From a7bc424a01d1923c7959355d322d6f509bd3a943 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Sat, 5 Apr 2025 15:13:27 +0200 Subject: [PATCH 1/2] chore: update to DNPM-Datamodel 2.1 preview --- .../mtb/{ValueWithUnit.java => Age.java} | 2 +- .../{ChromosomeCode.java => Chromosome.java} | 6 +- .../pcvolkmer/mv64e/mtb/ChromosomeSystem.java | 22 - .../java/dev/pcvolkmer/mv64e/mtb/Claim.java | 25 +- .../pcvolkmer/mv64e/mtb/ClaimResponse.java | 12 +- .../mv64e/mtb/ClaimResponseClaim.java | 18 - .../mv64e/mtb/ClaimResponseClaimType.java | 22 - .../java/dev/pcvolkmer/mv64e/mtb/Cnv.java | 46 +- ...a => CodingAtcUnregisteredMedication.java} | 14 +- .../mtb/CodingBaseVariantLocalization.java | 30 + .../CodingBaseVariantLocalizationCode.java | 30 + .../pcvolkmer/mv64e/mtb/CodingChromosome.java | 24 - .../mv64e/mtb/CodingClaimResponseStatus.java | 12 +- .../mtb/CodingClaimResponseStatusReason.java | 12 +- ... CodingClaimResponseStatusReasonCode.java} | 32 +- ...gTumorGrade.java => CodingClaimStage.java} | 8 +- ...pyStatusReason.java => CodingClinVar.java} | 8 +- .../mv64e/mtb/CodingClinVarCode.java | 30 + ...mmendationPriority.java => CodingCnv.java} | 14 +- .../mtb/{CNVType.java => CodingCnvCode.java} | 17 +- .../dev/pcvolkmer/mv64e/mtb/CodingEcog.java | 6 +- .../pcvolkmer/mv64e/mtb/CodingEcogCode.java | 32 + ....java => CodingFollowUpPatientStatus.java} | 14 +- .../dev/pcvolkmer/mv64e/mtb/CodingGender.java | 6 +- .../dev/pcvolkmer/mv64e/mtb/CodingGene.java | 24 - ...GeneticCounselingRecommendationReason.java | 30 + .../mv64e/mtb/CodingHealthInsurance.java | 30 + .../mv64e/mtb/CodingHealthInsuranceCode.java | 38 + .../mtb/CodingHrdScoreInterpretation.java | 30 + .../mtb/CodingLevelOfEvidenceGrading.java | 6 +- .../mtb/CodingMolecularDiagnosticReport.java | 30 + .../CodingMolecularDiagnosticReportCode.java | 44 + .../mtb/CodingMtbCarePlanStatusReason.java | 30 + .../CodingMtbCarePlanStatusReasonCode.java | 32 + .../mv64e/mtb/CodingMtbDiagnosis.java | 30 + .../mv64e/mtb/CodingMtbDiagnosisCode.java | 26 + ...gMtbDiagnosisGuidelineTreatmentStatus.java | 30 + ...ngMtbMedicationRecommendationCategory.java | 30 + ...bMedicationRecommendationCategoryCode.java | 32 + ...ingMtbMedicationRecommendationUseType.java | 30 + ...ingMtbProcedureRecommendationCategory.java | 30 + ...tbProcedureRecommendationCategoryCode.java | 32 + .../mtb/CodingMtbSystemicTherapyCategory.java | 30 + .../CodingMtbSystemicTherapyCategoryCode.java | 30 + ...herapyRecommendationFulfillmentStatus.java | 30 + ...vType.java => CodingMtbTherapyIntent.java} | 14 +- .../mtb/CodingMtbTherapyStatusReason.java | 30 + .../mtb/CodingMtbTherapyStatusReasonCode.java | 58 + .../pcvolkmer/mv64e/mtb/CodingNgsReport.java | 30 + .../mv64e/mtb/CodingNgsReportCode.java | 36 + .../mv64e/mtb/CodingOncoProcedure.java | 30 + .../mv64e/mtb/CodingOncoProcedureCode.java | 26 + .../mtb/CodingProteinExpressionResult.java | 6 +- .../CodingProteinExpressionResultCode.java | 32 + .../dev/pcvolkmer/mv64e/mtb/CodingRecist.java | 6 +- .../pcvolkmer/mv64e/mtb/CodingRecistCode.java | 32 + .../mtb/CodingRecommendationPriority.java | 30 + .../mv64e/mtb/CodingResponseMethod.java | 30 + .../mv64e/mtb/CodingResponseMethodCode.java | 24 + .../mv64e/mtb/CodingTherapyStatus.java | 12 +- ...atus.java => CodingTherapyStatusCode.java} | 23 +- .../mv64e/mtb/CodingTmbInterpretation.java | 30 + .../mtb/CodingTumorCellContentMethod.java | 12 +- ... => CodingTumorCellContentMethodCode.java} | 6 +- .../mv64e/mtb/CodingTumorSpecimen.java | 30 + ...Type.java => CodingTumorSpecimenCode.java} | 23 +- ...ngTumorSpecimenCollectionLocalization.java | 12 +- ...morSpecimenCollectionLocalizationCode.java | 32 + .../CodingTumorSpecimenCollectionMethod.java | 12 +- ...dingTumorSpecimenCollectionMethodCode.java | 30 + .../mv64e/mtb/CodingTumorSpread.java | 24 - .../mv64e/mtb/CodingTumorStagingMethod.java | 30 + .../mtb/CodingTumorStagingMethodCode.java | 24 + ...italStatus.java => CodingVitalStatus.java} | 8 +- .../dev/pcvolkmer/mv64e/mtb/Collection.java | 2 - .../dev/pcvolkmer/mv64e/mtb/DNAFusion.java | 19 + .../dev/pcvolkmer/mv64e/mtb/Diagnosis.java | 18 - .../mtb/DnaFusionFusionPartner3Prime.java | 12 +- .../mtb/DnaFusionFusionPartner5Prime.java | 12 +- .../dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java | 22 - .../dev/pcvolkmer/mv64e/mtb/EcogCode.java | 37 - .../pcvolkmer/mv64e/mtb/ExternalIdSystem.java | 28 + .../dev/pcvolkmer/mv64e/mtb/FollowUp.java | 21 + .../mtb/{Gender.java => GenderCode.java} | 20 +- .../java/dev/pcvolkmer/mv64e/mtb/Gene.java | 18 - .../mv64e/mtb/GeneAlterationReference.java | 24 + .../dev/pcvolkmer/mv64e/mtb/GeneSystem.java | 22 - .../mtb/GeneticCounselingRecommendation.java | 14 +- .../java/dev/pcvolkmer/mv64e/mtb/Grading.java | 13 + .../dev/pcvolkmer/mv64e/mtb/GradingCode.java | 49 - .../mtb/GuidelineTreatmentStatusCode.java | 30 + .../dev/pcvolkmer/mv64e/mtb/HRDScore.java | 6 +- .../pcvolkmer/mv64e/mtb/HealthInsurance.java | 22 +- .../mtb/HistologyReevaluationRequest.java | 33 + .../pcvolkmer/mv64e/mtb/HistologyReport.java | 12 +- .../mv64e/mtb/HistologyReportSpecimen.java | 18 - .../mtb/{StageHistory.java => History.java} | 12 +- .../dev/pcvolkmer/mv64e/mtb/ICScoreCode.java | 24 +- .../dev/pcvolkmer/mv64e/mtb/IHCReport.java | 50 +- .../pcvolkmer/mv64e/mtb/IhcReportResults.java | 19 + .../dev/pcvolkmer/mv64e/mtb/IntentCode.java | 28 + .../mv64e/mtb/InterpretationCode.java | 26 + .../pcvolkmer/mv64e/mtb/LevelOfEvidence.java | 6 +- .../mv64e/mtb/LevelOfEvidenceCode.java | 38 + .../mtb/{MSIMmrResult.java => MSIMmr.java} | 2 +- .../dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java | 68 +- .../dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java | 80 +- .../dev/pcvolkmer/mv64e/mtb/MTBEpisode.java | 24 - ...isodeOfCare.java => MTBEpisodeOfCare.java} | 8 +- .../mtb/MTBMedicationRecommendation.java | 56 +- .../mv64e/mtb/MTBMedicationTherapy.java | 80 - .../mtb/MTBStudyEnrollmentRecommendation.java | 64 + .../mv64e/mtb/MTBSystemicTherapy.java | 94 + .../mtb/{Metadatum.java => Metadata.java} | 2 +- .../pcvolkmer/mv64e/mtb/MolecularTherapy.java | 13 - .../java/dev/pcvolkmer/mv64e/mtb/Mtb.java | 78 +- .../dev/pcvolkmer/mv64e/mtb/MtbPatient.java | 57 - .../mv64e/mtb/NgsReportSpecimen.java | 18 - .../pcvolkmer/mv64e/mtb/NoTargetFinding.java | 25 - .../pcvolkmer/mv64e/mtb/OncoProcedure.java | 82 + .../pcvolkmer/mv64e/mtb/OncoProdecure.java | 79 - .../java/dev/pcvolkmer/mv64e/mtb/Patient.java | 55 +- .../mv64e/mtb/PatientStatusCode.java | 22 + .../dev/pcvolkmer/mv64e/mtb/PatientType.java | 22 - .../mv64e/mtb/PerformanceStatus.java | 6 +- .../{PeriodLocalDate.java => PeriodDate.java} | 2 +- .../mv64e/mtb/PriorDiagnosticReport.java | 52 + .../dev/pcvolkmer/mv64e/mtb/PriorityCode.java | 28 + .../mv64e/mtb/ProcedureRecommendation.java | 58 + ...sionResult.java => ProteinExpression.java} | 2 +- .../mtb/ProteinExpressionResultCode.java | 40 - .../mv64e/mtb/PublicationReference.java | 30 + .../mv64e/mtb/PublicationSystem.java | 24 + .../dev/pcvolkmer/mv64e/mtb/RNAFusion.java | 25 +- .../java/dev/pcvolkmer/mv64e/mtb/RNASeq.java | 77 +- .../dev/pcvolkmer/mv64e/mtb/ReasonCode.java | 30 + .../pcvolkmer/mv64e/mtb/RebiopsyRequest.java | 33 + .../dev/pcvolkmer/mv64e/mtb/RecistCode.java | 43 - .../pcvolkmer/mv64e/mtb/Recommendation.java | 18 - .../RecommendationFulfillmentStatusCode.java | 24 + .../dev/pcvolkmer/mv64e/mtb/Reference.java | 6 + .../mv64e/mtb/ReferencePublication.java | 24 - .../mv64e/mtb/RequestedMedicationSystem.java | 24 + .../dev/pcvolkmer/mv64e/mtb/Response.java | 18 +- .../pcvolkmer/mv64e/mtb/ResponseTherapy.java | 18 - .../mv64e/mtb/ResponseTherapyType.java | 22 - .../mtb/RnaFusionFusionPartner3Prime.java | 22 +- .../mtb/RnaFusionFusionPartner5Prime.java | 22 +- .../java/dev/pcvolkmer/mv64e/mtb/Snv.java | 66 +- .../pcvolkmer/mv64e/mtb/SomaticNgsReport.java | 56 - .../mv64e/mtb/SomaticNgsReportMetadata.java | 52 + .../dev/pcvolkmer/mv64e/mtb/SpecimenType.java | 22 - .../dev/pcvolkmer/mv64e/mtb/StageCode.java | 22 +- .../java/dev/pcvolkmer/mv64e/mtb/Staging.java | 13 + .../pcvolkmer/mv64e/mtb/StatusReasonCode.java | 73 - ...aimResponseStatus.java => StickyCode.java} | 17 +- .../java/dev/pcvolkmer/mv64e/mtb/Study.java | 18 - .../mtb/StudyEnrollmentRecommendation.java | 50 - .../pcvolkmer/mv64e/mtb/StudyReference.java | 30 + .../dev/pcvolkmer/mv64e/mtb/StudySystem.java | 28 + .../pcvolkmer/mv64e/mtb/SystemicTherapy.java | 13 + .../mv64e/mtb/{Value.java => TMBResult.java} | 2 +- .../dev/pcvolkmer/mv64e/mtb/TcScoreCode.java | 39 +- .../java/dev/pcvolkmer/mv64e/mtb/Therapy.java | 13 - .../mtb/TherapyRecommendationPriority.java | 34 - .../java/dev/pcvolkmer/mv64e/mtb/Tmb.java | 12 +- .../mv64e/mtb/TnmClassification.java | 24 + .../{ExternalId.java => TranscriptId.java} | 8 +- .../mv64e/mtb/TranscriptIdSystem.java | 24 + .../pcvolkmer/mv64e/mtb/TumorCellContent.java | 12 +- .../mv64e/mtb/TumorCellContentSpecimen.java | 18 - .../pcvolkmer/mv64e/mtb/TumorGradeCode.java | 37 - .../dev/pcvolkmer/mv64e/mtb/TumorGrading.java | 22 + .../pcvolkmer/mv64e/mtb/TumorMorphology.java | 12 +- .../mv64e/mtb/TumorMorphologySpecimen.java | 18 - .../pcvolkmer/mv64e/mtb/TumorSpecimen.java | 18 +- .../TumorSpecimenCollectionLocalization.java | 31 - .../mtb/TumorSpecimenCollectionMethod.java | 37 - .../dev/pcvolkmer/mv64e/mtb/TumorStaging.java | 34 + .../java/dev/pcvolkmer/mv64e/mtb/Type.java | 23 +- .../java/dev/pcvolkmer/mv64e/mtb/Unit.java | 4 +- .../dev/pcvolkmer/mv64e/mtb/UseTypeCode.java | 30 + .../{EXTId.java => VariantExternalId.java} | 8 +- .../resources/mv64e-mtb-fake-patient.json | 2244 ++++++++++++++++- 184 files changed, 5310 insertions(+), 1844 deletions(-) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ValueWithUnit.java => Age.java} (93%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ChromosomeCode.java => Chromosome.java} (93%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingCarePlanStatusReason.java => CodingAtcUnregisteredMedication.java} (53%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ClaimResponseStatusReason.java => CodingClaimResponseStatusReasonCode.java} (50%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorGrade.java => CodingClaimStage.java} (79%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTherapyStatusReason.java => CodingClinVar.java} (78%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTherapyRecommendationPriority.java => CodingCnv.java} (58%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CNVType.java => CodingCnvCode.java} (52%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenType.java => CodingFollowUpPatientStatus.java} (57%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingCnvType.java => CodingMtbTherapyIntent.java} (58%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{TherapyStatus.java => CodingTherapyStatusCode.java} (50%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{TumorCellContentMethod.java => CodingTumorCellContentMethodCode.java} (68%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{TumorSpecimenType.java => CodingTumorSpecimenCode.java} (50%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{VitalStatus.java => CodingVitalStatus.java} (74%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Gender.java => GenderCode.java} (51%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GeneAlterationReference.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Grading.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReevaluationRequest.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{StageHistory.java => History.java} (59%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReportResults.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MSIMmrResult.java => MSIMmr.java} (98%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{EpisodeOfCare.java => MTBEpisodeOfCare.java} (80%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Metadatum.java => Metadata.java} (98%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{PeriodLocalDate.java => PeriodDate.java} (94%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ProteinExpressionResult.java => ProteinExpression.java} (97%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationReference.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RebiopsyRequest.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Staging.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ClaimResponseStatus.java => StickyCode.java} (50%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/StudyReference.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Value.java => TMBResult.java} (94%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Therapy.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TnmClassification.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ExternalId.java => TranscriptId.java} (61%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGrading.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethod.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{EXTId.java => VariantExternalId.java} (61%) diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Age.java similarity index 93% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Age.java index 34eb272..10b8d5e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueWithUnit.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Age.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class ValueWithUnit { +public class Age { private Unit unit; private double value; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java similarity index 93% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java index 33522ea..92b2c18 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum ChromosomeCode { +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 @@ -38,7 +38,7 @@ public enum ChromosomeCode { } @JsonCreator - public static ChromosomeCode forValue(String value) throws IOException { + public static Chromosome forValue(String value) throws IOException { if (value.equals("chr1")) return CHR1; if (value.equals("chr10")) return CHR10; if (value.equals("chr11")) return CHR11; @@ -63,6 +63,6 @@ public enum ChromosomeCode { 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"); + throw new IOException("Cannot deserialize Chromosome"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java deleted file mode 100644 index a8337e0..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ChromosomeSystem.java +++ /dev/null @@ -1,22 +0,0 @@ -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 5bbdf4d..b5b1adf 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java @@ -2,13 +2,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.Date; +import java.util.List; public class Claim { private String id; private Date issuedOn; - private Patient patient; - private Recommendation recommendation; - private Coding stage; + private Reference patient; + private Reference recommendation; + private List requestedMedication; + private CodingClaimStage stage; @JsonProperty("id") public String getId() { return id; } @@ -23,17 +25,22 @@ public class Claim { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("recommendation") - public Recommendation getRecommendation() { return recommendation; } + public Reference getRecommendation() { return recommendation; } @JsonProperty("recommendation") - public void setRecommendation(Recommendation value) { this.recommendation = value; } + public void setRecommendation(Reference value) { this.recommendation = value; } + + @JsonProperty("requestedMedication") + public List getRequestedMedication() { return requestedMedication; } + @JsonProperty("requestedMedication") + public void setRequestedMedication(List value) { this.requestedMedication = value; } @JsonProperty("stage") - public Coding getStage() { return stage; } + public CodingClaimStage getStage() { return stage; } @JsonProperty("stage") - public void setStage(Coding value) { this.stage = value; } + public void setStage(CodingClaimStage 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 7b93ab5..657eb0e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java @@ -4,17 +4,17 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; public class ClaimResponse { - private ClaimResponseClaim claim; + private Reference claim; private String id; private Date issuedOn; - private Patient patient; + private Reference patient; private CodingClaimResponseStatus status; private CodingClaimResponseStatusReason statusReason; @JsonProperty("claim") - public ClaimResponseClaim getClaim() { return claim; } + public Reference getClaim() { return claim; } @JsonProperty("claim") - public void setClaim(ClaimResponseClaim value) { this.claim = value; } + public void setClaim(Reference value) { this.claim = value; } @JsonProperty("id") public String getId() { return id; } @@ -29,9 +29,9 @@ public class ClaimResponse { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("status") public CodingClaimResponseStatus getStatus() { return status; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java deleted file mode 100644 index 53bd5d6..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class ClaimResponseClaim { - private String id; - private ClaimResponseClaimType type; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("type") - public ClaimResponseClaimType getType() { return type; } - @JsonProperty("type") - public void setType(ClaimResponseClaimType value) { this.type = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java deleted file mode 100644 index e0f132e..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java +++ /dev/null @@ -1,22 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum ClaimResponseClaimType { - CLAIM; - - @JsonValue - public String toValue() { - switch (this) { - case CLAIM: return "Claim"; - } - return null; - } - - @JsonCreator - public static ClaimResponseClaimType forValue(String value) throws IOException { - if (value.equals("Claim")) return CLAIM; - throw new IOException("Cannot deserialize ClaimResponseClaimType"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java index 27c308f..d2ad364 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java @@ -4,25 +4,26 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class Cnv { - private CodingChromosome chromosome; + private Chromosome chromosome; private Double cnA; private Double cnB; - private List copyNumberNeutralLoH; + private List copyNumberNeutralLoH; private EndRange endRange; + private List externalIds; private String id; - private Reference indication; - private Patient patient; + private List localization; + private Reference patient; private Double relativeCopyNumber; - private List reportedAffectedGenes; + private List reportedAffectedGenes; private String reportedFocality; private StartRange startRange; private Long totalCopyNumber; - private CodingCnvType type; + private CodingCnv type; @JsonProperty("chromosome") - public CodingChromosome getChromosome() { return chromosome; } + public Chromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(CodingChromosome value) { this.chromosome = value; } + public void setChromosome(Chromosome value) { this.chromosome = value; } @JsonProperty("cnA") public Double getCnA() { return cnA; } @@ -35,29 +36,34 @@ 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; } @JsonProperty("endRange") public void setEndRange(EndRange value) { this.endRange = value; } + @JsonProperty("externalIds") + public List getExternalIds() { return externalIds; } + @JsonProperty("externalIds") + public void setExternalIds(List value) { this.externalIds = 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("localization") + public List getLocalization() { return localization; } + @JsonProperty("localization") + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("relativeCopyNumber") public Double getRelativeCopyNumber() { return relativeCopyNumber; } @@ -65,9 +71,9 @@ public class Cnv { 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; } @@ -85,7 +91,7 @@ public class Cnv { public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; } @JsonProperty("type") - public CodingCnvType getType() { return type; } + public CodingCnv getType() { return type; } @JsonProperty("type") - public void setType(CodingCnvType value) { this.type = value; } + public void setType(CodingCnv value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java similarity index 53% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java index 698acd9..ced0849 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCarePlanStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java @@ -2,10 +2,11 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingCarePlanStatusReason { +public class CodingAtcUnregisteredMedication { private String code; private String display; - private String system; + private RequestedMedicationSystem system; + private String version; @JsonProperty("code") public String getCode() { return code; } @@ -18,7 +19,12 @@ public class CodingCarePlanStatusReason { public void setDisplay(String value) { this.display = value; } @JsonProperty("system") - public String getSystem() { return system; } + public RequestedMedicationSystem getSystem() { return system; } @JsonProperty("system") - public void setSystem(String value) { this.system = value; } + public void setSystem(RequestedMedicationSystem value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java new file mode 100644 index 0000000..26d9c4f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingBaseVariantLocalization { + private CodingBaseVariantLocalizationCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingBaseVariantLocalizationCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingBaseVariantLocalizationCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java new file mode 100644 index 0000000..d06b221 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingBaseVariantLocalizationCode { + CODING_REGION, INTERGENIC, INTRONIC, REGULATORY_REGION, SPLICING_REGION; + + @JsonValue + public String toValue() { + switch (this) { + case CODING_REGION: return "coding-region"; + case INTERGENIC: return "intergenic"; + case INTRONIC: return "intronic"; + case REGULATORY_REGION: return "regulatory-region"; + case SPLICING_REGION: return "splicing-region"; + } + return null; + } + + @JsonCreator + public static CodingBaseVariantLocalizationCode forValue(String value) throws IOException { + if (value.equals("coding-region")) return CODING_REGION; + if (value.equals("intergenic")) return INTERGENIC; + if (value.equals("intronic")) return INTRONIC; + if (value.equals("regulatory-region")) return REGULATORY_REGION; + if (value.equals("splicing-region")) return SPLICING_REGION; + throw new IOException("Cannot deserialize CodingBaseVariantLocalizationCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java deleted file mode 100644 index f8c3e83..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingChromosome.java +++ /dev/null @@ -1,24 +0,0 @@ -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/CodingClaimResponseStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java index beff73d..bc4a36e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingClaimResponseStatus { - private ClaimResponseStatus code; + private StickyCode code; private String display; private String system; + private String version; @JsonProperty("code") - public ClaimResponseStatus getCode() { return code; } + public StickyCode getCode() { return code; } @JsonProperty("code") - public void setCode(ClaimResponseStatus value) { this.code = value; } + public void setCode(StickyCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingClaimResponseStatus { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java index ea49f6b..275505d 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingClaimResponseStatusReason { - private ClaimResponseStatusReason code; + private CodingClaimResponseStatusReasonCode code; private String display; private String system; + private String version; @JsonProperty("code") - public ClaimResponseStatusReason getCode() { return code; } + public CodingClaimResponseStatusReasonCode getCode() { return code; } @JsonProperty("code") - public void setCode(ClaimResponseStatusReason value) { this.code = value; } + public void setCode(CodingClaimResponseStatusReasonCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingClaimResponseStatusReason { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java similarity index 50% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java index 1cf35ab..843bf4f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum ClaimResponseStatusReason { +public enum CodingClaimResponseStatusReasonCode { APPROVAL_REVOCATION, FORMAL_REASONS, INCLUSION_IN_STUDY, INSUFFICIENT_EVIDENCE, OTHER, OTHER_THERAPY_RECOMMENDED, STANDARD_THERAPY_NOT_EXHAUSTED, UNKNOWN; @JsonValue @@ -22,25 +22,15 @@ public enum ClaimResponseStatusReason { } @JsonCreator - public static ClaimResponseStatusReason forValue(String value) throws IOException { - switch (value) { - case "approval-revocation": - return APPROVAL_REVOCATION; - case "formal-reasons": - return FORMAL_REASONS; - case "inclusion-in-study": - return INCLUSION_IN_STUDY; - case "insufficient-evidence": - return INSUFFICIENT_EVIDENCE; - case "other": - return OTHER; - case "other-therapy-recommended": - return OTHER_THERAPY_RECOMMENDED; - case "standard-therapy-not-exhausted": - return STANDARD_THERAPY_NOT_EXHAUSTED; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize ClaimResponseStatusReason"); + public static CodingClaimResponseStatusReasonCode forValue(String value) throws IOException { + if (value.equals("approval-revocation")) return APPROVAL_REVOCATION; + if (value.equals("formal-reasons")) return FORMAL_REASONS; + if (value.equals("inclusion-in-study")) return INCLUSION_IN_STUDY; + if (value.equals("insufficient-evidence")) return INSUFFICIENT_EVIDENCE; + if (value.equals("other")) return OTHER; + if (value.equals("other-therapy-recommended")) return OTHER_THERAPY_RECOMMENDED; + if (value.equals("standard-therapy-not-exhausted")) return STANDARD_THERAPY_NOT_EXHAUSTED; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingClaimResponseStatusReasonCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java index 1cb9881..e857200 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorGrade.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorGrade { - private TumorGradeCode code; +public class CodingClaimStage { + private StageCode code; private String display; private String system; private String version; @JsonProperty("code") - public TumorGradeCode getCode() { return code; } + public StageCode getCode() { return code; } @JsonProperty("code") - public void setCode(TumorGradeCode value) { this.code = value; } + public void setCode(StageCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java index 0b7284f..14d6cdf 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTherapyStatusReason { - private StatusReasonCode code; +public class CodingClinVar { + private CodingClinVarCode code; private String display; private String system; private String version; @JsonProperty("code") - public StatusReasonCode getCode() { return code; } + public CodingClinVarCode getCode() { return code; } @JsonProperty("code") - public void setCode(StatusReasonCode value) { this.code = value; } + public void setCode(CodingClinVarCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java new file mode 100644 index 0000000..57f4dad --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingClinVarCode { + THE_1, THE_2, THE_3, THE_4, THE_5; + + @JsonValue + public String toValue() { + switch (this) { + case THE_1: return "1"; + case THE_2: return "2"; + case THE_3: return "3"; + case THE_4: return "4"; + case THE_5: return "5"; + } + return null; + } + + @JsonCreator + public static CodingClinVarCode forValue(String value) throws IOException { + if (value.equals("1")) return THE_1; + if (value.equals("2")) return THE_2; + if (value.equals("3")) return THE_3; + if (value.equals("4")) return THE_4; + if (value.equals("5")) return THE_5; + throw new IOException("Cannot deserialize CodingClinVarCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java similarity index 58% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java index 040ef92..9c2997e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyRecommendationPriority.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java @@ -2,15 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTherapyRecommendationPriority { - private TherapyRecommendationPriority code; +public class CodingCnv { + private CodingCnvCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TherapyRecommendationPriority getCode() { return code; } + public CodingCnvCode getCode() { return code; } @JsonProperty("code") - public void setCode(TherapyRecommendationPriority value) { this.code = value; } + public void setCode(CodingCnvCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTherapyRecommendationPriority { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java similarity index 52% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java index 58338d3..aa36408 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CNVType.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CNVType { +public enum CodingCnvCode { HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN; @JsonValue @@ -17,15 +17,10 @@ public enum CNVType { } @JsonCreator - public static CNVType forValue(String value) throws IOException { - switch (value) { - case "high-level-gain": - return HIGH_LEVEL_GAIN; - case "loss": - return LOSS; - case "low-level-gain": - return LOW_LEVEL_GAIN; - } - throw new IOException("Cannot deserialize CNVType"); + public static CodingCnvCode forValue(String value) throws IOException { + if (value.equals("high-level-gain")) return HIGH_LEVEL_GAIN; + if (value.equals("loss")) return LOSS; + if (value.equals("low-level-gain")) return LOW_LEVEL_GAIN; + throw new IOException("Cannot deserialize CodingCnvCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java index 22fc01a..4f2cdd0 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingEcog { - private EcogCode code; + private CodingEcogCode code; private String display; private String system; private String version; @JsonProperty("code") - public EcogCode getCode() { return code; } + public CodingEcogCode getCode() { return code; } @JsonProperty("code") - public void setCode(EcogCode value) { this.code = value; } + public void setCode(CodingEcogCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java new file mode 100644 index 0000000..e65ff47 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingEcogCode { + THE_0, THE_1, THE_2, THE_3, THE_4, THE_5; + + @JsonValue + public String toValue() { + switch (this) { + case THE_0: return "0"; + case THE_1: return "1"; + case THE_2: return "2"; + case THE_3: return "3"; + case THE_4: return "4"; + case THE_5: return "5"; + } + return null; + } + + @JsonCreator + public static CodingEcogCode forValue(String value) throws IOException { + if (value.equals("0")) return THE_0; + if (value.equals("1")) return THE_1; + if (value.equals("2")) return THE_2; + if (value.equals("3")) return THE_3; + if (value.equals("4")) return THE_4; + if (value.equals("5")) return THE_5; + throw new IOException("Cannot deserialize CodingEcogCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java similarity index 57% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenType.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java index ff9ef3d..188421c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenType.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java @@ -2,15 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorSpecimenType { - private TumorSpecimenType code; +public class CodingFollowUpPatientStatus { + private PatientStatusCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TumorSpecimenType getCode() { return code; } + public PatientStatusCode getCode() { return code; } @JsonProperty("code") - public void setCode(TumorSpecimenType value) { this.code = value; } + public void setCode(PatientStatusCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTumorSpecimenType { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java index 9f67221..7f562b1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingGender { - private Gender code; + private GenderCode code; private String display; private String system; private String version; @JsonProperty("code") - public Gender getCode() { return code; } + public GenderCode getCode() { return code; } @JsonProperty("code") - public void setCode(Gender value) { this.code = value; } + public void setCode(GenderCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java deleted file mode 100644 index 78ab110..