From 50464681be07cdbc7785f0c30ddd94741b87c083 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Thu, 12 Dec 2024 17:14:12 +0100 Subject: [PATCH] Update model from schema and scala code --- .../dev/pcvolkmer/mv64e/mtb/BRCAness.java | 36 +++++++ .../mv64e/mtb/{CnvType.java => CNVType.java} | 4 +- .../dev/pcvolkmer/mv64e/mtb/Chromosome.java | 94 ------------------- .../pcvolkmer/mv64e/mtb/ChromosomeCode.java | 68 ++++++++++++++ .../pcvolkmer/mv64e/mtb/ChromosomeSystem.java | 22 +++++ .../java/dev/pcvolkmer/mv64e/mtb/Claim.java | 16 +++- .../pcvolkmer/mv64e/mtb/ClaimResponse.java | 12 +-- .../java/dev/pcvolkmer/mv64e/mtb/Cnv.java | 36 ++++--- .../mv64e/mtb/CodingCarePlanStatusReason.java | 24 +++++ .../pcvolkmer/mv64e/mtb/CodingChromosome.java | 24 +++++ .../mtb/CodingClaimResponseStatusReason.java | 24 +++++ .../pcvolkmer/mv64e/mtb/CodingCnvType.java | 24 +++++ .../dev/pcvolkmer/mv64e/mtb/CodingGene.java | 24 +++++ .../CodingTherapyRecommendationPriority.java | 24 +++++ .../mv64e/mtb/CodingTherapyStatus.java | 24 +++++ .../mv64e/mtb/CodingTherapyStatusReason.java | 6 +- .../mtb/CodingTumorCellContentMethod.java | 24 +++++ .../mtb/{Code.java => CodingTumorGrade.java} | 8 +- .../mv64e/mtb/CodingTumorSpread.java | 24 +++++ .../dev/pcvolkmer/mv64e/mtb/Components.java | 24 +++++ .../pcvolkmer/mv64e/mtb/ConfidenceRange.java | 18 ++++ .../java/dev/pcvolkmer/mv64e/mtb/Consent.java | 24 ----- .../pcvolkmer/mv64e/mtb/ConsentStatus.java | 24 ----- .../mv64e/mtb/CopyNumberNeutralLoH.java | 18 ---- .../mtb/{DnaFusion.java => DNAFusion.java} | 2 +- .../dev/pcvolkmer/mv64e/mtb/Diagnosis.java | 18 ++++ .../mtb/DnaFusionFusionPartner3Prime.java | 12 +-- .../mtb/DnaFusionFusionPartner5Prime.java | 12 +-- .../java/dev/pcvolkmer/mv64e/mtb/EXTId.java | 18 ++++ .../mtb/{SystemEnum.java => EXTIdSystem.java} | 6 +- .../pcvolkmer/mv64e/mtb/EpisodeOfCare.java | 31 ++++++ .../mv64e/mtb/{ExtId.java => ExternalId.java} | 8 +- .../dev/pcvolkmer/mv64e/mtb/FluffyGene.java | 18 ---- .../mv64e/mtb/{PurpleGene.java => Gene.java} | 2 +- .../dev/pcvolkmer/mv64e/mtb/GeneSystem.java | 22 +++++ .../mtb/GeneticCounselingRecommendation.java | 6 +- .../mv64e/mtb/GuidelineTreatmentStatus.java | 37 -------- .../dev/pcvolkmer/mv64e/mtb/HRDScore.java | 42 +++++++++ .../pcvolkmer/mv64e/mtb/HealthInsurance.java | 24 +++++ .../pcvolkmer/mv64e/mtb/HistologyReport.java | 18 ++-- .../mv64e/mtb/HistologyReportResults.java | 18 ++++ .../dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java | 74 +++++++++++++++ .../{MtbDiagnosis.java => MTBDiagnosis.java} | 30 ++++-- .../mtb/{MtbEpisode.java => MTBEpisode.java} | 2 +- ....java => MTBMedicationRecommendation.java} | 26 ++--- ...Therapy.java => MTBMedicationTherapy.java} | 42 ++++----- .../pcvolkmer/mv64e/mtb/MolecularTherapy.java | 6 +- .../java/dev/pcvolkmer/mv64e/mtb/Mtb.java | 64 +++++++------ .../dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java | 62 ------------ .../dev/pcvolkmer/mv64e/mtb/MtbPatient.java | 22 ++++- .../pcvolkmer/mv64e/mtb/NgsReportResults.java | 61 ++++++++++++ .../pcvolkmer/mv64e/mtb/OncoProdecure.java | 79 ++++++++++++++++ .../mtb/{StartEnd.java => Position.java} | 2 +- .../mtb/{RnaFusion.java => RNAFusion.java} | 2 +- ...FusionStrand.java => RNAFusionStrand.java} | 4 +- .../mv64e/mtb/{RnaSeq.java => RNASeq.java} | 8 +- .../pcvolkmer/mv64e/mtb/Recommendation.java | 18 ++++ .../dev/pcvolkmer/mv64e/mtb/Reference.java | 24 +++++ .../mv64e/mtb/ReferencePublication.java | 6 +- .../mv64e/mtb/ReportedAffectedGene.java | 18 ---- .../mtb/RnaFusionFusionPartner3Prime.java | 12 +-- .../mtb/RnaFusionFusionPartner5Prime.java | 12 +-- .../dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java | 18 ---- .../mv64e/mtb/SimpleVariantGene.java | 18 ---- .../java/dev/pcvolkmer/mv64e/mtb/Snv.java | 47 +++++++--- .../pcvolkmer/mv64e/mtb/SomaticNgsReport.java | 62 ++---------- ...agnosisTumorSpread.java => StageCode.java} | 6 +- .../{StatusHistory.java => StageHistory.java} | 12 +-- ...eReasonCode.java => StatusReasonCode.java} | 6 +- .../dev/pcvolkmer/mv64e/mtb/StickyGene.java | 18 ---- .../java/dev/pcvolkmer/mv64e/mtb/Study.java | 18 ++++ .../mtb/StudyEnrollmentRecommendation.java | 29 ++++-- .../pcvolkmer/mv64e/mtb/TentacledGene.java | 18 ---- .../java/dev/pcvolkmer/mv64e/mtb/Tmb.java | 36 +++++++ .../pcvolkmer/mv64e/mtb/TumorCellContent.java | 18 ++-- .../mv64e/mtb/TumorCellContentSpecimen.java | 18 ++++ .../pcvolkmer/mv64e/mtb/TumorGradeCode.java | 37 ++++++++ .../pcvolkmer/mv64e/mtb/TumorMorphology.java | 16 ++-- ...imen.java => TumorMorphologySpecimen.java} | 2 +- .../pcvolkmer/mv64e/mtb/TumorSpecimen.java | 10 +- .../java/dev/pcvolkmer/mv64e/mtb/Type.java | 22 +++++ .../java/dev/pcvolkmer/mv64e/mtb/Unit.java | 22 +++++ .../java/dev/pcvolkmer/mv64e/mtb/Value.java | 18 ++++ .../pcvolkmer/mv64e/mtb/ValueWithUnit.java | 18 ++++ .../dev/pcvolkmer/mv64e/mtb/VitalStatus.java | 24 +++++ .../pcvolkmer/mv64e/mtb/VitalStatusCode.java | 24 +++++ 86 files changed, 1372 insertions(+), 639 deletions(-) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CnvType.java => CNVType.java} (89%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Code.java => CodingTumorGrade.java} (79%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Components.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ConfidenceRange.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{DnaFusion.java => DNAFusion.java} (97%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{SystemEnum.java => EXTIdSystem.java} (73%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ExtId.java => ExternalId.java} (65%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{PurpleGene.java => Gene.java} (95%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportResults.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MtbDiagnosis.java => MTBDiagnosis.java} (65%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MtbEpisode.java => MTBEpisode.java} (96%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MtbMedicationRecommendation.java => MTBMedicationRecommendation.java} (68%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MtbMedicationTherapy.java => MTBMedicationTherapy.java} (65%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{StartEnd.java => Position.java} (94%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RnaFusion.java => RNAFusion.java} (98%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RnaFusionStrand.java => RNAFusionStrand.java} (85%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RnaSeq.java => RNASeq.java} (93%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MtbDiagnosisTumorSpread.java => StageCode.java} (79%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{StatusHistory.java => StageHistory.java} (56%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{NotDoneReasonCode.java => StatusReasonCode.java} (93%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Specimen.java => TumorMorphologySpecimen.java} (92%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java new file mode 100644 index 0000000..a8b02b3 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java @@ -0,0 +1,36 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class BRCAness { + private ConfidenceRange confidenceRange; + private String id; + private Reference patient; + private Reference specimen; + private double value; + + @JsonProperty("confidenceRange") + public ConfidenceRange getConfidenceRange() { return confidenceRange; } + @JsonProperty("confidenceRange") + public void setConfidenceRange(ConfidenceRange value) { this.confidenceRange = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("specimen") + public Reference getSpecimen() { return specimen; } + @JsonProperty("specimen") + public void setSpecimen(Reference value) { this.specimen = value; } + + @JsonProperty("value") + public double getValue() { return value; } + @JsonProperty("value") + public void setValue(double value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java similarity index 89% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java index e7866e8..58338d3 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CnvType { +public enum CNVType { HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN; @JsonValue @@ -17,7 +17,7 @@ public enum CnvType { } @JsonCreator - public static CnvType forValue(String value) throws IOException { + public static CNVType forValue(String value) throws IOException { switch (value) { case "high-level-gain": return HIGH_LEVEL_GAIN; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java deleted file mode 100644 index 241bb3f..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java +++ /dev/null @@ -1,94 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum Chromosome { - CHR1, CHR10, CHR11, CHR12, CHR13, CHR14, CHR15, CHR16, CHR17, CHR18, CHR19, CHR2, CHR20, CHR21, CHR22, CHR3, CHR4, CHR5, CHR6, CHR7, CHR8, CHR9, CHR_X, CHR_Y; - - @JsonValue - public String toValue() { - switch (this) { - case CHR1: return "chr1"; - case CHR10: return "chr10"; - case CHR11: return "chr11"; - case CHR12: return "chr12"; - case CHR13: return "chr13"; - case CHR14: return "chr14"; - case CHR15: return "chr15"; - case CHR16: return "chr16"; - case CHR17: return "chr17"; - case CHR18: return "chr18"; - case CHR19: return "chr19"; - case CHR2: return "chr2"; - case CHR20: return "chr20"; - case CHR21: return "chr21"; - case CHR22: return "chr22"; - case CHR3: return "chr3"; - case CHR4: return "chr4"; - case CHR5: return "chr5"; - case CHR6: return "chr6"; - case CHR7: return "chr7"; - case CHR8: return "chr8"; - case CHR9: return "chr9"; - case CHR_X: return "chrX"; - case CHR_Y: return "chrY"; - } - return null; - } - - @JsonCreator - public static Chromosome forValue(String value) throws IOException { - switch (value) { - case "chr1": - return CHR1; - case "chr10": - return CHR10; - case "chr11": - return CHR11; - case "chr12": - return CHR12; - case "chr13": - return CHR13; - case "chr14": - return CHR14; - case "chr15": - return CHR15; - case "chr16": - return CHR16; - case "chr17": - return CHR17; - case "chr18": - return CHR18; - case "chr19": - return CHR19; - case "chr2": - return CHR2; - case "chr20": - return CHR20; - case "chr21": - return CHR21; - case "chr22": - return CHR22; - case "chr3": - return CHR3; - case "chr4": - return CHR4; - case "chr5": - return CHR5; - case "chr6": - return CHR6; - case "chr7": - return CHR7; - case "chr8": - return CHR8; - case "chr9": - return CHR9; - case "chrX": - return CHR_X; - case "chrY": - return CHR_Y; - } - throw new IOException("Cannot deserialize Chromosome"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java new file mode 100644 index 0000000..33522ea --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java @@ -0,0 +1,68 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ChromosomeCode { + CHR1, CHR10, CHR11, CHR12, CHR13, CHR14, CHR15, CHR16, CHR17, CHR18, CHR19, CHR2, CHR20, CHR21, CHR22, CHR3, CHR4, CHR5, CHR6, CHR7, CHR8, CHR9, CHR_X, CHR_Y; + + @JsonValue + public String toValue() { + switch (this) { + case CHR1: return "chr1"; + case CHR10: return "chr10"; + case CHR11: return "chr11"; + case CHR12: return "chr12"; + case CHR13: return "chr13"; + case CHR14: return "chr14"; + case CHR15: return "chr15"; + case