pcvolkmer/mv64e-mtb-dto-java
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Update model from schema and scala code

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This commit is contained in:
Paul-Christian Volkmer
2024-12-12 17:14:12 +01:00
parent d5b1926945
commit 50464681be
86 changed files with 1372 additions and 639 deletions
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36
src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java Normal file
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@ -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; }
}

4
src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java → src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java
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@ -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;

94
src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java
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@ -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");
}
}

68
src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java Normal file
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@ -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");
}
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java Normal file
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@ -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");
}
}

16
src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java
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@ -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")
public String getTherapy() { return therapy; }
@JsonProperty("therapy")
public void setTherapy(String value) { this.therapy = value; }
@JsonProperty("recommendation")
public Recommendation getRecommendation() { return recommendation; }
@JsonProperty("recommendation")
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; }
}

12
src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java
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@ -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; }
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java Normal file
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@ -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; }
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java
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@ -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; }

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java Normal file
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@ -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; }
}

8
src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java → src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java
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@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Code {
private String code;
public class CodingTumorGrade {
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; }

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/Components.java Normal file
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@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ConfidenceRange.java Normal file
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java
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@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java
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@ -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");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java
View File

@ -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; }
}

2
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java → src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java
View File

@ -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;

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java Normal file
View File

@ -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; }
}

12
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java
View File

@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class DnaFusionFusionPartner3Prime {
private Chromosome chromosome;
private PurpleGene gene;
private CodingChromosome chromosome;
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; }

12
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java
View File

@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class DnaFusionFusionPartner5Prime {
private Chromosome chromosome;
private FluffyGene gene;
private CodingChromosome chromosome;
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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java Normal file
View File

@ -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; }
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java → src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java
View File

@ -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");
}
}

31
src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java Normal file
View File

@ -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; }
}

8
src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java → src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java
View File

@ -2,14 +2,14 @@ package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class ExtId {
private SystemEnum system;
public class ExternalId {
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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java
View File

@ -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; }
}

2
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java → src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java
View File

@ -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;

22
src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java Normal file
View File

@ -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");
}
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java
View File

@ -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; }
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java
View File

@ -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");
}
}

42
src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java Normal file
View File

@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java Normal file
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportResults.java Normal file
View File

@ -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; }
}

74
src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java Normal file
View File

@ -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; }
}

30
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java → src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java
View File

@ -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")
public List<StatusHistory> getStatusHistory() { return statusHistory; }
@JsonProperty("statusHistory")
public void setStatusHistory(List<StatusHistory> value) { this.statusHistory = value; }
@JsonProperty("stageHistory")
public List<StageHistory> getStageHistory() { return stageHistory; }
@JsonProperty("stageHistory")
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; }
}

2
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java → src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java
View File

@ -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;

26
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java → src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java
View File

@ -4,27 +4,27 @@ import com.fasterxml.jackson.annotation.*;
import java.util.Date;
import java.util.List;
public class MtbMedicationRecommendation {
private String diagnosis;
public class MTBMedicationRecommendation {
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 List<String> supportingVariants;
@JsonProperty("diagnosis")
public String getDiagnosis() { return diagnosis; }
@JsonProperty("diagnosis")
public void setDiagnosis(String value) { this.diagnosis = value; }
private CodingTherapyRecommendationPriority priority;
private List<Reference> supportingVariants;
@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; }
}

42
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java → src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java
View File

@ -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 note;
private String notes;
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")
public CodingTherapyStatusReason getNotDoneReason() { return notDoneReason; }
@JsonProperty("notDoneReason")
public void setNotDoneReason(CodingTherapyStatusReason value) { this.notDoneReason = value; }
@JsonProperty("note")
public String getNote() { return note; }
@JsonProperty("note")
public void setNote(String value) { this.note = 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; }
@ -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; }

6
src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java
View File

@ -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; }
}

64
src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java
View File

@ -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<PerformanceStatus> ecogStatus;
private MtbEpisode episode;
private List<MTBDiagnosis> diagnoses;
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<MtbMedicationRecommendation> recommendations;
private List<PerformanceStatus> performanceStatus;
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; }
@JsonProperty("ecogStatus")
public List<PerformanceStatus> getEcogStatus() { return ecogStatus; }
@JsonProperty("ecogStatus")
public void setEcogStatus(List<PerformanceStatus> value) { this.ecogStatus = value; }
public void setDiagnoses(List<MTBDiagnosis> value) { this.diagnoses = 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")
public List<MtbMedicationTherapy> getPreviousGuidelineTherapies() { return previousGuidelineTherapies; }
@JsonProperty("previousGuidelineTherapies")
public void setPreviousGuidelineTherapies(List<MtbMedicationTherapy> value) { this.previousGuidelineTherapies = value; }
@JsonProperty("performanceStatus")
public List<PerformanceStatus> getPerformanceStatus() { return performanceStatus; }
@JsonProperty("performanceStatus")
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; }

