pcvolkmer/mv64e-mtb-dto-java
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Paul-Christian Volkmer
2024-07-09 16:36:24 +02:00
commit c7386f1dc2
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34
src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum AddendumCode {
IS, IV, R, Z;
@JsonValue
public String toValue() {
switch (this) {
case IS: return "is";
case IV: return "iv";
case R: return "R";
case Z: return "Z";
}
return null;
}
@JsonCreator
public static AddendumCode forValue(String value) throws IOException {
switch (value) {
case "is":
return IS;
case "iv":
return IV;
case "R":
return R;
case "Z":
return Z;
}
throw new IOException("Cannot deserialize AddendumCode");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Address.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Address {
private String municipalityCode;
@JsonProperty("municipalityCode")
public String getMunicipalityCode() { return municipalityCode; }
@JsonProperty("municipalityCode")
public void setMunicipalityCode(String value) { this.municipalityCode = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java Normal file
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class Claim {
private String id;
private Date issuedOn;
private Patient patient;
private String therapy;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getIssuedOn() { return issuedOn; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setIssuedOn(Date value) { this.issuedOn = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class ClaimResponse {
private ClaimResponseClaim claim;
private String id;
private Date issuedOn;
private Patient patient;
private ClaimResponseStatusReason reason;
private CodingClaimResponseStatus status;
@JsonProperty("claim")
public ClaimResponseClaim getClaim() { return claim; }
@JsonProperty("claim")
public void setClaim(ClaimResponseClaim value) { this.claim = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getIssuedOn() { return issuedOn; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setIssuedOn(Date value) { this.issuedOn = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class ClaimResponseClaim {
private String id;
private ClaimResponseClaimType type;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("type")
public ClaimResponseClaimType getType() { return type; }
@JsonProperty("type")
public void setType(ClaimResponseClaimType value) { this.type = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum ClaimResponseClaimType {
CLAIM;
@JsonValue
public String toValue() {
switch (this) {
case CLAIM: return "Claim";
}
return null;
}
@JsonCreator
public static ClaimResponseClaimType forValue(String value) throws IOException {
if (value.equals("Claim")) return CLAIM;
throw new IOException("Cannot deserialize ClaimResponseClaimType");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatus.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum ClaimResponseStatus {
ACCEPTED, REJECTED, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case ACCEPTED: return "accepted";
case REJECTED: return "rejected";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static ClaimResponseStatus forValue(String value) throws IOException {
switch (value) {
case "accepted":
return ACCEPTED;
case "rejected":
return REJECTED;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize ClaimResponseStatus");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReason.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum ClaimResponseStatusReason {
APPROVAL_REVOCATION, FORMAL_REASONS, INCLUSION_IN_STUDY, INSUFFICIENT_EVIDENCE, OTHER, OTHER_THERAPY_RECOMMENDED, STANDARD_THERAPY_NOT_EXHAUSTED, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case APPROVAL_REVOCATION: return "approval-revocation";
case FORMAL_REASONS: return "formal-reasons";
case INCLUSION_IN_STUDY: return "inclusion-in-study";
case INSUFFICIENT_EVIDENCE: return "insufficient-evidence";
case OTHER: return "other";
case OTHER_THERAPY_RECOMMENDED: return "other-therapy-recommended";
case STANDARD_THERAPY_NOT_EXHAUSTED: return "standard-therapy-not-exhausted";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static ClaimResponseStatusReason forValue(String value) throws IOException {
switch (value) {
case "approval-revocation":
return APPROVAL_REVOCATION;
case "formal-reasons":
return FORMAL_REASONS;
case "inclusion-in-study":
return INCLUSION_IN_STUDY;
case "insufficient-evidence":
return INSUFFICIENT_EVIDENCE;
case "other":
return OTHER;
case "other-therapy-recommended":
return OTHER_THERAPY_RECOMMENDED;
case "standard-therapy-not-exhausted":
return STANDARD_THERAPY_NOT_EXHAUSTED;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize ClaimResponseStatusReason");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.List;
public class Cnv {
private Chromosome chromosome;
private Double cnA;
private Double cnB;
private List<CopyNumberNeutralLoH> copyNumberNeutralLoH;
private EndRange endRange;
private String id;
private Double relativeCopyNumber;
private List<ReportedAffectedGene> reportedAffectedGenes;
private String reportedFocality;
private StartRange startRange;
private Long totalCopyNumber;
private CnvType type;
@JsonProperty("chromosome")
public Chromosome getChromosome() { return chromosome; }
@JsonProperty("chromosome")
public void setChromosome(Chromosome value) { this.chromosome = value; }
@JsonProperty("cnA")
public Double getCnA() { return cnA; }
@JsonProperty("cnA")
public void setCnA(Double value) { this.cnA = value; }
@JsonProperty("cnB")
public Double getCnB() { return cnB; }
@JsonProperty("cnB")
public void setCnB(Double value) { this.cnB = value; }
@JsonProperty("copyNumberNeutralLoH")
public List<CopyNumberNeutralLoH> getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; }
@JsonProperty("copyNumberNeutralLoH")
public void setCopyNumberNeutralLoH(List<CopyNumberNeutralLoH> value) { this.copyNumberNeutralLoH = value; }
@JsonProperty("endRange")
public EndRange getEndRange() { return endRange; }
@JsonProperty("endRange")
public void setEndRange(EndRange value) { this.endRange = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = 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; }
@JsonProperty("reportedAffectedGenes")
public void setReportedAffectedGenes(List<ReportedAffectedGene> value) { this.reportedAffectedGenes = value; }
@JsonProperty("reportedFocality")
public String getReportedFocality() { return reportedFocality; }
@JsonProperty("reportedFocality")
public void setReportedFocality(String value) { this.reportedFocality = value; }
@JsonProperty("startRange")
public StartRange getStartRange() { return startRange; }
@JsonProperty("startRange")
public void setStartRange(StartRange value) { this.startRange = value; }
@JsonProperty("totalCopyNumber")
public Long getTotalCopyNumber() { return totalCopyNumber; }
@JsonProperty("totalCopyNumber")
public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; }
@JsonProperty("type")
public CnvType getType() { return type; }
@JsonProperty("type")
public void setType(CnvType value) { this.type = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum CnvType {
HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN;
@JsonValue
public String toValue() {
switch (this) {
case HIGH_LEVEL_GAIN: return "high-level-gain";
case LOSS: return "loss";
case LOW_LEVEL_GAIN: return "low-level-gain";
}
return null;
}
@JsonCreator
public static CnvType forValue(String value) throws IOException {
switch (value) {
case "high-level-gain":
return HIGH_LEVEL_GAIN;
case "loss":
return LOSS;
case "low-level-gain":
return LOW_LEVEL_GAIN;
}
throw new IOException("Cannot deserialize CNVType");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Code {
private String code;
private String display;
private String system;
private String version;
@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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Coding.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Coding {
private String code;
private String display;
private String system;
private String version;
@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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingClaimResponseStatus {
private ClaimResponseStatus code;
private String display;
private String system;
@JsonProperty("code")
public ClaimResponseStatus getCode() { return code; }
@JsonProperty("code")
public void setCode(ClaimResponseStatus 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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingEcog {
private PurpleCode code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public PurpleCode getCode() { return code; }
@JsonProperty("code")
public void setCode(PurpleCode 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingGender {
private Gender code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public Gender getCode() { return code; }
@JsonProperty("code")
public void setCode(Gender 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingLevelOfEvidenceAddendum {
private AddendumCode code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public AddendumCode getCode() { return code; }
@JsonProperty("code")
public void setCode(AddendumCode 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingLevelOfEvidenceGrading {
private GradingCode code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public GradingCode getCode() { return code; }
@JsonProperty("code")
public void setCode(GradingCode 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingRecist {
private FluffyCode code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public FluffyCode getCode() { return code; }
@JsonProperty("code")
public void setCode(FluffyCode 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingTherapyStatusReason {
private NotDoneReasonCode code;
private String display;
private String system;
private String version;
@JsonProperty("code")
public NotDoneReasonCode getCode() { return code; }
@JsonProperty("code")
public void setCode(NotDoneReasonCode 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; }
@JsonProperty("version")
public String getVersion() { return version; }
@JsonProperty("version")
public void setVersion(String value) { this.version = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingTumorSpecimenCollectionLocalization {
private TumorSpecimenCollectionLocalization code;
private String display;
private String system;
@JsonProperty("code")
public TumorSpecimenCollectionLocalization getCode() { return code; }
@JsonProperty("code")
public void setCode(TumorSpecimenCollectionLocalization 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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingTumorSpecimenCollectionMethod {
private TumorSpecimenCollectionMethod code;
private String display;
private String system;
@JsonProperty("code")
public TumorSpecimenCollectionMethod getCode() { return code; }
@JsonProperty("code")
public void setCode(TumorSpecimenCollectionMethod 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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class CodingTumorSpecimenType {
private TumorSpecimenType code;
private String display;
private String system;
@JsonProperty("code")
public TumorSpecimenType getCode() { return code; }
@JsonProperty("code")
public void setCode(TumorSpecimenType 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; }
}

