorCellContent() { return tumorCellContent; }
-    @JsonProperty("tumorCellContent")
-    public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
 }

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

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum MtbDiagnosisTumorSpread {
+public enum StageCode {
     LOCAL, METASTASIZED, TUMOR_FREE, UNKNOWN;
 
     @JsonValue
@@ -18,7 +18,7 @@ public enum MtbDiagnosisTumorSpread {
     }
 
     @JsonCreator
-    public static MtbDiagnosisTumorSpread forValue(String value) throws IOException {
+    public static StageCode forValue(String value) throws IOException {
         switch (value) {
             case "local":
                 return LOCAL;
@@ -29,6 +29,6 @@ public enum MtbDiagnosisTumorSpread {
             case "unknown":
                 return UNKNOWN;
         }
-        throw new IOException("Cannot deserialize MTBDiagnosisTumorSpread");
+        throw new IOException("Cannot deserialize StageCode");
     }
 }

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

@@ -3,9 +3,9 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 import java.util.Date;
 
-public class StatusHistory {
+public class StageHistory {
     private Date date;
-    private MtbDiagnosisTumorSpread status;
+    private CodingTumorSpread stage;
 
     @JsonProperty("date")
     @JsonFormat(pattern = "yyyy-MM-dd")
@@ -14,8 +14,8 @@ public class StatusHistory {
     @JsonFormat(pattern = "yyyy-MM-dd")
     public void setDate(Date value) { this.date = value; }
 
-    @JsonProperty("status")
+    @JsonProperty("stage")
-    public MtbDiagnosisTumorSpread getStatus() { return status; }
+    public CodingTumorSpread getStage() { return stage; }
-    @JsonProperty("status")
+    @JsonProperty("stage")
-    public void setStatus(MtbDiagnosisTumorSpread value) { this.status = value; }
+    public void setStage(CodingTumorSpread value) { this.stage = value; }
 }

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

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum NotDoneReasonCode {
+public enum StatusReasonCode {
     CHRONIC_REMISSION, CONTINUED_EXTERNALLY, DETERIORATION, LOST_TO_FU, MEDICAL_REASON, NO_INDICATION, OTHER, OTHER_THERAPY_CHOSEN, PATIENT_DEATH, PATIENT_REFUSAL, PATIENT_WISH, PAYMENT_ENDED, PAYMENT_PENDING, PAYMENT_REFUSED, PROGRESSION, TOXICITY, UNKNOWN;
 
     @JsonValue
@@ -31,7 +31,7 @@ public enum NotDoneReasonCode {
     }
 
     @JsonCreator
-    public static NotDoneReasonCode forValue(String value) throws IOException {
+    public static StatusReasonCode forValue(String value) throws IOException {
         switch (value) {
             case "chronic-remission":
                 return CHRONIC_REMISSION;
@@ -68,6 +68,6 @@ public enum NotDoneReasonCode {
             case "unknown":
                 return UNKNOWN;
         }
-        throw new IOException("Cannot deserialize NotDoneReasonCode");
+        throw new IOException("Cannot deserialize StatusReasonCode");
     }
 }

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class StickyGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Study {
+    private String system;
+    private String value;
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+
+    @JsonProperty("value")
+    public String getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(String value) { this.value = value; }
+}

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

@@ -2,13 +2,16 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 import java.util.Date;
+import java.util.List;
 
 public class StudyEnrollmentRecommendation {
     private String id;
     private Date issuedOn;
-    private String nctNumber;
+    private Coding levelOfEvidence;
     private Patient patient;
-    private String reason;
+    private Reference reason;
+    private List<Study> studies;
+    private List<Reference> supportingVariants;
 
     @JsonProperty("id")
     public String getId() { return id; }
@@ -20,10 +23,10 @@ public class StudyEnrollmentRecommendation {
     @JsonProperty("issuedOn")
     public void setIssuedOn(Date value) { this.issuedOn = value; }
 
-    @JsonProperty("nctNumber")
+    @JsonProperty("levelOfEvidence")
-    public String getNctNumber() { return nctNumber; }
+    public Coding getLevelOfEvidence() { return levelOfEvidence; }
-    @JsonProperty("nctNumber")
+    @JsonProperty("levelOfEvidence")
-    public void setNctNumber(String value) { this.nctNumber = value; }
+    public void setLevelOfEvidence(Coding value) { this.levelOfEvidence = value; }
 