CHR16: return "chr16"; + case CHR17: return "chr17"; + case CHR18: return "chr18"; + case CHR19: return "chr19"; + case CHR2: return "chr2"; + case CHR20: return "chr20"; + case CHR21: return "chr21"; + case CHR22: return "chr22"; + case CHR3: return "chr3"; + case CHR4: return "chr4"; + case CHR5: return "chr5"; + case CHR6: return "chr6"; + case CHR7: return "chr7"; + case CHR8: return "chr8"; + case CHR9: return "chr9"; + case CHR_X: return "chrX"; + case CHR_Y: return "chrY"; + } + return null; + } + + @JsonCreator + public static ChromosomeCode forValue(String value) throws IOException { + if (value.equals("chr1")) return CHR1; + if (value.equals("chr10")) return CHR10; + if (value.equals("chr11")) return CHR11; + if (value.equals("chr12")) return CHR12; + if (value.equals("chr13")) return CHR13; + if (value.equals("chr14")) return CHR14; + if (value.equals("chr15")) return CHR15; + if (value.equals("chr16")) return CHR16; + if (value.equals("chr17")) return CHR17; + if (value.equals("chr18")) return CHR18; + if (value.equals("chr19")) return CHR19; + if (value.equals("chr2")) return CHR2; + if (value.equals("chr20")) return CHR20; + if (value.equals("chr21")) return CHR21; + if (value.equals("chr22")) return CHR22; + if (value.equals("chr3")) return CHR3; + if (value.equals("chr4")) return CHR4; + if (value.equals("chr5")) return CHR5; + if (value.equals("chr6")) return CHR6; + if (value.equals("chr7")) return CHR7; + if (value.equals("chr8")) return CHR8; + if (value.equals("chr9")) return CHR9; + if (value.equals("chrX")) return CHR_X; + if (value.equals("chrY")) return CHR_Y; + throw new IOException("Cannot deserialize ChromosomeCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java new file mode 100644 index 0000000..a8337e0 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ChromosomeSystem { + CHROMOSOME; + + @JsonValue + public String toValue() { + switch (this) { + case CHROMOSOME: return "chromosome"; + } + return null; + } + + @JsonCreator + public static ChromosomeSystem forValue(String value) throws IOException { + if (value.equals("chromosome")) return CHROMOSOME; + throw new IOException("Cannot deserialize ChromosomeSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java index a182eff..5bbdf4d 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java @@ -7,7 +7,8 @@ public class Claim { private String id; private Date issuedOn; private Patient patient; - private String therapy; + private Recommendation recommendation; + private Coding stage; @JsonProperty("id") public String getId() { return id; } @@ -26,8 +27,13 @@ public class Claim { @JsonProperty("patient") public void setPatient(Patient value) { this.patient = value; } - @JsonProperty("therapy") - public String getTherapy() { return therapy; } - @JsonProperty("therapy") - public void setTherapy(String value) { this.therapy = value; } + @JsonProperty("recommendation") + public Recommendation getRecommendation() { return recommendation; } + @JsonProperty("recommendation") + public void setRecommendation(Recommendation value) { this.recommendation = value; } + + @JsonProperty("stage") + public Coding getStage() { return stage; } + @JsonProperty("stage") + public void setStage(Coding value) { this.stage = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java index 55af191..7b93ab5 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java @@ -8,8 +8,8 @@ public class ClaimResponse { private String id; private Date issuedOn; private Patient patient; - private ClaimResponseStatusReason reason; private CodingClaimResponseStatus status; + private CodingClaimResponseStatusReason statusReason; @JsonProperty("claim") public ClaimResponseClaim getClaim() { return claim; } @@ -33,13 +33,13 @@ public class ClaimResponse { @JsonProperty("patient") public void setPatient(Patient value) { this.patient = value; } - @JsonProperty("reason") - public ClaimResponseStatusReason getReason() { return reason; } - @JsonProperty("reason") - public void setReason(ClaimResponseStatusReason value) { this.reason = value; } - @JsonProperty("status") public CodingClaimResponseStatus getStatus() { return status; } @JsonProperty("status") public void setStatus(CodingClaimResponseStatus value) { this.status = value; } + + @JsonProperty("statusReason") + public CodingClaimResponseStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingClaimResponseStatusReason value) { this.statusReason = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java index 72f293f..27c308f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java @@ -4,23 +4,25 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class Cnv { - private Chromosome chromosome; + private CodingChromosome chromosome; private Double cnA; private Double cnB; - private List copyNumberNeutralLoH; + private List copyNumberNeutralLoH; private EndRange endRange; private String id; + private Reference indication; + private Patient patient; private Double relativeCopyNumber; - private List reportedAffectedGenes; + private List reportedAffectedGenes; private String reportedFocality; private StartRange startRange; private Long totalCopyNumber; - private CnvType type; + private CodingCnvType type; @JsonProperty("chromosome") - public Chromosome getChromosome() { return chromosome; } + public CodingChromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(Chromosome value) { this.chromosome = value; } + public void setChromosome(CodingChromosome value) { this.chromosome = value; } @JsonProperty("cnA") public Double getCnA() { return cnA; } @@ -33,9 +35,9 @@ public class Cnv { public void setCnB(Double value) { this.cnB = value; } @JsonProperty("copyNumberNeutralLoH") - public List getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; } + public List getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; } @JsonProperty("copyNumberNeutralLoH") - public void setCopyNumberNeutralLoH(List value) { this.copyNumberNeutralLoH = value; } + public void setCopyNumberNeutralLoH(List value) { this.copyNumberNeutralLoH = value; } @JsonProperty("endRange") public EndRange getEndRange() { return endRange; } @@ -47,15 +49,25 @@ public class Cnv { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("indication") + public Reference getIndication() { return indication; } + @JsonProperty("indication") + public void setIndication(Reference value) { this.indication = value; } + + @JsonProperty("patient") + public Patient getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Patient value) { this.patient = value; } + @JsonProperty("relativeCopyNumber") public Double getRelativeCopyNumber() { return relativeCopyNumber; } @JsonProperty("relativeCopyNumber") public void setRelativeCopyNumber(Double value) { this.relativeCopyNumber = value; } @JsonProperty("reportedAffectedGenes") - public List getReportedAffectedGenes() { return reportedAffectedGenes; } + public List getReportedAffectedGenes() { return reportedAffectedGenes; } @JsonProperty("reportedAffectedGenes") - public void setReportedAffectedGenes(List value) { this.reportedAffectedGenes = value; } + public void setReportedAffectedGenes(List value) { this.reportedAffectedGenes = value; } @JsonProperty("reportedFocality") public String getReportedFocality() { return reportedFocality; } @@ -73,7 +85,7 @@ public class Cnv { public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; } @JsonProperty("type") - public CnvType getType() { return type; } + public CodingCnvType getType() { return type; } @JsonProperty("type") - public void setType(CnvType value) { this.type = value; } + public void setType(CodingCnvType value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java new file mode 100644 index 0000000..698acd9 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingCarePlanStatusReason { + private String code; + private String display; + private String system; + + @JsonProperty("code") + public String getCode() { return code; } + @JsonProperty("code") + public void setCode(String value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java new file mode 100644 index 0000000..f8c3e83 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingChromosome { + private ChromosomeCode code; + private String display; + private ChromosomeSystem system; + + @JsonProperty("code") + public ChromosomeCode getCode() { return code; } + @JsonProperty("code") + public void setCode(ChromosomeCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public ChromosomeSystem getSystem() { return system; } + @JsonProperty("system") + public void setSystem(ChromosomeSystem value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java new file mode 100644 index 0000000..ea49f6b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingClaimResponseStatusReason { + private ClaimResponseStatusReason code; + private String display; + private String system; + + @JsonProperty("code") + public ClaimResponseStatusReason getCode() { return code; } + @JsonProperty("code") + public void setCode(ClaimResponseStatusReason value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java new file mode 100644 index 0000000..3bf6b07 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingCnvType { + private CNVType code; + private String display; + private String system; + + @JsonProperty("code") + public CNVType getCode() { return code; } + @JsonProperty("code") + public void setCode(CNVType value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java new file mode 100644 index 0000000..78ab110 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingGene { + private String code; + private String display; + private GeneSystem system; + + @JsonProperty("code") + public String getCode() { return code; } + @JsonProperty("code") + public void setCode(String value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public GeneSystem getSystem() { return system; } + @JsonProperty("system") + public void setSystem(GeneSystem value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java new file mode 100644 index 0000000..040ef92 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTherapyRecommendationPriority { + private TherapyRecommendationPriority code; + private String display; + private String system; + + @JsonProperty("code") + public TherapyRecommendationPriority getCode() { return code; } + @JsonProperty("code") + public void setCode(TherapyRecommendationPriority value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java new file mode 100644 index 0000000..ee51af0 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTherapyStatus { + private TherapyStatus code; + private String display; + private String system; + + @JsonProperty("code") + public TherapyStatus getCode() { return code; } + @JsonProperty("code") + public void setCode(TherapyStatus value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java index 8d093e2..0b7284f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingTherapyStatusReason { - private NotDoneReasonCode code; + private StatusReasonCode code; private String display; private String system; private String version; @JsonProperty("code") - public NotDoneReasonCode getCode() { return code; } + public StatusReasonCode getCode() { return code; } @JsonProperty("code") - public void setCode(NotDoneReasonCode value) { this.code = value; } + public void setCode(StatusReasonCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java new file mode 100644 index 0000000..868c44a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTumorCellContentMethod { + private TumorCellContentMethod code; + private String display; + private String system; + + @JsonProperty("code") + public TumorCellContentMethod getCode() { return code; } + @JsonProperty("code") + public void setCode(TumorCellContentMethod value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java index 24e7777..1cb9881 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class Code { - private String code; +public class CodingTumorGrade { + private TumorGradeCode code; private String display; private String system; private String version; @JsonProperty("code") - public String getCode() { return code; } + public TumorGradeCode getCode() { return code; } @JsonProperty("code") - public void setCode(String value) { this.code = value; } + public void setCode(TumorGradeCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java new file mode 100644 index 0000000..a228665 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTumorSpread { + private StageCode code; + private String display; + private String system; + + @JsonProperty("code") + public StageCode getCode() { return code; } + @JsonProperty("code") + public void setCode(StageCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Components.