27
src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class Collection {
private Date date;
private CodingTumorSpecimenCollectionLocalization localization;
private CodingTumorSpecimenCollectionMethod method;
@JsonProperty("date")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getDate() { return date; }
@JsonProperty("date")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setDate(Date value) { this.date = value; }
@JsonProperty("localization")
public CodingTumorSpecimenCollectionLocalization getLocalization() { return localization; }
@JsonProperty("localization")
public void setLocalization(CodingTumorSpecimenCollectionLocalization value) { this.localization = value; }
@JsonProperty("method")
public CodingTumorSpecimenCollectionMethod getMethod() { return method; }
@JsonProperty("method")
public void setMethod(CodingTumorSpecimenCollectionMethod value) { this.method = value; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java Normal file
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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 Normal file
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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");
}
}

107
src/main/java/dev/pcvolkmer/mv64e/mtb/Converter.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.*;
import com.fasterxml.jackson.databind.module.SimpleModule;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.Date;
public class Converter {
// Date-time helpers
private static final String[] DATE_TIME_FORMATS = {
"yyyy-MM-dd'T'HH:mm:ss.SX",
"yyyy-MM-dd'T'HH:mm:ss.S",
"yyyy-MM-dd'T'HH:mm:ssX",
"yyyy-MM-dd'T'HH:mm:ss",
"yyyy-MM-dd HH:mm:ss.SX",
"yyyy-MM-dd HH:mm:ss.S",
"yyyy-MM-dd HH:mm:ssX",
"yyyy-MM-dd HH:mm:ss",
"HH:mm:ss.SZ",
"HH:mm:ss.S",
"HH:mm:ssZ",
"HH:mm:ss",
"yyyy-MM-dd",
};
public static Date parseAllDateTimeString(String str) {
for (String format : DATE_TIME_FORMATS) {
try {
return new SimpleDateFormat(format).parse(str);
} catch (Exception ex) {
// Ignored
}
}
return null;
}
public static String serializeDateTime(Date datetime) {
return new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ssZ").format(datetime);
}
public static String serializeDate(Date datetime) {
return new SimpleDateFormat("yyyy-MM-dd").format(datetime);
}
public static String serializeTime(Date datetime) {
return new SimpleDateFormat("hh:mm:ssZ").format(datetime);
}
// Serialize/deserialize helpers
public static Mtb fromJsonString(String json) throws IOException {
return getObjectReader().readValue(json);
}
public static String toJsonString(Mtb obj) throws JsonProcessingException {
return getObjectWriter().writeValueAsString(obj);
}
private static ObjectReader reader;
private static ObjectWriter writer;
private static void instantiateMapper() {
ObjectMapper mapper = new ObjectMapper();
mapper.findAndRegisterModules();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
mapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
SimpleModule module = new SimpleModule();
module.addDeserializer(Date.class, new JsonDeserializer<>() {
@Override
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
String value = jsonParser.getText();
return Converter.parseAllDateTimeString(value);
}
});
module.addDeserializer(Date.class, new JsonDeserializer<>() {
@Override
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
String value = jsonParser.getText();
return Converter.parseAllDateTimeString(value);
}
});
module.addDeserializer(Date.class, new JsonDeserializer<>() {
@Override
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
String value = jsonParser.getText();
return Converter.parseAllDateTimeString(value);
}
});
mapper.registerModule(module);
reader = mapper.readerFor(Mtb.class);
writer = mapper.writerFor(Mtb.class);
}
private static ObjectReader getObjectReader() {
if (reader == null) instantiateMapper();
return reader;
}
private static ObjectWriter getObjectWriter() {
if (writer == null) instantiateMapper();
return writer;
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java Normal file
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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; }
}