     @JsonProperty("patient")
     public Patient getPatient() { return patient; }
@@ -31,7 +34,17 @@ public class StudyEnrollmentRecommendation {
     public void setPatient(Patient value) { this.patient = value; }
 
     @JsonProperty("reason")
-    public String getReason() { return reason; }
+    public Reference getReason() { return reason; }
     @JsonProperty("reason")
-    public void setReason(String value) { this.reason = value; }
+    public void setReason(Reference value) { this.reason = value; }
+
+    @JsonProperty("studies")
+    public List<Study> getStudies() { return studies; }
+    @JsonProperty("studies")
+    public void setStudies(List<Study> value) { this.studies = value; }
+
+    @JsonProperty("supportingVariants")
+    public List<Reference> getSupportingVariants() { return supportingVariants; }
+    @JsonProperty("supportingVariants")
+    public void setSupportingVariants(List<Reference> value) { this.supportingVariants = value; }
 }

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

@@ -1,18 +0,0 @@
-package dev.pcvolkmer.mv64e.mtb;
-
-import com.fasterxml.jackson.annotation.*;
-
-public class TentacledGene {
-    private String ensemblId;
-    private String hgncId;
-
-    @JsonProperty("ensemblId")
-    public String getEnsemblId() { return ensemblId; }
-    @JsonProperty("ensemblId")
-    public void setEnsemblId(String value) { this.ensemblId = value; }
-
-    @JsonProperty("hgncId")
-    public String getHgncId() { return hgncId; }
-    @JsonProperty("hgncId")
-    public void setHgncId(String value) { this.hgncId = value; }
-}

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

@@ -0,0 +1,36 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Tmb {
+    private String id;
+    private Coding interpretation;
+    private Reference patient;
+    private Reference specimen;
+    private Value value;
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("interpretation")
+    public Coding getInterpretation() { return interpretation; }
+    @JsonProperty("interpretation")
+    public void setInterpretation(Coding value) { this.interpretation = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("specimen")
+    public Reference getSpecimen() { return specimen; }
+    @JsonProperty("specimen")
+    public void setSpecimen(Reference value) { this.specimen = value; }
+
+    @JsonProperty("value")
+    public Value getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(Value value) { this.value = value; }
+}

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

@@ -4,8 +4,9 @@ import com.fasterxml.jackson.annotation.*;
 
 public class TumorCellContent {
     private String id;
-    private TumorCellContentMethod method;
+    private CodingTumorCellContentMethod method;
-    private String specimen;
+    private Patient patient;
+    private TumorCellContentSpecimen specimen;
     private double value;
 
     @JsonProperty("id")
@@ -14,14 +15,19 @@ public class TumorCellContent {
     public void setId(String value) { this.id = value; }
 
     @JsonProperty("method")
-    public TumorCellContentMethod getMethod() { return method; }
+    public CodingTumorCellContentMethod getMethod() { return method; }
     @JsonProperty("method")
-    public void setMethod(TumorCellContentMethod value) { this.method = value; }
+    public void setMethod(CodingTumorCellContentMethod value) { this.method = value; }
+
+    @JsonProperty("patient")
+    public Patient getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Patient value) { this.patient = value; }
 
     @JsonProperty("specimen")
-    public String getSpecimen() { return specimen; }
+    public TumorCellContentSpecimen getSpecimen() { return specimen; }
     @JsonProperty("specimen")
-    public void setSpecimen(String value) { this.specimen = value; }
+    public void setSpecimen(TumorCellContentSpecimen value) { this.specimen = value; }
 
     @JsonProperty("value")
     public double getValue() { return value; }

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class TumorCellContentSpecimen {
+    private String id;
+    private SpecimenType type;
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("type")
+    public SpecimenType getType() { return type; }
+    @JsonProperty("type")
+    public void setType(SpecimenType value) { this.type = value; }
+}

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

@@ -0,0 +1,37 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum TumorGradeCode {
+    G1, G2, G3, G4, GX;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case G1: return "G1";
+            case G2: return "G2";
+            case G3: return "G3";
+            case G4: return "G4";
+            case GX: return "GX";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static TumorGradeCode forValue(String value) throws IOException {
+        switch (value) {
+            case "G1":
+                return G1;
+            case "G2":
+                return G2;
+            case "G3":
+                return G3;
+            case "G4":
+                return G4;
+            case "GX":
+                return GX;
+        }
+        throw new IOException("Cannot deserialize TumorGradeCode");
+    }
+}