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGene.java +++ /dev/null @@ -1,24 +0,0 @@ -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/CodingGeneticCounselingRecommendationReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java new file mode 100644 index 0000000..2c55eba --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingGeneticCounselingRecommendationReason { + private ReasonCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public ReasonCode getCode() { return code; } + @JsonProperty("code") + public void setCode(ReasonCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java new file mode 100644 index 0000000..0de046a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingHealthInsurance { + private CodingHealthInsuranceCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingHealthInsuranceCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingHealthInsuranceCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java new file mode 100644 index 0000000..37ab3da --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java @@ -0,0 +1,38 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingHealthInsuranceCode { + BEI, BG, GKV, GPV, PKV, PPV, SEL, SOZ, UNK; + + @JsonValue + public String toValue() { + switch (this) { + case BEI: return "BEI"; + case BG: return "BG"; + case GKV: return "GKV"; + case GPV: return "GPV"; + case PKV: return "PKV"; + case PPV: return "PPV"; + case SEL: return "SEL"; + case SOZ: return "SOZ"; + case UNK: return "UNK"; + } + return null; + } + + @JsonCreator + public static CodingHealthInsuranceCode forValue(String value) throws IOException { + if (value.equals("BEI")) return BEI; + if (value.equals("BG")) return BG; + if (value.equals("GKV")) return GKV; + if (value.equals("GPV")) return GPV; + if (value.equals("PKV")) return PKV; + if (value.equals("PPV")) return PPV; + if (value.equals("SEL")) return SEL; + if (value.equals("SOZ")) return SOZ; + if (value.equals("UNK")) return UNK; + throw new IOException("Cannot deserialize CodingHealthInsuranceCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java new file mode 100644 index 0000000..c468a9f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingHrdScoreInterpretation { + private InterpretationCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public InterpretationCode getCode() { return code; } + @JsonProperty("code") + public void setCode(InterpretationCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java index f797266..9b2c543 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingLevelOfEvidenceGrading { - private GradingCode code; + private LevelOfEvidenceCode code; private String display; private String system; private String version; @JsonProperty("code") - public GradingCode getCode() { return code; } + public LevelOfEvidenceCode getCode() { return code; } @JsonProperty("code") - public void setCode(GradingCode value) { this.code = value; } + public void setCode(LevelOfEvidenceCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java new file mode 100644 index 0000000..df81875 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMolecularDiagnosticReport { + private CodingMolecularDiagnosticReportCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMolecularDiagnosticReportCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMolecularDiagnosticReportCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java new file mode 100644 index 0000000..f161aa6 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java @@ -0,0 +1,44 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMolecularDiagnosticReportCode { + ARRAY, EXOME, FISH, FUSION_PANEL, GENE_PANEL, GENOME_LONG_READ, GENOME_SHORT_READ, KARYOTYPING, OTHER, PANEL, PCR, SINGLE; + + @JsonValue + public String toValue() { + switch (this) { + case ARRAY: return "array"; + case EXOME: return "exome"; + case FISH: return "FISH"; + case FUSION_PANEL: return "fusion-panel"; + case GENE_PANEL: return "gene-panel"; + case GENOME_LONG_READ: return "genome-long-read"; + case GENOME_SHORT_READ: return "genome-short-read"; + case KARYOTYPING: return "karyotyping"; + case OTHER: return "other"; + case PANEL: return "panel"; + case PCR: return "PCR"; + case SINGLE: return "single"; + } + return null; + } + + @JsonCreator + public static CodingMolecularDiagnosticReportCode forValue(String value) throws IOException { + if (value.equals("array")) return ARRAY; + if (value.equals("exome")) return EXOME; + if (value.equals("FISH")) return FISH; + if (value.equals("fusion-panel")) return FUSION_PANEL; + if (value.equals("gene-panel")) return GENE_PANEL; + if (value.equals("genome-long-read")) return GENOME_LONG_READ; + if (value.equals("genome-short-read")) return GENOME_SHORT_READ; + if (value.equals("karyotyping")) return KARYOTYPING; + if (value.equals("other")) return OTHER; + if (value.equals("panel")) return PANEL; + if (value.equals("PCR")) return PCR; + if (value.equals("single")) return SINGLE; + throw new IOException("Cannot deserialize CodingMolecularDiagnosticReportCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java new file mode 100644 index 0000000..d45c114 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbCarePlanStatusReason { + private CodingMtbCarePlanStatusReasonCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbCarePlanStatusReasonCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbCarePlanStatusReasonCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java new file mode 100644 index 0000000..0e89c48 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbCarePlanStatusReasonCode { + NON_GENETIC_CAUSE, NOT_RARE_DISEASE, NO_TARGET, OTHER, PSYCHOSOMATIC, TARGETED_DIAGNOSTICS_RECOMMENDED; + + @JsonValue + public String toValue() { + switch (this) { + case NON_GENETIC_CAUSE: return "non-genetic-cause"; + case NOT_RARE_DISEASE: return "not-rare-disease"; + case NO_TARGET: return "no-target"; + case OTHER: return "other"; + case PSYCHOSOMATIC: return "psychosomatic"; + case TARGETED_DIAGNOSTICS_RECOMMENDED: return "targeted-diagnostics-recommended"; + } + return null; + } + + @JsonCreator + public static CodingMtbCarePlanStatusReasonCode forValue(String value) throws IOException { + if (value.equals("non-genetic-cause")) return NON_GENETIC_CAUSE; + if (value.equals("not-rare-disease")) return NOT_RARE_DISEASE; + if (value.equals("no-target")) return NO_TARGET; + if (value.equals("other")) return OTHER; + if (value.equals("psychosomatic")) return PSYCHOSOMATIC; + if (value.equals("targeted-diagnostics-recommended")) return TARGETED_DIAGNOSTICS_RECOMMENDED; + throw new IOException("Cannot deserialize CodingMtbCarePlanStatusReasonCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java new file mode 100644 index 0000000..63e1a41 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbDiagnosis { + private CodingMtbDiagnosisCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbDiagnosisCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbDiagnosisCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java new file mode 100644 index 0000000..db0afd2 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java @@ -0,0 +1,26 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbDiagnosisCode { + MAIN, METACHRONOUS, SECONDARY; + + @JsonValue + public String toValue() { + switch (this) { + case MAIN: return "main"; + case METACHRONOUS: return "metachronous"; + case SECONDARY: return "secondary"; + } + return null; + } + + @JsonCreator + public static CodingMtbDiagnosisCode forValue(String value) throws IOException { + if (value.equals("main")) return MAIN; + if (value.equals("metachronous")) return METACHRONOUS; + if (value.equals("secondary")) return SECONDARY; + throw new IOException("Cannot deserialize CodingMtbDiagnosisCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java new file mode 100644 index 0000000..779eb42 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbDiagnosisGuidelineTreatmentStatus { + private GuidelineTreatmentStatusCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public GuidelineTreatmentStatusCode getCode() { return code; } + @JsonProperty("code") + public void setCode(GuidelineTreatmentStatusCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java new file mode 100644 index 0000000..3e2dcae --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbMedicationRecommendationCategory { + private CodingMtbMedicationRecommendationCategoryCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbMedicationRecommendationCategoryCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbMedicationRecommendationCategoryCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java new file mode 100644 index 0000000..0662734 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbMedicationRecommendationCategoryCode { + CH, HO, IM, SO, SZ, ZS; + + @JsonValue + public String toValue() { + switch (this) { + case CH: return "CH"; + case HO: return "HO"; + case IM: return "IM"; + case SO: return "SO"; + case SZ: return "SZ"; + case ZS: return "ZS"; + } + return null; + } + + @JsonCreator + public static CodingMtbMedicationRecommendationCategoryCode forValue(String value) throws IOException { + if (value.equals("CH")) return CH; + if (value.equals("HO")) return HO; + if (value.equals("IM")) return IM; + if (value.equals("SO")) return SO; + if (value.equals("SZ")) return SZ; + if (value.equals("ZS")) return ZS; + throw new IOException("Cannot deserialize CodingMtbMedicationRecommendationCategoryCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java new file mode 100644 index 0000000..c285eca --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbMedicationRecommendationUseType { + private UseTypeCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public UseTypeCode getCode() { return code; } + @JsonProperty("code") + public void setCode(UseTypeCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java new file mode 100644 index 0000000..3d37fe2 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbProcedureRecommendationCategory { + private CodingMtbProcedureRecommendationCategoryCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbProcedureRecommendationCategoryCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbProcedureRecommendationCategoryCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java new file mode 100644 index 0000000..293cb02 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbProcedureRecommendationCategoryCode { + AS, OP, SO, ST, WS, WW; + + @JsonValue + public String toValue() { + switch (this) { + case AS: return "AS"; + case OP: return "OP"; + case SO: return "SO"; + case ST: return "ST"; + case WS: return "WS"; + case WW: return "WW"; + } + return null; + } + + @JsonCreator + public static CodingMtbProcedureRecommendationCategoryCode forValue(String value) throws IOException { + if (value.equals("AS")) return AS; + if (value.equals("OP")) return OP; + if (value.equals("SO")) return SO; + if (value.equals("ST")) return ST; + if (value.equals("WS")) return WS; + if (value.equals("WW")) return WW; + throw new IOException("Cannot deserialize CodingMtbProcedureRecommendationCategoryCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java new file mode 100644 index 0000000..86c9303 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbSystemicTherapyCategory { + private CodingMtbSystemicTherapyCategoryCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbSystemicTherapyCategoryCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbSystemicTherapyCategoryCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java new file mode 100644 index 0000000..807246b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbSystemicTherapyCategoryCode { + A, I, N, O, S; + + @JsonValue + public String toValue() { + switch (this) { + case A: return "A"; + case I: return "I"; + case N: return "N"; + case O: return "O"; + case S: return "S"; + } + return null; + } + + @JsonCreator + public static CodingMtbSystemicTherapyCategoryCode forValue(String value) throws IOException { + if (value.equals("A")) return A; + if (value.equals("I")) return I; + if (value.equals("N")) return N; + if (value.equals("O")) return O; + if (value.equals("S")) return S; + throw new IOException("Cannot deserialize CodingMtbSystemicTherapyCategoryCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java new file mode 100644 index 0000000..b66f927 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbSystemicTherapyRecommendationFulfillmentStatus { + private RecommendationFulfillmentStatusCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public RecommendationFulfillmentStatusCode getCode() { return code; } + @JsonProperty("code") + public void setCode(RecommendationFulfillmentStatusCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java similarity index 58% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java index 3bf6b07..664811b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvType.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java @@ -2,15 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingCnvType { - private CNVType code; +public class CodingMtbTherapyIntent { + private IntentCode code; private String display; private String system; + private String version; @JsonProperty("code") - public CNVType getCode() { return code; } + public IntentCode getCode() { return code; } @JsonProperty("code") - public void setCode(CNVType value) { this.code = value; } + public void setCode(IntentCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingCnvType { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java new file mode 100644 index 0000000..fae7df1 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingMtbTherapyStatusReason { + private CodingMtbTherapyStatusReasonCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingMtbTherapyStatusReasonCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbTherapyStatusReasonCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java new file mode 100644 index 0000000..c3fad95 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java @@ -0,0 +1,58 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingMtbTherapyStatusReasonCode { + BEST_SUPPORTIVE_CARE, CHRONIC_REMISSION, DETERIORATION, LOST_TO_FU, MEDICAL_REASONS, NO_INDICATION, OTHER, OTHER_THERAPY_CHOSEN, PATIENT_DEATH, PATIENT_REFUSAL, PATIENT_WISH, PAYMENT_ENDED, PAYMENT_PENDING, PAYMENT_REFUSED, PROGRESSION, REGULAR_COMPLETION, REGULAR_COMPLETION_WITH_DOSAGE_REDUCTION, REGULAR_COMPLETION_WITH_SUBSTANCE_CHANGE, TOXICITY; + + @JsonValue + public String toValue() { + switch (this) { + case BEST_SUPPORTIVE_CARE: return "best-supportive-care"; + case CHRONIC_REMISSION: return "chronic-remission"; + case DETERIORATION: return "deterioration"; + case LOST_TO_FU: return "lost-to-fu"; + case MEDICAL_REASONS: return "medical-reasons"; + case NO_INDICATION: return "no-indication"; + case OTHER: return "other"; + case OTHER_THERAPY_CHOSEN: return "other-therapy-chosen"; + case PATIENT_DEATH: return "patient-death"; + case PATIENT_REFUSAL: return "patient-refusal"; + case PATIENT_WISH: return "patient-wish"; + case PAYMENT_ENDED: return "payment-ended"; + case PAYMENT_PENDING: return "payment-pending"; + case PAYMENT_REFUSED: return "payment-refused"; + case PROGRESSION: return "progression"; + case REGULAR_COMPLETION: return "regular-completion"; + case REGULAR_COMPLETION_WITH_DOSAGE_REDUCTION: return "regular-completion-with-dosage-reduction"; + case REGULAR_COMPLETION_WITH_SUBSTANCE_CHANGE: return "regular-completion-with-substance-change"; + case TOXICITY: return "toxicity"; + } + return null; + } + + @JsonCreator + public static CodingMtbTherapyStatusReasonCode forValue(String value) throws IOException { + if (value.equals("best-supportive-care")) return BEST_SUPPORTIVE_CARE; + if (value.equals("chronic-remission")) return CHRONIC_REMISSION; + if (value.equals("deterioration")) return DETERIORATION; + if (value.equals("lost-to-fu")) return LOST_TO_FU; + if (value.equals("medical-reasons")) return MEDICAL_REASONS; + if (value.equals("no-indication")) return NO_INDICATION; + if (value.equals("other")) return OTHER; + if (value.equals("other-therapy-chosen")) return OTHER_THERAPY_CHOSEN; + if (value.equals("patient-death")) return PATIENT_DEATH; + if (value.equals("patient-refusal")) return PATIENT_REFUSAL; + if (value.equals("patient-wish")) return PATIENT_WISH; + if (value.equals("payment-ended")) return PAYMENT_ENDED; + if (value.equals("payment-pending")) return PAYMENT_PENDING; + if (value.equals("payment-refused")) return PAYMENT_REFUSED; + if (value.equals("progression")) return PROGRESSION; + if (value.equals("regular-completion")) return REGULAR_COMPLETION; + if (value.equals("regular-completion-with-dosage-reduction")) return REGULAR_COMPLETION_WITH_DOSAGE_REDUCTION; + if (value.equals("regular-completion-with-substance-change")) return REGULAR_COMPLETION_WITH_SUBSTANCE_CHANGE; + if (value.equals("toxicity")) return TOXICITY; + throw new IOException("Cannot deserialize CodingMtbTherapyStatusReasonCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java new file mode 100644 index 0000000..e4b0faa --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingNgsReport { + private CodingNgsReportCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingNgsReportCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingNgsReportCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java new file mode 100644 index 0000000..7e3f156 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java @@ -0,0 +1,36 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingNgsReportCode { + ARRAY, EXOME, GENOME_LONG_READ, GENOME_SHORT_READ, KARYOTYPING, OTHER, PANEL, SINGLE; + + @JsonValue + public String toValue() { + switch (this) { + case ARRAY: return "array"; + case EXOME: return "exome"; + case GENOME_LONG_READ: return "genome-long-read"; + case GENOME_SHORT_READ: return "genome-short-read"; + case KARYOTYPING: return "karyotyping"; + case OTHER: return "other"; + case PANEL: return "panel"; + case SINGLE: return "single"; + } + return null; + } + + @JsonCreator + public static CodingNgsReportCode forValue(String value) throws IOException { + if (value.equals("array")) return ARRAY; + if (value.equals("exome")) return EXOME; + if (value.equals("genome-long-read")) return GENOME_LONG_READ; + if (value.equals("genome-short-read")) return GENOME_SHORT_READ; + if (value.equals("karyotyping")) return KARYOTYPING; + if (value.equals("other")) return OTHER; + if (value.equals("panel")) return PANEL; + if (value.equals("single")) return SINGLE; + throw new IOException("Cannot deserialize CodingNgsReportCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java new file mode 100644 index 0000000..4fea654 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingOncoProcedure { + private CodingOncoProcedureCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingOncoProcedureCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingOncoProcedureCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java new file mode 100644 index 0000000..62eac67 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java @@ -0,0 +1,26 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingOncoProcedureCode { + NUCLEAR_MEDICINE, RADIO_THERAPY, SURGERY; + + @JsonValue + public String toValue() { + switch (this) { + case NUCLEAR_MEDICINE: return "nuclear-medicine"; + case RADIO_THERAPY: return "radio-therapy"; + case SURGERY: return "surgery"; + } + return null; + } + + @JsonCreator + public static CodingOncoProcedureCode forValue(String value) throws IOException { + if (value.equals("nuclear-medicine")) return NUCLEAR_MEDICINE; + if (value.equals("radio-therapy")) return RADIO_THERAPY; + if (value.equals("surgery")) return SURGERY; + throw new IOException("Cannot deserialize CodingOncoProcedureCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java index 9ed9ac8..33a1e70 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingProteinExpressionResult { - private ProteinExpressionResultCode code; + private CodingProteinExpressionResultCode code; private String display; private String system; private String version; @JsonProperty("code") - public ProteinExpressionResultCode getCode() { return code; } + public CodingProteinExpressionResultCode getCode() { return code; } @JsonProperty("code") - public void setCode(ProteinExpressionResultCode value) { this.code = value; } + public void setCode(CodingProteinExpressionResultCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java new file mode 100644 index 0000000..96889dc --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingProteinExpressionResultCode { + EXP, NOT_EXP, THE_1, THE_2, THE_3, UNKNOWN; + + @JsonValue + public String toValue() { + switch (this) { + case EXP: return "exp"; + case NOT_EXP: return "not-exp"; + case THE_1: return "1+"; + case THE_2: return "2+"; + case THE_3: return "3+"; + case UNKNOWN: return "unknown"; + } + return null; + } + + @JsonCreator + public static CodingProteinExpressionResultCode forValue(String value) throws IOException { + if (value.equals("exp")) return EXP; + if (value.equals("not-exp")) return NOT_EXP; + if (value.equals("1+")) return THE_1; + if (value.equals("2+")) return THE_2; + if (value.equals("3+")) return THE_3; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingProteinExpressionResultCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java index c05c8d0..478985f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java @@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingRecist { - private RecistCode code; + private CodingRecistCode code; private String display; private String system; private String version; @JsonProperty("code") - public RecistCode getCode() { return code; } + public CodingRecistCode getCode() { return code; } @JsonProperty("code") - public void setCode(RecistCode value) { this.code = value; } + public void setCode(CodingRecistCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java new file mode 100644 index 0000000..5b5ba47 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingRecistCode { + CR, MR, NA, PD, PR, SD; + + @JsonValue + public String toValue() { + switch (this) { + case CR: return "CR"; + case MR: return "MR"; + case NA: return "NA"; + case PD: return "PD"; + case PR: return "PR"; + case SD: return "SD"; + } + return null; + } + + @JsonCreator + public static CodingRecistCode forValue(String value) throws IOException { + if (value.equals("CR")) return CR; + if (value.equals("MR")) return MR; + if (value.equals("NA")) return NA; + if (value.equals("PD")) return PD; + if (value.equals("PR")) return PR; + if (value.equals("SD")) return SD; + throw new IOException("Cannot deserialize CodingRecistCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java new file mode 100644 index 0000000..a4ea759 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingRecommendationPriority { + private PriorityCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public PriorityCode getCode() { return code; } + @JsonProperty("code") + public void setCode(PriorityCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java new file mode 100644 index 0000000..2446beb --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingResponseMethod { + private CodingResponseMethodCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingResponseMethodCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingResponseMethodCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java new file mode 100644 index 0000000..68a5de5 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingResponseMethodCode { + RANO, RECIST; + + @JsonValue + public String toValue() { + switch (this) { + case RANO: return "RANO"; + case RECIST: return "RECIST"; + } + return null; + } + + @JsonCreator + public static CodingResponseMethodCode forValue(String value) throws IOException { + if (value.equals("RANO")) return RANO; + if (value.equals("RECIST")) return RECIST; + throw new IOException("Cannot deserialize CodingResponseMethodCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java index ee51af0..76c8a40 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingTherapyStatus { - private TherapyStatus code; + private CodingTherapyStatusCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TherapyStatus getCode() { return code; } + public CodingTherapyStatusCode getCode() { return code; } @JsonProperty("code") - public void setCode(TherapyStatus value) { this.code = value; } + public void setCode(CodingTherapyStatusCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTherapyStatus { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java similarity index 50% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java index 9379f04..8388a6f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum TherapyStatus { +public enum CodingTherapyStatusCode { COMPLETED, NOT_DONE, ON_GOING, STOPPED, UNKNOWN; @JsonValue @@ -19,19 +19,12 @@ public enum TherapyStatus { } @JsonCreator - public static TherapyStatus forValue(String value) throws IOException { - switch (value) { - case "completed": - return COMPLETED; - case "not-done": - return NOT_DONE; - case "on-going": - return ON_GOING; - case "stopped": - return STOPPED; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize TherapyStatus"); + public static CodingTherapyStatusCode forValue(String value) throws IOException { + if (value.equals("completed")) return COMPLETED; + if (value.equals("not-done")) return NOT_DONE; + if (value.equals("on-going")) return ON_GOING; + if (value.equals("stopped")) return STOPPED; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingTherapyStatusCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java new file mode 100644 index 0000000..02d57df --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTmbInterpretation { + private InterpretationCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public InterpretationCode getCode() { return code; } + @JsonProperty("code") + public void setCode(InterpretationCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java index 868c44a..e6826f5 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingTumorCellContentMethod { - private TumorCellContentMethod code; + private CodingTumorCellContentMethodCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TumorCellContentMethod getCode() { return code; } + public CodingTumorCellContentMethodCode getCode() { return code; } @JsonProperty("code") - public void setCode(TumorCellContentMethod value) { this.code = value; } + public void setCode(CodingTumorCellContentMethodCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTumorCellContentMethod { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java similarity index 68% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethod.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java index f3f2a06..bac8a5f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum TumorCellContentMethod { +public enum CodingTumorCellContentMethodCode { BIOINFORMATIC, HISTOLOGIC; @JsonValue @@ -16,9 +16,9 @@ public enum TumorCellContentMethod { } @JsonCreator - public static TumorCellContentMethod forValue(String value) throws IOException { + public static CodingTumorCellContentMethodCode forValue(String value) throws IOException { if (value.equals("bioinformatic")) return BIOINFORMATIC; if (value.equals("histologic")) return HISTOLOGIC; - throw new IOException("Cannot deserialize TumorCellContentMethod"); + throw new IOException("Cannot deserialize CodingTumorCellContentMethodCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java new file mode 100644 index 0000000..0f2431f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTumorSpecimen { + private CodingTumorSpecimenCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingTumorSpecimenCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingTumorSpecimenCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java similarity index 50% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenType.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java index 9c9b448..d1afbd9 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenType.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum TumorSpecimenType { +public enum CodingTumorSpecimenCode { CRYO_FROZEN, FFPE, FRESH_TISSUE, LIQUID_BIOPSY, UNKNOWN; @JsonValue @@ -19,19 +19,12 @@ public enum TumorSpecimenType { } @JsonCreator - public static TumorSpecimenType forValue(String value) throws IOException { - switch (value) { - case "cryo-frozen": - return CRYO_FROZEN; - case "FFPE": - return FFPE; - case "fresh-tissue": - return FRESH_TISSUE; - case "liquid-biopsy": - return LIQUID_BIOPSY; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize TumorSpecimenType"); + public static CodingTumorSpecimenCode forValue(String value) throws IOException { + if (value.equals("cryo-frozen")) return CRYO_FROZEN; + if (value.equals("FFPE")) return FFPE; + if (value.equals("fresh-tissue")) return FRESH_TISSUE; + if (value.equals("liquid-biopsy")) return LIQUID_BIOPSY; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingTumorSpecimenCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java index 31b0888..ee99f7c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingTumorSpecimenCollectionLocalization { - private TumorSpecimenCollectionLocalization code; + private CodingTumorSpecimenCollectionLocalizationCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TumorSpecimenCollectionLocalization getCode() { return code; } + public CodingTumorSpecimenCollectionLocalizationCode getCode() { return code; } @JsonProperty("code") - public void setCode(TumorSpecimenCollectionLocalization value) { this.code = value; } + public void setCode(CodingTumorSpecimenCollectionLocalizationCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTumorSpecimenCollectionLocalization { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java new file mode 100644 index 0000000..ad5e4e6 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingTumorSpecimenCollectionLocalizationCode { + CELLFREE_DNA, LOCAL_RECURRENCE, METASTASIS, PRIMARY_TUMOR, REGIONAL_LYMPH_NODES, UNKNOWN; + + @JsonValue + public String toValue() { + switch (this) { + case CELLFREE_DNA: return "cellfree-dna"; + case LOCAL_RECURRENCE: return "local-recurrence"; + case METASTASIS: return "metastasis"; + case PRIMARY_TUMOR: return "primary-tumor"; + case REGIONAL_LYMPH_NODES: return "regional-lymph-nodes"; + case UNKNOWN: return "unknown"; + } + return null; + } + + @JsonCreator + public static CodingTumorSpecimenCollectionLocalizationCode forValue(String value) throws IOException { + if (value.equals("cellfree-dna")) return CELLFREE_DNA; + if (value.equals("local-recurrence")) return LOCAL_RECURRENCE; + if (value.equals("metastasis")) return METASTASIS; + if (value.equals("primary-tumor")) return PRIMARY_TUMOR; + if (value.equals("regional-lymph-nodes")) return REGIONAL_LYMPH_NODES; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingTumorSpecimenCollectionLocalizationCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java index 9a44fdd..69563b3 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java @@ -3,14 +3,15 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class CodingTumorSpecimenCollectionMethod { - private TumorSpecimenCollectionMethod code; + private CodingTumorSpecimenCollectionMethodCode code; private String display; private String system; + private String version; @JsonProperty("code") - public TumorSpecimenCollectionMethod getCode() { return code; } + public CodingTumorSpecimenCollectionMethodCode getCode() { return code; } @JsonProperty("code") - public void setCode(TumorSpecimenCollectionMethod value) { this.code = value; } + public void setCode(CodingTumorSpecimenCollectionMethodCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } @@ -21,4 +22,9 @@ public class CodingTumorSpecimenCollectionMethod { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java new file mode 100644 index 0000000..49f859d --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingTumorSpecimenCollectionMethodCode { + BIOPSY, CYTOLOGY, LIQUID_BIOPSY, RESECTION, UNKNOWN; + + @JsonValue + public String toValue() { + switch (this) { + case BIOPSY: return "biopsy"; + case CYTOLOGY: return "cytology"; + case LIQUID_BIOPSY: return "liquid-biopsy"; + case RESECTION: return "resection"; + case UNKNOWN: return "unknown"; + } + return null; + } + + @JsonCreator + public static CodingTumorSpecimenCollectionMethodCode forValue(String value) throws IOException { + if (value.equals("biopsy")) return BIOPSY; + if (value.equals("cytology")) return CYTOLOGY; + if (value.equals("liquid-biopsy")) return LIQUID_BIOPSY; + if (value.equals("resection")) return RESECTION; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize CodingTumorSpecimenCollectionMethodCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java deleted file mode 100644 index a228665..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpread.java +++ /dev/null @@ -1,24 +0,0 @@ -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/CodingTumorStagingMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java new file mode 100644 index 0000000..d49812f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CodingTumorStagingMethod { + private CodingTumorStagingMethodCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public CodingTumorStagingMethodCode getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingTumorStagingMethodCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java new file mode 100644 index 0000000..9f48c71 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum CodingTumorStagingMethodCode { + CLINICAL, PATHOLOGIC; + + @JsonValue + public String toValue() { + switch (this) { + case CLINICAL: return "clinical"; + case PATHOLOGIC: return "pathologic"; + } + return null; + } + + @JsonCreator + public static CodingTumorStagingMethodCode forValue(String value) throws IOException { + if (value.equals("clinical")) return CLINICAL; + if (value.equals("pathologic")) return PATHOLOGIC; + throw new IOException("Cannot deserialize CodingTumorStagingMethodCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java similarity index 74% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java index c553e1b..d421742 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java @@ -2,10 +2,11 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class VitalStatus { +public class CodingVitalStatus { private VitalStatusCode code; private String display; private String system; + private String version; @JsonProperty("code") public VitalStatusCode getCode() { return code; } @@ -21,4 +22,9 @@ public class VitalStatus { public String getSystem() { return system; } @JsonProperty("system") public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java index c45b7cb..f8b585e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java @@ -9,10 +9,8 @@ public class Collection { private CodingTumorSpecimenCollectionMethod method; @JsonProperty("date") - @JsonFormat(pattern = "yyyy-MM-dd") public Date getDate() { return date; } @JsonProperty("date") - @JsonFormat(pattern = "yyyy-MM-dd") public void setDate(Date value) { this.date = value; } @JsonProperty("localization") diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java index 0a45733..6cd24c8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java @@ -1,13 +1,22 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; +import java.util.List; public class DNAFusion { + private List externalIds; private DnaFusionFusionPartner3Prime fusionPartner3Prime; private DnaFusionFusionPartner5Prime fusionPartner5Prime; private String id; + private List localization; + private Reference patient; private long reportedNumReads; + @JsonProperty("externalIds") + public List getExternalIds() { return externalIds; } + @JsonProperty("externalIds") + public void setExternalIds(List value) { this.externalIds = value; } + @JsonProperty("fusionPartner3prime") public DnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; } @JsonProperty("fusionPartner3prime") @@ -23,6 +32,16 @@ public class DNAFusion { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("localization") + public List getLocalization() { return localization; } + @JsonProperty("localization") + public void setLocalization(List value) { this.localization = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + @JsonProperty("reportedNumReads") public long getReportedNumReads() { return reportedNumReads; } @JsonProperty("reportedNumReads") diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java deleted file mode 100644 index eb339c1..