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Components.java new file mode 100644 index 0000000..aa4f340 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Components.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Components { + private double loh; + private double lst; + private double tai; + + @JsonProperty("loh") + public double getLoh() { return loh; } + @JsonProperty("loh") + public void setLoh(double value) { this.loh = value; } + + @JsonProperty("lst") + public double getLst() { return lst; } + @JsonProperty("lst") + public void setLst(double value) { this.lst = value; } + + @JsonProperty("tai") + public double getTai() { return tai; } + @JsonProperty("tai") + public void setTai(double value) { this.tai = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ConfidenceRange.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ConfidenceRange.java new file mode 100644 index 0000000..ce71b18 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ConfidenceRange.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class ConfidenceRange { + private double max; + private double min; + + @JsonProperty("max") + public double getMax() { return max; } + @JsonProperty("max") + public void setMax(double value) { this.max = value; } + + @JsonProperty("min") + public double getMin() { return min; } + @JsonProperty("min") + public void setMin(double value) { this.min = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java deleted file mode 100644 index 3aba7d1..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java +++ /dev/null @@ -1,24 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class Consent { - private String id; - private Patient patient; - private ConsentStatus status; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("patient") - public Patient getPatient() { return patient; } - @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } - - @JsonProperty("status") - public ConsentStatus getStatus() { return status; } - @JsonProperty("status") - public void setStatus(ConsentStatus value) { this.status = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java deleted file mode 100644 index f2894fc..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java +++ /dev/null @@ -1,24 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum ConsentStatus { - ACTIVE, REJECTED; - - @JsonValue - public String toValue() { - switch (this) { - case ACTIVE: return "active"; - case REJECTED: return "rejected"; - } - return null; - } - - @JsonCreator - public static ConsentStatus forValue(String value) throws IOException { - if (value.equals("active")) return ACTIVE; - if (value.equals("rejected")) return REJECTED; - throw new IOException("Cannot deserialize ConsentStatus"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java deleted file mode 100644 index 88dd27b..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CopyNumberNeutralLoH { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java similarity index 97% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java index a4c5dbb..0a45733 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class DnaFusion { +public class DNAFusion { private DnaFusionFusionPartner3Prime fusionPartner3Prime; private DnaFusionFusionPartner5Prime fusionPartner5Prime; private String id; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java new file mode 100644 index 0000000..eb339c1 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Diagnosis { + private String id; + private String type; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("type") + public String getType() { return type; } + @JsonProperty("type") + public void setType(String value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java index 71d65ab..2544f84 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java @@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class DnaFusionFusionPartner3Prime { - private Chromosome chromosome; - private PurpleGene gene; + private CodingChromosome chromosome; + private CodingGene gene; private double position; @JsonProperty("chromosome") - public Chromosome getChromosome() { return chromosome; } + public CodingChromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(Chromosome value) { this.chromosome = value; } + public void setChromosome(CodingChromosome value) { this.chromosome = value; } @JsonProperty("gene") - public PurpleGene getGene() { return gene; } + public CodingGene getGene() { return gene; } @JsonProperty("gene") - public void setGene(PurpleGene value) { this.gene = value; } + public void setGene(CodingGene value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java index 57fb8b5..ed9608a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java @@ -3,19 +3,19 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class DnaFusionFusionPartner5Prime { - private Chromosome chromosome; - private FluffyGene gene; + private CodingChromosome chromosome; + private Gene gene; private double position; @JsonProperty("chromosome") - public Chromosome getChromosome() { return chromosome; } + public CodingChromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(Chromosome value) { this.chromosome = value; } + public void setChromosome(CodingChromosome value) { this.chromosome = value; } @JsonProperty("gene") - public FluffyGene getGene() { return gene; } + public Gene getGene() { return gene; } @JsonProperty("gene") - public void setGene(FluffyGene value) { this.gene = value; } + public void setGene(Gene value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java new file mode 100644 index 0000000..1ce1acc --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class EXTId { + private EXTIdSystem system; + private String value; + + @JsonProperty("system") + public EXTIdSystem getSystem() { return system; } + @JsonProperty("system") + public void setSystem(EXTIdSystem value) { this.system = value; } + + @JsonProperty("value") + public String getValue() { return value; } + @JsonProperty("value") + public void setValue(String value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java similarity index 73% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java index d81a6d9..f9c31c5 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum SystemEnum { +public enum EXTIdSystem { HTTPS_PUBMED_NCBI_NLM_NIH_GOV; @JsonValue @@ -15,8 +15,8 @@ public enum SystemEnum { } @JsonCreator - public static SystemEnum forValue(String value) throws IOException { + public static EXTIdSystem forValue(String value) throws IOException { if (value.equals("https://pubmed.ncbi.nlm.nih.gov/")) return HTTPS_PUBMED_NCBI_NLM_NIH_GOV; - throw new IOException("Cannot deserialize SystemEnum"); + throw new IOException("Cannot deserialize EXTIdSystem"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java new file mode 100644 index 0000000..1ef9d50 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java @@ -0,0 +1,31 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class EpisodeOfCare { + private List diagnoses; + private String id; + private Reference patient; + private PeriodLocalDate period; + + @JsonProperty("diagnoses") + public List getDiagnoses() { return diagnoses; } + @JsonProperty("diagnoses") + public void setDiagnoses(List value) { this.diagnoses = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("period") + public PeriodLocalDate getPeriod() { return period; } + @JsonProperty("period") + public void setPeriod(PeriodLocalDate value) { this.period = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java similarity index 65% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java index b8c5a7b..fcad183 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java @@ -2,14 +2,14 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class ExtId { - private SystemEnum system; +public class ExternalId { + private String system; private String value; @JsonProperty("system") - public SystemEnum getSystem() { return system; } + public String getSystem() { return system; } @JsonProperty("system") - public void setSystem(SystemEnum value) { this.system = value; } + public void setSystem(String value) { this.system = value; } @JsonProperty("value") public String getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java deleted file mode 100644 index d5435db..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class FluffyGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java similarity index 95% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java index 1e2646f..84fd6b4 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class PurpleGene { +public class Gene { private String ensemblId; private String hgncId; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java new file mode 100644 index 0000000..8a41113 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum GeneSystem { + HTTPS_Www_GENENAMES_ORG; + + @JsonValue + public String toValue() { + switch (this) { + case HTTPS_Www_GENENAMES_ORG: return "https://www.genenames.org/"; + } + return null; + } + + @JsonCreator + public static GeneSystem forValue(String value) throws IOException { + if (value.equals("https://www.genenames.org/")) return HTTPS_Www_GENENAMES_ORG; + throw new IOException("Cannot deserialize GeneSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java index eed3a2c..0897302 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java @@ -7,7 +7,7 @@ public class GeneticCounselingRecommendation { private String id; private Date issuedOn; private Patient patient; - private String reason; + private Coding reason; @JsonProperty("id") public String getId() { return id; } @@ -25,7 +25,7 @@ public class GeneticCounselingRecommendation { public void setPatient(Patient value) { this.patient = value; } @JsonProperty("reason") - public String getReason() { return reason; } + public Coding getReason() { return reason; } @JsonProperty("reason") - public void setReason(String value) { this.reason = value; } + public void setReason(Coding value) { this.reason = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java deleted file mode 100644 index 5d64e0f..