30
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class DnaFusion {
private DnaFusionFusionPartner3Prime fusionPartner3Prime;
private DnaFusionFusionPartner5Prime fusionPartner5Prime;
private String id;
private long reportedNumReads;
@JsonProperty("fusionPartner3prime")
public DnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; }
@JsonProperty("fusionPartner3prime")
public void setFusionPartner3Prime(DnaFusionFusionPartner3Prime value) { this.fusionPartner3Prime = value; }
@JsonProperty("fusionPartner5prime")
public DnaFusionFusionPartner5Prime getFusionPartner5Prime() { return fusionPartner5Prime; }
@JsonProperty("fusionPartner5prime")
public void setFusionPartner5Prime(DnaFusionFusionPartner5Prime value) { this.fusionPartner5Prime = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("reportedNumReads")
public long getReportedNumReads() { return reportedNumReads; }
@JsonProperty("reportedNumReads")
public void setReportedNumReads(long value) { this.reportedNumReads = value; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class DnaFusionFusionPartner3Prime {
private Chromosome chromosome;
private PurpleGene gene;
private double position;
@JsonProperty("chromosome")
public Chromosome getChromosome() { return chromosome; }
@JsonProperty("chromosome")
public void setChromosome(Chromosome value) { this.chromosome = value; }
@JsonProperty("gene")
public PurpleGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(PurpleGene value) { this.gene = value; }
@JsonProperty("position")
public double getPosition() { return position; }
@JsonProperty("position")
public void setPosition(double value) { this.position = value; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class DnaFusionFusionPartner5Prime {
private Chromosome chromosome;
private FluffyGene gene;
private double position;
@JsonProperty("chromosome")
public Chromosome getChromosome() { return chromosome; }
@JsonProperty("chromosome")
public void setChromosome(Chromosome value) { this.chromosome = value; }
@JsonProperty("gene")
public FluffyGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(FluffyGene value) { this.gene = value; }
@JsonProperty("position")
public double getPosition() { return position; }
@JsonProperty("position")
public void setPosition(double value) { this.position = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/EndRange.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class EndRange {
private Double end;
private double start;
@JsonProperty("end")
public Double getEnd() { return end; }
@JsonProperty("end")
public void setEnd(Double value) { this.end = value; }
@JsonProperty("start")
public double getStart() { return start; }
@JsonProperty("start")
public void setStart(double value) { this.start = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class ExtId {
private SystemEnum system;
private String value;
@JsonProperty("system")
public SystemEnum getSystem() { return system; }
@JsonProperty("system")
public void setSystem(SystemEnum value) { this.system = value; }
@JsonProperty("value")
public String getValue() { return value; }
@JsonProperty("value")
public void setValue(String value) { this.value = value; }
}

43
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyCode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum FluffyCode {
CR, MR, NA, NYA, PD, PR, SD;
@JsonValue
public String toValue() {
switch (this) {
case CR: return "CR";
case MR: return "MR";
case NA: return "NA";
case NYA: return "NYA";
case PD: return "PD";
case PR: return "PR";
case SD: return "SD";
}
return null;
}
@JsonCreator
public static FluffyCode forValue(String value) throws IOException {
switch (value) {
case "CR":
return CR;
case "MR":
return MR;
case "NA":
return NA;
case "NYA":
return NYA;
case "PD":
return PD;
case "PR":
return PR;
case "SD":
return SD;
}
throw new IOException("Cannot deserialize FluffyCode");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java Normal file
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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; }
}

34
src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum Gender {
FEMALE, MALE, OTHER, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case FEMALE: return "female";
case MALE: return "male";
case OTHER: return "other";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static Gender forValue(String value) throws IOException {
switch (value) {
case "female":
return FEMALE;
case "male":
return MALE;
case "other":
return OTHER;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize Gender");
}
}

31
src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class GeneticCounselingRecommendation {
private String id;
private Date issuedOn;
private Patient patient;
private String reason;
@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("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = value; }
@JsonProperty("reason")
public String getReason() { return reason; }
@JsonProperty("reason")
public void setReason(String value) { this.reason = value; }
}

49
src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum GradingCode {
M1_A, M1_B, M1_C, M2_A, M2_B, M2_C, M3, M4, UNDEFINED;
@JsonValue
public String toValue() {
switch (this) {
case M1_A: return "m1A";
case M1_B: return "m1B";
case M1_C: return "m1C";
case M2_A: return "m2A";
case M2_B: return "m2B";
case M2_C: return "m2C";
case M3: return "m3";
case M4: return "m4";
case UNDEFINED: return "undefined";
}
return null;
}
@JsonCreator
public static GradingCode forValue(String value) throws IOException {
switch (value) {
case "m1A":
return M1_A;
case "m1B":
return M1_B;
case "m1C":
return M1_C;
case "m2A":
return M2_A;
case "m2B":
return M2_B;
case "m2C":
return M2_C;
case "m3":
return M3;
case "m4":
return M4;
case "undefined":
return UNDEFINED;
}
throw new IOException("Cannot deserialize GradingCode");
}
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java Normal file
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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");
}
}