62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java
View File

@ -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; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java
View File

@ -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")
public String getInsurance() { return insurance; }
@JsonProperty("insurance")
public void setInsurance(String value) { this.insurance = value; }
@JsonProperty("vitalStatus")
public VitalStatus getVitalStatus() { return vitalStatus; }
@JsonProperty("vitalStatus")
public void setVitalStatus(VitalStatus value) { this.vitalStatus = value; }
}

61
src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java Normal file
View File

@ -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; }
}

79
src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java Normal file
View File

@ -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; }
}

2
src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java → src/main/java/dev/pcvolkmer/mv64e/mtb/Position.java
View File

@ -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;

2
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java → src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java
View File

@ -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;

4
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java → src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java
View File

@ -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");

8
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java → src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java
View File

@ -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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java Normal file
View File

@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java Normal file
View File

@ -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; }
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java
View File

@ -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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java
View File

@ -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; }
}

12
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java
View File

@ -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; }

12
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java
View File

@ -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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java
View File

@ -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; }
}

47
src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java
View File

@ -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")
public StartEnd getStartEnd() { return startEnd; }
@JsonProperty("startEnd")
public void setStartEnd(StartEnd value) { this.startEnd = value; }
@JsonProperty("transcriptId")
public ExternalId getTranscriptId() { return transcriptId; }
@JsonProperty("transcriptId")
public void setTranscriptId(ExternalId value) { this.transcriptId = value; }
}

62
src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java
View File

@ -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 List<RnaSeq> rnaSeqs;
private NgsReportResults results;
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")
public Date getIssueDate() { return issueDate; }
@JsonProperty("issueDate")
public void setIssueDate(Date value) { this.issueDate = value; }
@JsonProperty("issuedOn")
public Date getIssuedOn() { return issuedOn; }
@JsonProperty("issuedOn")
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")
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("results")
public NgsReportResults getResults() { return results; }
@JsonProperty("results")
public void setResults(NgsReportResults value) { this.results = 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; }
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java → src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java
View File

@ -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");
}
}

12
src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java → src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java
View File

@ -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")
public MtbDiagnosisTumorSpread getStatus() { return status; }
@JsonProperty("status")
public void setStatus(MtbDiagnosisTumorSpread value) { this.status = value; }
@JsonProperty("stage")
public CodingTumorSpread getStage() { return stage; }
@JsonProperty("stage")
public void setStage(CodingTumorSpread value) { this.stage = value; }
}

6
src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java → src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java
View File

@ -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");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java Normal file
View File

@ -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; }
}

29
src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java
View File

@ -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")
public String getNctNumber() { return nctNumber; }
@JsonProperty("nctNumber")
public void setNctNumber(String value) { this.nctNumber = value; }
@JsonProperty("levelOfEvidence")
public Coding getLevelOfEvidence() { return levelOfEvidence; }
@JsonProperty("levelOfEvidence")
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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java
View File

@ -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; }
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java Normal file
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java
View File

@ -4,8 +4,9 @@ import com.fasterxml.jackson.annotation.*;
public class TumorCellContent {
private String id;
private TumorCellContentMethod method;
private String specimen;
private CodingTumorCellContentMethod method;
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; }

18
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java Normal file
View File

@ -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; }
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java Normal file
View File

@ -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");
}
}

16
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java
View File

@ -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")
public String getNote() { return note; }
@JsonProperty("note")
public void setNote(String value) { this.note = 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; }
@ -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; }

2
src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java → src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java
View File

@ -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;

10
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java
View File

@ -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")
public Coding getIcd10() { return icd10; }
@JsonProperty("icd10")
public void setIcd10(Coding value) { this.icd10 = value; }
@JsonProperty("diagnosis")
public Diagnosis getDiagnosis() { return diagnosis; }
@JsonProperty("diagnosis")
public void setDiagnosis(Diagnosis value) { this.diagnosis = value; }
@JsonProperty("id")
public String getId() { return id; }

22
src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java Normal file
View File

@ -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");
}
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java Normal file
View File

@ -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");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java Normal file
View File

@ -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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java Normal file
View File

@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java Normal file
View File

@ -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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java Normal file
View File

@ -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");
}
}