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java +++ /dev/null @@ -1,37 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum GuidelineTreatmentStatus { - EXHAUSTED, IMPOSSIBLE, NON_EXHAUSTED, NO_GUIDELINES_AVAILABLE, UNKNOWN; - - @JsonValue - public String toValue() { - switch (this) { - case EXHAUSTED: return "exhausted"; - case IMPOSSIBLE: return "impossible"; - case NON_EXHAUSTED: return "non-exhausted"; - case NO_GUIDELINES_AVAILABLE: return "no-guidelines-available"; - case UNKNOWN: return "unknown"; - } - return null; - } - - @JsonCreator - public static GuidelineTreatmentStatus forValue(String value) throws IOException { - switch (value) { - case "exhausted": - return EXHAUSTED; - case "impossible": - return IMPOSSIBLE; - case "non-exhausted": - return NON_EXHAUSTED; - case "no-guidelines-available": - return NO_GUIDELINES_AVAILABLE; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize GuidelineTreatmentStatus"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java new file mode 100644 index 0000000..4945a09 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java @@ -0,0 +1,42 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class HRDScore { + private Components components; + private String id; + private Coding interpretation; + private Reference patient; + private Reference specimen; + private double value; + + @JsonProperty("components") + public Components getComponents() { return components; } + @JsonProperty("components") + public void setComponents(Components value) { this.components = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("interpretation") + public Coding getInterpretation() { return interpretation; } + @JsonProperty("interpretation") + public void setInterpretation(Coding value) { this.interpretation = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("specimen") + public Reference getSpecimen() { return specimen; } + @JsonProperty("specimen") + public void setSpecimen(Reference value) { this.specimen = value; } + + @JsonProperty("value") + public double getValue() { return value; } + @JsonProperty("value") + public void setValue(double value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java new file mode 100644 index 0000000..a79c185 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class HealthInsurance { + private String display; + private ExternalId extId; + private Type type; + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("extId") + public ExternalId getExtId() { return extId; } + @JsonProperty("extId") + public void setExtId(ExternalId value) { this.extId = value; } + + @JsonProperty("type") + public Type getType() { return type; } + @JsonProperty("type") + public void setType(Type value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java index f58ee64..a808216 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java @@ -7,9 +7,8 @@ public class HistologyReport { private String id; private Date issuedOn; private Patient patient; + private HistologyReportResults results; private HistologyReportSpecimen specimen; - private TumorCellContent tumorCellContent; - private TumorMorphology tumorMorphology; @JsonProperty("id") public String getId() { return id; } @@ -28,18 +27,13 @@ public class HistologyReport { @JsonProperty("patient") public void setPatient(Patient value) { this.patient = value; } + @JsonProperty("results") + public HistologyReportResults getResults() { return results; } + @JsonProperty("results") + public void setResults(HistologyReportResults value) { this.results = value; } + @JsonProperty("specimen") public HistologyReportSpecimen getSpecimen() { return specimen; } @JsonProperty("specimen") public void setSpecimen(HistologyReportSpecimen value) { this.specimen = value; } - - @JsonProperty("tumorCellContent") - public TumorCellContent getTumorCellContent() { return tumorCellContent; } - @JsonProperty("tumorCellContent") - public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; } - - @JsonProperty("tumorMorphology") - public TumorMorphology getTumorMorphology() { return tumorMorphology; } - @JsonProperty("tumorMorphology") - public void setTumorMorphology(TumorMorphology value) { this.tumorMorphology = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportResults.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportResults.java new file mode 100644 index 0000000..0445f30 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportResults.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class HistologyReportResults { + private TumorCellContent tumorCellContent; + private TumorMorphology tumorMorphology; + + @JsonProperty("tumorCellContent") + public TumorCellContent getTumorCellContent() { return tumorCellContent; } + @JsonProperty("tumorCellContent") + public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; } + + @JsonProperty("tumorMorphology") + public TumorMorphology getTumorMorphology() { return tumorMorphology; } + @JsonProperty("tumorMorphology") + public void setTumorMorphology(TumorMorphology value) { this.tumorMorphology = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java new file mode 100644 index 0000000..f1440ed --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java @@ -0,0 +1,74 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class MTBCarePlan { + private String diagnosis; + private GeneticCounselingRecommendation geneticCounselingRecommendation; + private String id; + private Reference indication; + private Date issuedOn; + private List medicationRecommendations; + private NoTargetFinding noTargetFinding; + private String notes; + private Patient patient; + private CodingCarePlanStatusReason statusReason; + private List studyEnrollmentRecommendations; + + @JsonProperty("diagnosis") + public String getDiagnosis() { return diagnosis; } + @JsonProperty("diagnosis") + public void setDiagnosis(String value) { this.diagnosis = value; } + + @JsonProperty("geneticCounselingRecommendation") + public GeneticCounselingRecommendation getGeneticCounselingRecommendation() { return geneticCounselingRecommendation; } + @JsonProperty("geneticCounselingRecommendation") + public void setGeneticCounselingRecommendation(GeneticCounselingRecommendation value) { this.geneticCounselingRecommendation = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("indication") + public Reference getIndication() { return indication; } + @JsonProperty("indication") + public void setIndication(Reference value) { this.indication = value; } + + @JsonProperty("issuedOn") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("medicationRecommendations") + public List getMedicationRecommendations() { return medicationRecommendations; } + @JsonProperty("medicationRecommendations") + public void setMedicationRecommendations(List value) { this.medicationRecommendations = value; } + + @JsonProperty("noTargetFinding") + public NoTargetFinding getNoTargetFinding() { return noTargetFinding; } + @JsonProperty("noTargetFinding") + public void setNoTargetFinding(NoTargetFinding value) { this.noTargetFinding = value; } + + @JsonProperty("notes") + public String getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(String value) { this.notes = value; } + + @JsonProperty("patient") + public Patient getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Patient value) { this.patient = value; } + + @JsonProperty("statusReason") + public CodingCarePlanStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingCarePlanStatusReason value) { this.statusReason = value; } + + @JsonProperty("studyEnrollmentRecommendations") + public List getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; } + @JsonProperty("studyEnrollmentRecommendations") + public void setStudyEnrollmentRecommendations(List value) { this.studyEnrollmentRecommendations = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java similarity index 65% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java index 5341a88..c8c26ed 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MtbDiagnosis { +public class MTBDiagnosis { private Coding code; private Coding guidelineTreatmentStatus; private List histologyResults; @@ -12,8 +12,11 @@ public class MtbDiagnosis { private String id; private Patient patient; private Date recordedOn; - private List statusHistory; + private List stageHistory; + private Coding topography; + private CodingTumorGrade tumorGrade; private Coding whoGrade; + private Coding whoGrading; @JsonProperty("code") public Coding getCode() { return code; } @@ -50,13 +53,28 @@ public class MtbDiagnosis { @JsonProperty("recordedOn") public void setRecordedOn(Date value) { this.recordedOn = value; } - @JsonProperty("statusHistory") - public List getStatusHistory() { return statusHistory; } - @JsonProperty("statusHistory") - public void setStatusHistory(List value) { this.statusHistory = value; } + @JsonProperty("stageHistory") + public List getStageHistory() { return stageHistory; } + @JsonProperty("stageHistory") + public void setStageHistory(List value) { this.stageHistory = value; } + + @JsonProperty("topography") + public Coding getTopography() { return topography; } + @JsonProperty("topography") + public void setTopography(Coding value) { this.topography = value; } + + @JsonProperty("tumorGrade") + public CodingTumorGrade getTumorGrade() { return tumorGrade; } + @JsonProperty("tumorGrade") + public void setTumorGrade(CodingTumorGrade value) { this.tumorGrade = value; } @JsonProperty("whoGrade") public Coding getWhoGrade() { return whoGrade; } @JsonProperty("whoGrade") public void setWhoGrade(Coding value) { this.whoGrade = value; } + + @JsonProperty("whoGrading") + public Coding getWhoGrading() { return whoGrading; } + @JsonProperty("whoGrading") + public void setWhoGrading(Coding value) { this.whoGrading = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java similarity index 96% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java index 7ed7705..ae9cfd0 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class MtbEpisode { +public class MTBEpisode { private String id; private Patient patient; private PeriodLocalDate period; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java similarity index 68% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java index b309aac..7abc6b3 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java @@ -4,27 +4,27 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MtbMedicationRecommendation { - private String diagnosis; +public class MTBMedicationRecommendation { private String id; + private Reference indication; private Date issuedOn; private LevelOfEvidence levelOfEvidence; private List medication; private String ngsReport; private Patient patient; - private TherapyRecommendationPriority priority; - private List supportingVariants; - - @JsonProperty("diagnosis") - public String getDiagnosis() { return diagnosis; } - @JsonProperty("diagnosis") - public void setDiagnosis(String value) { this.diagnosis = value; } + private CodingTherapyRecommendationPriority priority; + private List supportingVariants; @JsonProperty("id") public