45
src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class HistologyReport {
private String id;
private Date issuedOn;
private Patient patient;
private HistologyReportSpecimen specimen;
private TumorCellContent tumorCellContent;
private TumorMorphology tumorMorphology;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getIssuedOn() { return issuedOn; }
@JsonProperty("issuedOn")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setIssuedOn(Date value) { this.issuedOn = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = 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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class HistologyReportSpecimen {
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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.List;
public class LevelOfEvidence {
private List<CodingLevelOfEvidenceAddendum> addendums;
private CodingLevelOfEvidenceGrading grading;
private List<ReferencePublication> publications;
@JsonProperty("addendums")
public List<CodingLevelOfEvidenceAddendum> getAddendums() { return addendums; }
@JsonProperty("addendums")
public void setAddendums(List<CodingLevelOfEvidenceAddendum> value) { this.addendums = value; }
@JsonProperty("grading")
public CodingLevelOfEvidenceGrading getGrading() { return grading; }
@JsonProperty("grading")
public void setGrading(CodingLevelOfEvidenceGrading value) { this.grading = value; }
@JsonProperty("publications")
public List<ReferencePublication> getPublications() { return publications; }
@JsonProperty("publications")
public void setPublications(List<ReferencePublication> value) { this.publications = value; }
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/Metadatum.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Metadatum {
private String kitManufacturer;
private String kitType;
private String pipeline;
private String referenceGenome;
private String sequencer;
@JsonProperty("kitManufacturer")
public String getKitManufacturer() { return kitManufacturer; }
@JsonProperty("kitManufacturer")
public void setKitManufacturer(String value) { this.kitManufacturer = value; }
@JsonProperty("kitType")
public String getKitType() { return kitType; }
@JsonProperty("kitType")
public void setKitType(String value) { this.kitType = value; }
@JsonProperty("pipeline")
public String getPipeline() { return pipeline; }
@JsonProperty("pipeline")
public void setPipeline(String value) { this.pipeline = value; }
@JsonProperty("referenceGenome")
public String getReferenceGenome() { return referenceGenome; }
@JsonProperty("referenceGenome")
public void setReferenceGenome(String value) { this.referenceGenome = value; }
@JsonProperty("sequencer")
public String getSequencer() { return sequencer; }
@JsonProperty("sequencer")
public void setSequencer(String value) { this.sequencer = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.List;
public class MolecularTherapy {
private List<MtbMedicationTherapy> history;
@JsonProperty("history")
public List<MtbMedicationTherapy> getHistory() { return history; }
@JsonProperty("history")
public void setHistory(List<MtbMedicationTherapy> value) { this.history = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.List;
public class Mtb {
private List<MtbCarePlan> carePlans;
private List<ClaimResponse> claimResponses;
private List<Claim> claims;
private Consent consent;
private List<MtbDiagnosis> diagnoses;
private List<PerformanceStatus> ecogStatus;
private MtbEpisode episode;
private List<GeneticCounselingRecommendation> geneticCounsellingRequests;
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<Response> responses;
private List<TumorSpecimen> specimens;
private List<StudyEnrollmentRecommendation> studyInclusionRequests;
@JsonProperty("carePlans")
public List<MtbCarePlan> getCarePlans() { return carePlans; }
@JsonProperty("carePlans")
public void setCarePlans(List<MtbCarePlan> value) { this.carePlans = value; }
@JsonProperty("claimResponses")
public List<ClaimResponse> getClaimResponses() { return claimResponses; }
@JsonProperty("claimResponses")
public void setClaimResponses(List<ClaimResponse> value) { this.claimResponses = value; }
@JsonProperty("claims")
public List<Claim> getClaims() { return claims; }
@JsonProperty("claims")
public void setClaims(List<Claim> value) { this.claims = value; }
@JsonProperty("consent")
public Consent getConsent() { return consent; }
@JsonProperty("consent")
public void setConsent(Consent value) { this.consent = value; }
@JsonProperty("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; }
@JsonProperty("episode")
public MtbEpisode getEpisode() { return episode; }
@JsonProperty("episode")
public void setEpisode(MtbEpisode value) { this.episode = value; }
@JsonProperty("geneticCounsellingRequests")
public List<GeneticCounselingRecommendation> getGeneticCounsellingRequests() { return geneticCounsellingRequests; }
@JsonProperty("geneticCounsellingRequests")
public void setGeneticCounsellingRequests(List<GeneticCounselingRecommendation> value) { this.geneticCounsellingRequests = 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")
public void setMolecularTherapies(List<MolecularTherapy> value) { this.molecularTherapies = value; }
@JsonProperty("ngsReports")
public List<SomaticNgsReport> getNgsReports() { return ngsReports; }
@JsonProperty("ngsReports")
public void setNgsReports(List<SomaticNgsReport> value) { this.ngsReports = value; }
@JsonProperty("patient")
public MtbPatient getPatient() { return patient; }
@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("recommendations")
public List<MtbMedicationRecommendation> getRecommendations() { return recommendations; }
@JsonProperty("recommendations")
public void setRecommendations(List<MtbMedicationRecommendation> value) { this.recommendations = value; }
@JsonProperty("responses")
public List<Response> getResponses() { return responses; }
@JsonProperty("responses")
public void setResponses(List<Response> value) { this.responses = value; }
@JsonProperty("specimens")
public List<TumorSpecimen> getSpecimens() { return specimens; }
@JsonProperty("specimens")
public void setSpecimens(List<TumorSpecimen> value) { this.specimens = value; }
@JsonProperty("studyInclusionRequests")
public List<StudyEnrollmentRecommendation> getStudyInclusionRequests() { return studyInclusionRequests; }
@JsonProperty("studyInclusionRequests")
public void setStudyInclusionRequests(List<StudyEnrollmentRecommendation> value) { this.studyInclusionRequests = value; }
}

62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java Normal file
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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; }
}

62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
import java.util.List;
public class MtbDiagnosis {
private Coding code;
private Coding guidelineTreatmentStatus;
private List<String> histologyResults;
private Coding icdO3T;
private String id;
private Patient patient;
private Date recordedOn;
private List<StatusHistory> statusHistory;
private Coding whoGrade;
@JsonProperty("code")
public Coding getCode() { return code; }
@JsonProperty("code")
public void setCode(Coding value) { this.code = value; }
@JsonProperty("guidelineTreatmentStatus")
public Coding getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; }
@JsonProperty("guidelineTreatmentStatus")
public void setGuidelineTreatmentStatus(Coding value) { this.guidelineTreatmentStatus = value; }
@JsonProperty("histologyResults")
public List<String> getHistologyResults() { return histologyResults; }
@JsonProperty("histologyResults")
public void setHistologyResults(List<String> value) { this.histologyResults = value; }
@JsonProperty("icdO3T")
public Coding getIcdO3T() { return icdO3T; }
@JsonProperty("icdO3T")
public void setIcdO3T(Coding value) { this.icdO3T = value; }
@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("recordedOn")
public Date getRecordedOn() { return recordedOn; }
@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("whoGrade")
public Coding getWhoGrade() { return whoGrade; }
@JsonProperty("whoGrade")
public void setWhoGrade(Coding value) { this.whoGrade = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum MtbDiagnosisTumorSpread {
LOCAL, METASTASIZED, TUMOR_FREE, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case LOCAL: return "local";
case METASTASIZED: return "metastasized";
case TUMOR_FREE: return "tumor-free";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static MtbDiagnosisTumorSpread forValue(String value) throws IOException {
switch (value) {
case "local":
return LOCAL;
case "metastasized":
return METASTASIZED;
case "tumor-free":
return TUMOR_FREE;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize MTBDiagnosisTumorSpread");
}
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class MtbEpisode {
private String id;
private Patient patient;
private PeriodLocalDate period;
@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("period")
public PeriodLocalDate getPeriod() { return period; }
@JsonProperty("period")
public void setPeriod(PeriodLocalDate value) { this.period = value; }
}