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Diagnosis.java +++ /dev/null @@ -1,18 +0,0 @@ -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 2544f84..ee7170c 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 CodingChromosome chromosome; - private CodingGene gene; + private Chromosome chromosome; + private Coding gene; private double position; @JsonProperty("chromosome") - public CodingChromosome getChromosome() { return chromosome; } + public Chromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(CodingChromosome value) { this.chromosome = value; } + public void setChromosome(Chromosome value) { this.chromosome = value; } @JsonProperty("gene") - public CodingGene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(CodingGene value) { this.gene = value; } + public void setGene(Coding 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 ed9608a..83b9414 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 CodingChromosome chromosome; - private Gene gene; + private Chromosome chromosome; + private Coding gene; private double position; @JsonProperty("chromosome") - public CodingChromosome getChromosome() { return chromosome; } + public Chromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(CodingChromosome value) { this.chromosome = value; } + public void setChromosome(Chromosome value) { this.chromosome = value; } @JsonProperty("gene") - public Gene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(Gene value) { this.gene = value; } + public void setGene(Coding value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java deleted file mode 100644 index f9c31c5..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTIdSystem.java +++ /dev/null @@ -1,22 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum EXTIdSystem { - HTTPS_PUBMED_NCBI_NLM_NIH_GOV; - - @JsonValue - public String toValue() { - switch (this) { - case HTTPS_PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov/"; - } - return null; - } - - @JsonCreator - public static 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 EXTIdSystem"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCode.java deleted file mode 100644 index b32991c..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCode.java +++ /dev/null @@ -1,37 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum EcogCode { - CODE_0, CODE_1, CODE_2, CODE_3, CODE_4; - - @JsonValue - public String toValue() { - switch (this) { - case CODE_0: return "0"; - case CODE_1: return "1"; - case CODE_2: return "2"; - case CODE_3: return "3"; - case CODE_4: return "4"; - } - return null; - } - - @JsonCreator - public static EcogCode forValue(String value) throws IOException { - switch (value) { - case "0": - return CODE_0; - case "1": - return CODE_1; - case "2": - return CODE_2; - case "3": - return CODE_3; - case "4": - return CODE_4; - } - throw new IOException("Cannot deserialize EcogCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java new file mode 100644 index 0000000..9c3862f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ExternalIdSystem { + HTTPS_CANCER_SANGER_Ac_UK_COSMIC, HTTPS_Www_ENSEMBL_ORG, HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ, HTTPS_Www_NCBI_NLM_NIH_GOV_SNP; + + @JsonValue + public String toValue() { + switch (this) { + case HTTPS_CANCER_SANGER_Ac_UK_COSMIC: return "https://cancer.sanger.ac.uk/cosmic"; + case HTTPS_Www_ENSEMBL_ORG: return "https://www.ensembl.org"; + case HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ: return "https://www.ncbi.nlm.nih.gov/entrez"; + case HTTPS_Www_NCBI_NLM_NIH_GOV_SNP: return "https://www.ncbi.nlm.nih.gov/snp"; + } + return null; + } + + @JsonCreator + public static ExternalIdSystem forValue(String value) throws IOException { + if (value.equals("https://cancer.sanger.ac.uk/cosmic")) return HTTPS_CANCER_SANGER_Ac_UK_COSMIC; + if (value.equals("https://www.ensembl.org")) return HTTPS_Www_ENSEMBL_ORG; + if (value.equals("https://www.ncbi.nlm.nih.gov/entrez")) return HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ; + if (value.equals("https://www.ncbi.nlm.nih.gov/snp")) return HTTPS_Www_NCBI_NLM_NIH_GOV_SNP; + throw new IOException("Cannot deserialize ExternalIdSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java new file mode 100644 index 0000000..12fcfd8 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java @@ -0,0 +1,21 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; + +public class FollowUp { + private Date date; + private CodingFollowUpPatientStatus patientStatus; + + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getDate() { return date; } + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setDate(Date value) { this.date = value; } + + @JsonProperty("patientStatus") + public CodingFollowUpPatientStatus getPatientStatus() { return patientStatus; } + @JsonProperty("patientStatus") + public void setPatientStatus(CodingFollowUpPatientStatus value) { this.patientStatus = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java similarity index 51% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java index aa8970f..137883f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum Gender { +public enum GenderCode { FEMALE, MALE, OTHER, UNKNOWN; @JsonValue @@ -18,17 +18,11 @@ public enum Gender { } @JsonCreator - public static Gender forValue(String value) throws IOException { - switch (value) { - case "female": - return FEMALE; - case "male": - return MALE; - case "other": - return OTHER; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize Gender"); + public static GenderCode forValue(String value) throws IOException { + if (value.equals("female")) return FEMALE; + if (value.equals("male")) return MALE; + if (value.equals("other")) return OTHER; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize GenderCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java deleted file mode 100644 index 84fd6b4..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Gene.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class Gene { - 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/GeneAlterationReference.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneAlterationReference.java new file mode 100644 index 0000000..99c60b4 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneAlterationReference.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class GeneAlterationReference { + private String display; + private Coding gene; + private Reference variant; + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("gene") + public Coding getGene() { return gene; } + @JsonProperty("gene") + public void setGene(Coding value) { this.gene = value; } + + @JsonProperty("variant") + public Reference getVariant() { return variant; } + @JsonProperty("variant") + public void setVariant(Reference value) { this.variant = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java deleted file mode 100644 index 8a41113..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneSystem.java +++ /dev/null @@ -1,22 +0,0 @@ -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 0897302..77b41df 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java @@ -6,8 +6,8 @@ import java.util.Date; public class GeneticCounselingRecommendation { private String id; private Date issuedOn; - private Patient patient; - private Coding reason; + private Reference patient; + private CodingGeneticCounselingRecommendationReason reason; @JsonProperty("id") public String getId() { return id; } @@ -15,17 +15,19 @@ public class GeneticCounselingRecommendation { public void setId(String value) { this.id = value; } @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public Date getIssuedOn() { return issuedOn; } @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("reason") - public Coding getReason() { return reason; } + public CodingGeneticCounselingRecommendationReason getReason() { return reason; } @JsonProperty("reason") - public void setReason(Coding value) { this.reason = value; } + public void setReason(CodingGeneticCounselingRecommendationReason value) { this.reason = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Grading.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Grading.java new file mode 100644 index 0000000..bad3bfb --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Grading.java @@ -0,0 +1,13 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class Grading { + private List history; + + @JsonProperty("history") + public List getHistory() { return history; } + @JsonProperty("history") + public void setHistory(List value) { this.history = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java deleted file mode 100644 index 4fd92f7..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java +++ /dev/null @@ -1,49 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum GradingCode { - M1_A, M1_B, M1_C, M2_A, M2_B, M2_C, M3, M4, UNDEFINED; - - @JsonValue - public String toValue() { - switch (this) { - case M1_A: return "m1A"; - case M1_B: return "m1B"; - case M1_C: return "m1C"; - case M2_A: return "m2A"; - case M2_B: return "m2B"; - case M2_C: return "m2C"; - case M3: return "m3"; - case M4: return "m4"; - case UNDEFINED: return "undefined"; - } - return null; - } - - @JsonCreator - public static GradingCode forValue(String value) throws IOException { - switch (value) { - case "m1A": - return M1_A; - case "m1B": - return M1_B; - case "m1C": - return M1_C; - case "m2A": - return M2_A; - case "m2B": - return M2_B; - case "m2C": - return M2_C; - case "m3": - return M3; - case "m4": - return M4; - case "undefined": - return UNDEFINED; - } - throw new IOException("Cannot deserialize GradingCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java new file mode 100644 index 0000000..80d237c --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum GuidelineTreatmentStatusCode { + 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 GuidelineTreatmentStatusCode forValue(String value) throws IOException { + if (value.equals("exhausted")) return EXHAUSTED; + if (value.equals("impossible")) return IMPOSSIBLE; + if (value.equals("non-exhausted")) return NON_EXHAUSTED; + if (value.equals("no-guidelines-available")) return NO_GUIDELINES_AVAILABLE; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize GuidelineTreatmentStatusCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java index 4945a09..59946ed 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java @@ -5,7 +5,7 @@ import com.fasterxml.jackson.annotation.*; public class HRDScore { private Components components; private String id; - private Coding interpretation; + private CodingHrdScoreInterpretation interpretation; private Reference patient; private Reference specimen; private double value; @@ -21,9 +21,9 @@ public class HRDScore { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public Coding getInterpretation() { return interpretation; } + public CodingHrdScoreInterpretation getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(Coding value) { this.interpretation = value; } + public void setInterpretation(CodingHrdScoreInterpretation value) { this.interpretation = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java index a79c185..5e951aa 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java @@ -3,22 +3,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class HealthInsurance { - private String display; - private ExternalId extId; - private Type type; + private Reference reference; + private CodingHealthInsurance 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("reference") + public Reference getReference() { return reference; } + @JsonProperty("reference") + public void setReference(Reference value) { this.reference = value; } @JsonProperty("type") - public Type getType() { return type; } + public CodingHealthInsurance getType() { return type; } @JsonProperty("type") - public void setType(Type value) { this.type = value; } + public void setType(CodingHealthInsurance value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReevaluationRequest.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReevaluationRequest.java new file mode 100644 index 0000000..5738fe1 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReevaluationRequest.java @@ -0,0 +1,33 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; + +public class HistologyReevaluationRequest { + private String id; + private Date issuedOn; + private Reference patient; + private Reference specimen; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("patient") + public 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; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java index a808216..ca47785 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java @@ -6,9 +6,9 @@ import java.util.Date; public class HistologyReport { private String id; private Date issuedOn; - private Patient patient; + private Reference patient; private HistologyReportResults results; - private HistologyReportSpecimen specimen; + private Reference specimen; @JsonProperty("id") public String getId() { return id; } @@ -23,9 +23,9 @@ public class HistologyReport { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("results") public HistologyReportResults getResults() { return results; } @@ -33,7 +33,7 @@ public class HistologyReport { public void setResults(HistologyReportResults value) { this.results = value; } @JsonProperty("specimen") - public HistologyReportSpecimen getSpecimen() { return specimen; } + public Reference getSpecimen() { return specimen; } @JsonProperty("specimen") - public void setSpecimen(HistologyReportSpecimen value) { this.specimen = value; } + public void setSpecimen(Reference value) { this.specimen = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java deleted file mode 100644 index 9f08941..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class HistologyReportSpecimen { - private String id; - private SpecimenType type; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("type") - public SpecimenType getType() { return type; } - @JsonProperty("type") - public void setType(SpecimenType value) { this.type = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java similarity index 59% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/History.java index aa8c1dd..e1f7e0c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageHistory.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java @@ -3,9 +3,9 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.Date; -public class StageHistory { +public class History { private Date date; - private CodingTumorSpread stage; + private CodingMtbDiagnosis value; @JsonProperty("date") @JsonFormat(pattern = "yyyy-MM-dd") @@ -14,8 +14,8 @@ public class StageHistory { @JsonFormat(pattern = "yyyy-MM-dd") public void setDate(Date value) { this.date = value; } - @JsonProperty("stage") - public CodingTumorSpread getStage() { return stage; } - @JsonProperty("stage") - public void setStage(CodingTumorSpread value) { this.stage = value; } + @JsonProperty("value") + public CodingMtbDiagnosis getValue() { return value; } + @JsonProperty("value") + public void setValue(CodingMtbDiagnosis value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java index 0122265..297c4ba 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java @@ -4,31 +4,25 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum ICScoreCode { - CODE_0, CODE_1, CODE_2, CODE_3; + THE_0, THE_1, THE_2, THE_3; @JsonValue public String toValue() { switch (this) { - case CODE_0: return "0"; - case CODE_1: return "1"; - case CODE_2: return "2"; - case CODE_3: return "3"; + case THE_0: return "0"; + case THE_1: return "1"; + case THE_2: return "2"; + case THE_3: return "3"; } return null; } @JsonCreator public static ICScoreCode forValue(String value) throws IOException { - switch (value) { - case "0": - return CODE_0; - case "1": - return CODE_1; - case "2": - return CODE_2; - case "3": - return CODE_3; - } + if (value.equals("0")) return THE_0; + if (value.equals("1")) return THE_1; + if (value.equals("2")) return THE_2; + if (value.equals("3")) return THE_3; throw new IOException("Cannot deserialize ICScoreCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java index 722dee6..0d315f8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java @@ -5,51 +5,45 @@ import java.util.Date; import java.util.List; public class IHCReport { - private ExternalId blockId; - private Date date; + private List blockIds; private String id; - private ExternalId journalId; - private List msiMmrResults; + private Date issuedOn; + private String journalId; private Reference patient; - private List proteinExpressionResults; + private IhcReportResults results; private Reference specimen; - @JsonProperty("blockId") - public ExternalId getBlockId() { return blockId; } - @JsonProperty("blockId") - public void setBlockId(ExternalId value) { this.blockId = value; } - - @JsonProperty("date") - @JsonFormat(pattern = "yyyy-MM-dd") - public Date getDate() { return date; } - @JsonProperty("date") - @JsonFormat(pattern = "yyyy-MM-dd") - public void setDate(Date value) { this.date = value; } + @JsonProperty("blockIds") + public List getBlockIds() { return blockIds; } + @JsonProperty("blockIds") + public void setBlockIds(List value) { this.blockIds = value; } @JsonProperty("id") public String getId() { return id; } @JsonProperty("id") public void setId(String value) { this.id = value; } - @JsonProperty("journalId") - public ExternalId getJournalId() { return journalId; } - @JsonProperty("journalId") - public void setJournalId(ExternalId value) { this.journalId = value; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } - @JsonProperty("msiMmrResults") - public List getMsiMmrResults() { return msiMmrResults; } - @JsonProperty("msiMmrResults") - public void setMsiMmrResults(List value) { this.msiMmrResults = value; } + @JsonProperty("journalId") + public String getJournalId() { return journalId; } + @JsonProperty("journalId") + public void setJournalId(String value) { this.journalId = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @JsonProperty("patient") public void setPatient(Reference value) { this.patient = value; } - @JsonProperty("proteinExpressionResults") - public List getProteinExpressionResults() { return proteinExpressionResults; } - @JsonProperty("proteinExpressionResults") - public void setProteinExpressionResults(List value) { this.proteinExpressionResults = value; } + @JsonProperty("results") + public IhcReportResults getResults() { return results; } + @JsonProperty("results") + public void setResults(IhcReportResults value) { this.results = value; } @JsonProperty("specimen") public Reference getSpecimen() { return specimen; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReportResults.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReportResults.java new file mode 100644 index 0000000..c074484 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReportResults.java @@ -0,0 +1,19 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class IhcReportResults { + private List msiMmr; + private List proteinExpression; + + @JsonProperty("msiMmr") + public List getMsiMmr() { return msiMmr; } + @JsonProperty("msiMmr") + public void setMsiMmr(List value) { this.msiMmr = value; } + + @JsonProperty("proteinExpression") + public List getProteinExpression() { return proteinExpression; } + @JsonProperty("proteinExpression") + public void setProteinExpression(List value) { this.proteinExpression = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java new file mode 100644 index 0000000..2fc318f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum IntentCode { + K, P, S, X; + + @JsonValue + public String toValue() { + switch (this) { + case K: return "K"; + case P: return "P"; + case S: return "S"; + case X: return "X"; + } + return null; + } + + @JsonCreator + public static IntentCode forValue(String value) throws IOException { + if (value.equals("K")) return K; + if (value.equals("P")) return P; + if (value.equals("S")) return S; + if (value.equals("X")) return X; + throw new IOException("Cannot deserialize IntentCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java new file mode 100644 index 0000000..47ca825 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java @@ -0,0 +1,26 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum InterpretationCode { + HIGH, INTERMEDIATE, LOW; + + @JsonValue + public String toValue() { + switch (this) { + case HIGH: return "high"; + case INTERMEDIATE: return "intermediate"; + case LOW: return "low"; + } + return null; + } + + @JsonCreator + public static InterpretationCode forValue(String value) throws IOException { + if (value.equals("high")) return HIGH; + if (value.equals("intermediate")) return INTERMEDIATE; + if (value.equals("low")) return LOW; + throw new IOException("Cannot deserialize InterpretationCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java index 6e3e79f..d70b239 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java @@ -6,7 +6,7 @@ import java.util.List; public class LevelOfEvidence { private List addendums; private CodingLevelOfEvidenceGrading grading; - private List publications; + private List publications; @JsonProperty("addendums") public List getAddendums() { return addendums; } @@ -19,7 +19,7 @@ public class LevelOfEvidence { public void setGrading(CodingLevelOfEvidenceGrading value) { this.grading = value; } @JsonProperty("publications") - public List getPublications() { return publications; } + public List getPublications() { return publications; } @JsonProperty("publications") - public void setPublications(List value) { this.publications = value; } + public void setPublications(List value) { this.publications = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java new file mode 100644 index 0000000..4bb2456 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java @@ -0,0 +1,38 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum LevelOfEvidenceCode { + M1_A, M1_B, M1_C, M2_A, M2_B, M2_C, M3, M4, UNDEFINED; + + @JsonValue + public String toValue() { + switch (this) { + case M1_A: return "m1A"; + case M1_B: return "m1B"; + case M1_C: return "m1C"; + case M2_A: return "m2A"; + case M2_B: return "m2B"; + case M2_C: return "m2C"; + case M3: return "m3"; + case M4: return "m4"; + case UNDEFINED: return "undefined"; + } + return null; + } + + @JsonCreator + public static LevelOfEvidenceCode forValue(String value) throws IOException { + if (value.equals("m1A")) return M1_A; + if (value.equals("m1B")) return M1_B; + if (value.equals("m1C")) return M1_C; + if (value.equals("m2A")) return M2_A; + if (value.equals("m2B")) return M2_B; + if (value.equals("m2C")) return M2_C; + if (value.equals("m3")) return M3; + if (value.equals("m4")) return M4; + if (value.equals("undefined")) return UNDEFINED; + throw new IOException("Cannot deserialize LevelOfEvidenceCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmrResult.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java similarity index 98% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmrResult.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java index 5311eb6..1fbb70c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmrResult.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class MSIMmrResult { +public class MSIMmr { private CodingProteinExpressionIcScore icScore; private String id; private Reference patient; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java index f1440ed..ebaf766 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java @@ -5,41 +5,39 @@ import java.util.Date; import java.util.List; public class MTBCarePlan { - private String diagnosis; private GeneticCounselingRecommendation geneticCounselingRecommendation; + private List histologyReevaluationRequests; 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; } + private List notes; + private Reference patient; + private List procedureRecommendations; + private Reference reason; + private List rebiopsyRequests; + private CodingMtbCarePlanStatusReason statusReason; + private List studyEnrollmentRecommendations; @JsonProperty("geneticCounselingRecommendation") public GeneticCounselingRecommendation getGeneticCounselingRecommendation() { return geneticCounselingRecommendation; } @JsonProperty("geneticCounselingRecommendation") public void setGeneticCounselingRecommendation(GeneticCounselingRecommendation value) { this.geneticCounselingRecommendation = value; } + @JsonProperty("histologyReevaluationRequests") + public List getHistologyReevaluationRequests() { return histologyReevaluationRequests; } + @JsonProperty("histologyReevaluationRequests") + public void setHistologyReevaluationRequests(List value) { this.histologyReevaluationRequests = 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") + @JsonFormat(pattern = "yyyy-MM-dd") public Date getIssuedOn() { return issuedOn; } @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("medicationRecommendations") @@ -47,28 +45,38 @@ public class MTBCarePlan { @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; } + public List getNotes() { return notes; } @JsonProperty("notes") - public void setNotes(String value) { this.notes = value; } + public void setNotes(List value) { this.notes = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("procedureRecommendations") + public List getProcedureRecommendations() { return procedureRecommendations; } + @JsonProperty("procedureRecommendations") + public void setProcedureRecommendations(List value) { this.procedureRecommendations = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = value; } + + @JsonProperty("rebiopsyRequests") + public List getRebiopsyRequests() { return rebiopsyRequests; } + @JsonProperty("rebiopsyRequests") + public void setRebiopsyRequests(List value) { this.rebiopsyRequests = value; } @JsonProperty("statusReason") - public CodingCarePlanStatusReason getStatusReason() { return statusReason; } + public CodingMtbCarePlanStatusReason getStatusReason() { return statusReason; } @JsonProperty("statusReason") - public void setStatusReason(CodingCarePlanStatusReason value) { this.statusReason = value; } + public void setStatusReason(CodingMtbCarePlanStatusReason value) { this.statusReason = value; } @JsonProperty("studyEnrollmentRecommendations") - public List getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; } + public List getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; } @JsonProperty("studyEnrollmentRecommendations") - public void setStudyEnrollmentRecommendations(List value) { this.studyEnrollmentRecommendations = value; } + 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 index c8c26ed..0c20afd 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java @@ -6,75 +6,75 @@ import java.util.List; public class MTBDiagnosis { private Coding code; - private Coding guidelineTreatmentStatus; - private List histologyResults; - private Coding icdO3T; + private List germlineCodes; + private Grading grading; + private CodingMtbDiagnosisGuidelineTreatmentStatus guidelineTreatmentStatus; + private List histology; private String id; - private Patient patient; + private List notes; + private Reference patient; private Date recordedOn; - private List stageHistory; + private Staging staging; private Coding topography; - private CodingTumorGrade tumorGrade; - private Coding whoGrade; - private Coding whoGrading; + private Type type; @JsonProperty("code") public Coding getCode() { return code; } @JsonProperty("code") public void setCode(Coding value) { this.code = value; } - @JsonProperty("guidelineTreatmentStatus") - public Coding getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; } - @JsonProperty("guidelineTreatmentStatus") - public void setGuidelineTreatmentStatus(Coding value) { this.guidelineTreatmentStatus = value; } + @JsonProperty("germlineCodes") + public List getGermlineCodes() { return germlineCodes; } + @JsonProperty("germlineCodes") + public void setGermlineCodes(List value) { this.germlineCodes = value; } - @JsonProperty("histologyResults") - public List getHistologyResults() { return histologyResults; } - @JsonProperty("histologyResults") - public void setHistologyResults(List value) { this.histologyResults = value; } + @JsonProperty("grading") + public Grading getGrading() { return grading; } + @JsonProperty("grading") + public void setGrading(Grading value) { this.grading = value; } - @JsonProperty("icdO3T") - public Coding getIcdO3T() { return icdO3T; } - @JsonProperty("icdO3T") - public void setIcdO3T(Coding value) { this.icdO3T = value; } + @JsonProperty("guidelineTreatmentStatus") + public CodingMtbDiagnosisGuidelineTreatmentStatus getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; } + @JsonProperty("guidelineTreatmentStatus") + public void setGuidelineTreatmentStatus(CodingMtbDiagnosisGuidelineTreatmentStatus value) { this.guidelineTreatmentStatus = value; } + + @JsonProperty("histology") + public List getHistology() { return histology; } + @JsonProperty("histology") + public void setHistology(List value) { this.histology = value; } @JsonProperty("id") public String getId() { return id; } @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("notes") + public List getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(List value) { this.notes = value; } + @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("recordedOn") public Date getRecordedOn() { return recordedOn; } @JsonProperty("recordedOn") public void setRecordedOn(Date value) { this.recordedOn = value; } - @JsonProperty("stageHistory") - public List getStageHistory() { return stageHistory; } - @JsonProperty("stageHistory") - public void setStageHistory(List value) { this.stageHistory = value; } + @JsonProperty("staging") + public Staging getStaging() { return staging; } + @JsonProperty("staging") + public void setStaging(Staging value) { this.staging = 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; } + @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/MTBEpisode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java deleted file mode 100644 index ae9cfd0..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisode.java +++ /dev/null @@ -1,24 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class MTBEpisode { - private String id; - private Patient patient; - private PeriodLocalDate period; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("patient") - public Patient getPatient() { return patient; } - @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } - - @JsonProperty("period") - public PeriodLocalDate getPeriod() { return period; } - @JsonProperty("period") - public void setPeriod(PeriodLocalDate value) { this.period = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java index 1ef9d50..f167a36 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/EpisodeOfCare.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java @@ -3,11 +3,11 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.List; -public class EpisodeOfCare { +public class MTBEpisodeOfCare { private List diagnoses; private String id; private Reference patient; - private PeriodLocalDate period; + private PeriodDate period; @JsonProperty("diagnoses") public List getDiagnoses() { return diagnoses; } @@ -25,7 +25,7 @@ public class EpisodeOfCare { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("period") - public PeriodLocalDate getPeriod() { return period; } + public PeriodDate getPeriod() { return period; } @JsonProperty("period") - public void setPeriod(PeriodLocalDate value) { this.period = value; } + public void setPeriod(PeriodDate value) { this.period = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java index 7abc6b3..79e0f3a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java @@ -5,29 +5,32 @@ import java.util.Date; import java.util.List; public class MTBMedicationRecommendation { + private CodingMtbMedicationRecommendationCategory category; private String id; - private Reference indication; private Date issuedOn; private LevelOfEvidence levelOfEvidence; - private List medication; - private String ngsReport; - private Patient patient; - private CodingTherapyRecommendationPriority priority; - private List supportingVariants; + private List medication; + private Reference patient; + private CodingRecommendationPriority priority; + private Reference reason; + private List supportingVariants; + private CodingMtbMedicationRecommendationUseType useType; + + @JsonProperty("category") + public CodingMtbMedicationRecommendationCategory getCategory() { return category; } + @JsonProperty("category") + public void setCategory(CodingMtbMedicationRecommendationCategory value) { this.category = 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") + @JsonFormat(pattern = "yyyy-MM-dd") public Date getIssuedOn() { return issuedOn; } @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("levelOfEvidence") @@ -36,27 +39,32 @@ public class MTBMedicationRecommendation { public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; } @JsonProperty("medication") - public List getMedication() { return medication; } + public List getMedication() { return medication; } @JsonProperty("medication") - public void setMedication(List value) { this.medication = value; } - - @JsonProperty("ngsReport") - public String getNgsReport() { return ngsReport; } - @JsonProperty("ngsReport") - public void setNgsReport(String value) { this.ngsReport = value; } + public void setMedication(List value) { this.medication = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("priority") - public CodingTherapyRecommendationPriority getPriority() { return priority; } + public CodingRecommendationPriority getPriority() { return priority; } @JsonProperty("priority") - public void setPriority(CodingTherapyRecommendationPriority value) { this.priority = value; } + public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = 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; } + + @JsonProperty("useType") + public CodingMtbMedicationRecommendationUseType getUseType() { return useType; } + @JsonProperty("useType") + public void setUseType(CodingMtbMedicationRecommendationUseType value) { this.useType = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java deleted file mode 100644 index 265cf3d..