String getId() { return id; } @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("indication") + public Reference getIndication() { return indication; } + @JsonProperty("indication") + public void setIndication(Reference value) { this.indication = value; } + @JsonProperty("issuedOn") public Date getIssuedOn() { return issuedOn; } @JsonProperty("issuedOn") @@ -51,12 +51,12 @@ public class MtbMedicationRecommendation { public void setPatient(Patient value) { this.patient = value; } @JsonProperty("priority") - public TherapyRecommendationPriority getPriority() { return priority; } + public CodingTherapyRecommendationPriority getPriority() { return priority; } @JsonProperty("priority") - public void setPriority(TherapyRecommendationPriority value) { this.priority = value; } + public void setPriority(CodingTherapyRecommendationPriority value) { this.priority = value; } @JsonProperty("supportingVariants") - public List getSupportingVariants() { return supportingVariants; } + public List getSupportingVariants() { return supportingVariants; } @JsonProperty("supportingVariants") - public void setSupportingVariants(List value) { this.supportingVariants = value; } + public void setSupportingVariants(List value) { this.supportingVariants = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java similarity index 65% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java index e5ddf1d..d8cacd0 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java @@ -4,18 +4,18 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MtbMedicationTherapy { +public class MTBMedicationTherapy { private String basedOn; private String diagnosis; private String id; + private Reference indication; private List medication; - private CodingTherapyStatusReason notDoneReason; - private String note; + private String notes; private Patient patient; private PeriodLocalDate period; - private CodingTherapyStatusReason reasonStopped; private Date recordedOn; - private TherapyStatus status; + private CodingTherapyStatus status; + private CodingTherapyStatusReason statusReason; private Long therapyLine; @JsonProperty("basedOn") @@ -33,20 +33,20 @@ public class MtbMedicationTherapy { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("indication") + public Reference getIndication() { return indication; } + @JsonProperty("indication") + public void setIndication(Reference value) { this.indication = value; } + @JsonProperty("medication") public List getMedication() { return medication; } @JsonProperty("medication") public void setMedication(List value) { this.medication = value; } - @JsonProperty("notDoneReason") - public CodingTherapyStatusReason getNotDoneReason() { return notDoneReason; } - @JsonProperty("notDoneReason") - public void setNotDoneReason(CodingTherapyStatusReason value) { this.notDoneReason = value; } - - @JsonProperty("note") - public String getNote() { return note; } - @JsonProperty("note") - public void setNote(String value) { this.note = value; } + @JsonProperty("notes") + public String getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(String value) { this.notes = value; } @JsonProperty("patient") public Patient getPatient() { return patient; } @@ -58,20 +58,20 @@ public class MtbMedicationTherapy { @JsonProperty("period") public void setPeriod(PeriodLocalDate value) { this.period = value; } - @JsonProperty("reasonStopped") - public CodingTherapyStatusReason getReasonStopped() { return reasonStopped; } - @JsonProperty("reasonStopped") - public void setReasonStopped(CodingTherapyStatusReason value) { this.reasonStopped = value; } - @JsonProperty("recordedOn") public Date getRecordedOn() { return recordedOn; } @JsonProperty("recordedOn") public void setRecordedOn(Date value) { this.recordedOn = value; } @JsonProperty("status") - public TherapyStatus getStatus() { return status; } + public CodingTherapyStatus getStatus() { return status; } @JsonProperty("status") - public void setStatus(TherapyStatus value) { this.status = value; } + public void setStatus(CodingTherapyStatus value) { this.status = value; } + + @JsonProperty("statusReason") + public CodingTherapyStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingTherapyStatusReason value) { this.statusReason = value; } @JsonProperty("therapyLine") public Long getTherapyLine() { return therapyLine; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java index b2f4967..6222040 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java @@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class MolecularTherapy { - private List history; + private List history; @JsonProperty("history") - public List getHistory() { return history; } + public List getHistory() { return history; } @JsonProperty("history") - public void setHistory(List value) { this.history = value; } + public void setHistory(List value) { this.history = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java index 0a1e994..9a8ae51 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java @@ -4,28 +4,29 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class Mtb { - private List carePlans; + private List carePlans; private List claimResponses; private List claims; - private List diagnoses; - private List ecogStatus; - private MtbEpisode episode; + private List diagnoses; + private MTBEpisode episode; + private List episodesOfCare; private List geneticCounsellingRequests; + private List guidelineProcedures; + private List guidelineTherapies; private List histologyReports; - private List lastGuidelineTherapies; private List molecularTherapies; private List ngsReports; private MtbPatient patient; - private List previousGuidelineTherapies; - private List recommendations; + private List performanceStatus; + private List recommendations; private List responses; private List specimens; private List studyInclusionRequests; @JsonProperty("carePlans") - public List getCarePlans() { return carePlans; } + public List getCarePlans() { return carePlans; } @JsonProperty("carePlans") - public void setCarePlans(List value) { this.carePlans = value; } + public void setCarePlans(List value) { this.carePlans = value; } @JsonProperty("claimResponses") public List getClaimResponses() { return claimResponses; } @@ -38,35 +39,40 @@ public class Mtb { public void setClaims(List value) { this.claims = value; } @JsonProperty("diagnoses") - public List getDiagnoses() { return diagnoses; } + public List getDiagnoses() { return diagnoses; } @JsonProperty("diagnoses") - public void setDiagnoses(List value) { this.diagnoses = value; } - - @JsonProperty("ecogStatus") - public List getEcogStatus() { return ecogStatus; } - @JsonProperty("ecogStatus") - public void setEcogStatus(List value) { this.ecogStatus = value; } + public void setDiagnoses(List value) { this.diagnoses = value; } @JsonProperty("episode") - public MtbEpisode getEpisode() { return episode; } + public MTBEpisode getEpisode() { return episode; } @JsonProperty("episode") - public void setEpisode(MtbEpisode value) { this.episode = value; } + public void setEpisode(MTBEpisode value) { this.episode = value; } + + @JsonProperty("episodesOfCare") + public List getEpisodesOfCare() { return episodesOfCare; } + @JsonProperty("episodesOfCare") + public void setEpisodesOfCare(List value) { this.episodesOfCare = value; } @JsonProperty("geneticCounsellingRequests") public List getGeneticCounsellingRequests() { return geneticCounsellingRequests; } @JsonProperty("geneticCounsellingRequests") public void setGeneticCounsellingRequests(List value) { this.geneticCounsellingRequests = value; } + @JsonProperty("guidelineProcedures") + public List getGuidelineProcedures() { return guidelineProcedures; } + @JsonProperty("guidelineProcedures") + public void setGuidelineProcedures(List value) { this.guidelineProcedures = value; } + + @JsonProperty("guidelineTherapies") + public List getGuidelineTherapies() { return guidelineTherapies; } + @JsonProperty("guidelineTherapies") + public void setGuidelineTherapies(List value) { this.guidelineTherapies = value; } + @JsonProperty("histologyReports") public List getHistologyReports() { return histologyReports; } @JsonProperty("histologyReports") public void setHistologyReports(List value) { this.histologyReports = value; } - @JsonProperty("lastGuidelineTherapies") - public List getLastGuidelineTherapies() { return lastGuidelineTherapies; } - @JsonProperty("lastGuidelineTherapies") - public void setLastGuidelineTherapies(List value) { this.lastGuidelineTherapies = value; } - @JsonProperty("molecularTherapies") public List getMolecularTherapies() { return molecularTherapies; } @JsonProperty("molecularTherapies") @@ -82,15 +88,15 @@ public class Mtb { @JsonProperty("patient") public void setPatient(MtbPatient value) { this.patient = value; } - @JsonProperty("previousGuidelineTherapies") - public List getPreviousGuidelineTherapies() { return previousGuidelineTherapies; } - @JsonProperty("previousGuidelineTherapies") - public void setPreviousGuidelineTherapies(List value) { this.previousGuidelineTherapies = value; } + @JsonProperty("performanceStatus") + public List getPerformanceStatus() { return performanceStatus; } + @JsonProperty("performanceStatus") + public void setPerformanceStatus(List value) { this.performanceStatus = value; } @JsonProperty("recommendations") - public List getRecommendations() { return recommendations; } + public List getRecommendations() { return recommendations; } @JsonProperty("recommendations") - public void setRecommendations(List value) { this.recommendations = value; } + public void setRecommendations(List value) { this.recommendations = value; } @JsonProperty("responses") public List getResponses() { return responses; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java deleted file mode 100644 index 566de3e..