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

@@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*;
 
 public class TumorMorphology {
     private String id;
-    private String note;
+    private String notes;
     private Patient patient;
-    private String specimen;
+    private TumorMorphologySpecimen specimen;
     private Coding value;
 
     @JsonProperty("id")
@@ -14,10 +14,10 @@ public class TumorMorphology {
     @JsonProperty("id")
     public void setId(String value) { this.id = value; }
 
-    @JsonProperty("note")
+    @JsonProperty("notes")
-    public String getNote() { return note; }
+    public String getNotes() { return notes; }
-    @JsonProperty("note")
+    @JsonProperty("notes")
-    public void setNote(String value) { this.note = value; }
+    public void setNotes(String value) { this.notes = value; }
 
     @JsonProperty("patient")
     public Patient getPatient() { return patient; }
@@ -25,9 +25,9 @@ public class TumorMorphology {
     public void setPatient(Patient value) { this.patient = value; }
 
     @JsonProperty("specimen")
-    public String getSpecimen() { return specimen; }
+    public TumorMorphologySpecimen getSpecimen() { return specimen; }
     @JsonProperty("specimen")
-    public void setSpecimen(String value) { this.specimen = value; }
+    public void setSpecimen(TumorMorphologySpecimen value) { this.specimen = value; }
 
     @JsonProperty("value")
     public Coding getValue() { return value; }

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

@@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb;
 
 import com.fasterxml.jackson.annotation.*;
 
-public class Specimen {
+public class TumorMorphologySpecimen {
     private String id;
     private SpecimenType type;
 

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

@@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*;
 
 public class TumorSpecimen {
     private Collection collection;
-    private Coding icd10;
+    private Diagnosis diagnosis;
     private String id;
     private Patient patient;
     private CodingTumorSpecimenType type;
@@ -14,10 +14,10 @@ public class TumorSpecimen {
     @JsonProperty("collection")
     public void setCollection(Collection value) { this.collection = value; }
 
-    @JsonProperty("icd10")
+    @JsonProperty("diagnosis")
-    public Coding getIcd10() { return icd10; }
+    public Diagnosis getDiagnosis() { return diagnosis; }
-    @JsonProperty("icd10")
+    @JsonProperty("diagnosis")
-    public void setIcd10(Coding value) { this.icd10 = value; }
+    public void setDiagnosis(Diagnosis value) { this.diagnosis = value; }
 
     @JsonProperty("id")
     public String getId() { return id; }

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

@@ -0,0 +1,22 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum Type {
+    ORGANIZATION;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case ORGANIZATION: return "Organization";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static Type forValue(String value) throws IOException {
+        if (value.equals("Organization")) return ORGANIZATION;
+        throw new IOException("Cannot deserialize Type");
+    }
+}

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

@@ -0,0 +1,22 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum Unit {
+    YEARS;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case YEARS: return "Years";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static Unit forValue(String value) throws IOException {
+        if (value.equals("Years")) return YEARS;
+        throw new IOException("Cannot deserialize Unit");
+    }
+}

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class Value {
+    private String unit;
+    private double value;
+
+    @JsonProperty("unit")
+    public String getUnit() { return unit; }
+    @JsonProperty("unit")
+    public void setUnit(String value) { this.unit = value; }
+
+    @JsonProperty("value")
+    public double getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(double value) { this.value = value; }
+}

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

@@ -0,0 +1,18 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class ValueWithUnit {
+    private Unit unit;
+    private double value;
+
+    @JsonProperty("unit")
+    public Unit getUnit() { return unit; }
+    @JsonProperty("unit")
+    public void setUnit(Unit value) { this.unit = value; }
+
+    @JsonProperty("value")
+    public double getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(double value) { this.value = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class VitalStatus {
+    private VitalStatusCode code;
+    private String display;
+    private String system;
+
+    @JsonProperty("code")
+    public VitalStatusCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(VitalStatusCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+}

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

@@ -0,0 +1,24 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum VitalStatusCode {
+    ALIVE, DECEASED;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case ALIVE: return "alive";
+            case DECEASED: return "deceased";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static VitalStatusCode forValue(String value) throws IOException {
+        if (value.equals("alive")) return ALIVE;
+        if (value.equals("deceased")) return DECEASED;
+        throw new IOException("Cannot deserialize VitalStatusCode");
+    }
+}