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java +++ /dev/null @@ -1,80 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.Date; -import java.util.List; - -public class MTBMedicationTherapy { - private Reference basedOn; - private String diagnosis; - private String id; - private Reference indication; - private List medication; - private String notes; - private Patient patient; - private PeriodLocalDate period; - private Date recordedOn; - private CodingTherapyStatus status; - private CodingTherapyStatusReason statusReason; - private Long therapyLine; - - @JsonProperty("basedOn") - public Reference getBasedOn() { return basedOn; } - @JsonProperty("basedOn") - public void setBasedOn(Reference value) { this.basedOn = value; } - - @JsonProperty("diagnosis") - public String getDiagnosis() { return diagnosis; } - @JsonProperty("diagnosis") - public void setDiagnosis(String value) { this.diagnosis = value; } - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("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("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/MTBStudyEnrollmentRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java new file mode 100644 index 0000000..989825e --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java @@ -0,0 +1,64 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class MTBStudyEnrollmentRecommendation { + private String id; + private Date issuedOn; + private CodingLevelOfEvidenceGrading levelOfEvidence; + private List medication; + private Reference patient; + private CodingRecommendationPriority priority; + private Reference reason; + private List study; + private List supportingVariants; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("levelOfEvidence") + public CodingLevelOfEvidenceGrading getLevelOfEvidence() { return levelOfEvidence; } + @JsonProperty("levelOfEvidence") + public void setLevelOfEvidence(CodingLevelOfEvidenceGrading value) { this.levelOfEvidence = value; } + + @JsonProperty("medication") + public List getMedication() { return medication; } + @JsonProperty("medication") + public void setMedication(List value) { this.medication = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("priority") + public CodingRecommendationPriority getPriority() { return priority; } + @JsonProperty("priority") + public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = value; } + + @JsonProperty("study") + public List getStudy() { return study; } + @JsonProperty("study") + public void setStudy(List value) { this.study = 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/MTBSystemicTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java new file mode 100644 index 0000000..ce76755 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java @@ -0,0 +1,94 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class MTBSystemicTherapy { + private Reference basedOn; + private CodingMtbSystemicTherapyCategory category; + private String id; + private CodingMtbTherapyIntent intent; + private List medication; + private List notes; + private Reference patient; + private PeriodDate period; + private Reference reason; + private CodingMtbSystemicTherapyRecommendationFulfillmentStatus recommendationFulfillmentStatus; + private Date recordedOn; + private CodingTherapyStatus status; + private CodingMtbTherapyStatusReason statusReason; + private Long therapyLine; + + @JsonProperty("basedOn") + public Reference getBasedOn() { return basedOn; } + @JsonProperty("basedOn") + public void setBasedOn(Reference value) { this.basedOn = value; } + + @JsonProperty("category") + public CodingMtbSystemicTherapyCategory getCategory() { return category; } + @JsonProperty("category") + public void setCategory(CodingMtbSystemicTherapyCategory value) { this.category = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("intent") + public CodingMtbTherapyIntent getIntent() { return intent; } + @JsonProperty("intent") + public void setIntent(CodingMtbTherapyIntent value) { this.intent = value; } + + @JsonProperty("medication") + public List getMedication() { return medication; } + @JsonProperty("medication") + public void setMedication(List value) { this.medication = value; } + + @JsonProperty("notes") + public List getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(List value) { this.notes = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("period") + public PeriodDate getPeriod() { return period; } + @JsonProperty("period") + public void setPeriod(PeriodDate value) { this.period = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = value; } + + @JsonProperty("recommendationFulfillmentStatus") + public CodingMtbSystemicTherapyRecommendationFulfillmentStatus getRecommendationFulfillmentStatus() { return recommendationFulfillmentStatus; } + @JsonProperty("recommendationFulfillmentStatus") + public void setRecommendationFulfillmentStatus(CodingMtbSystemicTherapyRecommendationFulfillmentStatus value) { this.recommendationFulfillmentStatus = value; } + + @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getRecordedOn() { return recordedOn; } + @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + 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 CodingMtbTherapyStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingMtbTherapyStatusReason 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/Metadatum.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java similarity index 98% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Metadatum.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java index 010cf44..dab2b86 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Metadatum.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class Metadatum { +public class Metadata { private String kitManufacturer; private String kitType; private String pipeline; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java deleted file mode 100644 index 6222040..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java +++ /dev/null @@ -1,13 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.List; - -public class MolecularTherapy { - private List history; - - @JsonProperty("history") - public List getHistory() { return history; } - @JsonProperty("history") - 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 3b9baab..ab8073e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java @@ -8,22 +8,19 @@ public class Mtb { private List claimResponses; private List claims; private List diagnoses; - private MTBEpisode episode; - private List episodesOfCare; - private List geneticCounsellingRequests; - private List guidelineProcedures; - private List guidelineTherapies; + private List episodesOfCare; + private List followUps; + private List guidelineProcedures; + private List guidelineTherapies; private List histologyReports; private List ihcReports; - private List molecularTherapies; - private List ngsReports; - private MtbPatient patient; + private List ngsReports; + private Patient patient; private List performanceStatus; - private List recommendations; + private List priorDiagnosticReports; private List responses; private List specimens; - private List studyInclusionRequests; - private List therapies; + private List systemicTherapies; @JsonProperty("carePlans") public List getCarePlans() { return carePlans; } @@ -45,30 +42,25 @@ public class Mtb { @JsonProperty("diagnoses") public void setDiagnoses(List value) { this.diagnoses = value; } - @JsonProperty("episode") - public MTBEpisode getEpisode() { return episode; } - @JsonProperty("episode") - public void setEpisode(MTBEpisode value) { this.episode = value; } - @JsonProperty("episodesOfCare") - public List getEpisodesOfCare() { return episodesOfCare; } + public List getEpisodesOfCare() { return episodesOfCare; } @JsonProperty("episodesOfCare") - public void setEpisodesOfCare(List value) { this.episodesOfCare = value; } + 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("followUps") + public List getFollowUps() { return followUps; } + @JsonProperty("followUps") + public void setFollowUps(List value) { this.followUps = value; } @JsonProperty("guidelineProcedures") - public List getGuidelineProcedures() { return guidelineProcedures; } + public List getGuidelineProcedures() { return guidelineProcedures; } @JsonProperty("guidelineProcedures") - public void setGuidelineProcedures(List value) { this.guidelineProcedures = value; } + public void setGuidelineProcedures(List value) { this.guidelineProcedures = value; } @JsonProperty("guidelineTherapies") - public List getGuidelineTherapies() { return guidelineTherapies; } + public List getGuidelineTherapies() { return guidelineTherapies; } @JsonProperty("guidelineTherapies") - public void setGuidelineTherapies(List value) { this.guidelineTherapies = value; } + public void setGuidelineTherapies(List value) { this.guidelineTherapies = value; } @JsonProperty("histologyReports") public List getHistologyReports() { return histologyReports; } @@ -80,30 +72,25 @@ public class Mtb { @JsonProperty("ihcReports") public void setIhcReports(List value) { this.ihcReports = value; } - @JsonProperty("molecularTherapies") - public List getMolecularTherapies() { return molecularTherapies; } - @JsonProperty("molecularTherapies") - public void setMolecularTherapies(List value) { this.molecularTherapies = value; } - @JsonProperty("ngsReports") - public List getNgsReports() { return ngsReports; } + public List getNgsReports() { return ngsReports; } @JsonProperty("ngsReports") - public void setNgsReports(List value) { this.ngsReports = value; } + public void setNgsReports(List value) { this.ngsReports = value; } @JsonProperty("patient") - public MtbPatient getPatient() { return patient; } + public Patient getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(MtbPatient value) { this.patient = value; } + public void setPatient(Patient value) { this.patient = 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; } - @JsonProperty("recommendations") - public void setRecommendations(List value) { this.recommendations = value; } + @JsonProperty("priorDiagnosticReports") + public List getPriorDiagnosticReports() { return priorDiagnosticReports; } + @JsonProperty("priorDiagnosticReports") + public void setPriorDiagnosticReports(List value) { this.priorDiagnosticReports = value; } @JsonProperty("responses") public List getResponses() { return responses; } @@ -115,13 +102,8 @@ public class Mtb { @JsonProperty("specimens") public void setSpecimens(List value) { this.specimens = value; } - @JsonProperty("studyInclusionRequests") - public List getStudyInclusionRequests() { return studyInclusionRequests; } - @JsonProperty("studyInclusionRequests") - public void setStudyInclusionRequests(List value) { this.studyInclusionRequests = value; } - - @JsonProperty("therapies") - public List getTherapies() { return therapies; } - @JsonProperty("therapies") - public void setTherapies(List value) { this.therapies = value; } + @JsonProperty("systemicTherapies") + public List getSystemicTherapies() { return systemicTherapies; } + @JsonProperty("systemicTherapies") + public void setSystemicTherapies(List value) { this.systemicTherapies = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java deleted file mode 100644 index 8722cee..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java +++ /dev/null @@ -1,57 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -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 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; } - @JsonProperty("birthDate") - @JsonFormat(pattern = "yyyy-MM-dd") - public void setBirthDate(Date value) { this.birthDate = value; } - - @JsonProperty("dateOfDeath") - public Date getDateOfDeath() { return dateOfDeath; } - @JsonProperty("dateOfDeath") - public void setDateOfDeath(Date value) { this.dateOfDeath = value; } - - @JsonProperty("gender") - public CodingGender getGender() { return gender; } - @JsonProperty("gender") - public void setGender(CodingGender value) { this.gender = value; } - - @JsonProperty("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("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/NgsReportSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java deleted file mode 100644 index efb64ce..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class NgsReportSpecimen { - private String id; - private SpecimenType type; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("type") - public SpecimenType getType() { return type; } - @JsonProperty("type") - public void setType(SpecimenType value) { this.type = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java deleted file mode 100644 index 91eacd3..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java +++ /dev/null @@ -1,25 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.Date; - -public class NoTargetFinding { - private String diagnosis; - private Date issuedOn; - private Patient patient; - - @JsonProperty("diagnosis") - public String getDiagnosis() { return diagnosis; } - @JsonProperty("diagnosis") - public void setDiagnosis(String value) { this.diagnosis = value; } - - @JsonProperty("issuedOn") - public Date getIssuedOn() { return issuedOn; } - @JsonProperty("issuedOn") - public void setIssuedOn(Date value) { this.issuedOn = value; } - - @JsonProperty("patient") - public Patient getPatient() { return patient; } - @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java new file mode 100644 index 0000000..8a8d037 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java @@ -0,0 +1,82 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class OncoProcedure { + private Reference basedOn; + private CodingOncoProcedure code; + private String id; + private CodingMtbTherapyIntent intent; + private List notes; + private Reference patient; + private PeriodDate period; + private Reference reason; + private Date recordedOn; + private CodingTherapyStatus status; + private CodingMtbTherapyStatusReason statusReason; + private Long therapyLine; + + @JsonProperty("basedOn") + public Reference getBasedOn() { return basedOn; } + @JsonProperty("basedOn") + public void setBasedOn(Reference value) { this.basedOn = value; } + + @JsonProperty("code") + public CodingOncoProcedure getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingOncoProcedure value) { this.code = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("intent") + public CodingMtbTherapyIntent getIntent() { return intent; } + @JsonProperty("intent") + public void setIntent(CodingMtbTherapyIntent value) { this.intent = value; } + + @JsonProperty("notes") + public List getNotes() { return notes; } + @JsonProperty("notes") + public void setNotes(List value) { this.notes = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("period") + public PeriodDate getPeriod() { return period; } + @JsonProperty("period") + public void setPeriod(PeriodDate value) { this.period = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = value; } + + @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getRecordedOn() { return recordedOn; } + @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + 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 CodingMtbTherapyStatusReason getStatusReason() { return statusReason; } + @JsonProperty("statusReason") + public void setStatusReason(CodingMtbTherapyStatusReason 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/OncoProdecure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java deleted file mode 100644 index ea16b1b..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProdecure.java +++ /dev/null @@ -1,79 +0,0 @@ -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/Patient.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java index 2f6abcd..0ee6d26 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java @@ -1,18 +1,63 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; +import java.util.Date; public class Patient { + private Address address; + private Age age; + private Date birthDate; + private Date dateOfDeath; + private CodingGender gender; + private HealthInsurance healthInsurance; private String id; - private PatientType type; + private Coding managingSite; + private CodingVitalStatus vitalStatus; + + @JsonProperty("address") + public Address getAddress() { return address; } + @JsonProperty("address") + public void setAddress(Address value) { this.address = value; } + + @JsonProperty("age") + public Age getAge() { return age; } + @JsonProperty("age") + public void setAge(Age value) { this.age = value; } + + @JsonProperty("birthDate") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getBirthDate() { return birthDate; } + @JsonProperty("birthDate") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setBirthDate(Date value) { this.birthDate = value; } + + @JsonProperty("dateOfDeath") + public Date getDateOfDeath() { return dateOfDeath; } + @JsonProperty("dateOfDeath") + public void setDateOfDeath(Date value) { this.dateOfDeath = value; } + + @JsonProperty("gender") + public CodingGender getGender() { return gender; } + @JsonProperty("gender") + public void setGender(CodingGender value) { this.gender = value; } + + @JsonProperty("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("type") - public PatientType getType() { return type; } - @JsonProperty("type") - public void setType(PatientType value) { this.type = value; } + @JsonProperty("managingSite") + public Coding getManagingSite() { return managingSite; } + @JsonProperty("managingSite") + public void setManagingSite(Coding value) { this.managingSite = value; } + + @JsonProperty("vitalStatus") + public CodingVitalStatus getVitalStatus() { return vitalStatus; } + @JsonProperty("vitalStatus") + public void setVitalStatus(CodingVitalStatus value) { this.vitalStatus = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java new file mode 100644 index 0000000..b9b4e9e --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum PatientStatusCode { + LOST_TO_FU; + + @JsonValue + public String toValue() { + switch (this) { + case LOST_TO_FU: return "lost-to-fu"; + } + return null; + } + + @JsonCreator + public static PatientStatusCode forValue(String value) throws IOException { + if (value.equals("lost-to-fu")) return LOST_TO_FU; + throw new IOException("Cannot deserialize PatientStatusCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java deleted file mode 100644 index e992e68..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java +++ /dev/null @@ -1,22 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum PatientType { - PATIENT; - - @JsonValue - public String toValue() { - switch (this) { - case PATIENT: return "Patient"; - } - return null; - } - - @JsonCreator - public static PatientType forValue(String value) throws IOException { - if (value.equals("Patient")) return PATIENT; - throw new IOException("Cannot deserialize PatientType"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java index 24d0e82..c9d473e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java @@ -6,7 +6,7 @@ import java.util.Date; public class PerformanceStatus { private Date effectiveDate; private String id; - private Patient patient; + private Reference patient; private CodingEcog value; @JsonProperty("effectiveDate") @@ -22,9 +22,9 @@ public class PerformanceStatus { public void setId(String value) { this.id = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("value") public CodingEcog getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodDate.java similarity index 94% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodDate.java index 1175184..a1004d6 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodDate.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.Date; -public class PeriodLocalDate { +public class PeriodDate { private Date end; private Date start; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java new file mode 100644 index 0000000..6c74b87 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java @@ -0,0 +1,52 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class PriorDiagnosticReport { + private String id; + private Date issuedOn; + private Reference patient; + private Reference performer; + private List results; + private Reference specimen; + private CodingMolecularDiagnosticReport type; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("performer") + public Reference getPerformer() { return performer; } + @JsonProperty("performer") + public void setPerformer(Reference value) { this.performer = value; } + + @JsonProperty("results") + public List getResults() { return results; } + @JsonProperty("results") + public void setResults(List value) { this.results = value; } + + @JsonProperty("specimen") + public Reference getSpecimen() { return specimen; } + @JsonProperty("specimen") + public void setSpecimen(Reference value) { this.specimen = value; } + + @JsonProperty("type") + public CodingMolecularDiagnosticReport getType() { return type; } + @JsonProperty("type") + public void setType(CodingMolecularDiagnosticReport value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java new file mode 100644 index 0000000..2775a5c --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum PriorityCode { + THE_1, THE_2, THE_3, THE_4; + + @JsonValue + public String toValue() { + switch (this) { + case THE_1: return "1"; + case THE_2: return "2"; + case THE_3: return "3"; + case THE_4: return "4"; + } + return null; + } + + @JsonCreator + public static PriorityCode forValue(String value) throws IOException { + if (value.equals("1")) return THE_1; + if (value.equals("2")) return THE_2; + if (value.equals("3")) return THE_3; + if (value.equals("4")) return THE_4; + throw new IOException("Cannot deserialize PriorityCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java new file mode 100644 index 0000000..aa88124 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java @@ -0,0 +1,58 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class ProcedureRecommendation { + private CodingMtbProcedureRecommendationCategory code; + private String id; + private Date issuedOn; + private LevelOfEvidence levelOfEvidence; + private Reference patient; + private CodingRecommendationPriority priority; + private Reference reason; + private List supportingVariants; + + @JsonProperty("code") + public CodingMtbProcedureRecommendationCategory getCode() { return code; } + @JsonProperty("code") + public void setCode(CodingMtbProcedureRecommendationCategory value) { this.code = value; } + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("levelOfEvidence") + public LevelOfEvidence getLevelOfEvidence() { return levelOfEvidence; } + @JsonProperty("levelOfEvidence") + public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("priority") + public CodingRecommendationPriority getPriority() { return priority; } + @JsonProperty("priority") + public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + + @JsonProperty("reason") + public Reference getReason() { return reason; } + @JsonProperty("reason") + public void setReason(Reference value) { this.reason = 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/ProteinExpressionResult.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java similarity index 97% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResult.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java index e004417..64b9b46 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResult.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class ProteinExpressionResult { +public class ProteinExpression { private CodingProteinExpressionIcScore icScore; private String id; private Reference patient; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCode.java deleted file mode 100644 index 2348bdd..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCode.java +++ /dev/null @@ -1,40 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum ProteinExpressionResultCode { - EXP, NOT_EXP, CODE_1_PLUS, CODE_2_PLUS, CODE_3_PLUS, UNKNOWN; - - @JsonValue - public String toValue() { - switch (this) { - case EXP: return "exp"; - case NOT_EXP: return "not-exp"; - case CODE_1_PLUS: return "1+"; - case CODE_2_PLUS: return "2+"; - case CODE_3_PLUS: return "3+"; - case UNKNOWN: return "unknown"; - } - return null; - } - - @JsonCreator - public static ProteinExpressionResultCode forValue(String value) throws IOException { - switch (value) { - case "exp": - return EXP; - case "not-exp": - return NOT_EXP; - case "1+": - return CODE_1_PLUS; - case "2+": - return CODE_2_PLUS; - case "3+": - return CODE_3_PLUS; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize PurpleCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationReference.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationReference.java new file mode 100644 index 0000000..3a17d9e --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationReference.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class PublicationReference { + private String display; + private String id; + private PublicationSystem system; + 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("system") + public PublicationSystem getSystem() { return system; } + @JsonProperty("system") + public void setSystem(PublicationSystem value) { this.system = 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/PublicationSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java new file mode 100644 index 0000000..fcfc0ec --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum PublicationSystem { + HTTPS_PUBMED_NCBI_NLM_NIH_GOV, HTTPS_Www_DOI_ORG; + + @JsonValue + public String toValue() { + switch (this) { + case HTTPS_PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov"; + case HTTPS_Www_DOI_ORG: return "https://www.doi.org"; + } + return null; + } + + @JsonCreator + public static PublicationSystem forValue(String value) throws IOException { + if (value.equals("https://pubmed.ncbi.nlm.nih.gov")) return HTTPS_PUBMED_NCBI_NLM_NIH_GOV; + if (value.equals("https://www.doi.org")) return HTTPS_Www_DOI_ORG; + throw new IOException("Cannot deserialize PublicationSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java index 7152835..11494ee 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java @@ -1,25 +1,28 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; +import java.util.List; public class RNAFusion { - private String cosmicId; private String effect; + private List externalIds; private RnaFusionFusionPartner3Prime fusionPartner3Prime; private RnaFusionFusionPartner5Prime fusionPartner5Prime; private String id; + private List localization; + private Reference patient; private long reportedNumReads; - @JsonProperty("cosmicId") - public String getCosmicId() { return cosmicId; } - @JsonProperty("cosmicId") - public void setCosmicId(String value) { this.cosmicId = value; } - @JsonProperty("effect") public String getEffect() { return effect; } @JsonProperty("effect") public void setEffect(String value) { this.effect = value; } + @JsonProperty("externalIds") + public List getExternalIds() { return externalIds; } + @JsonProperty("externalIds") + public void setExternalIds(List value) { this.externalIds = value; } + @JsonProperty("fusionPartner3prime") public RnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; } @JsonProperty("fusionPartner3prime") @@ -35,6 +38,16 @@ public class RNAFusion { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("localization") + public List getLocalization() { return localization; } + @JsonProperty("localization") + public void setLocalization(List value) { this.localization = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + @JsonProperty("reportedNumReads") public long getReportedNumReads() { return reportedNumReads; } @JsonProperty("reportedNumReads") diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java index 5757db3..73b09b7 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java @@ -1,49 +1,36 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; +import java.util.List; public class RNASeq { private Long cohortRanking; - private String ensemblId; - private String entrezId; - private double fragmentsPerKilobaseMillion; - private boolean fromNgs; - private CodingGene gene; + private List externalIds; + private Coding gene; private String id; - private long librarySize; + private Long librarySize; + private List localization; + private Reference patient; private long rawCounts; - private boolean tissueCorrectedExpression; - private String transcriptId; + private Boolean tissueCorrectedExpression; + private TranscriptId transcriptId; + private double transcriptsPerMillion; + private Reference variant; @JsonProperty("cohortRanking") public Long getCohortRanking() { return cohortRanking; } @JsonProperty("cohortRanking") public void setCohortRanking(Long value) { this.cohortRanking = value; } - @JsonProperty("ensemblId") - public String getEnsemblId() { return ensemblId; } - @JsonProperty("ensemblId") - public void setEnsemblId(String value) { this.ensemblId = value; } - - @JsonProperty("entrezId") - public String getEntrezId() { return entrezId; } - @JsonProperty("entrezId") - public void setEntrezId(String value) { this.entrezId = value; } - - @JsonProperty("fragmentsPerKilobaseMillion") - public double getFragmentsPerKilobaseMillion() { return fragmentsPerKilobaseMillion; } - @JsonProperty("fragmentsPerKilobaseMillion") - public void setFragmentsPerKilobaseMillion(double value) { this.fragmentsPerKilobaseMillion = value; } - - @JsonProperty("fromNGS") - public boolean getFromNgs() { return fromNgs; } - @JsonProperty("fromNGS") - public void setFromNgs(boolean value) { this.fromNgs = value; } + @JsonProperty("externalIds") + public List getExternalIds() { return externalIds; } + @JsonProperty("externalIds") + public void setExternalIds(List value) { this.externalIds = value; } @JsonProperty("gene") - public CodingGene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(CodingGene value) { this.gene = value; } + public void setGene(Coding value) { this.gene = value; } @JsonProperty("id") public String getId() { return id; } @@ -51,9 +38,19 @@ public class RNASeq { public void setId(String value) { this.id = value; } @JsonProperty("librarySize") - public long getLibrarySize() { return librarySize; } + public Long getLibrarySize() { return librarySize; } @JsonProperty("librarySize") - public void setLibrarySize(long value) { this.librarySize = value; } + public void setLibrarySize(Long value) { this.librarySize = value; } + + @JsonProperty("localization") + public List getLocalization() { return localization; } + @JsonProperty("localization") + public void setLocalization(List value) { this.localization = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("rawCounts") public long getRawCounts() { return rawCounts; } @@ -61,12 +58,22 @@ public class RNASeq { public void setRawCounts(long value) { this.rawCounts = value; } @JsonProperty("tissueCorrectedExpression") - public boolean getTissueCorrectedExpression() { return tissueCorrectedExpression; } + public Boolean getTissueCorrectedExpression() { return tissueCorrectedExpression; } @JsonProperty("tissueCorrectedExpression") - public void setTissueCorrectedExpression(boolean value) { this.tissueCorrectedExpression = value; } + public void setTissueCorrectedExpression(Boolean value) { this.tissueCorrectedExpression = value; } @JsonProperty("transcriptId") - public String getTranscriptId() { return transcriptId; } + public TranscriptId getTranscriptId() { return transcriptId; } @JsonProperty("transcriptId") - public void setTranscriptId(String value) { this.transcriptId = value; } + public void setTranscriptId(TranscriptId value) { this.transcriptId = value; } + + @JsonProperty("transcriptsPerMillion") + public double getTranscriptsPerMillion() { return transcriptsPerMillion; } + @JsonProperty("transcriptsPerMillion") + public void setTranscriptsPerMillion(double value) { this.transcriptsPerMillion = value; } + + @JsonProperty("variant") + public Reference getVariant() { return variant; } + @JsonProperty("variant") + public void setVariant(Reference value) { this.variant = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java new file mode 100644 index 0000000..ff1ef7f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ReasonCode { + FAMILY_ANAMNESIS, OTHER, SECONDARY_TUMOR, SELF_ANAMNESIS, UNKNOWN; + + @JsonValue + public String toValue() { + switch (this) { + case FAMILY_ANAMNESIS: return "family-anamnesis"; + case OTHER: return "other"; + case SECONDARY_TUMOR: return "secondary-tumor"; + case SELF_ANAMNESIS: return "self-anamnesis"; + case UNKNOWN: return "unknown"; + } + return null; + } + + @JsonCreator + public static ReasonCode forValue(String value) throws IOException { + if (value.equals("family-anamnesis")) return FAMILY_ANAMNESIS; + if (value.equals("other")) return OTHER; + if (value.equals("secondary-tumor")) return SECONDARY_TUMOR; + if (value.equals("self-anamnesis")) return SELF_ANAMNESIS; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize ReasonCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RebiopsyRequest.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RebiopsyRequest.java new file mode 100644 index 0000000..0a6727a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RebiopsyRequest.java @@ -0,0 +1,33 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; + +public class RebiopsyRequest { + private String id; + private Date issuedOn; + private Reference patient; + private Reference tumorEntity; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("tumorEntity") + public Reference getTumorEntity() { return tumorEntity; } + @JsonProperty("tumorEntity") + public void setTumorEntity(Reference value) { this.tumorEntity = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCode.java deleted file mode 100644 index 702e551..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCode.java +++ /dev/null @@ -1,43 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum RecistCode { - CR, MR, NA, NYA, PD, PR, SD; - - @JsonValue - public String toValue() { - switch (this) { - case CR: return "CR"; - case MR: return "MR"; - case NA: return "NA"; - case NYA: return "NYA"; - case PD: return "PD"; - case PR: return "PR"; - case SD: return "SD"; - } - return null; - } - - @JsonCreator - public static RecistCode forValue(String value) throws IOException { - switch (value) { - case "CR": - return CR; - case "MR": - return MR; - case "NA": - return NA; - case "NYA": - return NYA; - case "PD": - return PD; - case "PR": - return PR; - case "SD": - return SD; - } - throw new IOException("Cannot deserialize RecistCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java deleted file mode 100644 index 4d7a898..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Recommendation.java +++ /dev/null @@ -1,18 +0,0 @@ -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/RecommendationFulfillmentStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java new file mode 100644 index 0000000..3fc4269 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum RecommendationFulfillmentStatusCode { + COMPLETE, PARTIAL; + + @JsonValue + public String toValue() { + switch (this) { + case COMPLETE: return "complete"; + case PARTIAL: return "partial"; + } + return null; + } + + @JsonCreator + public static RecommendationFulfillmentStatusCode forValue(String value) throws IOException { + if (value.equals("complete")) return COMPLETE; + if (value.equals("partial")) return PARTIAL; + throw new IOException("Cannot deserialize RecommendationFulfillmentStatusCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java index 21dda4d..ea2cf94 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Reference.java @@ -5,6 +5,7 @@ import com.fasterxml.jackson.annotation.*; public class Reference { private String display; private String id; + private String system; private String type; @JsonProperty("display") @@ -17,6 +18,11 @@ public class Reference { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + @JsonProperty("type") public String getType() { return type; } @JsonProperty("type") diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java deleted file mode 100644 index b50e9eb..