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java +++ /dev/null @@ -1,62 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.Date; -import java.util.List; - -public class MtbCarePlan { - private String description; - private String diagnosis; - private String geneticCounsellingRequest; - private String id; - private Date issuedOn; - private NoTargetFinding noTargetFinding; - private Patient patient; - private List recommendations; - private List 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 getRecommendations() { return recommendations; } - @JsonProperty("recommendations") - public void setRecommendations(List value) { this.recommendations = value; } - - @JsonProperty("studyInclusionRequests") - public List getStudyInclusionRequests() { return studyInclusionRequests; } - @JsonProperty("studyInclusionRequests") - public void setStudyInclusionRequests(List value) { this.studyInclusionRequests = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java index 2bf4c4a..8722cee 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java @@ -5,17 +5,24 @@ import java.util.Date; public class MtbPatient { private Address address; + private ValueWithUnit age; private Date birthDate; private Date dateOfDeath; private CodingGender gender; + private HealthInsurance healthInsurance; private String id; - private String insurance; + private VitalStatus vitalStatus; @JsonProperty("address") public Address getAddress() { return address; } @JsonProperty("address") public void setAddress(Address value) { this.address = value; } + @JsonProperty("age") + public ValueWithUnit getAge() { return age; } + @JsonProperty("age") + public void setAge(ValueWithUnit value) { this.age = value; } + @JsonProperty("birthDate") @JsonFormat(pattern = "yyyy-MM-dd") public Date getBirthDate() { return birthDate; } @@ -33,13 +40,18 @@ public class MtbPatient { @JsonProperty("gender") public void setGender(CodingGender value) { this.gender = value; } + @JsonProperty("healthInsurance") + public HealthInsurance getHealthInsurance() { return healthInsurance; } + @JsonProperty("healthInsurance") + public void setHealthInsurance(HealthInsurance value) { this.healthInsurance = value; } + @JsonProperty("id") public String getId() { return id; } @JsonProperty("id") public void setId(String value) { this.id = value; } - @JsonProperty("insurance") - public String getInsurance() { return insurance; } - @JsonProperty("insurance") - public void setInsurance(String value) { this.insurance = value; } + @JsonProperty("vitalStatus") + public VitalStatus getVitalStatus() { return vitalStatus; } + @JsonProperty("vitalStatus") + public void setVitalStatus(VitalStatus value) { this.vitalStatus = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java new file mode 100644 index 0000000..567aa4b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java @@ -0,0 +1,61 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class NgsReportResults { + private BRCAness brcaness; + private List copyNumberVariants; + private List dnaFusions; + private HRDScore hrdScore; + private List rnaFusions; + private List rnaSeqs; + private List simpleVariants; + private Tmb tmb; + private TumorCellContent tumorCellContent; + + @JsonProperty("brcaness") + public BRCAness getBrcaness() { return brcaness; } + @JsonProperty("brcaness") + public void setBrcaness(BRCAness value) { this.brcaness = value; } + + @JsonProperty("copyNumberVariants") + public List getCopyNumberVariants() { return copyNumberVariants; } + @JsonProperty("copyNumberVariants") + public void setCopyNumberVariants(List value) { this.copyNumberVariants = value; } + + @JsonProperty("dnaFusions") + public List getDnaFusions() { return dnaFusions; } + @JsonProperty("dnaFusions") + public void setDnaFusions(List value) { this.dnaFusions = value; } + + @JsonProperty("hrdScore") + public HRDScore getHrdScore() { return hrdScore; } + @JsonProperty("hrdScore") + public void setHrdScore(HRDScore value) { this.hrdScore = value; } + + @JsonProperty("rnaFusions") + public List getRnaFusions() { return rnaFusions; } + @JsonProperty("rnaFusions") + public void setRnaFusions(List value) { this.rnaFusions = value; } + + @JsonProperty("rnaSeqs") + public List getRnaSeqs() { return rnaSeqs; } + @JsonProperty("rnaSeqs") + public void setRnaSeqs(List value) { this.rnaSeqs = value; } + + @JsonProperty("simpleVariants") + public List getSimpleVariants() { return simpleVariants; } + @JsonProperty("simpleVariants") + public void setSimpleVariants(List value) { this.simpleVariants = value; } + + @JsonProperty("tmb") + public Tmb getTmb() { return tmb; } + @JsonProperty("tmb") + public void setTmb(Tmb value) { this.tmb = value; } + + @JsonProperty("tumorCellContent") + public TumorCellContent getTumorCellContent() { return tumorCellContent; } + @JsonProperty("tumorCellContent") + public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java new file mode 100644 index 0000000..ea16b1b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java @@ -0,0 +1,79 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; + +public class OncoProdecure { + private String basedOn; + private Coding code; + private String diagnosis; + private String id; + private Reference indication; + private String notes; + private Patient patient; + private PeriodLocalDate period; + private Date recordedOn; + private CodingTherapyStatus status; + private CodingTherapyStatusReason statusReason; + private Long therapyLine; + + @JsonProperty("basedOn") + public String getBasedOn() { return basedOn; } + @JsonProperty("basedOn") + public void setBasedOn(String value) { this.basedOn = value; } + + @JsonProperty("code") + public Coding getCode() { return code; } + @JsonProperty("code") + public void setCode(Coding value) { this.code = value; } + + @JsonProperty("diagnosis") + public String getDiagnosis() { return diagnosis; } + @JsonProperty("diagnosis") + public void setDiagnosis(String value) { this.diagnosis = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("indication") + public Reference getIndication() { return indication; } + @JsonProperty("indication") + public void setIndication(Reference value) { this.indication = value; } + + @JsonProperty("notes") + public String getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(String value) { this.notes = value; } + + @JsonProperty("patient") + public Patient getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Patient value) { this.patient = value; } + + @JsonProperty("period") + public PeriodLocalDate getPeriod() { return period; } + @JsonProperty("period") + public void setPeriod(PeriodLocalDate value) { this.period = value; } + + @JsonProperty("recordedOn") + public Date getRecordedOn() { return recordedOn; } + @JsonProperty("recordedOn") + public void setRecordedOn(Date value) { this.recordedOn = value; } + + @JsonProperty("status") + public CodingTherapyStatus getStatus() { return status; } + @JsonProperty("status") + public void setStatus(CodingTherapyStatus value) { this.status = value; } + + @JsonProperty("statusReason") + public CodingTherapyStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingTherapyStatusReason value) { this.statusReason = value; } + + @JsonProperty("therapyLine") + public Long getTherapyLine() { return therapyLine; } + @JsonProperty("therapyLine") + public void setTherapyLine(Long value) { this.therapyLine = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Position.java similarity index 94% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Position.java index 7109491..471258a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Position.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class StartEnd { +public class Position { private Double end; private double start; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java similarity index 98% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java index 292f387..7152835 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class RnaFusion { +public class RNAFusion { private String cosmicId; private String effect; private RnaFusionFusionPartner3Prime fusionPartner3Prime; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java similarity index 85% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java index 237b6af..8de16d9 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum RnaFusionStrand { +public enum RNAFusionStrand { EMPTY, RNA_FUSION_STRAND; @JsonValue @@ -16,7 +16,7 @@ public enum RnaFusionStrand { } @JsonCreator - public static RnaFusionStrand forValue(String value) throws IOException { + public static RNAFusionStrand forValue(String value) throws IOException { if (value.equals("+")) return EMPTY; if (value.equals("-")) return RNA_FUSION_STRAND; throw new IOException("Cannot deserialize RNAFusionStrand"); diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java similarity index 93% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java index ed6c568..5757db3 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java @@ -2,13 +2,13 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class RnaSeq { +public class RNASeq { private Long cohortRanking; private String ensemblId; private String entrezId; private double fragmentsPerKilobaseMillion; private boolean fromNgs; - private RnaSeqGene gene; + private CodingGene gene; private String id; private long librarySize; private long rawCounts; @@ -41,9 +41,9 @@ public class RnaSeq { public void setFromNgs(boolean value) { this.fromNgs = value; } @JsonProperty("gene") - public RnaSeqGene getGene() { return gene; } + public CodingGene getGene() { return gene; } @JsonProperty("gene") - public void setGene(RnaSeqGene value) { this.gene = value; } + public void setGene(CodingGene value) { this.gene = value; } @JsonProperty("id") public String getId() { return id; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java new file mode 100644 index 0000000..4d7a898 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Recommendation { + private String id; + private String type; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("type") + public String getType() { return type; } + @JsonProperty("type") + public void setType(String value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java new file mode 100644 index 0000000..21dda4d --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Reference { + private String display; + private String id; + private String type; + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("type") + public String getType() { return type; } + @JsonProperty("type") + public void setType(String value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java index 4af27ae..b50e9eb 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java @@ -3,14 +3,14 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class ReferencePublication { - private ExtId extId; + private EXTId extId; private String type; private String uri; @JsonProperty("extId") - public ExtId getExtId() { return extId; } + public EXTId getExtId() { return extId; } @JsonProperty("extId") - public void setExtId(ExtId value) { this.extId = value; } + public void setExtId(EXTId value) { this.extId = value; } @JsonProperty("type") public String getType() { return type; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java deleted file mode 100644 index 1127c22..