62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
import java.util.List;
public class MtbMedicationRecommendation {
private String diagnosis;
private String id;
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; }
@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("levelOfEvidence")
public LevelOfEvidence getLevelOfEvidence() { return levelOfEvidence; }
@JsonProperty("levelOfEvidence")
public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; }
@JsonProperty("medication")
public List<Coding> getMedication() { return medication; }
@JsonProperty("medication")
public void setMedication(List<Coding> value) { this.medication = value; }
@JsonProperty("ngsReport")
public String getNgsReport() { return ngsReport; }
@JsonProperty("ngsReport")
public void setNgsReport(String value) { this.ngsReport = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = value; }
@JsonProperty("priority")
public TherapyRecommendationPriority getPriority() { return priority; }
@JsonProperty("priority")
public void setPriority(TherapyRecommendationPriority value) { this.priority = value; }
@JsonProperty("supportingVariants")
public List<String> getSupportingVariants() { return supportingVariants; }
@JsonProperty("supportingVariants")
public void setSupportingVariants(List<String> value) { this.supportingVariants = value; }
}

80
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
import java.util.List;
public class MtbMedicationTherapy {
private String basedOn;
private String diagnosis;
private String id;
private List<Coding> medication;
private CodingTherapyStatusReason notDoneReason;
private String note;
private Patient patient;
private PeriodLocalDate period;
private CodingTherapyStatusReason reasonStopped;
private Date recordedOn;
private TherapyStatus status;
private Long therapyLine;
@JsonProperty("basedOn")
public String getBasedOn() { return basedOn; }
@JsonProperty("basedOn")
public void setBasedOn(String value) { this.basedOn = 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("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("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("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; }
@JsonProperty("status")
public void setStatus(TherapyStatus value) { this.status = value; }
@JsonProperty("therapyLine")
public Long getTherapyLine() { return therapyLine; }
@JsonProperty("therapyLine")
public void setTherapyLine(Long value) { this.therapyLine = value; }
}

45
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class MtbPatient {
private Address address;
private Date birthDate;
private Date dateOfDeath;
private CodingGender gender;
private String id;
private String insurance;
@JsonProperty("address")
public Address getAddress() { return address; }
@JsonProperty("address")
public void setAddress(Address value) { this.address = value; }
@JsonProperty("birthDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getBirthDate() { return birthDate; }
@JsonProperty("birthDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setBirthDate(Date value) { this.birthDate = value; }
@JsonProperty("dateOfDeath")
public Date getDateOfDeath() { return dateOfDeath; }
@JsonProperty("dateOfDeath")
public void setDateOfDeath(Date value) { this.dateOfDeath = value; }
@JsonProperty("gender")
public CodingGender getGender() { return gender; }
@JsonProperty("gender")
public void setGender(CodingGender value) { this.gender = 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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class NgsReportSpecimen {
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; }
}

25
src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class NoTargetFinding {
private String diagnosis;
private Date issuedOn;
private Patient patient;
@JsonProperty("diagnosis")
public String getDiagnosis() { return diagnosis; }
@JsonProperty("diagnosis")
public void setDiagnosis(String value) { this.diagnosis = value; }
@JsonProperty("issuedOn")
public Date getIssuedOn() { return issuedOn; }
@JsonProperty("issuedOn")
public void setIssuedOn(Date value) { this.issuedOn = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = value; }
}

73
src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum NotDoneReasonCode {
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
public String toValue() {
switch (this) {
case CHRONIC_REMISSION: return "chronic-remission";
case CONTINUED_EXTERNALLY: return "continued-externally";
case DETERIORATION: return "deterioration";
case LOST_TO_FU: return "lost-to-fu";
case MEDICAL_REASON: return "medical-reason";
case NO_INDICATION: return "no-indication";
case OTHER: return "other";
case OTHER_THERAPY_CHOSEN: return "other-therapy-chosen";
case PATIENT_DEATH: return "patient-death";
case PATIENT_REFUSAL: return "patient-refusal";
case PATIENT_WISH: return "patient-wish";
case PAYMENT_ENDED: return "payment-ended";
case PAYMENT_PENDING: return "payment-pending";
case PAYMENT_REFUSED: return "payment-refused";
case PROGRESSION: return "progression";
case TOXICITY: return "toxicity";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static NotDoneReasonCode forValue(String value) throws IOException {
switch (value) {
case "chronic-remission":
return CHRONIC_REMISSION;
case "continued-externally":
return CONTINUED_EXTERNALLY;
case "deterioration":
return DETERIORATION;
case "lost-to-fu":
return LOST_TO_FU;
case "medical-reason":
return MEDICAL_REASON;
case "no-indication":
return NO_INDICATION;
case "other":
return OTHER;
case "other-therapy-chosen":
return OTHER_THERAPY_CHOSEN;
case "patient-death":
return PATIENT_DEATH;
case "patient-refusal":
return PATIENT_REFUSAL;
case "patient-wish":
return PATIENT_WISH;
case "payment-ended":
return PAYMENT_ENDED;
case "payment-pending":
return PAYMENT_PENDING;
case "payment-refused":
return PAYMENT_REFUSED;
case "progression":
return PROGRESSION;
case "toxicity":
return TOXICITY;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize NotDoneReasonCode");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Patient {
private String id;
private PatientType type;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("type")
public PatientType getType() { return type; }
@JsonProperty("type")
public void setType(PatientType value) { this.type = value; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum PatientType {
PATIENT;
@JsonValue
public String toValue() {
switch (this) {
case PATIENT: return "Patient";
}
return null;
}
@JsonCreator
public static PatientType forValue(String value) throws IOException {
if (value.equals("Patient")) return PATIENT;
throw new IOException("Cannot deserialize PatientType");
}
}

33
src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class PerformanceStatus {
private Date effectiveDate;
private String id;
private Patient patient;
private CodingEcog value;
@JsonProperty("effectiveDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getEffectiveDate() { return effectiveDate; }
@JsonProperty("effectiveDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setEffectiveDate(Date value) { this.effectiveDate = value; }
@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("value")
public CodingEcog getValue() { return value; }
@JsonProperty("value")
public void setValue(CodingEcog value) { this.value = value; }
}