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java +++ /dev/null @@ -1,24 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class ReferencePublication { - private EXTId extId; - private String type; - private String uri; - - @JsonProperty("extId") - public EXTId getExtId() { return extId; } - @JsonProperty("extId") - public void setExtId(EXTId value) { this.extId = value; } - - @JsonProperty("type") - public String getType() { return type; } - @JsonProperty("type") - public void setType(String value) { this.type = value; } - - @JsonProperty("uri") - public String getUri() { return uri; } - @JsonProperty("uri") - public void setUri(String value) { this.uri = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java new file mode 100644 index 0000000..a1b5992 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum RequestedMedicationSystem { + HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC, UNDEFINED; + + @JsonValue + public String toValue() { + switch (this) { + case HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC: return "http://fhir.de/CodeSystem/bfarm/atc"; + case UNDEFINED: return "undefined"; + } + return null; + } + + @JsonCreator + public static RequestedMedicationSystem forValue(String value) throws IOException { + if (value.equals("http://fhir.de/CodeSystem/bfarm/atc")) return HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC; + if (value.equals("undefined")) return UNDEFINED; + throw new IOException("Cannot deserialize RequestedMedicationSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java index 3cf56b3..d4bf8cb 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java @@ -6,8 +6,9 @@ import java.util.Date; public class Response { private Date effectiveDate; private String id; - private Patient patient; - private ResponseTherapy therapy; + private CodingResponseMethod method; + private Reference patient; + private Reference therapy; private CodingRecist value; @JsonProperty("effectiveDate") @@ -22,15 +23,20 @@ public class Response { @JsonProperty("id") public void setId(String value) { this.id = value; } + @JsonProperty("method") + public CodingResponseMethod getMethod() { return method; } + @JsonProperty("method") + public void setMethod(CodingResponseMethod value) { this.method = value; } + @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("therapy") - public ResponseTherapy getTherapy() { return therapy; } + public Reference getTherapy() { return therapy; } @JsonProperty("therapy") - public void setTherapy(ResponseTherapy value) { this.therapy = value; } + public void setTherapy(Reference value) { this.therapy = value; } @JsonProperty("value") public CodingRecist getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java deleted file mode 100644 index a2a304b..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class ResponseTherapy { - private String id; - private ResponseTherapyType type; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("type") - public ResponseTherapyType getType() { return type; } - @JsonProperty("type") - public void setType(ResponseTherapyType value) { this.type = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java deleted file mode 100644 index bdfcd08..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java +++ /dev/null @@ -1,22 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum ResponseTherapyType { - MTB_MEDICATION_THERAPY; - - @JsonValue - public String toValue() { - switch (this) { - case MTB_MEDICATION_THERAPY: return "MTBMedicationTherapy"; - } - return null; - } - - @JsonCreator - public static ResponseTherapyType forValue(String value) throws IOException { - if (value.equals("MTBMedicationTherapy")) return MTB_MEDICATION_THERAPY; - throw new IOException("Cannot deserialize ResponseTherapyType"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java index 4160c4e..777886d 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java @@ -3,21 +3,21 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class RnaFusionFusionPartner3Prime { - private String exon; - private CodingGene gene; + private String exonId; + private Coding gene; private double position; private RNAFusionStrand strand; - private String transcriptId; + private TranscriptId transcriptId; - @JsonProperty("exon") - public String getExon() { return exon; } - @JsonProperty("exon") - public void setExon(String value) { this.exon = value; } + @JsonProperty("exonId") + public String getExonId() { return exonId; } + @JsonProperty("exonId") + public void setExonId(String value) { this.exonId = value; } @JsonProperty("gene") - public CodingGene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(CodingGene value) { this.gene = value; } + public void setGene(Coding value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } @@ -30,7 +30,7 @@ public class RnaFusionFusionPartner3Prime { public void setStrand(RNAFusionStrand value) { this.strand = value; } @JsonProperty("transcriptId") - public String getTranscriptId() { return transcriptId; } + public TranscriptId getTranscriptId() { return transcriptId; } @JsonProperty("transcriptId") - public void setTranscriptId(String value) { this.transcriptId = value; } + public void setTranscriptId(TranscriptId value) { this.transcriptId = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java index 946f076..bf1767d 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java @@ -3,21 +3,21 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class RnaFusionFusionPartner5Prime { - private String exon; - private CodingGene gene; + private String exonId; + private Coding gene; private double position; private RNAFusionStrand strand; - private String transcriptId; + private TranscriptId transcriptId; - @JsonProperty("exon") - public String getExon() { return exon; } - @JsonProperty("exon") - public void setExon(String value) { this.exon = value; } + @JsonProperty("exonId") + public String getExonId() { return exonId; } + @JsonProperty("exonId") + public void setExonId(String value) { this.exonId = value; } @JsonProperty("gene") - public CodingGene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(CodingGene value) { this.gene = value; } + public void setGene(Coding value) { this.gene = value; } @JsonProperty("position") public double getPosition() { return position; } @@ -30,7 +30,7 @@ public class RnaFusionFusionPartner5Prime { public void setStrand(RNAFusionStrand value) { this.strand = value; } @JsonProperty("transcriptId") - public String getTranscriptId() { return transcriptId; } + public TranscriptId getTranscriptId() { return transcriptId; } @JsonProperty("transcriptId") - public void setTranscriptId(String value) { this.transcriptId = value; } + public void setTranscriptId(TranscriptId value) { this.transcriptId = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java index 3811672..733c8b8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java @@ -6,21 +6,20 @@ import java.util.List; public class Snv { private double allelicFrequency; private String altAllele; - private Coding aminoAcidChange; - private CodingChromosome chromosome; - private String cosmicId; - private String dbSnpId; + private Chromosome chromosome; private Coding dnaChange; - private List externalIds; - private CodingGene gene; + private String exonId; + private List externalIds; + private Coding gene; private String id; - private Coding interpretation; - private Patient patient; + private CodingClinVar interpretation; + private List localization; + private Reference patient; private Position position; private Coding proteinChange; private long readDepth; private String refAllele; - private ExternalId transcriptId; + private TranscriptId transcriptId; @JsonProperty("allelicFrequency") public double getAllelicFrequency() { return allelicFrequency; } @@ -32,40 +31,30 @@ public class Snv { @JsonProperty("altAllele") public void setAltAllele(String value) { this.altAllele = value; } - @JsonProperty("aminoAcidChange") - public Coding getAminoAcidChange() { return aminoAcidChange; } - @JsonProperty("aminoAcidChange") - public void setAminoAcidChange(Coding value) { this.aminoAcidChange = value; } - @JsonProperty("chromosome") - public CodingChromosome getChromosome() { return chromosome; } + public Chromosome getChromosome() { return chromosome; } @JsonProperty("chromosome") - public void setChromosome(CodingChromosome value) { this.chromosome = value; } - - @JsonProperty("cosmicId") - public String getCosmicId() { return cosmicId; } - @JsonProperty("cosmicId") - public void setCosmicId(String value) { this.cosmicId = value; } - - @JsonProperty("dbSNPId") - public String getDbSnpId() { return dbSnpId; } - @JsonProperty("dbSNPId") - public void setDbSnpId(String value) { this.dbSnpId = value; } + public void setChromosome(Chromosome value) { this.chromosome = value; } @JsonProperty("dnaChange") public Coding getDnaChange() { return dnaChange; } @JsonProperty("dnaChange") public void setDnaChange(Coding value) { this.dnaChange = value; } + @JsonProperty("exonId") + public String getExonId() { return exonId; } + @JsonProperty("exonId") + public void setExonId(String value) { this.exonId = value; } + @JsonProperty("externalIds") - public List getExternalIds() { return externalIds; } + public List getExternalIds() { return externalIds; } @JsonProperty("externalIds") - public void setExternalIds(List value) { this.externalIds = value; } + public void setExternalIds(List value) { this.externalIds = value; } @JsonProperty("gene") - public CodingGene getGene() { return gene; } + public Coding getGene() { return gene; } @JsonProperty("gene") - public void setGene(CodingGene value) { this.gene = value; } + public void setGene(Coding value) { this.gene = value; } @JsonProperty("id") public String getId() { return id; } @@ -73,14 +62,19 @@ public class Snv { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public Coding getInterpretation() { return interpretation; } + public CodingClinVar getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(Coding value) { this.interpretation = value; } + public void setInterpretation(CodingClinVar value) { this.interpretation = value; } + + @JsonProperty("localization") + public List getLocalization() { return localization; } + @JsonProperty("localization") + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("position") public Position getPosition() { return position; } @@ -103,7 +97,7 @@ public class Snv { public void setRefAllele(String value) { this.refAllele = value; } @JsonProperty("transcriptId") - public ExternalId getTranscriptId() { return transcriptId; } + public TranscriptId getTranscriptId() { return transcriptId; } @JsonProperty("transcriptId") - public void setTranscriptId(ExternalId value) { this.transcriptId = value; } + public void setTranscriptId(TranscriptId 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 deleted file mode 100644 index ad6e57f..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java +++ /dev/null @@ -1,56 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.Date; -import java.util.List; - -public class SomaticNgsReport { - private String id; - private Date issuedOn; - private List metadata; - private Double msi; - private Patient patient; - private NgsReportResults results; - private Coding sequencingType; - private NgsReportSpecimen specimen; - - @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("metadata") - public List getMetadata() { return metadata; } - @JsonProperty("metadata") - public void setMetadata(List value) { this.metadata = value; } - - @JsonProperty("msi") - public Double getMsi() { return msi; } - @JsonProperty("msi") - public void setMsi(Double value) { this.msi = value; } - - @JsonProperty("patient") - public Patient getPatient() { return patient; } - @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } - - @JsonProperty("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("specimen") - public NgsReportSpecimen getSpecimen() { return specimen; } - @JsonProperty("specimen") - public void setSpecimen(NgsReportSpecimen value) { this.specimen = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java new file mode 100644 index 0000000..3ec147b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java @@ -0,0 +1,52 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class SomaticNgsReportMetadata { + private String id; + private Date issuedOn; + private List metadata; + private Reference patient; + private NgsReportResults results; + private Reference specimen; + private CodingNgsReport type; + + @JsonProperty("id") + public String getId() { return id; } + @JsonProperty("id") + public void setId(String value) { this.id = value; } + + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getIssuedOn() { return issuedOn; } + @JsonProperty("issuedOn") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setIssuedOn(Date value) { this.issuedOn = value; } + + @JsonProperty("metadata") + public List getMetadata() { return metadata; } + @JsonProperty("metadata") + public void setMetadata(List value) { this.metadata = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + + @JsonProperty("results") + public NgsReportResults getResults() { return results; } + @JsonProperty("results") + public void setResults(NgsReportResults value) { this.results = value; } + + @JsonProperty("specimen") + public Reference getSpecimen() { return specimen; } + @JsonProperty("specimen") + public void setSpecimen(Reference value) { this.specimen = value; } + + @JsonProperty("type") + public CodingNgsReport getType() { return type; } + @JsonProperty("type") + public void setType(CodingNgsReport value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java deleted file mode 100644 index 7d3fb74..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java +++ /dev/null @@ -1,22 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum SpecimenType { - TUMOR_SPECIMEN; - - @JsonValue - public String toValue() { - switch (this) { - case TUMOR_SPECIMEN: return "TumorSpecimen"; - } - return null; - } - - @JsonCreator - public static SpecimenType forValue(String value) throws IOException { - if (value.equals("TumorSpecimen")) return TUMOR_SPECIMEN; - throw new IOException("Cannot deserialize SpecimenType"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java index bd06407..fb8a6f3 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java @@ -4,14 +4,14 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum StageCode { - LOCAL, METASTASIZED, TUMOR_FREE, UNKNOWN; + FOLLOW_UP_CLAIM, INITIAL_CLAIM, REVOCATION, UNKNOWN; @JsonValue public String toValue() { switch (this) { - case LOCAL: return "local"; - case METASTASIZED: return "metastasized"; - case TUMOR_FREE: return "tumor-free"; + case FOLLOW_UP_CLAIM: return "follow-up-claim"; + case INITIAL_CLAIM: return "initial-claim"; + case REVOCATION: return "revocation"; case UNKNOWN: return "unknown"; } return null; @@ -19,16 +19,10 @@ public enum StageCode { @JsonCreator public static StageCode forValue(String value) throws IOException { - switch (value) { - case "local": - return LOCAL; - case "metastasized": - return METASTASIZED; - case "tumor-free": - return TUMOR_FREE; - case "unknown": - return UNKNOWN; - } + if (value.equals("follow-up-claim")) return FOLLOW_UP_CLAIM; + if (value.equals("initial-claim")) return INITIAL_CLAIM; + if (value.equals("revocation")) return REVOCATION; + if (value.equals("unknown")) return UNKNOWN; throw new IOException("Cannot deserialize StageCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Staging.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Staging.java new file mode 100644 index 0000000..84be81b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Staging.java @@ -0,0 +1,13 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class Staging { + private List history; + + @JsonProperty("history") + public List getHistory() { return history; } + @JsonProperty("history") + public void setHistory(List value) { this.history = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java deleted file mode 100644 index b3f1f5d..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StatusReasonCode.java +++ /dev/null @@ -1,73 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -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 - public String toValue() { - switch (this) { - case CHRONIC_REMISSION: return "chronic-remission"; - case CONTINUED_EXTERNALLY: return "continued-externally"; - case DETERIORATION: return "deterioration"; - case LOST_TO_FU: return "lost-to-fu"; - case MEDICAL_REASON: return "medical-reason"; - case NO_INDICATION: return "no-indication"; - case OTHER: return "other"; - case OTHER_THERAPY_CHOSEN: return "other-therapy-chosen"; - case PATIENT_DEATH: return "patient-death"; - case PATIENT_REFUSAL: return "patient-refusal"; - case PATIENT_WISH: return "patient-wish"; - case PAYMENT_ENDED: return "payment-ended"; - case PAYMENT_PENDING: return "payment-pending"; - case PAYMENT_REFUSED: return "payment-refused"; - case PROGRESSION: return "progression"; - case TOXICITY: return "toxicity"; - case UNKNOWN: return "unknown"; - } - return null; - } - - @JsonCreator - public static StatusReasonCode forValue(String value) throws IOException { - switch (value) { - case "chronic-remission": - return CHRONIC_REMISSION; - case "continued-externally": - return CONTINUED_EXTERNALLY; - case "deterioration": - return DETERIORATION; - case "lost-to-fu": - return LOST_TO_FU; - case "medical-reason": - return MEDICAL_REASON; - case "no-indication": - return NO_INDICATION; - case "other": - return OTHER; - case "other-therapy-chosen": - return OTHER_THERAPY_CHOSEN; - case "patient-death": - return PATIENT_DEATH; - case "patient-refusal": - return PATIENT_REFUSAL; - case "patient-wish": - return PATIENT_WISH; - case "payment-ended": - return PAYMENT_ENDED; - case "payment-pending": - return PAYMENT_PENDING; - case "payment-refused": - return PAYMENT_REFUSED; - case "progression": - return PROGRESSION; - case "toxicity": - return TOXICITY; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize StatusReasonCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java similarity index 50% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatus.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java index 6e9c34c..031dc9e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum ClaimResponseStatus { +public enum StickyCode { ACCEPTED, REJECTED, UNKNOWN; @JsonValue @@ -17,15 +17,10 @@ public enum ClaimResponseStatus { } @JsonCreator - public static ClaimResponseStatus forValue(String value) throws IOException { - switch (value) { - case "accepted": - return ACCEPTED; - case "rejected": - return REJECTED; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize ClaimResponseStatus"); + public static StickyCode forValue(String value) throws IOException { + if (value.equals("accepted")) return ACCEPTED; + if (value.equals("rejected")) return REJECTED; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize StickyCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java deleted file mode 100644 index 791abe2..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Study.java +++ /dev/null @@ -1,18 +0,0 @@ -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 deleted file mode 100644 index 7b68a1e..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java +++ /dev/null @@ -1,50 +0,0 @@ -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 Coding levelOfEvidence; - private Patient patient; - private Reference reason; - private List studies; - private List supportingVariants; - - @JsonProperty("id") - public String getId() { return id; } - @JsonProperty("id") - public void setId(String value) { this.id = value; } - - @JsonProperty("issuedOn") - public Date getIssuedOn() { return issuedOn; } - @JsonProperty("issuedOn") - public void setIssuedOn(Date value) { this.issuedOn = value; } - - @JsonProperty("levelOfEvidence") - public Coding getLevelOfEvidence() { return levelOfEvidence; } - @JsonProperty("levelOfEvidence") - public void setLevelOfEvidence(Coding value) { this.levelOfEvidence = value; } - - @JsonProperty("patient") - public Patient getPatient() { return patient; } - @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } - - @JsonProperty("reason") - public Reference getReason() { return reason; } - @JsonProperty("reason") - 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/StudyReference.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyReference.java new file mode 100644 index 0000000..f5114a9 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudyReference.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class StudyReference { + private String display; + private String id; + private StudySystem system; + 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("system") + public StudySystem getSystem() { return system; } + @JsonProperty("system") + public void setSystem(StudySystem value) { this.system = 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/StudySystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java new file mode 100644 index 0000000..4447e0a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum StudySystem { + DRKS, EUDAMED, EUDRA_Ct, NCT; + + @JsonValue + public String toValue() { + switch (this) { + case DRKS: return "DRKS"; + case EUDAMED: return "EUDAMED"; + case EUDRA_Ct: return "Eudra-CT"; + case NCT: return "NCT"; + } + return null; + } + + @JsonCreator + public static StudySystem forValue(String value) throws IOException { + if (value.equals("DRKS")) return DRKS; + if (value.equals("EUDAMED")) return EUDAMED; + if (value.equals("Eudra-CT")) return EUDRA_Ct; + if (value.equals("NCT")) return NCT; + throw new IOException("Cannot deserialize StudySystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java new file mode 100644 index 0000000..ac7441a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java @@ -0,0 +1,13 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; + +public class SystemicTherapy { + private List history; + + @JsonProperty("history") + public List getHistory() { return history; } + @JsonProperty("history") + public void setHistory(List value) { this.history = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java similarity index 94% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java index 9cafbb7..e49ae10 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Value.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class Value { +public class TMBResult { private String unit; private double value; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java index 9024092..833bac4 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java @@ -4,40 +4,31 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum TcScoreCode { - CODE_0, CODE_1, CODE_2, CODE_3, CODE_4, CODE_5, CODE_6; + THE_0, THE_1, THE_2, THE_3, THE_4, THE_5, THE_6; @JsonValue public String toValue() { switch (this) { - case CODE_0: return "0"; - case CODE_1: return "1"; - case CODE_2: return "2"; - case CODE_3: return "3"; - case CODE_4: return "4"; - case CODE_5: return "5"; - case CODE_6: return "6"; + case THE_0: return "0"; + case THE_1: return "1"; + case THE_2: return "2"; + case THE_3: return "3"; + case THE_4: return "4"; + case THE_5: return "5"; + case THE_6: return "6"; } return null; } @JsonCreator public static TcScoreCode forValue(String value) throws IOException { - switch (value) { - case "0": - return CODE_0; - case "1": - return CODE_1; - case "2": - return CODE_2; - case "3": - return CODE_3; - case "4": - return CODE_4; - case "5": - return CODE_5; - case "6": - return CODE_6; - } + if (value.equals("0")) return THE_0; + if (value.equals("1")) return THE_1; + if (value.equals("2")) return THE_2; + if (value.equals("3")) return THE_3; + if (value.equals("4")) return THE_4; + if (value.equals("5")) return THE_5; + if (value.equals("6")) return THE_6; throw new IOException("Cannot deserialize TcScoreCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Therapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Therapy.java deleted file mode 100644 index 78fe4c4..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Therapy.java +++ /dev/null @@ -1,13 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; -import java.util.List; - -public class Therapy { - private List history; - - @JsonProperty("history") - public List getHistory() { return history; } - @JsonProperty("history") - public void setHistory(List value) { this.history = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java deleted file mode 100644 index 88eee99..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java +++ /dev/null @@ -1,34 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum TherapyRecommendationPriority { - PRIORITY_1, PRIORITY_2, PRIORITY_3, PRIORITY_4; - - @JsonValue - public String toValue() { - switch (this) { - case PRIORITY_1: return "1"; - case PRIORITY_2: return "2"; - case PRIORITY_3: return "3"; - case PRIORITY_4: return "4"; - } - return null; - } - - @JsonCreator - public static TherapyRecommendationPriority forValue(String value) throws IOException { - switch (value) { - case "1": - return PRIORITY_1; - case "2": - return PRIORITY_2; - case "3": - return PRIORITY_3; - case "4": - return PRIORITY_4; - } - throw new IOException("Cannot deserialize TherapyRecommendationPriority"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java index 507bc64..605cefd 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java @@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*; public class Tmb { private String id; - private Coding interpretation; + private CodingTmbInterpretation interpretation; private Reference patient; private Reference specimen; - private Value value; + private TMBResult value; @JsonProperty("id") public String getId() { return id; } @@ -15,9 +15,9 @@ public class Tmb { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public Coding getInterpretation() { return interpretation; } + public CodingTmbInterpretation getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(Coding value) { this.interpretation = value; } + public void setInterpretation(CodingTmbInterpretation value) { this.interpretation = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -30,7 +30,7 @@ public class Tmb { public void setSpecimen(Reference value) { this.specimen = value; } @JsonProperty("value") - public Value getValue() { return value; } + public TMBResult getValue() { return value; } @JsonProperty("value") - public void setValue(Value value) { this.value = value; } + public void setValue(TMBResult value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TnmClassification.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TnmClassification.java new file mode 100644 index 0000000..9f80c34 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TnmClassification.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class TnmClassification { + private Coding metastasis; + private Coding nodes; + private Coding tumor; + + @JsonProperty("metastasis") + public Coding getMetastasis() { return metastasis; } + @JsonProperty("metastasis") + public void setMetastasis(Coding value) { this.metastasis = value; } + + @JsonProperty("nodes") + public Coding getNodes() { return nodes; } + @JsonProperty("nodes") + public void setNodes(Coding value) { this.nodes = value; } + + @JsonProperty("tumor") + public Coding getTumor() { return tumor; } + @JsonProperty("tumor") + public void setTumor(Coding value) { this.tumor = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptId.java similarity index 61% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptId.java index fcad183..f447b9a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalId.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptId.java @@ -2,14 +2,14 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class ExternalId { - private String system; +public class TranscriptId { + private TranscriptIdSystem system; private String value; @JsonProperty("system") - public String getSystem() { return system; } + public TranscriptIdSystem getSystem() { return system; } @JsonProperty("system") - public void setSystem(String value) { this.system = value; } + public void setSystem(TranscriptIdSystem value) { this.system = value; } @JsonProperty("value") public String getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java new file mode 100644 index 0000000..f6041ca --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum TranscriptIdSystem { + HTTPS_Www_ENSEMBL_ORG, HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ; + + @JsonValue + public String toValue() { + switch (this) { + case HTTPS_Www_ENSEMBL_ORG: return "https://www.ensembl.org"; + case HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ: return "https://www.ncbi.nlm.nih.gov/refseq"; + } + return null; + } + + @JsonCreator + public static TranscriptIdSystem forValue(String value) throws IOException { + if (value.equals("https://www.ensembl.org")) return HTTPS_Www_ENSEMBL_ORG; + if (value.equals("https://www.ncbi.nlm.nih.gov/refseq")) return HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ; + throw new IOException("Cannot deserialize TranscriptIdSystem"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java index bc8a08b..3b4f970 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java @@ -5,8 +5,8 @@ import com.fasterxml.jackson.annotation.*; public class TumorCellContent { private String id; private CodingTumorCellContentMethod method; - private Patient patient; - private TumorCellContentSpecimen specimen; + private Reference patient; + private Reference specimen; private double value; @JsonProperty("id") @@ -20,14 +20,14 @@ public class TumorCellContent { public void setMethod(CodingTumorCellContentMethod value) { this.method = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("specimen") - public TumorCellContentSpecimen getSpecimen() { return specimen; } + public Reference getSpecimen() { return specimen; } @JsonProperty("specimen") - public void setSpecimen(TumorCellContentSpecimen value) { this.specimen = value; } + public void setSpecimen(Reference 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 deleted file mode 100644 index 9ba1e38..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentSpecimen.java +++ /dev/null @@ -1,18 +0,0 @@ -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 deleted file mode 100644 index 45b9be9..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGradeCode.java +++ /dev/null @@ -1,37 +0,0 @@ -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/TumorGrading.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGrading.java new file mode 100644 index 0000000..a4418c4 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorGrading.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class TumorGrading { + private List codes; + private Date date; + + @JsonProperty("codes") + public List getCodes() { return codes; } + @JsonProperty("codes") + public void setCodes(List value) { this.codes = value; } + + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getDate() { return date; } + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setDate(Date value) { this.date = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java index 3e2f139..24aac0f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java @@ -5,8 +5,8 @@ import com.fasterxml.jackson.annotation.*; public class TumorMorphology { private String id; private String notes; - private Patient patient; - private TumorMorphologySpecimen specimen; + private Reference patient; + private Reference specimen; private Coding value; @JsonProperty("id") @@ -20,14 +20,14 @@ public class TumorMorphology { public void setNotes(String value) { this.notes = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("specimen") - public TumorMorphologySpecimen getSpecimen() { return specimen; } + public Reference getSpecimen() { return specimen; } @JsonProperty("specimen") - public void setSpecimen(TumorMorphologySpecimen value) { this.specimen = value; } + public void setSpecimen(Reference value) { this.specimen = value; } @JsonProperty("value") public Coding getValue() { return value; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java deleted file mode 100644 index 5f28551..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphologySpecimen.java +++ /dev/null @@ -1,18 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class TumorMorphologySpecimen { - 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/TumorSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java index bb504ba..c971e19 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java @@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*; public class TumorSpecimen { private Collection collection; - private Diagnosis diagnosis; + private Reference diagnosis; private String id; - private Patient patient; - private CodingTumorSpecimenType type; + private Reference patient; + private CodingTumorSpecimen type; @JsonProperty("collection") public Collection getCollection() { return collection; } @@ -15,9 +15,9 @@ public class TumorSpecimen { public void setCollection(Collection value) { this.collection = value; } @JsonProperty("diagnosis") - public Diagnosis getDiagnosis() { return diagnosis; } + public Reference getDiagnosis() { return diagnosis; } @JsonProperty("diagnosis") - public void setDiagnosis(Diagnosis value) { this.diagnosis = value; } + public void setDiagnosis(Reference value) { this.diagnosis = value; } @JsonProperty("id") public String getId() { return id; } @@ -25,12 +25,12 @@ public class TumorSpecimen { public void setId(String value) { this.id = value; } @JsonProperty("patient") - public Patient getPatient() { return patient; } + public Reference getPatient() { return patient; } @JsonProperty("patient") - public void setPatient(Patient value) { this.patient = value; } + public void setPatient(Reference value) { this.patient = value; } @JsonProperty("type") - public CodingTumorSpecimenType getType() { return type; } + public CodingTumorSpecimen getType() { return type; } @JsonProperty("type") - public void setType(CodingTumorSpecimenType value) { this.type = value; } + public void setType(CodingTumorSpecimen value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java deleted file mode 100644 index 2843b9c..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java +++ /dev/null @@ -1,31 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum TumorSpecimenCollectionLocalization { - METASTASIS, PRIMARY_TUMOR, UNKNOWN; - - @JsonValue - public String toValue() { - switch (this) { - case METASTASIS: return "metastasis"; - case PRIMARY_TUMOR: return "primary-tumor"; - case UNKNOWN: return "unknown"; - } - return null; - } - - @JsonCreator - public static TumorSpecimenCollectionLocalization forValue(String value) throws IOException { - switch (value) { - case "metastasis": - return METASTASIS; - case "primary-tumor": - return PRIMARY_TUMOR; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize TumorSpecimenCollectionLocalization"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethod.java deleted file mode 100644 index 36ec4c9..