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class ReportedAffectedGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java index 6857753..4160c4e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java @@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*; public class RnaFusionFusionPartner3Prime { private String exon; - private TentacledGene gene; + private CodingGene gene; private double position; - private RnaFusionStrand strand; + private RNAFusionStrand strand; private String transcriptId; @JsonProperty("exon") @@ -15,9 +15,9 @@ public class RnaFusionFusionPartner3Prime { public void setExon(String value) { this.exon = value; } @JsonProperty("gene") - public TentacledGene getGene() { return gene; } + public CodingGene getGene() { return gene; } @JsonProperty("gene") - public void setGene(TentacledGene value) { this.gene = value; } + public void setGene(CodingGene value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } @@ -25,9 +25,9 @@ public class RnaFusionFusionPartner3Prime { public void setPosition(double value) { this.position = value; } @JsonProperty("strand") - public RnaFusionStrand getStrand() { return strand; } + public RNAFusionStrand getStrand() { return strand; } @JsonProperty("strand") - public void setStrand(RnaFusionStrand value) { this.strand = value; } + public void setStrand(RNAFusionStrand value) { this.strand = value; } @JsonProperty("transcriptId") public String getTranscriptId() { return transcriptId; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java index 24541d3..946f076 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java @@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*; public class RnaFusionFusionPartner5Prime { private String exon; - private StickyGene gene; + private CodingGene gene; private double position; - private RnaFusionStrand strand; + private RNAFusionStrand strand; private String transcriptId; @JsonProperty("exon") @@ -15,9 +15,9 @@ public class RnaFusionFusionPartner5Prime { public void setExon(String value) { this.exon = value; } @JsonProperty("gene") - public StickyGene getGene() { return gene; } + public CodingGene getGene() { return gene; } @JsonProperty("gene") - public void setGene(StickyGene value) { this.gene = value; } + public void setGene(CodingGene value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } @@ -25,9 +25,9 @@ public class RnaFusionFusionPartner5Prime { public void setPosition(double value) { this.position = value; } @JsonProperty("strand") - public RnaFusionStrand getStrand() { return strand; } + public RNAFusionStrand getStrand() { return strand; } @JsonProperty("strand") - public void setStrand(RnaFusionStrand value) { this.strand = value; } + public void setStrand(RNAFusionStrand value) { this.strand = value; } @JsonProperty("transcriptId") public String getTranscriptId() { return transcriptId; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java deleted file mode 100644 index 681e537..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class RnaSeqGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java deleted file mode 100644 index 7696ec8..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class SimpleVariantGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java index f03bb85..3811672 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java @@ -1,21 +1,26 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; +import java.util.List; public class Snv { private double allelicFrequency; private String altAllele; private Coding aminoAcidChange; - private Chromosome chromosome; + private CodingChromosome chromosome; private String cosmicId; private String dbSnpId; private Coding dnaChange; - private SimpleVariantGene gene; + private List externalIds; + private CodingGene gene; private String id; private Coding interpretation; + private Patient patient; + private Position position; + private Coding proteinChange; private long readDepth; private String refAllele; - private StartEnd startEnd; + private ExternalId transcriptId; @JsonProperty("allelicFrequency") public double getAllelicFrequency() { return allelicFrequency; } @@ -33,9 +38,9 @@ public class Snv { public void setAminoAcidChange(Coding value) { this.aminoAcidChange = value; } @JsonProperty("chromosome") - public Chromosome getChromosome() { return chromosome; } + public CodingChromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(Chromosome value) { this.chromosome = value; } + public void setChromosome(CodingChromosome value) { this.chromosome = value; } @JsonProperty("cosmicId") public String getCosmicId() { return cosmicId; } @@ -52,10 +57,15 @@ public class Snv { @JsonProperty("dnaChange") public void setDnaChange(Coding value) { this.dnaChange = value; } + @JsonProperty("externalIds") + public List getExternalIds() { return externalIds; } + @JsonProperty("externalIds") + public void setExternalIds(List value) { this.externalIds = value; } + @JsonProperty("gene") - public SimpleVariantGene getGene() { return gene; } + public CodingGene getGene() { return gene; } @JsonProperty("gene") - public void setGene(SimpleVariantGene value) { this.gene = value; } + public void setGene(CodingGene value) { this.gene = value; } @JsonProperty("id") public String getId() { return id; } @@ -67,6 +77,21 @@ public class Snv { @JsonProperty("interpretation") public void setInterpretation(Coding value) { this.interpretation = value; } + @JsonProperty("patient") + public Patient getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Patient value) { this.patient = value; } + + @JsonProperty("position") + public Position getPosition() { return position; } + @JsonProperty("position") + public void setPosition(Position value) { this.position = value; } + + @JsonProperty("proteinChange") + public Coding getProteinChange() { return proteinChange; } + @JsonProperty("proteinChange") + public void setProteinChange(Coding value) { this.proteinChange = value; } + @JsonProperty("readDepth") public long getReadDepth() { return readDepth; } @JsonProperty("readDepth") @@ -77,8 +102,8 @@ public class Snv { @JsonProperty("refAllele") public void setRefAllele(String value) { this.refAllele = value; } - @JsonProperty("startEnd") - public StartEnd getStartEnd() { return startEnd; } - @JsonProperty("startEnd") - public void setStartEnd(StartEnd value) { this.startEnd = value; } + @JsonProperty("transcriptId") + public ExternalId getTranscriptId() { return transcriptId; } + @JsonProperty("transcriptId") + public void setTranscriptId(ExternalId value) { this.transcriptId = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java index c8fc940..ad6e57f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java @@ -5,46 +5,24 @@ import java.util.Date; import java.util.List; public class SomaticNgsReport { - private Double brcaness; - private List copyNumberVariants; - private List dnaFusions; private String id; - private Date issueDate; + private Date issuedOn; private List metadata; private Double msi; private Patient patient; - private List rnaFusions; - private List rnaSeqs; + private NgsReportResults results; private Coding sequencingType; - private List 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 getCopyNumberVariants() { return copyNumberVariants; } - @JsonProperty("copyNumberVariants") - public void setCopyNumberVariants(List value) { this.copyNumberVariants = value; } - - @JsonProperty("dnaFusions") - public List getDnaFusions() { return dnaFusions; } - @JsonProperty("dnaFusions") - public void setDnaFusions(List value) { this.dnaFusions = value; } @JsonProperty("id") public String getId() { return id; } @JsonProperty("id") public void setId(String value) { this.id = value; } - @JsonProperty("issueDate") - public Date getIssueDate() { return issueDate; } - @JsonProperty("issueDate") - public void setIssueDate(Date value) { this.issueDate = value; } + @JsonProperty("issuedOn") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("metadata") public List getMetadata() { return metadata; } @@ -61,38 +39,18 @@ public class SomaticNgsReport { @JsonProperty("patient") public void setPatient(Patient value) { this.patient = value; } - @JsonProperty("rnaFusions") - public List getRnaFusions() { return rnaFusions; } - @JsonProperty("rnaFusions") - public void setRnaFusions(List value) { this.rnaFusions = value; } - - @JsonProperty("rnaSeqs") - public List getRnaSeqs() { return rnaSeqs; } - @JsonProperty("rnaSeqs") - public void setRnaSeqs(List value) { this.rnaSeqs = value; } + @JsonProperty("results") + public NgsReportResults getResults() { return results; } + @JsonProperty("results") + public void setResults(NgsReportResults value) { this.results = value; } @JsonProperty("sequencingType") public Coding getSequencingType() { return sequencingType; } @JsonProperty("sequencingType") public void setSequencingType(Coding value) { this.sequencingType = value; } - @JsonProperty("simpleVariants") - public List getSimpleVariants() { return simpleVariants; } - @JsonProperty("simpleVariants") - public void setSimpleVariants(List 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; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java index 55b3211..bd06407 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum MtbDiagnosisTumorSpread { +public enum StageCode { LOCAL, METASTASIZED, TUMOR_FREE, UNKNOWN; @JsonValue @@ -18,7 +18,7 @@ public enum MtbDiagnosisTumorSpread { } @JsonCreator - public static MtbDiagnosisTumorSpread forValue(String value) throws IOException { + public static StageCode forValue(String value) throws IOException { switch (value) { case "local": return LOCAL; @@ -29,6 +29,6 @@ public enum MtbDiagnosisTumorSpread { case "unknown": return UNKNOWN; } - throw new IOException("Cannot deserialize MTBDiagnosisTumorSpread"); + throw new IOException("Cannot deserialize StageCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java similarity index 56% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java index cc97faa..aa8c1dd 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java @@ -3,9 +3,9 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.Date; -public class StatusHistory { +public class StageHistory { private Date date; - private MtbDiagnosisTumorSpread status; + private CodingTumorSpread stage; @JsonProperty("date") @JsonFormat(pattern = "yyyy-MM-dd") @@ -14,8 +14,8 @@ public class StatusHistory { @JsonFormat(pattern = "yyyy-MM-dd") public void setDate(Date value) { this.date = value; } - @JsonProperty("status") - public MtbDiagnosisTumorSpread getStatus() { return status; } - @JsonProperty("status") - public void setStatus(MtbDiagnosisTumorSpread value) { this.status = value; } + @JsonProperty("stage") + public CodingTumorSpread getStage() { return stage; } + @JsonProperty("stage") + public void setStage(CodingTumorSpread value) { this.stage = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java similarity index 93% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java index 281c11d..b3f1f5d 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum NotDoneReasonCode { +public enum StatusReasonCode { CHRONIC_REMISSION, CONTINUED_EXTERNALLY, DETERIORATION, LOST_TO_FU, MEDICAL_REASON, NO_INDICATION, OTHER, OTHER_THERAPY_CHOSEN, PATIENT_DEATH, PATIENT_REFUSAL, PATIENT_WISH, PAYMENT_ENDED, PAYMENT_PENDING, PAYMENT_REFUSED, PROGRESSION, TOXICITY, UNKNOWN; @JsonValue @@ -31,7 +31,7 @@ public enum NotDoneReasonCode { } @JsonCreator - public static NotDoneReasonCode forValue(String value) throws IOException { + public static StatusReasonCode forValue(String value) throws IOException { switch (value) { case "chronic-remission": return CHRONIC_REMISSION; @@ -68,6 +68,6 @@ public enum NotDoneReasonCode { case "unknown": return UNKNOWN; } - throw new IOException("Cannot deserialize NotDoneReasonCode"); + throw new IOException("Cannot deserialize StatusReasonCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java deleted file mode 100644 index bafb125..