21
src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class PeriodLocalDate {
private Date end;
private Date start;
@JsonProperty("end")
public Date getEnd() { return end; }
@JsonProperty("end")
public void setEnd(Date value) { this.end = value; }
@JsonProperty("start")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getStart() { return start; }
@JsonProperty("start")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setStart(Date value) { this.start = value; }
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleCode.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum PurpleCode {
THE_0, THE_1, THE_2, THE_3, THE_4;
@JsonValue
public String toValue() {
switch (this) {
case THE_0: return "0";
case THE_1: return "1";
case THE_2: return "2";
case THE_3: return "3";
case THE_4: return "4";
}
return null;
}
@JsonCreator
public static PurpleCode forValue(String value) throws IOException {
switch (value) {
case "0":
return THE_0;
case "1":
return THE_1;
case "2":
return THE_2;
case "3":
return THE_3;
case "4":
return THE_4;
}
throw new IOException("Cannot deserialize PurpleCode");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class PurpleGene {
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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class RNAFusion {
private String cosmicId;
private String effect;
private RnaFusionFusionPartner3Prime fusionPartner3Prime;
private RnaFusionFusionPartner5Prime fusionPartner5Prime;
private String id;
private long reportedNumReads;
@JsonProperty("cosmicId")
public String getCosmicId() { return cosmicId; }
@JsonProperty("cosmicId")
public void setCosmicId(String value) { this.cosmicId = value; }
@JsonProperty("effect")
public String getEffect() { return effect; }
@JsonProperty("effect")
public void setEffect(String value) { this.effect = value; }
@JsonProperty("fusionPartner3prime")
public RnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; }
@JsonProperty("fusionPartner3prime")
public void setFusionPartner3Prime(RnaFusionFusionPartner3Prime value) { this.fusionPartner3Prime = value; }
@JsonProperty("fusionPartner5prime")
public RnaFusionFusionPartner5Prime getFusionPartner5Prime() { return fusionPartner5Prime; }
@JsonProperty("fusionPartner5prime")
public void setFusionPartner5Prime(RnaFusionFusionPartner5Prime value) { this.fusionPartner5Prime = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("reportedNumReads")
public long getReportedNumReads() { return reportedNumReads; }
@JsonProperty("reportedNumReads")
public void setReportedNumReads(long value) { this.reportedNumReads = value; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class ReferencePublication {
private ExtId extId;
private String type;
private String uri;
@JsonProperty("extId")
public ExtId getExtId() { return extId; }
@JsonProperty("extId")
public void setExtId(ExtId value) { this.extId = value; }
@JsonProperty("type")
public String getType() { return type; }
@JsonProperty("type")
public void setType(String value) { this.type = value; }
@JsonProperty("uri")
public String getUri() { return uri; }
@JsonProperty("uri")
public void setUri(String value) { this.uri = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java Normal file
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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; }
}

39
src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class Response {
private Date effectiveDate;
private String id;
private Patient patient;
private ResponseTherapy therapy;
private CodingRecist value;
@JsonProperty("effectiveDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getEffectiveDate() { return effectiveDate; }
@JsonProperty("effectiveDate")
@JsonFormat(pattern = "yyyy-MM-dd")
public void setEffectiveDate(Date value) { this.effectiveDate = value; }
@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("therapy")
public ResponseTherapy getTherapy() { return therapy; }
@JsonProperty("therapy")
public void setTherapy(ResponseTherapy value) { this.therapy = value; }
@JsonProperty("value")
public CodingRecist getValue() { return value; }
@JsonProperty("value")
public void setValue(CodingRecist value) { this.value = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class ResponseTherapy {
private String id;
private ResponseTherapyType type;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("type")
public ResponseTherapyType getType() { return type; }
@JsonProperty("type")
public void setType(ResponseTherapyType value) { this.type = value; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum ResponseTherapyType {
MTB_MEDICATION_THERAPY;
@JsonValue
public String toValue() {
switch (this) {
case MTB_MEDICATION_THERAPY: return "MTBMedicationTherapy";
}
return null;
}
@JsonCreator
public static ResponseTherapyType forValue(String value) throws IOException {
if (value.equals("MTBMedicationTherapy")) return MTB_MEDICATION_THERAPY;
throw new IOException("Cannot deserialize ResponseTherapyType");
}
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class RnaFusionFusionPartner3Prime {
private String exon;
private TentacledGene gene;
private double position;
private RnaFusionStrand strand;
private String transcriptId;
@JsonProperty("exon")
public String getExon() { return exon; }
@JsonProperty("exon")
public void setExon(String value) { this.exon = value; }
@JsonProperty("gene")
public TentacledGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(TentacledGene value) { this.gene = value; }
@JsonProperty("position")
public double getPosition() { return position; }
@JsonProperty("position")
public void setPosition(double value) { this.position = value; }
@JsonProperty("strand")
public RnaFusionStrand getStrand() { return strand; }
@JsonProperty("strand")
public void setStrand(RnaFusionStrand value) { this.strand = value; }
@JsonProperty("transcriptId")
public String getTranscriptId() { return transcriptId; }
@JsonProperty("transcriptId")
public void setTranscriptId(String value) { this.transcriptId = value; }
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class RnaFusionFusionPartner5Prime {
private String exon;
private StickyGene gene;
private double position;
private RnaFusionStrand strand;
private String transcriptId;
@JsonProperty("exon")
public String getExon() { return exon; }
@JsonProperty("exon")
public void setExon(String value) { this.exon = value; }
@JsonProperty("gene")
public StickyGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(StickyGene value) { this.gene = value; }
@JsonProperty("position")
public double getPosition() { return position; }
@JsonProperty("position")
public void setPosition(double value) { this.position = value; }
@JsonProperty("strand")
public RnaFusionStrand getStrand() { return strand; }
@JsonProperty("strand")
public void setStrand(RnaFusionStrand value) { this.strand = value; }
@JsonProperty("transcriptId")
public String getTranscriptId() { return transcriptId; }
@JsonProperty("transcriptId")
public void setTranscriptId(String value) { this.transcriptId = value; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum RnaFusionStrand {
EMPTY, RNA_FUSION_STRAND;
@JsonValue
public String toValue() {
switch (this) {
case EMPTY: return "+";
case RNA_FUSION_STRAND: return "-";
}
return null;
}
@JsonCreator
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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class RnaSeq {
private Long cohortRanking;
private String ensemblId;
private String entrezId;
private double fragmentsPerKilobaseMillion;
private boolean fromNgs;
private RnaSeqGene gene;
private String id;
private long librarySize;
private long rawCounts;
private boolean tissueCorrectedExpression;
private String transcriptId;
@JsonProperty("cohortRanking")
public Long getCohortRanking() { return cohortRanking; }
@JsonProperty("cohortRanking")
public void setCohortRanking(Long value) { this.cohortRanking = value; }
@JsonProperty("ensemblId")
public String getEnsemblId() { return ensemblId; }
@JsonProperty("ensemblId")
public void setEnsemblId(String value) { this.ensemblId = value; }
@JsonProperty("entrezId")
public String getEntrezId() { return entrezId; }
@JsonProperty("entrezId")
public void setEntrezId(String value) { this.entrezId = value; }
@JsonProperty("fragmentsPerKilobaseMillion")
public double getFragmentsPerKilobaseMillion() { return fragmentsPerKilobaseMillion; }
@JsonProperty("fragmentsPerKilobaseMillion")
public void setFragmentsPerKilobaseMillion(double value) { this.fragmentsPerKilobaseMillion = value; }
@JsonProperty("fromNGS")
public boolean getFromNgs() { return fromNgs; }
@JsonProperty("fromNGS")
public void setFromNgs(boolean value) { this.fromNgs = value; }
@JsonProperty("gene")
public RnaSeqGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(RnaSeqGene value) { this.gene = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("librarySize")
public long getLibrarySize() { return librarySize; }
@JsonProperty("librarySize")
public void setLibrarySize(long value) { this.librarySize = value; }
@JsonProperty("rawCounts")
public long getRawCounts() { return rawCounts; }
@JsonProperty("rawCounts")
public void setRawCounts(long value) { this.rawCounts = value; }
@JsonProperty("tissueCorrectedExpression")
public boolean getTissueCorrectedExpression() { return tissueCorrectedExpression; }
@JsonProperty("tissueCorrectedExpression")
public void setTissueCorrectedExpression(boolean value) { this.tissueCorrectedExpression = value; }
@JsonProperty("transcriptId")
public String getTranscriptId() { return transcriptId; }
@JsonProperty("transcriptId")
public void setTranscriptId(String value) { this.transcriptId = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java Normal file
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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 Normal file
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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; }
}