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethod.java +++ /dev/null @@ -1,37 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum TumorSpecimenCollectionMethod { - BIOPSY, CYTOLOGY, LIQUID_BIOPSY, RESECTION, UNKNOWN; - - @JsonValue - public String toValue() { - switch (this) { - case BIOPSY: return "biopsy"; - case CYTOLOGY: return "cytology"; - case LIQUID_BIOPSY: return "liquid-biopsy"; - case RESECTION: return "resection"; - case UNKNOWN: return "unknown"; - } - return null; - } - - @JsonCreator - public static TumorSpecimenCollectionMethod forValue(String value) throws IOException { - switch (value) { - case "biopsy": - return BIOPSY; - case "cytology": - return CYTOLOGY; - case "liquid-biopsy": - return LIQUID_BIOPSY; - case "resection": - return RESECTION; - case "unknown": - return UNKNOWN; - } - throw new IOException("Cannot deserialize TumorSpecimenCollectionMethod"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java new file mode 100644 index 0000000..72dd26a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java @@ -0,0 +1,34 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class TumorStaging { + private Date date; + private CodingTumorStagingMethod method; + private List otherClassifications; + private TnmClassification tnmClassification; + + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getDate() { return date; } + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setDate(Date value) { this.date = value; } + + @JsonProperty("method") + public CodingTumorStagingMethod getMethod() { return method; } + @JsonProperty("method") + public void setMethod(CodingTumorStagingMethod value) { this.method = value; } + + @JsonProperty("otherClassifications") + public List getOtherClassifications() { return otherClassifications; } + @JsonProperty("otherClassifications") + public void setOtherClassifications(List value) { this.otherClassifications = value; } + + @JsonProperty("tnmClassification") + public TnmClassification getTnmClassification() { return tnmClassification; } + @JsonProperty("tnmClassification") + public void setTnmClassification(TnmClassification value) { this.tnmClassification = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java index c8e3303..2319f2b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Type.java @@ -1,22 +1,13 @@ package dev.pcvolkmer.mv64e.mtb; -import java.io.IOException; import com.fasterxml.jackson.annotation.*; +import java.util.List; -public enum Type { - ORGANIZATION; +public class Type { + private List history; - @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"); - } + @JsonProperty("history") + public List getHistory() { return history; } + @JsonProperty("history") + public void setHistory(List value) { this.history = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java index 0ce88dc..32f1ce1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Unit.java @@ -4,11 +4,12 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum Unit { - YEARS; + MONTHS, YEARS; @JsonValue public String toValue() { switch (this) { + case MONTHS: return "Months"; case YEARS: return "Years"; } return null; @@ -16,6 +17,7 @@ public enum Unit { @JsonCreator public static Unit forValue(String value) throws IOException { + if (value.equals("Months")) return MONTHS; if (value.equals("Years")) return YEARS; throw new IOException("Cannot deserialize Unit"); } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java new file mode 100644 index 0000000..bd8453b --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum UseTypeCode { + COMPASSIONATE, IN_LABEL, OFF_LABEL, SEC_PREVENTIVE, UNKNOWN; + + @JsonValue + public String toValue() { + switch (this) { + case COMPASSIONATE: return "compassionate"; + case IN_LABEL: return "in-label"; + case OFF_LABEL: return "off-label"; + case SEC_PREVENTIVE: return "sec-preventive"; + case UNKNOWN: return "unknown"; + } + return null; + } + + @JsonCreator + public static UseTypeCode forValue(String value) throws IOException { + if (value.equals("compassionate")) return COMPASSIONATE; + if (value.equals("in-label")) return IN_LABEL; + if (value.equals("off-label")) return OFF_LABEL; + if (value.equals("sec-preventive")) return SEC_PREVENTIVE; + if (value.equals("unknown")) return UNKNOWN; + throw new IOException("Cannot deserialize UseTypeCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/VariantExternalId.java similarity index 61% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/VariantExternalId.java index 1ce1acc..97a307e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/EXTId.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/VariantExternalId.java @@ -2,14 +2,14 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class EXTId { - private EXTIdSystem system; +public class VariantExternalId { + private ExternalIdSystem system; private String value; @JsonProperty("system") - public EXTIdSystem getSystem() { return system; } + public ExternalIdSystem getSystem() { return system; } @JsonProperty("system") - public void setSystem(EXTIdSystem value) { this.system = value; } + public void setSystem(ExternalIdSystem value) { this.system = value; } @JsonProperty("value") public String getValue() { return value; } diff --git a/src/test/resources/mv64e-mtb-fake-patient.json b/src/test/resources/mv64e-mtb-fake-patient.json index 94ec8ad..c82d951 100644 --- a/src/test/resources/mv64e-mtb-fake-patient.json +++ b/src/test/resources/mv64e-mtb-fake-patient.json @@ -1 +1,2243 @@ 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"744bf622-ba4b-4e64-867c-0807847d9da4", + "display" : "Bösartige Neubildung: Konjunktiva", + "type" : "MTBDiagnosis" + }, + "intent" : { + "code" : "X", + "display" : "Keine Angabe", + "system" : "dnpm-dip/therapy/intent" + }, + "category" : { + "code" : "A", + "display" : "Adjuvant", + "system" : "dnpm-dip/therapy/category" + }, + "basedOn" : { + "id" : "5650387b-2f3b-4f77-863c-9af4d02294fb", + "type" : "MTBMedicationRecommendation" + }, + "recordedOn" : "2025-04-03", + "status" : { + "code" : "stopped", + "display" : "Abgebrochen", + "system" : "dnpm-dip/therapy/status" + }, + "statusReason" : { + "code" : "progression", + "display" : "Progression", + "system" : "dnpm-dip/therapy/status-reason" + }, + "recommendationFulfillmentStatus" : { + "code" : "partial", + "display" : "Partiell", + "system" : "dnpm-dip/therapy/recommendation-fulfillment-status" + }, + "period" : { + "start" : "2006-10-29", + "end" : "2007-02-25" + }, + "medication" : [ { + "code" : "L01FX33", + "display" : "Tarlatamab", + "system" : "http://fhir.de/CodeSystem/bfarm/atc", + "version" : "2024" + } ], + "notes" : [ "Notes on the therapy..." ] + } ] + } ], + "responses" : [ { + "id" : "bbbbbaaf-8486-454c-ba59-28593519342c", + "patient" : { + "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", + "type" : "Patient" + }, + "therapy" : { + "id" : "6b150d30-1c82-4663-833f-6a12ac582ca4", + "type" : "MTBSystemicTherapy" + }, + "effectiveDate" : "2006-12-10", + "method" : { + "code" : "RECIST", + "display" : "Nach RECIST-Kriterien", + "system" : "dnpm-dip/mtb/response/method" + }, + "value" : { + "code" : "SD", + "display" : "Stable Disease", + "system" : "RECIST" + } + }, { + "id" : "6b93b820-4d03-4883-af96-cf504fa6798e", + "patient" : { + "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", + "type" : "Patient" + }, + "therapy" : { + "id" : "27b6eddc-1a4f-4d68-a027-190a2c38754b", + "type" : "MTBSystemicTherapy" + }, + "effectiveDate" : "2007-02-11", + "method" : { + "code" : "RECIST", + "display" : "Nach RECIST-Kriterien", + "system" : "dnpm-dip/mtb/response/method" + }, + "value" : { + "code" : "PD", + "display" : "Progressive Disease", + "system" : "RECIST" + } + } ] +} From 1cefda4bbaf3913e17f722f2e5b5fa261765bb33 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Fri, 30 May 2025 16:28:22 +0200 Subject: [PATCH 2/2] Update to latest data model version --- .../dev/pcvolkmer/mv64e/mtb/AddendumCode.java | 34 - ...a => AtcUnregisteredMedicationCoding.java} | 2 +- ...ava => BaseVariantLocalizationCoding.java} | 8 +- ...=> BaseVariantLocalizationCodingCode.java} | 6 +- .../mtb/{BRCAness.java => Brcaness.java} | 2 +- ...PlanNoSequencingPerformedReasonCoding.java | 30 + .../java/dev/pcvolkmer/mv64e/mtb/Claim.java | 12 +- .../pcvolkmer/mv64e/mtb/ClaimResponse.java | 12 +- .../mv64e/mtb/ClaimResponseStatusCoding.java | 30 + ...ava => ClaimResponseStatusCodingCode.java} | 6 +- ...a => ClaimResponseStatusReasonCoding.java} | 8 +- ... ClaimResponseStatusReasonCodingCode.java} | 6 +- ...gClaimStage.java => ClaimStageCoding.java} | 8 +- ...ageCode.java => ClaimStageCodingCode.java} | 6 +- ...{CodingClinVar.java => ClinVarCoding.java} | 8 +- .../mv64e/mtb/ClinVarCodingCode.java | 30 + .../java/dev/pcvolkmer/mv64e/mtb/Cnv.java | 12 +- .../mtb/{CodingCnv.java => CnvCoding.java} | 8 +- ...{CodingCnvCode.java => CnvCodingCode.java} | 6 +- .../mv64e/mtb/CodingClinVarCode.java | 30 - .../pcvolkmer/mv64e/mtb/CodingEcogCode.java | 32 - .../mtb/CodingFollowUpPatientStatus.java | 30 - .../mtb/CodingHrdScoreInterpretation.java | 30 - .../mtb/CodingLevelOfEvidenceAddendum.java | 30 - .../mtb/CodingLevelOfEvidenceGrading.java | 30 - .../mv64e/mtb/CodingMtbDiagnosis.java | 30 - ...gMtbDiagnosisGuidelineTreatmentStatus.java | 30 - ...ingMtbMedicationRecommendationUseType.java | 30 - ...herapyRecommendationFulfillmentStatus.java | 30 - .../mtb/CodingProteinExpressionIcScore.java | 30 - .../mtb/CodingProteinExpressionTcScore.java | 30 - .../mtb/CodingRecommendationPriority.java | 30 - .../mv64e/mtb/CodingTmbInterpretation.java | 30 - .../mv64e/mtb/CodingVitalStatus.java | 30 - .../dev/pcvolkmer/mv64e/mtb/Collection.java | 12 +- .../pcvolkmer/mv64e/mtb/ConsentProvision.java | 24 + .../mtb/{DNAFusion.java => DnaFusion.java} | 8 +- .../mtb/{CodingEcog.java => EcogCoding.java} | 8 +- .../pcvolkmer/mv64e/mtb/EcogCodingCode.java | 32 + .../pcvolkmer/mv64e/mtb/ExternalIdSystem.java | 18 +- .../dev/pcvolkmer/mv64e/mtb/FollowUp.java | 18 +- .../mtb/FollowUpPatientStatusCoding.java | 30 + ...a => FollowUpPatientStatusCodingCode.java} | 6 +- .../{CodingRecist.java => GenderCoding.java} | 8 +- ...{GenderCode.java => GenderCodingCode.java} | 6 +- .../mtb/GeneticCounselingRecommendation.java | 6 +- ...cCounselingRecommendationReasonCoding.java | 30 + ...selingRecommendationReasonCodingCode.java} | 6 +- .../pcvolkmer/mv64e/mtb/HealthInsurance.java | 6 +- ...urance.java => HealthInsuranceCoding.java} | 8 +- ...de.java => HealthInsuranceCodingCode.java} | 10 +- .../java/dev/pcvolkmer/mv64e/mtb/History.java | 6 +- .../mtb/{HRDScore.java => HrdScore.java} | 8 +- .../mtb/HrdScoreInterpretationCoding.java | 30 + .../dev/pcvolkmer/mv64e/mtb/ICScoreCode.java | 28 - .../mtb/{IHCReport.java => IhcReport.java} | 2 +- ...ode.java => InterpretationCodingCode.java} | 6 +- .../pcvolkmer/mv64e/mtb/LevelOfEvidence.java | 12 +- ...ava => LevelOfEvidenceAddendumCoding.java} | 8 +- .../LevelOfEvidenceAddendumCodingCode.java | 28 + .../mv64e/mtb/LevelOfEvidenceCode.java | 38 - ...java => LevelOfEvidenceGradingCoding.java} | 8 +- .../mtb/LevelOfEvidenceGradingCodingCode.java | 38 + .../java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java | 18 +- .../mv64e/mtb/ModelProjectConsent.java | 26 + .../mv64e/mtb/ModelProjectConsentPurpose.java | 26 + ...a => MolecularDiagnosticReportCoding.java} | 8 +- ... MolecularDiagnosticReportCodingCode.java} | 6 +- .../java/dev/pcvolkmer/mv64e/mtb/Mtb.java | 42 +- .../{MTBCarePlan.java => MtbCarePlan.java} | 30 +- ...lanRecommendationsMissingReasonCoding.java | 30 + ...ecommendationsMissingReasonCodingCode.java | 22 + .../{MTBDiagnosis.java => MtbDiagnosis.java} | 10 +- ...ingGender.java => MtbDiagnosisCoding.java} | 8 +- ...gnosisGuidelineTreatmentStatusCoding.java} | 8 +- ...isGuidelineTreatmentStatusCodingCode.java} | 6 +- ...isodeOfCare.java => MtbEpisodeOfCare.java} | 2 +- ....java => MtbMedicationRecommendation.java} | 26 +- ...dicationRecommendationCategoryCoding.java} | 8 +- ...tionRecommendationCategoryCodingCode.java} | 6 +- ...edicationRecommendationUseTypeCoding.java} | 8 +- ...ationRecommendationUseTypeCodingCode.java} | 6 +- ...ProcedureRecommendationCategoryCoding.java | 30 + ...dureRecommendationCategoryCodingCode.java} | 6 +- ... => MtbStudyEnrollmentRecommendation.java} | 20 +- ...icTherapy.java => MtbSystemicTherapy.java} | 44 +- ... => MtbSystemicTherapyCategoryCoding.java} | 8 +- ...MtbSystemicTherapyCategoryCodingCode.java} | 6 +- ...MtbSystemicTherapyDosageDensityCoding.java | 30 + ...ystemicTherapyDosageDensityCodingCode.java | 24 + ...RecommendationFulfillmentStatusCoding.java | 30 + ...mendationFulfillmentStatusCodingCode.java} | 6 +- ...eason.java => MtbTherapyIntentCoding.java} | 8 +- ...e.java => MtbTherapyIntentCodingCode.java} | 6 +- ...java => MtbTherapyStatusReasonCoding.java} | 8 +- ... => MtbTherapyStatusReasonCodingCode.java} | 6 +- .../dev/pcvolkmer/mv64e/mtb/MvhMetadata.java | 32 + .../mv64e/mtb/MvhSubmissionType.java | 28 + ...ingNgsReport.java => NgsReportCoding.java} | 8 +- ...portCode.java => NgsReportCodingCode.java} | 6 +- .../{Metadata.java => NgsReportMetadata.java} | 2 +- .../pcvolkmer/mv64e/mtb/NgsReportResults.java | 30 +- ...a => NoSequencingPerformedReasonCode.java} | 10 +- .../pcvolkmer/mv64e/mtb/OncoProcedure.java | 24 +- ...rocedure.java => OncoProcedureCoding.java} | 8 +- ...Code.java => OncoProcedureCodingCode.java} | 6 +- .../java/dev/pcvolkmer/mv64e/mtb/Patient.java | 12 +- .../mv64e/mtb/PerformanceStatus.java | 6 +- .../mv64e/mtb/PriorDiagnosticReport.java | 6 +- .../dev/pcvolkmer/mv64e/mtb/PriorityCode.java | 28 - .../mv64e/mtb/ProcedureRecommendation.java | 12 +- .../mv64e/mtb/ProteinExpression.java | 18 +- .../mtb/ProteinExpressionIcScoreCoding.java | 30 + .../ProteinExpressionIcScoreCodingCode.java | 28 + ...ava => ProteinExpressionResultCoding.java} | 8 +- ...=> ProteinExpressionResultCodingCode.java} | 20 +- .../mtb/ProteinExpressionTcScoreCoding.java | 30 + .../ProteinExpressionTcScoreCodingCode.java | 34 + .../dev/pcvolkmer/mv64e/mtb/Provision.java | 27 + .../mv64e/mtb/PublicationSystem.java | 10 +- ...mResponseStatus.java => RecistCoding.java} | 8 +- ...gRecistCode.java => RecistCodingCode.java} | 6 +- .../mtb/RecommendationPriorityCoding.java | 30 + .../mtb/RecommendationPriorityCodingCode.java | 28 + .../mv64e/mtb/RequestedMedicationSystem.java | 6 +- .../dev/pcvolkmer/mv64e/mtb/Response.java | 12 +- ...eMethod.java => ResponseMethodCoding.java} | 8 +- ...ode.java => ResponseMethodCodingCode.java} | 6 +- .../mtb/{RNAFusion.java => RnaFusion.java} | 8 +- .../mtb/RnaFusionFusionPartner3Prime.java | 6 +- .../mtb/RnaFusionFusionPartner5Prime.java | 6 +- ...FusionStrand.java => RnaFusionStrand.java} | 6 +- .../mv64e/mtb/{RNASeq.java => RnaSeq.java} | 8 +- .../java/dev/pcvolkmer/mv64e/mtb/Snv.java | 24 +- ...ortMetadata.java => SomaticNgsReport.java} | 14 +- .../dev/pcvolkmer/mv64e/mtb/StudySystem.java | 6 +- .../pcvolkmer/mv64e/mtb/SystemicTherapy.java | 6 +- .../dev/pcvolkmer/mv64e/mtb/TcScoreCode.java | 34 - ...pyStatus.java => TherapyStatusCoding.java} | 8 +- ...Code.java => TherapyStatusCodingCode.java} | 6 +- .../java/dev/pcvolkmer/mv64e/mtb/Tmb.java | 12 +- .../mv64e/mtb/TmbInterpretationCoding.java | 30 + .../mtb/{TMBResult.java => TmbResult.java} | 2 +- .../mv64e/mtb/TranscriptIdSystem.java | 10 +- .../pcvolkmer/mv64e/mtb/TumorCellContent.java | 6 +- .../mtb/TumorCellContentMethodCoding.java | 30 + ... => TumorCellContentMethodCodingCode.java} | 6 +- .../pcvolkmer/mv64e/mtb/TumorMorphology.java | 10 +- .../pcvolkmer/mv64e/mtb/TumorSpecimen.java | 6 +- ...Specimen.java => TumorSpecimenCoding.java} | 8 +- ...Code.java => TumorSpecimenCodingCode.java} | 6 +- ...SpecimenCollectionLocalizationCoding.java} | 8 +- ...imenCollectionLocalizationCodingCode.java} | 6 +- ... TumorSpecimenCollectionMethodCoding.java} | 8 +- ...orSpecimenCollectionMethodCodingCode.java} | 6 +- .../dev/pcvolkmer/mv64e/mtb/TumorStaging.java | 6 +- ...hod.java => TumorStagingMethodCoding.java} | 8 +- ...java => TumorStagingMethodCodingCode.java} | 6 +- ...ngMtbDiagnosisCode.java => ValueCode.java} | 6 +- .../mv64e/mtb/VitalStatusCoding.java | 30 + ...usCode.java => VitalStatusCodingCode.java} | 6 +- .../resources/mv64e-mtb-fake-patient.json | 4771 +++++++++-------- 162 files changed, 3983 insertions(+), 3325 deletions(-) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingAtcUnregisteredMedication.java => AtcUnregisteredMedicationCoding.java} (95%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbCarePlanStatusReason.java => BaseVariantLocalizationCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingBaseVariantLocalizationCode.java => BaseVariantLocalizationCodingCode.java} (82%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{BRCAness.java => Brcaness.java} (97%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CarePlanNoSequencingPerformedReasonCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{StickyCode.java => ClaimResponseStatusCodingCode.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingClaimResponseStatusReason.java => ClaimResponseStatusReasonCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingClaimResponseStatusReasonCode.java => ClaimResponseStatusReasonCodingCode.java} (88%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingClaimStage.java => ClaimStageCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{StageCode.java => ClaimStageCodingCode.java} (79%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingClinVar.java => ClinVarCoding.java} (80%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCodingCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingCnv.java => CnvCoding.java} (81%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingCnvCode.java => CnvCodingCode.java} (80%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionIcScore.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionTcScore.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentProvision.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{DNAFusion.java => DnaFusion.java} (87%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingEcog.java => EcogCoding.java} (80%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCodingCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{PatientStatusCode.java => FollowUpPatientStatusCodingCode.java} (61%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingRecist.java => GenderCoding.java} (80%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{GenderCode.java => GenderCodingCode.java} (77%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{ReasonCode.java => GeneticCounselingRecommendationReasonCodingCode.java} (76%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingHealthInsurance.java => HealthInsuranceCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingHealthInsuranceCode.java => HealthInsuranceCodingCode.java} (75%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{HRDScore.java => HrdScore.java} (85%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScoreInterpretationCoding.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{IHCReport.java => IhcReport.java} (98%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{InterpretationCode.java => InterpretationCodingCode.java} (81%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingProteinExpressionResult.java => LevelOfEvidenceAddendumCoding.java} (77%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCodingCode.java delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbTherapyStatusReason.java => LevelOfEvidenceGradingCoding.java} (77%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCodingCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsent.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsentPurpose.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMolecularDiagnosticReport.java => MolecularDiagnosticReportCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMolecularDiagnosticReportCode.java => MolecularDiagnosticReportCodingCode.java} (88%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBCarePlan.java => MtbCarePlan.java} (71%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCodingCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBDiagnosis.java => MtbDiagnosis.java} (87%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingGender.java => MtbDiagnosisCoding.java} (80%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbTherapyIntent.java => MtbDiagnosisGuidelineTreatmentStatusCoding.java} (70%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{GuidelineTreatmentStatusCode.java => MtbDiagnosisGuidelineTreatmentStatusCodingCode.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBEpisodeOfCare.java => MtbEpisodeOfCare.java} (96%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBMedicationRecommendation.java => MtbMedicationRecommendation.java} (68%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbMedicationRecommendationCategory.java => MtbMedicationRecommendationCategoryCoding.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbMedicationRecommendationCategoryCode.java => MtbMedicationRecommendationCategoryCodingCode.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbProcedureRecommendationCategory.java => MtbMedicationRecommendationUseTypeCoding.java} (76%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{UseTypeCode.java => MtbMedicationRecommendationUseTypeCodingCode.java} (76%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbProcedureRecommendationCategoryCode.java => MtbProcedureRecommendationCategoryCodingCode.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBStudyEnrollmentRecommendation.java => MtbStudyEnrollmentRecommendation.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{MTBSystemicTherapy.java => MtbSystemicTherapy.java} (60%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbSystemicTherapyCategory.java => MtbSystemicTherapyCategoryCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbSystemicTherapyCategoryCode.java => MtbSystemicTherapyCategoryCodingCode.java} (76%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCodingCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RecommendationFulfillmentStatusCode.java => MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.java} (59%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingGeneticCounselingRecommendationReason.java => MtbTherapyIntentCoding.java} (76%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{IntentCode.java => MtbTherapyIntentCodingCode.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorCellContentMethod.java => MtbTherapyStatusReasonCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbTherapyStatusReasonCode.java => MtbTherapyStatusReasonCodingCode.java} (94%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MvhMetadata.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/MvhSubmissionType.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingNgsReport.java => NgsReportCoding.java} (79%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingNgsReportCode.java => NgsReportCodingCode.java} (87%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{Metadata.java => NgsReportMetadata.java} (97%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbCarePlanStatusReasonCode.java => NoSequencingPerformedReasonCode.java} (67%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingOncoProcedure.java => OncoProcedureCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingOncoProcedureCode.java => OncoProcedureCodingCode.java} (78%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCodingCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingBaseVariantLocalization.java => ProteinExpressionResultCoding.java} (77%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingProteinExpressionResultCode.java => ProteinExpressionResultCodingCode.java} (50%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCodingCode.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/Provision.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingClaimResponseStatus.java => RecistCoding.java} (79%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingRecistCode.java => RecistCodingCode.java} (82%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCoding.java create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCodingCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingResponseMethod.java => ResponseMethodCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingResponseMethodCode.java => ResponseMethodCodingCode.java} (71%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RNAFusion.java => RnaFusion.java} (88%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RNAFusionStrand.java => RnaFusionStrand.java} (75%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{RNASeq.java => RnaSeq.java} (91%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{SomaticNgsReportMetadata.java => SomaticNgsReport.java} (78%) delete mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTherapyStatus.java => TherapyStatusCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTherapyStatusCode.java => TherapyStatusCodingCode.java} (81%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TmbInterpretationCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{TMBResult.java => TmbResult.java} (94%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorCellContentMethodCode.java => TumorCellContentMethodCodingCode.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimen.java => TumorSpecimenCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenCode.java => TumorSpecimenCodingCode.java} (82%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenCollectionLocalization.java => TumorSpecimenCollectionLocalizationCoding.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenCollectionLocalizationCode.java => TumorSpecimenCollectionLocalizationCodingCode.java} (83%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenCollectionMethod.java => TumorSpecimenCollectionMethodCoding.java} (76%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorSpecimenCollectionMethodCode.java => TumorSpecimenCollectionMethodCodingCode.java} (80%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorStagingMethod.java => TumorStagingMethodCoding.java} (78%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingTumorStagingMethodCode.java => TumorStagingMethodCodingCode.java} (72%) rename src/main/java/dev/pcvolkmer/mv64e/mtb/{CodingMtbDiagnosisCode.java => ValueCode.java} (74%) create mode 100644 src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCoding.java rename src/main/java/dev/pcvolkmer/mv64e/mtb/{VitalStatusCode.java => VitalStatusCodingCode.java} (79%) diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java deleted file mode 100644 index 7b36a77..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java +++ /dev/null @@ -1,34 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum AddendumCode { - IS, IV, R, Z; - - @JsonValue - public String toValue() { - switch (this) { - case IS: return "is"; - case IV: return "iv"; - case R: return "R"; - case Z: return "Z"; - } - return null; - } - - @JsonCreator - public static AddendumCode forValue(String value) throws IOException { - switch (value) { - case "is": - return IS; - case "iv": - return IV; - case "R": - return R; - case "Z": - return Z; - } - throw new IOException("Cannot deserialize AddendumCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/AtcUnregisteredMedicationCoding.java similarity index 95% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/AtcUnregisteredMedicationCoding.java index ced0849..56441ce 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingAtcUnregisteredMedication.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/AtcUnregisteredMedicationCoding.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingAtcUnregisteredMedication { +public class AtcUnregisteredMedicationCoding { private String code; private String display; private RequestedMedicationSystem system; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCoding.java index d45c114..d21eb00 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbCarePlanStatusReason { - private CodingMtbCarePlanStatusReasonCode code; +public class BaseVariantLocalizationCoding { + private BaseVariantLocalizationCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMtbCarePlanStatusReasonCode getCode() { return code; } + public BaseVariantLocalizationCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbCarePlanStatusReasonCode value) { this.code = value; } + public void setCode(BaseVariantLocalizationCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCodingCode.java similarity index 82% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCodingCode.java index d06b221..4634632 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalizationCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/BaseVariantLocalizationCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingBaseVariantLocalizationCode { +public enum BaseVariantLocalizationCodingCode { CODING_REGION, INTERGENIC, INTRONIC, REGULATORY_REGION, SPLICING_REGION; @JsonValue @@ -19,12 +19,12 @@ public enum CodingBaseVariantLocalizationCode { } @JsonCreator - public static CodingBaseVariantLocalizationCode forValue(String value) throws IOException { + public static BaseVariantLocalizationCodingCode forValue(String value) throws IOException { if (value.equals("coding-region")) return CODING_REGION; if (value.equals("intergenic")) return INTERGENIC; if (value.equals("intronic")) return INTRONIC; if (value.equals("regulatory-region")) return REGULATORY_REGION; if (value.equals("splicing-region")) return SPLICING_REGION; - throw new IOException("Cannot deserialize CodingBaseVariantLocalizationCode"); + throw new IOException("Cannot deserialize BaseVariantLocalizationCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Brcaness.java similarity index 97% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/Brcaness.java index a8b02b3..c0f731b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/BRCAness.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Brcaness.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class BRCAness { +public class Brcaness { private ConfidenceRange confidenceRange; private String id; private Reference patient; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CarePlanNoSequencingPerformedReasonCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CarePlanNoSequencingPerformedReasonCoding.java new file mode 100644 index 0000000..22949b3 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CarePlanNoSequencingPerformedReasonCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class CarePlanNoSequencingPerformedReasonCoding { + private NoSequencingPerformedReasonCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public NoSequencingPerformedReasonCode getCode() { return code; } + @JsonProperty("code") + public void setCode(NoSequencingPerformedReasonCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java index b5b1adf..7de8f51 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java @@ -9,8 +9,8 @@ public class Claim { private Date issuedOn; private Reference patient; private Reference recommendation; - private List requestedMedication; - private CodingClaimStage stage; + private List requestedMedication; + private ClaimStageCoding stage; @JsonProperty("id") public String getId() { return id; } @@ -35,12 +35,12 @@ public class Claim { public void setRecommendation(Reference value) { this.recommendation = value; } @JsonProperty("requestedMedication") - public List getRequestedMedication() { return requestedMedication; } + public List getRequestedMedication() { return requestedMedication; } @JsonProperty("requestedMedication") - public void setRequestedMedication(List value) { this.requestedMedication = value; } + public void setRequestedMedication(List value) { this.requestedMedication = value; } @JsonProperty("stage") - public CodingClaimStage getStage() { return stage; } + public ClaimStageCoding getStage() { return stage; } @JsonProperty("stage") - public void setStage(CodingClaimStage value) { this.stage = value; } + public void setStage(ClaimStageCoding 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 657eb0e..9304d51 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 Reference patient; - private CodingClaimResponseStatus status; - private CodingClaimResponseStatusReason statusReason; + private ClaimResponseStatusCoding status; + private ClaimResponseStatusReasonCoding statusReason; @JsonProperty("claim") public Reference getClaim() { return claim; } @@ -34,12 +34,12 @@ public class ClaimResponse { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("status") - public CodingClaimResponseStatus getStatus() { return status; } + public ClaimResponseStatusCoding getStatus() { return status; } @JsonProperty("status") - public void setStatus(CodingClaimResponseStatus value) { this.status = value; } + public void setStatus(ClaimResponseStatusCoding value) { this.status = value; } @JsonProperty("statusReason") - public CodingClaimResponseStatusReason getStatusReason() { return statusReason; } + public ClaimResponseStatusReasonCoding getStatusReason() { return statusReason; } @JsonProperty("statusReason") - public void setStatusReason(CodingClaimResponseStatusReason value) { this.statusReason = value; } + public void setStatusReason(ClaimResponseStatusReasonCoding value) { this.statusReason = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCoding.java new file mode 100644 index 0000000..37e3f44 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class ClaimResponseStatusCoding { + private ClaimResponseStatusCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public ClaimResponseStatusCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(ClaimResponseStatusCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCodingCode.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCodingCode.java index 031dc9e..79be481 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StickyCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum StickyCode { +public enum ClaimResponseStatusCodingCode { ACCEPTED, REJECTED, UNKNOWN; @JsonValue @@ -17,10 +17,10 @@ public enum StickyCode { } @JsonCreator - public static StickyCode forValue(String value) throws IOException { + public static ClaimResponseStatusCodingCode forValue(String value) throws IOException { if (value.equals("accepted")) return ACCEPTED; if (value.equals("rejected")) return REJECTED; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize StickyCode"); + throw new IOException("Cannot deserialize ClaimResponseStatusCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCoding.java index 275505d..1d09a1b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingClaimResponseStatusReason { - private CodingClaimResponseStatusReasonCode code; +public class ClaimResponseStatusReasonCoding { + private ClaimResponseStatusReasonCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingClaimResponseStatusReasonCode getCode() { return code; } + public ClaimResponseStatusReasonCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingClaimResponseStatusReasonCode value) { this.code = value; } + public void setCode(ClaimResponseStatusReasonCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCodingCode.java similarity index 88% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCodingCode.java index 843bf4f..581e8a8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatusReasonCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatusReasonCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingClaimResponseStatusReasonCode { +public enum ClaimResponseStatusReasonCodingCode { APPROVAL_REVOCATION, FORMAL_REASONS, INCLUSION_IN_STUDY, INSUFFICIENT_EVIDENCE, OTHER, OTHER_THERAPY_RECOMMENDED, STANDARD_THERAPY_NOT_EXHAUSTED, UNKNOWN; @JsonValue @@ -22,7 +22,7 @@ public enum CodingClaimResponseStatusReasonCode { } @JsonCreator - public static CodingClaimResponseStatusReasonCode forValue(String value) throws IOException { + public static ClaimResponseStatusReasonCodingCode forValue(String value) throws IOException { if (value.equals("approval-revocation")) return APPROVAL_REVOCATION; if (value.equals("formal-reasons")) return FORMAL_REASONS; if (value.equals("inclusion-in-study")) return INCLUSION_IN_STUDY; @@ -31,6 +31,6 @@ public enum CodingClaimResponseStatusReasonCode { if (value.equals("other-therapy-recommended")) return OTHER_THERAPY_RECOMMENDED; if (value.equals("standard-therapy-not-exhausted")) return STANDARD_THERAPY_NOT_EXHAUSTED; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingClaimResponseStatusReasonCode"); + throw new IOException("Cannot deserialize ClaimResponseStatusReasonCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCoding.java index e857200..8c8d7fb 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimStage.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingClaimStage { - private StageCode code; +public class ClaimStageCoding { + private ClaimStageCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public StageCode getCode() { return code; } + public ClaimStageCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(StageCode value) { this.code = value; } + public void setCode(ClaimStageCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCodingCode.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCodingCode.java index fb8a6f3..d879dd6 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StageCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimStageCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum StageCode { +public enum ClaimStageCodingCode { FOLLOW_UP_CLAIM, INITIAL_CLAIM, REVOCATION, UNKNOWN; @JsonValue @@ -18,11 +18,11 @@ public enum StageCode { } @JsonCreator - public static StageCode forValue(String value) throws IOException { + public static ClaimStageCodingCode forValue(String value) throws IOException { if (value.equals("follow-up-claim")) return FOLLOW_UP_CLAIM; if (value.equals("initial-claim")) return INITIAL_CLAIM; if (value.equals("revocation")) return REVOCATION; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize StageCode"); + throw new IOException("Cannot deserialize ClaimStageCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCoding.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCoding.java index 14d6cdf..0a36498 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVar.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingClinVar { - private CodingClinVarCode code; +public class ClinVarCoding { + private ClinVarCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingClinVarCode getCode() { return code; } + public ClinVarCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingClinVarCode value) { this.code = value; } + public void setCode(ClinVarCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCodingCode.java new file mode 100644 index 0000000..34f203c --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ClinVarCodingCode.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ClinVarCodingCode { + CODE_1, CODE_2, CODE_3, CODE_4, CODE_5; + + @JsonValue + public String toValue() { + switch (this) { + case CODE_1: return "1"; + case CODE_2: return "2"; + case CODE_3: return "3"; + case CODE_4: return "4"; + case CODE_5: return "5"; + } + return null; + } + + @JsonCreator + public static ClinVarCodingCode forValue(String value) throws IOException { + if (value.equals("1")) return CODE_1; + if (value.equals("2")) return CODE_2; + if (value.equals("3")) return CODE_3; + if (value.equals("4")) return CODE_4; + if (value.equals("5")) return CODE_5; + throw new IOException("Cannot deserialize ClinVarCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java index d2ad364..b36a812 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java @@ -11,14 +11,14 @@ public class Cnv { private EndRange endRange; private List externalIds; private String id; - private List localization; + private List localization; private Reference patient; private Double relativeCopyNumber; private List reportedAffectedGenes; private String reportedFocality; private StartRange startRange; private Long totalCopyNumber; - private CodingCnv type; + private CnvCoding type; @JsonProperty("chromosome") public Chromosome getChromosome() { return chromosome; } @@ -56,9 +56,9 @@ public class Cnv { public void setId(String value) { this.id = value; } @JsonProperty("localization") - public List getLocalization() { return localization; } + public List getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(List value) { this.localization = value; } + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -91,7 +91,7 @@ public class Cnv { public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; } @JsonProperty("type") - public CodingCnv getType() { return type; } + public CnvCoding getType() { return type; } @JsonProperty("type") - public void setType(CodingCnv value) { this.type = value; } + public void setType(CnvCoding value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCoding.java similarity index 81% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCoding.java index 9c2997e..9081da5 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingCnv { - private CodingCnvCode code; +public class CnvCoding { + private CnvCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingCnvCode getCode() { return code; } + public CnvCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingCnvCode value) { this.code = value; } + public void setCode(CnvCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCodingCode.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCodingCode.java index aa36408..858c544 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingCnvCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/CnvCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingCnvCode { +public enum CnvCodingCode { HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN; @JsonValue @@ -17,10 +17,10 @@ public enum CodingCnvCode { } @JsonCreator - public static CodingCnvCode forValue(String value) throws IOException { + public static CnvCodingCode forValue(String value) throws IOException { if (value.equals("high-level-gain")) return HIGH_LEVEL_GAIN; if (value.equals("loss")) return LOSS; if (value.equals("low-level-gain")) return LOW_LEVEL_GAIN; - throw new IOException("Cannot deserialize CodingCnvCode"); + throw new IOException("Cannot deserialize CnvCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java deleted file mode 100644 index 57f4dad..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClinVarCode.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum CodingClinVarCode { - THE_1, THE_2, THE_3, THE_4, THE_5; - - @JsonValue - public String toValue() { - switch (this) { - case THE_1: return "1"; - case THE_2: return "2"; - case THE_3: return "3"; - case THE_4: return "4"; - case THE_5: return "5"; - } - return null; - } - - @JsonCreator - public static CodingClinVarCode forValue(String value) throws IOException { - if (value.equals("1")) return THE_1; - if (value.equals("2")) return THE_2; - if (value.equals("3")) return THE_3; - if (value.equals("4")) return THE_4; - if (value.equals("5")) return THE_5; - throw new IOException("Cannot deserialize CodingClinVarCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java deleted file mode 100644 index e65ff47..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcogCode.java +++ /dev/null @@ -1,32 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum CodingEcogCode { - THE_0, THE_1, THE_2, THE_3, THE_4, THE_5; - - @JsonValue - public String toValue() { - switch (this) { - case THE_0: return "0"; - case THE_1: return "1"; - case THE_2: return "2"; - case THE_3: return "3"; - case THE_4: return "4"; - case THE_5: return "5"; - } - return null; - } - - @JsonCreator - public static CodingEcogCode forValue(String value) throws IOException { - if (value.equals("0")) return THE_0; - if (value.equals("1")) return THE_1; - if (value.equals("2")) return THE_2; - if (value.equals("3")) return THE_3; - if (value.equals("4")) return THE_4; - if (value.equals("5")) return THE_5; - throw new IOException("Cannot deserialize CodingEcogCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java deleted file mode 100644 index 188421c..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingFollowUpPatientStatus.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingFollowUpPatientStatus { - private PatientStatusCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public PatientStatusCode getCode() { return code; } - @JsonProperty("code") - public void setCode(PatientStatusCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java deleted file mode 100644 index c468a9f..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHrdScoreInterpretation.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingHrdScoreInterpretation { - private InterpretationCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public InterpretationCode getCode() { return code; } - @JsonProperty("code") - public void setCode(InterpretationCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java deleted file mode 100644 index 4efe15e..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingLevelOfEvidenceAddendum { - private AddendumCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public AddendumCode getCode() { return code; } - @JsonProperty("code") - public void setCode(AddendumCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java deleted file mode 100644 index 9b2c543..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingLevelOfEvidenceGrading { - private LevelOfEvidenceCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public LevelOfEvidenceCode getCode() { return code; } - @JsonProperty("code") - public void setCode(LevelOfEvidenceCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java deleted file mode 100644 index 63e1a41..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosis.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingMtbDiagnosis { - private CodingMtbDiagnosisCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public CodingMtbDiagnosisCode getCode() { return code; } - @JsonProperty("code") - public void setCode(CodingMtbDiagnosisCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java deleted file mode 100644 index 779eb42..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisGuidelineTreatmentStatus.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingMtbDiagnosisGuidelineTreatmentStatus { - private GuidelineTreatmentStatusCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public GuidelineTreatmentStatusCode getCode() { return code; } - @JsonProperty("code") - public void setCode(GuidelineTreatmentStatusCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java deleted file mode 100644 index c285eca..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationUseType.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingMtbMedicationRecommendationUseType { - private UseTypeCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public UseTypeCode getCode() { return code; } - @JsonProperty("code") - public void setCode(UseTypeCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java deleted file mode 100644 index b66f927..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyRecommendationFulfillmentStatus.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingMtbSystemicTherapyRecommendationFulfillmentStatus { - private RecommendationFulfillmentStatusCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public RecommendationFulfillmentStatusCode getCode() { return code; } - @JsonProperty("code") - public void setCode(RecommendationFulfillmentStatusCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionIcScore.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionIcScore.java deleted file mode 100644 index fb10972..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionIcScore.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingProteinExpressionIcScore { - private ICScoreCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public ICScoreCode getCode() { return code; } - @JsonProperty("code") - public void setCode(ICScoreCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionTcScore.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionTcScore.java deleted file mode 100644 index ec33755..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionTcScore.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingProteinExpressionTcScore { - private TcScoreCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public TcScoreCode getCode() { return code; } - @JsonProperty("code") - public void setCode(TcScoreCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java deleted file mode 100644 index a4ea759..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecommendationPriority.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingRecommendationPriority { - private PriorityCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public PriorityCode getCode() { return code; } - @JsonProperty("code") - public void setCode(PriorityCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java deleted file mode 100644 index 02d57df..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTmbInterpretation.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingTmbInterpretation { - private InterpretationCode code; - private String display; - private String system; - private String version; - - @JsonProperty("code") - public InterpretationCode getCode() { return code; } - @JsonProperty("code") - public void setCode(InterpretationCode value) { this.code = value; } - - @JsonProperty("display") - public String getDisplay() { return display; } - @JsonProperty("display") - public void setDisplay(String value) { this.display = value; } - - @JsonProperty("system") - public String getSystem() { return system; } - @JsonProperty("system") - public void setSystem(String value) { this.system = value; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java deleted file mode 100644 index d421742..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingVitalStatus.java +++ /dev/null @@ -1,30 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import com.fasterxml.jackson.annotation.*; - -public class CodingVitalStatus { - private VitalStatusCode code; - private String display; - private String system; - private String version; - - @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; } - - @JsonProperty("version") - public String getVersion() { return version; } - @JsonProperty("version") - public void setVersion(String value) { this.version = value; } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java index f8b585e..5518efa 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java @@ -5,8 +5,8 @@ import java.util.Date; public class Collection { private Date date; - private CodingTumorSpecimenCollectionLocalization localization; - private CodingTumorSpecimenCollectionMethod method; + private TumorSpecimenCollectionLocalizationCoding localization; + private TumorSpecimenCollectionMethodCoding method; @JsonProperty("date") public Date getDate() { return date; } @@ -14,12 +14,12 @@ public class Collection { public void setDate(Date value) { this.date = value; } @JsonProperty("localization") - public CodingTumorSpecimenCollectionLocalization getLocalization() { return localization; } + public TumorSpecimenCollectionLocalizationCoding getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(CodingTumorSpecimenCollectionLocalization value) { this.localization = value; } + public void setLocalization(TumorSpecimenCollectionLocalizationCoding value) { this.localization = value; } @JsonProperty("method") - public CodingTumorSpecimenCollectionMethod getMethod() { return method; } + public TumorSpecimenCollectionMethodCoding getMethod() { return method; } @JsonProperty("method") - public void setMethod(CodingTumorSpecimenCollectionMethod value) { this.method = value; } + public void setMethod(TumorSpecimenCollectionMethodCoding value) { this.method = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentProvision.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentProvision.java new file mode 100644 index 0000000..5698f9d --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentProvision.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ConsentProvision { + DENY, PERMIT; + + @JsonValue + public String toValue() { + switch (this) { + case DENY: return "deny"; + case PERMIT: return "permit"; + } + return null; + } + + @JsonCreator + public static ConsentProvision forValue(String value) throws IOException { + if (value.equals("deny")) return DENY; + if (value.equals("permit")) return PERMIT; + throw new IOException("Cannot deserialize ConsentProvision"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java similarity index 87% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java index 6cd24c8..48b32cc 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/DNAFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java @@ -3,12 +3,12 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.List; -public class DNAFusion { +public class DnaFusion { private List externalIds; private DnaFusionFusionPartner3Prime fusionPartner3Prime; private DnaFusionFusionPartner5Prime fusionPartner5Prime; private String id; - private List localization; + private List localization; private Reference patient; private long reportedNumReads; @@ -33,9 +33,9 @@ public class DNAFusion { public void setId(String value) { this.id = value; } @JsonProperty("localization") - public List getLocalization() { return localization; } + public List getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(List value) { this.localization = value; } + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCoding.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCoding.java index 4f2cdd0..668ead2 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingEcog { - private CodingEcogCode code; +public class EcogCoding { + private EcogCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingEcogCode getCode() { return code; } + public EcogCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingEcogCode value) { this.code = value; } + public void setCode(EcogCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCodingCode.java new file mode 100644 index 0000000..2101049 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCodingCode.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum EcogCodingCode { + CODE_0, CODE_1, CODE_2, CODE_3, CODE_4, CODE_5; + + @JsonValue + public String toValue() { + switch (this) { + case CODE_0: return "0"; + case CODE_1: return "1"; + case CODE_2: return "2"; + case CODE_3: return "3"; + case CODE_4: return "4"; + case CODE_5: return "5"; + } + return null; + } + + @JsonCreator + public static EcogCodingCode forValue(String value) throws IOException { + if (value.equals("0")) return CODE_0; + if (value.equals("1")) return CODE_1; + if (value.equals("2")) return CODE_2; + if (value.equals("3")) return CODE_3; + if (value.equals("4")) return CODE_4; + if (value.equals("5")) return CODE_5; + throw new IOException("Cannot deserialize EcogCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java index 9c3862f..967450c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ExternalIdSystem.java @@ -4,25 +4,25 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum ExternalIdSystem { - HTTPS_CANCER_SANGER_Ac_UK_COSMIC, HTTPS_Www_ENSEMBL_ORG, HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ, HTTPS_Www_NCBI_NLM_NIH_GOV_SNP; + CANCER_SANGER_AC_UK_COSMIC, ENSEMBL_ORG, NCBI_NLM_NIH_GOV_ENTREZ, NCBI_NLM_NIH_GOV_SNP; @JsonValue public String toValue() { switch (this) { - case HTTPS_CANCER_SANGER_Ac_UK_COSMIC: return "https://cancer.sanger.ac.uk/cosmic"; - case HTTPS_Www_ENSEMBL_ORG: return "https://www.ensembl.org"; - case HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ: return "https://www.ncbi.nlm.nih.gov/entrez"; - case HTTPS_Www_NCBI_NLM_NIH_GOV_SNP: return "https://www.ncbi.nlm.nih.gov/snp"; + case CANCER_SANGER_AC_UK_COSMIC: return "https://cancer.sanger.ac.uk/cosmic"; + case ENSEMBL_ORG: return "https://www.ensembl.org"; + case NCBI_NLM_NIH_GOV_ENTREZ: return "https://www.ncbi.nlm.nih.gov/entrez"; + case NCBI_NLM_NIH_GOV_SNP: return "https://www.ncbi.nlm.nih.gov/snp"; } return null; } @JsonCreator public static ExternalIdSystem forValue(String value) throws IOException { - if (value.equals("https://cancer.sanger.ac.uk/cosmic")) return HTTPS_CANCER_SANGER_Ac_UK_COSMIC; - if (value.equals("https://www.ensembl.org")) return HTTPS_Www_ENSEMBL_ORG; - if (value.equals("https://www.ncbi.nlm.nih.gov/entrez")) return HTTPS_Www_NCBI_NLM_NIH_GOV_ENTREZ; - if (value.equals("https://www.ncbi.nlm.nih.gov/snp")) return HTTPS_Www_NCBI_NLM_NIH_GOV_SNP; + if (value.equals("https://cancer.sanger.ac.uk/cosmic")) return CANCER_SANGER_AC_UK_COSMIC; + if (value.equals("https://www.ensembl.org")) return ENSEMBL_ORG; + if (value.equals("https://www.ncbi.nlm.nih.gov/entrez")) return NCBI_NLM_NIH_GOV_ENTREZ; + if (value.equals("https://www.ncbi.nlm.nih.gov/snp")) return NCBI_NLM_NIH_GOV_SNP; throw new IOException("Cannot deserialize ExternalIdSystem"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java index 12fcfd8..6e9c011 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUp.java @@ -5,7 +5,9 @@ import java.util.Date; public class FollowUp { private Date date; - private CodingFollowUpPatientStatus patientStatus; + private Date lastContactDate; + private Reference patient; + private FollowUpPatientStatusCoding patientStatus; @JsonProperty("date") @JsonFormat(pattern = "yyyy-MM-dd") @@ -14,8 +16,18 @@ public class FollowUp { @JsonFormat(pattern = "yyyy-MM-dd") public void setDate(Date value) { this.date = value; } + @JsonProperty("lastContactDate") + public Date getLastContactDate() { return lastContactDate; } + @JsonProperty("lastContactDate") + public void setLastContactDate(Date value) { this.lastContactDate = value; } + + @JsonProperty("patient") + public Reference getPatient() { return patient; } + @JsonProperty("patient") + public void setPatient(Reference value) { this.patient = value; } + @JsonProperty("patientStatus") - public CodingFollowUpPatientStatus getPatientStatus() { return patientStatus; } + public FollowUpPatientStatusCoding getPatientStatus() { return patientStatus; } @JsonProperty("patientStatus") - public void setPatientStatus(CodingFollowUpPatientStatus value) { this.patientStatus = value; } + public void setPatientStatus(FollowUpPatientStatusCoding value) { this.patientStatus = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCoding.java new file mode 100644 index 0000000..bf63271 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class FollowUpPatientStatusCoding { + private FollowUpPatientStatusCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public FollowUpPatientStatusCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(FollowUpPatientStatusCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCodingCode.java similarity index 61% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCodingCode.java index b9b4e9e..d4fd47a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PatientStatusCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/FollowUpPatientStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum PatientStatusCode { +public enum FollowUpPatientStatusCodingCode { LOST_TO_FU; @JsonValue @@ -15,8 +15,8 @@ public enum PatientStatusCode { } @JsonCreator - public static PatientStatusCode forValue(String value) throws IOException { + public static FollowUpPatientStatusCodingCode forValue(String value) throws IOException { if (value.equals("lost-to-fu")) return LOST_TO_FU; - throw new IOException("Cannot deserialize PatientStatusCode"); + throw new IOException("Cannot deserialize FollowUpPatientStatusCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCoding.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCoding.java index 478985f..924e282 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingRecist { - private CodingRecistCode code; +public class GenderCoding { + private GenderCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingRecistCode getCode() { return code; } + public GenderCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingRecistCode value) { this.code = value; } + public void setCode(GenderCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCodingCode.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCodingCode.java index 137883f..dcc094e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GenderCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum GenderCode { +public enum GenderCodingCode { FEMALE, MALE, OTHER, UNKNOWN; @JsonValue @@ -18,11 +18,11 @@ public enum GenderCode { } @JsonCreator - public static GenderCode forValue(String value) throws IOException { + public static GenderCodingCode forValue(String value) throws IOException { if (value.equals("female")) return FEMALE; if (value.equals("male")) return MALE; if (value.equals("other")) return OTHER; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize GenderCode"); + throw new IOException("Cannot deserialize GenderCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java index 77b41df..57b3f65 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 Reference patient; - private CodingGeneticCounselingRecommendationReason reason; + private GeneticCounselingRecommendationReasonCoding reason; @JsonProperty("id") public String getId() { return id; } @@ -27,7 +27,7 @@ public class GeneticCounselingRecommendation { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("reason") - public CodingGeneticCounselingRecommendationReason getReason() { return reason; } + public GeneticCounselingRecommendationReasonCoding getReason() { return reason; } @JsonProperty("reason") - public void setReason(CodingGeneticCounselingRecommendationReason value) { this.reason = value; } + public void setReason(GeneticCounselingRecommendationReasonCoding value) { this.reason = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCoding.java new file mode 100644 index 0000000..47cdd8d --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class GeneticCounselingRecommendationReasonCoding { + private GeneticCounselingRecommendationReasonCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public GeneticCounselingRecommendationReasonCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(GeneticCounselingRecommendationReasonCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCodingCode.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCodingCode.java index ff1ef7f..290130b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ReasonCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendationReasonCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum ReasonCode { +public enum GeneticCounselingRecommendationReasonCodingCode { FAMILY_ANAMNESIS, OTHER, SECONDARY_TUMOR, SELF_ANAMNESIS, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum ReasonCode { } @JsonCreator - public static ReasonCode forValue(String value) throws IOException { + public static GeneticCounselingRecommendationReasonCodingCode forValue(String value) throws IOException { if (value.equals("family-anamnesis")) return FAMILY_ANAMNESIS; if (value.equals("other")) return OTHER; if (value.equals("secondary-tumor")) return SECONDARY_TUMOR; if (value.equals("self-anamnesis")) return SELF_ANAMNESIS; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize ReasonCode"); + throw new IOException("Cannot deserialize GeneticCounselingRecommendationReasonCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java index 5e951aa..912a090 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsurance.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; public class HealthInsurance { private Reference reference; - private CodingHealthInsurance type; + private HealthInsuranceCoding type; @JsonProperty("reference") public Reference getReference() { return reference; } @@ -12,7 +12,7 @@ public class HealthInsurance { public void setReference(Reference value) { this.reference = value; } @JsonProperty("type") - public CodingHealthInsurance getType() { return type; } + public HealthInsuranceCoding getType() { return type; } @JsonProperty("type") - public void setType(CodingHealthInsurance value) { this.type = value; } + public void setType(HealthInsuranceCoding value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCoding.java index 0de046a..0b8c011 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsurance.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingHealthInsurance { - private CodingHealthInsuranceCode code; +public class HealthInsuranceCoding { + private HealthInsuranceCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingHealthInsuranceCode getCode() { return code; } + public HealthInsuranceCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingHealthInsuranceCode value) { this.code = value; } + public void setCode(HealthInsuranceCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCodingCode.java similarity index 75% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCodingCode.java index 37ab3da..0c93b4a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingHealthInsuranceCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HealthInsuranceCodingCode.java @@ -3,8 +3,8 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingHealthInsuranceCode { - BEI, BG, GKV, GPV, PKV, PPV, SEL, SOZ, UNK; +public enum HealthInsuranceCodingCode { + BEI, BG, GKV, GPV, PKV, PPV, SEL, SKT, SOZ, UNK; @JsonValue public String toValue() { @@ -16,6 +16,7 @@ public enum CodingHealthInsuranceCode { case PKV: return "PKV"; case PPV: return "PPV"; case SEL: return "SEL"; + case SKT: return "SKT"; case SOZ: return "SOZ"; case UNK: return "UNK"; } @@ -23,7 +24,7 @@ public enum CodingHealthInsuranceCode { } @JsonCreator - public static CodingHealthInsuranceCode forValue(String value) throws IOException { + public static HealthInsuranceCodingCode forValue(String value) throws IOException { if (value.equals("BEI")) return BEI; if (value.equals("BG")) return BG; if (value.equals("GKV")) return GKV; @@ -31,8 +32,9 @@ public enum CodingHealthInsuranceCode { if (value.equals("PKV")) return PKV; if (value.equals("PPV")) return PPV; if (value.equals("SEL")) return SEL; + if (value.equals("SKT")) return SKT; if (value.equals("SOZ")) return SOZ; if (value.equals("UNK")) return UNK; - throw new IOException("Cannot deserialize CodingHealthInsuranceCode"); + throw new IOException("Cannot deserialize HealthInsuranceCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java index e1f7e0c..71ffc74 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/History.java @@ -5,7 +5,7 @@ import java.util.Date; public class History { private Date date; - private CodingMtbDiagnosis value; + private MtbDiagnosisCoding value; @JsonProperty("date") @JsonFormat(pattern = "yyyy-MM-dd") @@ -15,7 +15,7 @@ public class History { public void setDate(Date value) { this.date = value; } @JsonProperty("value") - public CodingMtbDiagnosis getValue() { return value; } + public MtbDiagnosisCoding getValue() { return value; } @JsonProperty("value") - public void setValue(CodingMtbDiagnosis value) { this.value = value; } + public void setValue(MtbDiagnosisCoding value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScore.java similarity index 85% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScore.java index 59946ed..d552859 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/HRDScore.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScore.java @@ -2,10 +2,10 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class HRDScore { +public class HrdScore { private Components components; private String id; - private CodingHrdScoreInterpretation interpretation; + private HrdScoreInterpretationCoding interpretation; private Reference patient; private Reference specimen; private double value; @@ -21,9 +21,9 @@ public class HRDScore { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public CodingHrdScoreInterpretation getInterpretation() { return interpretation; } + public HrdScoreInterpretationCoding getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(CodingHrdScoreInterpretation value) { this.interpretation = value; } + public void setInterpretation(HrdScoreInterpretationCoding value) { this.interpretation = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScoreInterpretationCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScoreInterpretationCoding.java new file mode 100644 index 0000000..d69bf48 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/HrdScoreInterpretationCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class HrdScoreInterpretationCoding { + private InterpretationCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public InterpretationCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(InterpretationCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java deleted file mode 100644 index 297c4ba..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java +++ /dev/null @@ -1,28 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum ICScoreCode { - THE_0, THE_1, THE_2, THE_3; - - @JsonValue - public String toValue() { - switch (this) { - case THE_0: return "0"; - case THE_1: return "1"; - case THE_2: return "2"; - case THE_3: return "3"; - } - return null; - } - - @JsonCreator - public static ICScoreCode forValue(String value) throws IOException { - if (value.equals("0")) return THE_0; - if (value.equals("1")) return THE_1; - if (value.equals("2")) return THE_2; - if (value.equals("3")) return THE_3; - throw new IOException("Cannot deserialize ICScoreCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReport.java similarity index 98% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReport.java index 0d315f8..c24ebfa 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/IhcReport.