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class StickyGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java new file mode 100644 index 0000000..791abe2 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Study { + private String system; + private String value; + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("value") + public String getValue() { return value; } + @JsonProperty("value") + public void setValue(String value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java index a854c28..7b68a1e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java @@ -2,13 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.Date; +import java.util.List; public class StudyEnrollmentRecommendation { private String id; private Date issuedOn; - private String nctNumber; + private Coding levelOfEvidence; private Patient patient; - private String reason; + private Reference reason; + private List studies; + private List supportingVariants; @JsonProperty("id") public String getId() { return id; } @@ -20,10 +23,10 @@ public class StudyEnrollmentRecommendation { @JsonProperty("issuedOn") public void setIssuedOn(Date value) { this.issuedOn = value; } - @JsonProperty("nctNumber") - public String getNctNumber() { return nctNumber; } - @JsonProperty("nctNumber") - public void setNctNumber(String value) { this.nctNumber = value; } + @JsonProperty("levelOfEvidence") + public Coding getLevelOfEvidence() { return levelOfEvidence; } + @JsonProperty("levelOfEvidence") + public void setLevelOfEvidence(Coding value) { this.levelOfEvidence = value; } @JsonProperty("patient") public Patient getPatient() { return patient; } @@ -31,7 +34,17 @@ public class StudyEnrollmentRecommendation { public void setPatient(Patient value) { this.patient = value; } @JsonProperty("reason") - public String getReason() { return reason; } + public Reference getReason() { return reason; } @JsonProperty("reason") - public void setReason(String value) { this.reason = value; } + public void setReason(Reference value) { this.reason = value; } + + @JsonProperty("studies") + public List getStudies() { return studies; } + @JsonProperty("studies") + public void setStudies(List value) { this.studies = value; } + + @JsonProperty("supportingVariants") + public List getSupportingVariants() { return supportingVariants; } + @JsonProperty("supportingVariants") + public void setSupportingVariants(List value) { this.supportingVariants = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java deleted file mode 100644 index 254ed42..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class TentacledGene { - private String ensemblId; - private String hgncId; - - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("hgncId") - public String getHgncId() { return hgncId; } - @JsonProperty("hgncId") - public void setHgncId(String value) { this.hgncId = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java new file mode 100644 index 0000000..507bc64 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java @@ -0,0 +1,36 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Tmb { + private String id; + private Coding interpretation; + private Reference patient; + private Reference specimen; + private Value value; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("interpretation") + public Coding getInterpretation() { return interpretation; } + @JsonProperty("interpretation") + public void setInterpretation(Coding value) { this.interpretation = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("specimen") + public Reference getSpecimen() { return specimen; } + @JsonProperty("specimen") + public void setSpecimen(Reference value) { this.specimen = value; } + + @JsonProperty("value") + public Value getValue() { return value; } + @JsonProperty("value") + public void setValue(Value value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java index f23fe52..bc8a08b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java @@ -4,8 +4,9 @@ import com.fasterxml.jackson.annotation.*; public class TumorCellContent { private String id; - private TumorCellContentMethod method; - private String specimen; + private CodingTumorCellContentMethod method; + private Patient patient; + private TumorCellContentSpecimen specimen; private double value; @JsonProperty("id") @@ -14,14 +15,19 @@ public class TumorCellContent { public void setId(String value) { this.id = value; } @JsonProperty("method") - public TumorCellContentMethod getMethod() { return method; } + public CodingTumorCellContentMethod getMethod() { return method; } @JsonProperty("method") - public void setMethod(TumorCellContentMethod value) { this.method = value; } + public void setMethod(CodingTumorCellContentMethod value) { this.method = value; } + + @JsonProperty("patient") + public Patient getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Patient value) { this.patient = value; } @JsonProperty("specimen") - public String getSpecimen() { return specimen; } + public TumorCellContentSpecimen getSpecimen() { return specimen; } @JsonProperty("specimen") - public void setSpecimen(String value) { this.specimen = value; } + public void setSpecimen(TumorCellContentSpecimen value) { this.specimen = value; } @JsonProperty("value") public double getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java new file mode 100644 index 0000000..9ba1e38 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class TumorCellContentSpecimen { + private String id; + private SpecimenType type; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("type") + public SpecimenType getType() { return type; } + @JsonProperty("type") + public void setType(SpecimenType value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java new file mode 100644 index 0000000..45b9be9 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java @@ -0,0 +1,37 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum TumorGradeCode { + G1, G2, G3, G4, GX; + + @JsonValue + public String toValue() { + switch (this) { + case G1: return "G1"; + case G2: return "G2"; + case G3: return "G3"; + case G4: return "G4"; + case GX: return "GX"; + } + return null; + } + + @JsonCreator + public static TumorGradeCode forValue(String value) throws IOException { + switch (value) { + case "G1": + return G1; + case "G2": + return G2; + case "G3": + return G3; + case "G4": + return G4; + case "GX": + return GX; + } + throw new IOException("Cannot deserialize TumorGradeCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java index cff772c..3e2f139 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java @@ -4,9 +4,9 @@ import com.fasterxml.jackson.annotation.*; public class TumorMorphology { private String id; - private String note; + private String notes; private Patient patient; - private String specimen; + private TumorMorphologySpecimen specimen; private Coding value; @JsonProperty("id") @@ -14,10 +14,10 @@ public class TumorMorphology { @JsonProperty("id") public void setId(String value) { this.id = value; } - @JsonProperty("note") - public String getNote() { return note; } - @JsonProperty("note") - public void setNote(String value) { this.note = value; } + @JsonProperty("notes") + public String getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(String value) { this.notes = value; } @JsonProperty("patient") public Patient getPatient() { return patient; } @@ -25,9 +25,9 @@ public class TumorMorphology { public void setPatient(Patient value) { this.patient = value; } @JsonProperty("specimen") - public String getSpecimen() { return specimen; } + public TumorMorphologySpecimen getSpecimen() { return specimen; } @JsonProperty("specimen") - public void setSpecimen(String value) { this.specimen = value; } + public void setSpecimen(TumorMorphologySpecimen value) { this.specimen = value; } @JsonProperty("value") public Coding getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java similarity index 92% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java index ce66fde..5f28551 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class Specimen { +public class TumorMorphologySpecimen { private String id; private SpecimenType type; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java index 3dce7db..bb504ba 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; public class TumorSpecimen { private Collection collection; - private Coding icd10; + private Diagnosis diagnosis; private String id; private Patient patient; private CodingTumorSpecimenType type; @@ -14,10 +14,10 @@ public class TumorSpecimen { @JsonProperty("collection") public void setCollection(Collection value) { this.collection = value; } - @JsonProperty("icd10") - public Coding getIcd10() { return icd10; } - @JsonProperty("icd10") - public void setIcd10(Coding value) { this.icd10 = value; } + @JsonProperty("diagnosis") + public Diagnosis getDiagnosis() { return diagnosis; } + @JsonProperty("diagnosis") + public void setDiagnosis(Diagnosis value) { this.diagnosis = value; } @JsonProperty("id") public String getId() { return id; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java new file mode 100644 index 0000000..c8e3303 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum Type { + ORGANIZATION; + + @JsonValue + public String toValue() { + switch (this) { + case ORGANIZATION: return "Organization"; + } + return null; + } + + @JsonCreator + public static Type forValue(String value) throws IOException { + if (value.equals("Organization")) return ORGANIZATION; + throw new IOException("Cannot deserialize Type"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java new file mode 100644 index 0000000..0ce88dc --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum Unit { + YEARS; + + @JsonValue + public String toValue() { + switch (this) { + case YEARS: return "Years"; + } + return null; + } + + @JsonCreator + public static Unit forValue(String value) throws IOException { + if (value.equals("Years")) return YEARS; + throw new IOException("Cannot deserialize Unit"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java new file mode 100644 index 0000000..9cafbb7 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class Value { + private String unit; + private double value; + + @JsonProperty("unit") + public String getUnit() { return unit; } + @JsonProperty("unit") + public void setUnit(String value) { this.unit = value; } + + @JsonProperty("value") + public double getValue() { return value; } + @JsonProperty("value") + public void setValue(double value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java new file mode 100644 index 0000000..34eb272 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java @@ -0,0 +1,18 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class ValueWithUnit { + private Unit unit; + private double value; + + @JsonProperty("unit") + public Unit getUnit() { return unit; } + @JsonProperty("unit") + public void setUnit(Unit value) { this.unit = value; } + + @JsonProperty("value") + public double getValue() { return value; } + @JsonProperty("value") + public void setValue(double value) { this.value = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java new file mode 100644 index 0000000..c553e1b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class VitalStatus { + private VitalStatusCode code; + private String display; + private String system; + + @JsonProperty("code") + public VitalStatusCode getCode() { return code; } + @JsonProperty("code") + public void setCode(VitalStatusCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java new file mode 100644 index 0000000..1bd604f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum VitalStatusCode { + ALIVE, DECEASED; + + @JsonValue + public String toValue() { + switch (this) { + case ALIVE: return "alive"; + case DECEASED: return "deceased"; + } + return null; + } + + @JsonCreator + public static VitalStatusCode forValue(String value) throws IOException { + if (value.equals("alive")) return ALIVE; + if (value.equals("deceased")) return DECEASED; + throw new IOException("Cannot deserialize VitalStatusCode"); + } +}