84
src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Snv {
private double allelicFrequency;
private String altAllele;
private Coding aminoAcidChange;
private Chromosome chromosome;
private String cosmicId;
private String dbSnpId;
private Coding dnaChange;
private SimpleVariantGene gene;
private String id;
private Coding interpretation;
private long readDepth;
private String refAllele;
private StartEnd startEnd;
@JsonProperty("allelicFrequency")
public double getAllelicFrequency() { return allelicFrequency; }
@JsonProperty("allelicFrequency")
public void setAllelicFrequency(double value) { this.allelicFrequency = value; }
@JsonProperty("altAllele")
public String getAltAllele() { return altAllele; }
@JsonProperty("altAllele")
public void setAltAllele(String value) { this.altAllele = value; }
@JsonProperty("aminoAcidChange")
public Coding getAminoAcidChange() { return aminoAcidChange; }
@JsonProperty("aminoAcidChange")
public void setAminoAcidChange(Coding value) { this.aminoAcidChange = value; }
@JsonProperty("chromosome")
public Chromosome getChromosome() { return chromosome; }
@JsonProperty("chromosome")
public void setChromosome(Chromosome value) { this.chromosome = value; }
@JsonProperty("cosmicId")
public String getCosmicId() { return cosmicId; }
@JsonProperty("cosmicId")
public void setCosmicId(String value) { this.cosmicId = value; }
@JsonProperty("dbSNPId")
public String getDbSnpId() { return dbSnpId; }
@JsonProperty("dbSNPId")
public void setDbSnpId(String value) { this.dbSnpId = value; }
@JsonProperty("dnaChange")
public Coding getDnaChange() { return dnaChange; }
@JsonProperty("dnaChange")
public void setDnaChange(Coding value) { this.dnaChange = value; }
@JsonProperty("gene")
public SimpleVariantGene getGene() { return gene; }
@JsonProperty("gene")
public void setGene(SimpleVariantGene value) { this.gene = 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("readDepth")
public long getReadDepth() { return readDepth; }
@JsonProperty("readDepth")
public void setReadDepth(long value) { this.readDepth = value; }
@JsonProperty("refAllele")
public String getRefAllele() { return refAllele; }
@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; }
}

98
src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
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 List<Metadatum> metadata;
private Double msi;
private Patient patient;
private List<RNAFusion> rnaFusions;
private List<RnaSeq> rnaSeqs;
private Coding sequencingType;
private List<Snv> simpleVariants;
private NgsReportSpecimen specimen;
private Double tmb;
private TumorCellContent tumorCellContent;
@JsonProperty("brcaness")
public Double getBrcaness() { return brcaness; }
@JsonProperty("brcaness")
public void setBrcaness(Double value) { this.brcaness = value; }
@JsonProperty("copyNumberVariants")
public List<Cnv> getCopyNumberVariants() { return copyNumberVariants; }
@JsonProperty("copyNumberVariants")
public void setCopyNumberVariants(List<Cnv> value) { this.copyNumberVariants = value; }
@JsonProperty("dnaFusions")
public List<DnaFusion> getDnaFusions() { return dnaFusions; }
@JsonProperty("dnaFusions")
public void setDnaFusions(List<DnaFusion> value) { this.dnaFusions = value; }
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("issueDate")
public Date getIssueDate() { return issueDate; }
@JsonProperty("issueDate")
public void setIssueDate(Date value) { this.issueDate = value; }
@JsonProperty("metadata")
public List<Metadatum> getMetadata() { return metadata; }
@JsonProperty("metadata")
public void setMetadata(List<Metadatum> value) { this.metadata = value; }
@JsonProperty("msi")
public Double getMsi() { return msi; }
@JsonProperty("msi")
public void setMsi(Double value) { this.msi = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@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("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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class Specimen {
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; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum SpecimenType {
TUMOR_SPECIMEN;
@JsonValue
public String toValue() {
switch (this) {
case TUMOR_SPECIMEN: return "TumorSpecimen";
}
return null;
}
@JsonCreator
public static SpecimenType forValue(String value) throws IOException {
if (value.equals("TumorSpecimen")) return TUMOR_SPECIMEN;
throw new IOException("Cannot deserialize SpecimenType");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class StartEnd {
private Double end;
private double start;
@JsonProperty("end")
public Double getEnd() { return end; }
@JsonProperty("end")
public void setEnd(Double value) { this.end = value; }
@JsonProperty("start")
public double getStart() { return start; }
@JsonProperty("start")
public void setStart(double value) { this.start = value; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartRange.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class StartRange {
private Double end;
private double start;
@JsonProperty("end")
public Double getEnd() { return end; }
@JsonProperty("end")
public void setEnd(Double value) { this.end = value; }
@JsonProperty("start")
public double getStart() { return start; }
@JsonProperty("start")
public void setStart(double value) { this.start = value; }
}

21
src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class StatusHistory {
private Date date;
private MtbDiagnosisTumorSpread status;
@JsonProperty("date")
@JsonFormat(pattern = "yyyy-MM-dd")
public Date getDate() { return date; }
@JsonProperty("date")
@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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java Normal file
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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; }
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
import java.util.Date;
public class StudyEnrollmentRecommendation {
private String id;
private Date issuedOn;
private String nctNumber;
private Patient patient;
private String reason;
@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("nctNumber")
public String getNctNumber() { return nctNumber; }
@JsonProperty("nctNumber")
public void setNctNumber(String value) { this.nctNumber = value; }
@JsonProperty("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = value; }
@JsonProperty("reason")
public String getReason() { return reason; }
@JsonProperty("reason")
public void setReason(String value) { this.reason = value; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum SystemEnum {
HTTPS_PUBMED_NCBI_NLM_NIH_GOV;
@JsonValue
public String toValue() {
switch (this) {
case HTTPS_PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov/";
}
return null;
}
@JsonCreator
public static SystemEnum 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");
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java Normal file
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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; }
}

34
src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TherapyRecommendationPriority {
PRIORITY_1, PRIORITY_2, PRIORITY_3, PRIORITY_4;
@JsonValue
public String toValue() {
switch (this) {
case PRIORITY_1: return "1";
case PRIORITY_2: return "2";
case PRIORITY_3: return "3";
case PRIORITY_4: return "4";
}
return null;
}
@JsonCreator
public static TherapyRecommendationPriority forValue(String value) throws IOException {
switch (value) {
case "1":
return PRIORITY_1;
case "2":
return PRIORITY_2;
case "3":
return PRIORITY_3;
case "4":
return PRIORITY_4;
}
throw new IOException("Cannot deserialize TherapyRecommendationPriority");
}
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TherapyStatus {
COMPLETED, NOT_DONE, ON_GOING, STOPPED, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case COMPLETED: return "completed";
case NOT_DONE: return "not-done";
case ON_GOING: return "on-going";
case STOPPED: return "stopped";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static TherapyStatus forValue(String value) throws IOException {
switch (value) {
case "completed":
return COMPLETED;
case "not-done":
return NOT_DONE;
case "on-going":
return ON_GOING;
case "stopped":
return STOPPED;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize TherapyStatus");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class TumorCellContent {
private String id;
private TumorCellContentMethod method;
private String specimen;
private double value;
@JsonProperty("id")
public String getId() { return id; }
@JsonProperty("id")
public void setId(String value) { this.id = value; }
@JsonProperty("method")
public TumorCellContentMethod getMethod() { return method; }
@JsonProperty("method")
public void setMethod(TumorCellContentMethod value) { this.method = value; }
@JsonProperty("specimen")
public String getSpecimen() { return specimen; }
@JsonProperty("specimen")
public void setSpecimen(String 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/TumorCellContentMethod.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TumorCellContentMethod {
BIOINFORMATIC, HISTOLOGIC;
@JsonValue
public String toValue() {
switch (this) {
case BIOINFORMATIC: return "bioinformatic";
case HISTOLOGIC: return "histologic";
}
return null;
}
@JsonCreator
public static TumorCellContentMethod forValue(String value) throws IOException {
if (value.equals("bioinformatic")) return BIOINFORMATIC;
if (value.equals("histologic")) return HISTOLOGIC;
throw new IOException("Cannot deserialize TumorCellContentMethod");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class TumorMorphology {
private String id;
private String note;
private Patient patient;
private String specimen;
private Coding value;
@JsonProperty("id")
public String getId() { return id; }
@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("patient")
public Patient getPatient() { return patient; }
@JsonProperty("patient")
public void setPatient(Patient value) { this.patient = value; }
@JsonProperty("specimen")
public String getSpecimen() { return specimen; }
@JsonProperty("specimen")
public void setSpecimen(String value) { this.specimen = value; }
@JsonProperty("value")
public Coding getValue() { return value; }
@JsonProperty("value")
public void setValue(Coding value) { this.value = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import com.fasterxml.jackson.annotation.*;
public class TumorSpecimen {
private Collection collection;
private Coding icd10;
private String id;
private Patient patient;
private CodingTumorSpecimenType type;
@JsonProperty("collection")
public Collection getCollection() { return collection; }
@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("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("type")
public CodingTumorSpecimenType getType() { return type; }
@JsonProperty("type")
public void setType(CodingTumorSpecimenType value) { this.type = value; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TumorSpecimenCollectionLocalization {
METASTASIS, PRIMARY_TUMOR, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case METASTASIS: return "metastasis";
case PRIMARY_TUMOR: return "primary-tumor";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static TumorSpecimenCollectionLocalization forValue(String value) throws IOException {
switch (value) {
case "metastasis":
return METASTASIS;
case "primary-tumor":
return PRIMARY_TUMOR;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize TumorSpecimenCollectionLocalization");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethod.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TumorSpecimenCollectionMethod {
BIOPSY, CYTOLOGY, LIQUID_BIOPSY, RESECTION, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case BIOPSY: return "biopsy";
case CYTOLOGY: return "cytology";
case LIQUID_BIOPSY: return "liquid-biopsy";
case RESECTION: return "resection";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static TumorSpecimenCollectionMethod forValue(String value) throws IOException {
switch (value) {
case "biopsy":
return BIOPSY;
case "cytology":
return CYTOLOGY;
case "liquid-biopsy":
return LIQUID_BIOPSY;
case "resection":
return RESECTION;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize TumorSpecimenCollectionMethod");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenType.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import java.io.IOException;
import com.fasterxml.jackson.annotation.*;
public enum TumorSpecimenType {
CRYO_FROZEN, FFPE, FRESH_TISSUE, LIQUID_BIOPSY, UNKNOWN;
@JsonValue
public String toValue() {
switch (this) {
case CRYO_FROZEN: return "cryo-frozen";
case FFPE: return "FFPE";
case FRESH_TISSUE: return "fresh-tissue";
case LIQUID_BIOPSY: return "liquid-biopsy";
case UNKNOWN: return "unknown";
}
return null;
}
@JsonCreator
public static TumorSpecimenType forValue(String value) throws IOException {
switch (value) {
case "cryo-frozen":
return CRYO_FROZEN;
case "FFPE":
return FFPE;
case "fresh-tissue":
return FRESH_TISSUE;
case "liquid-biopsy":
return LIQUID_BIOPSY;
case "unknown":
return UNKNOWN;
}
throw new IOException("Cannot deserialize TumorSpecimenType");
}
}

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src/test/java/dev/pcvolkmer/mv64e/mtb/ConverterTest.java Normal file
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package dev.pcvolkmer.mv64e.mtb;
import org.junit.jupiter.api.Test;
import java.io.IOException;
public class ConverterTest {
@Test
void shouldDeserializeJsonString() throws IOException {
var ressource = getClass().getClassLoader().getResource("mv64e-mtb-fake-patient.json");
Converter.fromJsonString(new String(ressource.openStream().readAllBytes()));
}
}

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src/test/resources/mv64e-mtb-fake-patient.json Normal file
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