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class IHCReport { +public class IhcReport { private List blockIds; private String id; private Date issuedOn; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCodingCode.java similarity index 81% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCodingCode.java index 47ca825..1704310 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/InterpretationCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum InterpretationCode { +public enum InterpretationCodingCode { HIGH, INTERMEDIATE, LOW; @JsonValue @@ -17,10 +17,10 @@ public enum InterpretationCode { } @JsonCreator - public static InterpretationCode forValue(String value) throws IOException { + public static InterpretationCodingCode forValue(String value) throws IOException { if (value.equals("high")) return HIGH; if (value.equals("intermediate")) return INTERMEDIATE; if (value.equals("low")) return LOW; - throw new IOException("Cannot deserialize InterpretationCode"); + throw new IOException("Cannot deserialize InterpretationCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java index d70b239..c1d2cff 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java @@ -4,19 +4,19 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class LevelOfEvidence { - private List addendums; - private CodingLevelOfEvidenceGrading grading; + private List addendums; + private LevelOfEvidenceGradingCoding grading; private List publications; @JsonProperty("addendums") - public List getAddendums() { return addendums; } + public List getAddendums() { return addendums; } @JsonProperty("addendums") - public void setAddendums(List value) { this.addendums = value; } + public void setAddendums(List value) { this.addendums = value; } @JsonProperty("grading") - public CodingLevelOfEvidenceGrading getGrading() { return grading; } + public LevelOfEvidenceGradingCoding getGrading() { return grading; } @JsonProperty("grading") - public void setGrading(CodingLevelOfEvidenceGrading value) { this.grading = value; } + public void setGrading(LevelOfEvidenceGradingCoding value) { this.grading = value; } @JsonProperty("publications") public List getPublications() { return publications; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCoding.java index 33a1e70..09f9821 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingProteinExpressionResult { - private CodingProteinExpressionResultCode code; +public class LevelOfEvidenceAddendumCoding { + private LevelOfEvidenceAddendumCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingProteinExpressionResultCode getCode() { return code; } + public LevelOfEvidenceAddendumCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingProteinExpressionResultCode value) { this.code = value; } + public void setCode(LevelOfEvidenceAddendumCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCodingCode.java new file mode 100644 index 0000000..3c74d8f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceAddendumCodingCode.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum LevelOfEvidenceAddendumCodingCode { + IS, IV, R, Z; + + @JsonValue + public String toValue() { + switch (this) { + case IS: return "is"; + case IV: return "iv"; + case R: return "R"; + case Z: return "Z"; + } + return null; + } + + @JsonCreator + public static LevelOfEvidenceAddendumCodingCode forValue(String value) throws IOException { + if (value.equals("is")) return IS; + if (value.equals("iv")) return IV; + if (value.equals("R")) return R; + if (value.equals("Z")) return Z; + throw new IOException("Cannot deserialize LevelOfEvidenceAddendumCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java deleted file mode 100644 index 4bb2456..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceCode.java +++ /dev/null @@ -1,38 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum LevelOfEvidenceCode { - M1_A, M1_B, M1_C, M2_A, M2_B, M2_C, M3, M4, UNDEFINED; - - @JsonValue - public String toValue() { - switch (this) { - case M1_A: return "m1A"; - case M1_B: return "m1B"; - case M1_C: return "m1C"; - case M2_A: return "m2A"; - case M2_B: return "m2B"; - case M2_C: return "m2C"; - case M3: return "m3"; - case M4: return "m4"; - case UNDEFINED: return "undefined"; - } - return null; - } - - @JsonCreator - public static LevelOfEvidenceCode forValue(String value) throws IOException { - if (value.equals("m1A")) return M1_A; - if (value.equals("m1B")) return M1_B; - if (value.equals("m1C")) return M1_C; - if (value.equals("m2A")) return M2_A; - if (value.equals("m2B")) return M2_B; - if (value.equals("m2C")) return M2_C; - if (value.equals("m3")) return M3; - if (value.equals("m4")) return M4; - if (value.equals("undefined")) return UNDEFINED; - throw new IOException("Cannot deserialize LevelOfEvidenceCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCoding.java index fae7df1..f9f0433 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbTherapyStatusReason { - private CodingMtbTherapyStatusReasonCode code; +public class LevelOfEvidenceGradingCoding { + private LevelOfEvidenceGradingCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMtbTherapyStatusReasonCode getCode() { return code; } + public LevelOfEvidenceGradingCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbTherapyStatusReasonCode value) { this.code = value; } + public void setCode(LevelOfEvidenceGradingCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCodingCode.java new file mode 100644 index 0000000..d836518 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidenceGradingCodingCode.java @@ -0,0 +1,38 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum LevelOfEvidenceGradingCodingCode { + M1A, M1B, M1C, M2A, M2B, M2C, M3, M4, UNDEFINED; + + @JsonValue + public String toValue() { + switch (this) { + case M1A: return "m1A"; + case M1B: return "m1B"; + case M1C: return "m1C"; + case M2A: return "m2A"; + case M2B: return "m2B"; + case M2C: return "m2C"; + case M3: return "m3"; + case M4: return "m4"; + case UNDEFINED: return "undefined"; + } + return null; + } + + @JsonCreator + public static LevelOfEvidenceGradingCodingCode forValue(String value) throws IOException { + if (value.equals("m1A")) return M1A; + if (value.equals("m1B")) return M1B; + if (value.equals("m1C")) return M1C; + if (value.equals("m2A")) return M2A; + if (value.equals("m2B")) return M2B; + if (value.equals("m2C")) return M2C; + if (value.equals("m3")) return M3; + if (value.equals("m4")) return M4; + if (value.equals("undefined")) return UNDEFINED; + throw new IOException("Cannot deserialize LevelOfEvidenceGradingCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java index 1fbb70c..c7c8b69 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmr.java @@ -3,18 +3,18 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class MSIMmr { - private CodingProteinExpressionIcScore icScore; + private ProteinExpressionIcScoreCoding icScore; private String id; private Reference patient; private Coding protein; - private CodingProteinExpressionTcScore tcScore; + private ProteinExpressionTcScoreCoding tcScore; private Long tpsScore; - private CodingProteinExpressionResult value; + private ProteinExpressionResultCoding value; @JsonProperty("icScore") - public CodingProteinExpressionIcScore getIcScore() { return icScore; } + public ProteinExpressionIcScoreCoding getIcScore() { return icScore; } @JsonProperty("icScore") - public void setIcScore(CodingProteinExpressionIcScore value) { this.icScore = value; } + public void setIcScore(ProteinExpressionIcScoreCoding value) { this.icScore = value; } @JsonProperty("id") public String getId() { return id; } @@ -32,9 +32,9 @@ public class MSIMmr { public void setProtein(Coding value) { this.protein = value; } @JsonProperty("tcScore") - public CodingProteinExpressionTcScore getTcScore() { return tcScore; } + public ProteinExpressionTcScoreCoding getTcScore() { return tcScore; } @JsonProperty("tcScore") - public void setTcScore(CodingProteinExpressionTcScore value) { this.tcScore = value; } + public void setTcScore(ProteinExpressionTcScoreCoding value) { this.tcScore = value; } @JsonProperty("tpsScore") public Long getTpsScore() { return tpsScore; } @@ -42,7 +42,7 @@ public class MSIMmr { public void setTpsScore(Long value) { this.tpsScore = value; } @JsonProperty("value") - public CodingProteinExpressionResult getValue() { return value; } + public ProteinExpressionResultCoding getValue() { return value; } @JsonProperty("value") - public void setValue(CodingProteinExpressionResult value) { this.value = value; } + public void setValue(ProteinExpressionResultCoding value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsent.java new file mode 100644 index 0000000..db8a0f9 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsent.java @@ -0,0 +1,26 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; +import java.util.List; + +public class ModelProjectConsent { + private Date date; + private List provisions; + private String version; + + @JsonProperty("date") + public Date getDate() { return date; } + @JsonProperty("date") + public void setDate(Date value) { this.date = value; } + + @JsonProperty("provisions") + public List getProvisions() { return provisions; } + @JsonProperty("provisions") + public void setProvisions(List value) { this.provisions = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsentPurpose.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsentPurpose.java new file mode 100644 index 0000000..05626da --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ModelProjectConsentPurpose.java @@ -0,0 +1,26 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ModelProjectConsentPurpose { + CASE_IDENTIFICATION, REIDENTIFICATION, SEQUENCING; + + @JsonValue + public String toValue() { + switch (this) { + case CASE_IDENTIFICATION: return "case-identification"; + case REIDENTIFICATION: return "reidentification"; + case SEQUENCING: return "sequencing"; + } + return null; + } + + @JsonCreator + public static ModelProjectConsentPurpose forValue(String value) throws IOException { + if (value.equals("case-identification")) return CASE_IDENTIFICATION; + if (value.equals("reidentification")) return REIDENTIFICATION; + if (value.equals("sequencing")) return SEQUENCING; + throw new IOException("Cannot deserialize ModelProjectConsentPurpose"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCoding.java index df81875..429f2ed 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMolecularDiagnosticReport { - private CodingMolecularDiagnosticReportCode code; +public class MolecularDiagnosticReportCoding { + private MolecularDiagnosticReportCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMolecularDiagnosticReportCode getCode() { return code; } + public MolecularDiagnosticReportCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMolecularDiagnosticReportCode value) { this.code = value; } + public void setCode(MolecularDiagnosticReportCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCodingCode.java similarity index 88% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCodingCode.java index f161aa6..9f7380e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMolecularDiagnosticReportCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularDiagnosticReportCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMolecularDiagnosticReportCode { +public enum MolecularDiagnosticReportCodingCode { ARRAY, EXOME, FISH, FUSION_PANEL, GENE_PANEL, GENOME_LONG_READ, GENOME_SHORT_READ, KARYOTYPING, OTHER, PANEL, PCR, SINGLE; @JsonValue @@ -26,7 +26,7 @@ public enum CodingMolecularDiagnosticReportCode { } @JsonCreator - public static CodingMolecularDiagnosticReportCode forValue(String value) throws IOException { + public static MolecularDiagnosticReportCodingCode forValue(String value) throws IOException { if (value.equals("array")) return ARRAY; if (value.equals("exome")) return EXOME; if (value.equals("FISH")) return FISH; @@ -39,6 +39,6 @@ public enum CodingMolecularDiagnosticReportCode { if (value.equals("panel")) return PANEL; if (value.equals("PCR")) return PCR; if (value.equals("single")) return SINGLE; - throw new IOException("Cannot deserialize CodingMolecularDiagnosticReportCode"); + throw new IOException("Cannot deserialize MolecularDiagnosticReportCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java index ab8073e..d2081d7 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java @@ -4,17 +4,18 @@ 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 episodesOfCare; + private List diagnoses; + private List episodesOfCare; private List followUps; private List guidelineProcedures; - private List guidelineTherapies; + private List guidelineTherapies; private List histologyReports; - private List ihcReports; - private List ngsReports; + private List ihcReports; + private MvhMetadata metadata; + private List ngsReports; private Patient patient; private List performanceStatus; private List priorDiagnosticReports; @@ -23,9 +24,9 @@ public class Mtb { private List systemicTherapies; @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; } @@ -38,14 +39,14 @@ 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; } + public void setDiagnoses(List value) { this.diagnoses = value; } @JsonProperty("episodesOfCare") - public List getEpisodesOfCare() { return episodesOfCare; } + public List getEpisodesOfCare() { return episodesOfCare; } @JsonProperty("episodesOfCare") - public void setEpisodesOfCare(List value) { this.episodesOfCare = value; } + public void setEpisodesOfCare(List value) { this.episodesOfCare = value; } @JsonProperty("followUps") public List getFollowUps() { return followUps; } @@ -58,9 +59,9 @@ public class Mtb { public void setGuidelineProcedures(List value) { this.guidelineProcedures = value; } @JsonProperty("guidelineTherapies") - public List getGuidelineTherapies() { return guidelineTherapies; } + public List getGuidelineTherapies() { return guidelineTherapies; } @JsonProperty("guidelineTherapies") - public void setGuidelineTherapies(List value) { this.guidelineTherapies = value; } + public void setGuidelineTherapies(List value) { this.guidelineTherapies = value; } @JsonProperty("histologyReports") public List getHistologyReports() { return histologyReports; } @@ -68,14 +69,19 @@ public class Mtb { public void setHistologyReports(List value) { this.histologyReports = value; } @JsonProperty("ihcReports") - public List getIhcReports() { return ihcReports; } + public List getIhcReports() { return ihcReports; } @JsonProperty("ihcReports") - public void setIhcReports(List value) { this.ihcReports = value; } + public void setIhcReports(List value) { this.ihcReports = value; } + + @JsonProperty("metadata") + public MvhMetadata getMetadata() { return metadata; } + @JsonProperty("metadata") + public void setMetadata(MvhMetadata value) { this.metadata = value; } @JsonProperty("ngsReports") - public List getNgsReports() { return ngsReports; } + public List getNgsReports() { return ngsReports; } @JsonProperty("ngsReports") - public void setNgsReports(List value) { this.ngsReports = value; } + public void setNgsReports(List value) { this.ngsReports = value; } @JsonProperty("patient") public Patient getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java similarity index 71% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java index ebaf766..15d1286 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBCarePlan.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java @@ -4,19 +4,20 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MTBCarePlan { +public class MtbCarePlan { private GeneticCounselingRecommendation geneticCounselingRecommendation; private List histologyReevaluationRequests; private String id; private Date issuedOn; - private List medicationRecommendations; + private List medicationRecommendations; + private CarePlanNoSequencingPerformedReasonCoding noSequencingPerformedReason; private List notes; private Reference patient; private List procedureRecommendations; private Reference reason; private List rebiopsyRequests; - private CodingMtbCarePlanStatusReason statusReason; - private List studyEnrollmentRecommendations; + private MtbCarePlanRecommendationsMissingReasonCoding recommendationsMissingReason; + private List studyEnrollmentRecommendations; @JsonProperty("geneticCounselingRecommendation") public GeneticCounselingRecommendation getGeneticCounselingRecommendation() { return geneticCounselingRecommendation; } @@ -41,9 +42,14 @@ public class MTBCarePlan { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("medicationRecommendations") - public List getMedicationRecommendations() { return medicationRecommendations; } + public List getMedicationRecommendations() { return medicationRecommendations; } @JsonProperty("medicationRecommendations") - public void setMedicationRecommendations(List value) { this.medicationRecommendations = value; } + public void setMedicationRecommendations(List value) { this.medicationRecommendations = value; } + + @JsonProperty("noSequencingPerformedReason") + public CarePlanNoSequencingPerformedReasonCoding getNoSequencingPerformedReason() { return noSequencingPerformedReason; } + @JsonProperty("noSequencingPerformedReason") + public void setNoSequencingPerformedReason(CarePlanNoSequencingPerformedReasonCoding value) { this.noSequencingPerformedReason = value; } @JsonProperty("notes") public List getNotes() { return notes; } @@ -70,13 +76,13 @@ public class MTBCarePlan { @JsonProperty("rebiopsyRequests") public void setRebiopsyRequests(List value) { this.rebiopsyRequests = value; } - @JsonProperty("statusReason") - public CodingMtbCarePlanStatusReason getStatusReason() { return statusReason; } - @JsonProperty("statusReason") - public void setStatusReason(CodingMtbCarePlanStatusReason value) { this.statusReason = value; } + @JsonProperty("recommendationsMissingReason") + public MtbCarePlanRecommendationsMissingReasonCoding getRecommendationsMissingReason() { return recommendationsMissingReason; } + @JsonProperty("recommendationsMissingReason") + public void setRecommendationsMissingReason(MtbCarePlanRecommendationsMissingReasonCoding value) { this.recommendationsMissingReason = value; } @JsonProperty("studyEnrollmentRecommendations") - public List getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; } + public List getStudyEnrollmentRecommendations() { return studyEnrollmentRecommendations; } @JsonProperty("studyEnrollmentRecommendations") - public void setStudyEnrollmentRecommendations(List value) { this.studyEnrollmentRecommendations = value; } + public void setStudyEnrollmentRecommendations(List value) { this.studyEnrollmentRecommendations = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCoding.java new file mode 100644 index 0000000..4c1ee61 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class MtbCarePlanRecommendationsMissingReasonCoding { + private MtbCarePlanRecommendationsMissingReasonCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public MtbCarePlanRecommendationsMissingReasonCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(MtbCarePlanRecommendationsMissingReasonCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCodingCode.java new file mode 100644 index 0000000..eb48fbc --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlanRecommendationsMissingReasonCodingCode.java @@ -0,0 +1,22 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum MtbCarePlanRecommendationsMissingReasonCodingCode { + NO_TARGET; + + @JsonValue + public String toValue() { + switch (this) { + case NO_TARGET: return "no-target"; + } + return null; + } + + @JsonCreator + public static MtbCarePlanRecommendationsMissingReasonCodingCode forValue(String value) throws IOException { + if (value.equals("no-target")) return NO_TARGET; + throw new IOException("Cannot deserialize MtbCarePlanRecommendationsMissingReasonCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java similarity index 87% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java index 0c20afd..bdf6e3b 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBDiagnosis.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java @@ -4,11 +4,11 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MTBDiagnosis { +public class MtbDiagnosis { private Coding code; private List germlineCodes; private Grading grading; - private CodingMtbDiagnosisGuidelineTreatmentStatus guidelineTreatmentStatus; + private MtbDiagnosisGuidelineTreatmentStatusCoding guidelineTreatmentStatus; private List histology; private String id; private List notes; @@ -34,9 +34,9 @@ public class MTBDiagnosis { public void setGrading(Grading value) { this.grading = value; } @JsonProperty("guidelineTreatmentStatus") - public CodingMtbDiagnosisGuidelineTreatmentStatus getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; } + public MtbDiagnosisGuidelineTreatmentStatusCoding getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; } @JsonProperty("guidelineTreatmentStatus") - public void setGuidelineTreatmentStatus(CodingMtbDiagnosisGuidelineTreatmentStatus value) { this.guidelineTreatmentStatus = value; } + public void setGuidelineTreatmentStatus(MtbDiagnosisGuidelineTreatmentStatusCoding value) { this.guidelineTreatmentStatus = value; } @JsonProperty("histology") public List getHistology() { return histology; } @@ -59,8 +59,10 @@ public class MTBDiagnosis { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public Date getRecordedOn() { return recordedOn; } @JsonProperty("recordedOn") + @JsonFormat(pattern = "yyyy-MM-dd") public void setRecordedOn(Date value) { this.recordedOn = value; } @JsonProperty("staging") diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisCoding.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisCoding.java index 7f562b1..c2c7fa1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingGender { - private GenderCode code; +public class MtbDiagnosisCoding { + private ValueCode code; private String display; private String system; private String version; @JsonProperty("code") - public GenderCode getCode() { return code; } + public ValueCode getCode() { return code; } @JsonProperty("code") - public void setCode(GenderCode value) { this.code = value; } + public void setCode(ValueCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCoding.java similarity index 70% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCoding.java index 664811b..42bf335 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyIntent.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbTherapyIntent { - private IntentCode code; +public class MtbDiagnosisGuidelineTreatmentStatusCoding { + private MtbDiagnosisGuidelineTreatmentStatusCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public IntentCode getCode() { return code; } + public MtbDiagnosisGuidelineTreatmentStatusCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(IntentCode value) { this.code = value; } + public void setCode(MtbDiagnosisGuidelineTreatmentStatusCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCodingCode.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCodingCode.java index 80d237c..7b376ac 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatusCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisGuidelineTreatmentStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum GuidelineTreatmentStatusCode { +public enum MtbDiagnosisGuidelineTreatmentStatusCodingCode { EXHAUSTED, IMPOSSIBLE, NON_EXHAUSTED, NO_GUIDELINES_AVAILABLE, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum GuidelineTreatmentStatusCode { } @JsonCreator - public static GuidelineTreatmentStatusCode forValue(String value) throws IOException { + public static MtbDiagnosisGuidelineTreatmentStatusCodingCode forValue(String value) throws IOException { if (value.equals("exhausted")) return EXHAUSTED; if (value.equals("impossible")) return IMPOSSIBLE; if (value.equals("non-exhausted")) return NON_EXHAUSTED; if (value.equals("no-guidelines-available")) return NO_GUIDELINES_AVAILABLE; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize GuidelineTreatmentStatusCode"); + throw new IOException("Cannot deserialize MtbDiagnosisGuidelineTreatmentStatusCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisodeOfCare.java similarity index 96% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisodeOfCare.java index f167a36..ce70f33 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBEpisodeOfCare.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisodeOfCare.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.List; -public class MTBEpisodeOfCare { +public class MtbEpisodeOfCare { private List diagnoses; private String id; private Reference patient; 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 79e0f3a..1f5de01 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java @@ -4,22 +4,22 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MTBMedicationRecommendation { - private CodingMtbMedicationRecommendationCategory category; +public class MtbMedicationRecommendation { + private MtbMedicationRecommendationCategoryCoding category; private String id; private Date issuedOn; private LevelOfEvidence levelOfEvidence; - private List medication; + private List medication; private Reference patient; - private CodingRecommendationPriority priority; + private RecommendationPriorityCoding priority; private Reference reason; private List supportingVariants; - private CodingMtbMedicationRecommendationUseType useType; + private MtbMedicationRecommendationUseTypeCoding useType; @JsonProperty("category") - public CodingMtbMedicationRecommendationCategory getCategory() { return category; } + public MtbMedicationRecommendationCategoryCoding getCategory() { return category; } @JsonProperty("category") - public void setCategory(CodingMtbMedicationRecommendationCategory value) { this.category = value; } + public void setCategory(MtbMedicationRecommendationCategoryCoding value) { this.category = value; } @JsonProperty("id") public String getId() { return id; } @@ -39,9 +39,9 @@ public class MTBMedicationRecommendation { public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; } @JsonProperty("medication") - public List getMedication() { return medication; } + public List getMedication() { return medication; } @JsonProperty("medication") - public void setMedication(List value) { this.medication = value; } + public void setMedication(List value) { this.medication = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -49,9 +49,9 @@ public class MTBMedicationRecommendation { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("priority") - public CodingRecommendationPriority getPriority() { return priority; } + public RecommendationPriorityCoding getPriority() { return priority; } @JsonProperty("priority") - public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + public void setPriority(RecommendationPriorityCoding value) { this.priority = value; } @JsonProperty("reason") public Reference getReason() { return reason; } @@ -64,7 +64,7 @@ public class MTBMedicationRecommendation { public void setSupportingVariants(List value) { this.supportingVariants = value; } @JsonProperty("useType") - public CodingMtbMedicationRecommendationUseType getUseType() { return useType; } + public MtbMedicationRecommendationUseTypeCoding getUseType() { return useType; } @JsonProperty("useType") - public void setUseType(CodingMtbMedicationRecommendationUseType value) { this.useType = value; } + public void setUseType(MtbMedicationRecommendationUseTypeCoding value) { this.useType = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCoding.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCoding.java index 3e2dcae..0cc5589 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategory.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbMedicationRecommendationCategory { - private CodingMtbMedicationRecommendationCategoryCode code; +public class MtbMedicationRecommendationCategoryCoding { + private MtbMedicationRecommendationCategoryCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMtbMedicationRecommendationCategoryCode getCode() { return code; } + public MtbMedicationRecommendationCategoryCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbMedicationRecommendationCategoryCode value) { this.code = value; } + public void setCode(MtbMedicationRecommendationCategoryCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCodingCode.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCodingCode.java index 0662734..6ca31ca 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbMedicationRecommendationCategoryCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationCategoryCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbMedicationRecommendationCategoryCode { +public enum MtbMedicationRecommendationCategoryCodingCode { CH, HO, IM, SO, SZ, ZS; @JsonValue @@ -20,13 +20,13 @@ public enum CodingMtbMedicationRecommendationCategoryCode { } @JsonCreator - public static CodingMtbMedicationRecommendationCategoryCode forValue(String value) throws IOException { + public static MtbMedicationRecommendationCategoryCodingCode forValue(String value) throws IOException { if (value.equals("CH")) return CH; if (value.equals("HO")) return HO; if (value.equals("IM")) return IM; if (value.equals("SO")) return SO; if (value.equals("SZ")) return SZ; if (value.equals("ZS")) return ZS; - throw new IOException("Cannot deserialize CodingMtbMedicationRecommendationCategoryCode"); + throw new IOException("Cannot deserialize MtbMedicationRecommendationCategoryCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCoding.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCoding.java index 3d37fe2..c0fd439 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategory.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbProcedureRecommendationCategory { - private CodingMtbProcedureRecommendationCategoryCode code; +public class MtbMedicationRecommendationUseTypeCoding { + private MtbMedicationRecommendationUseTypeCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMtbProcedureRecommendationCategoryCode getCode() { return code; } + public MtbMedicationRecommendationUseTypeCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbProcedureRecommendationCategoryCode value) { this.code = value; } + public void setCode(MtbMedicationRecommendationUseTypeCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCodingCode.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCodingCode.java index bd8453b..08e2c5c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/UseTypeCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendationUseTypeCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum UseTypeCode { +public enum MtbMedicationRecommendationUseTypeCodingCode { COMPASSIONATE, IN_LABEL, OFF_LABEL, SEC_PREVENTIVE, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum UseTypeCode { } @JsonCreator - public static UseTypeCode forValue(String value) throws IOException { + public static MtbMedicationRecommendationUseTypeCodingCode forValue(String value) throws IOException { if (value.equals("compassionate")) return COMPASSIONATE; if (value.equals("in-label")) return IN_LABEL; if (value.equals("off-label")) return OFF_LABEL; if (value.equals("sec-preventive")) return SEC_PREVENTIVE; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize UseTypeCode"); + throw new IOException("Cannot deserialize MtbMedicationRecommendationUseTypeCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCoding.java new file mode 100644 index 0000000..6257192 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class MtbProcedureRecommendationCategoryCoding { + private MtbProcedureRecommendationCategoryCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public MtbProcedureRecommendationCategoryCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(MtbProcedureRecommendationCategoryCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCodingCode.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCodingCode.java index 293cb02..5b2b21e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbProcedureRecommendationCategoryCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbProcedureRecommendationCategoryCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbProcedureRecommendationCategoryCode { +public enum MtbProcedureRecommendationCategoryCodingCode { AS, OP, SO, ST, WS, WW; @JsonValue @@ -20,13 +20,13 @@ public enum CodingMtbProcedureRecommendationCategoryCode { } @JsonCreator - public static CodingMtbProcedureRecommendationCategoryCode forValue(String value) throws IOException { + public static MtbProcedureRecommendationCategoryCodingCode forValue(String value) throws IOException { if (value.equals("AS")) return AS; if (value.equals("OP")) return OP; if (value.equals("SO")) return SO; if (value.equals("ST")) return ST; if (value.equals("WS")) return WS; if (value.equals("WW")) return WW; - throw new IOException("Cannot deserialize CodingMtbProcedureRecommendationCategoryCode"); + throw new IOException("Cannot deserialize MtbProcedureRecommendationCategoryCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbStudyEnrollmentRecommendation.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbStudyEnrollmentRecommendation.java index 989825e..bc780a1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBStudyEnrollmentRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbStudyEnrollmentRecommendation.java @@ -4,13 +4,13 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MTBStudyEnrollmentRecommendation { +public class MtbStudyEnrollmentRecommendation { private String id; private Date issuedOn; - private CodingLevelOfEvidenceGrading levelOfEvidence; - private List medication; + private LevelOfEvidence levelOfEvidence; + private List medication; private Reference patient; - private CodingRecommendationPriority priority; + private RecommendationPriorityCoding priority; private Reference reason; private List study; private List supportingVariants; @@ -28,14 +28,14 @@ public class MTBStudyEnrollmentRecommendation { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("levelOfEvidence") - public CodingLevelOfEvidenceGrading getLevelOfEvidence() { return levelOfEvidence; } + public LevelOfEvidence getLevelOfEvidence() { return levelOfEvidence; } @JsonProperty("levelOfEvidence") - public void setLevelOfEvidence(CodingLevelOfEvidenceGrading value) { this.levelOfEvidence = value; } + public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; } @JsonProperty("medication") - public List getMedication() { return medication; } + public List getMedication() { return medication; } @JsonProperty("medication") - public void setMedication(List value) { this.medication = value; } + public void setMedication(List value) { this.medication = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -43,9 +43,9 @@ public class MTBStudyEnrollmentRecommendation { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("priority") - public CodingRecommendationPriority getPriority() { return priority; } + public RecommendationPriorityCoding getPriority() { return priority; } @JsonProperty("priority") - public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + public void setPriority(RecommendationPriorityCoding value) { this.priority = value; } @JsonProperty("reason") public Reference getReason() { return reason; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapy.java similarity index 60% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapy.java index ce76755..a542e7a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/MTBSystemicTherapy.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapy.java @@ -4,20 +4,21 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class MTBSystemicTherapy { +public class MtbSystemicTherapy { private Reference basedOn; - private CodingMtbSystemicTherapyCategory category; + private MtbSystemicTherapyCategoryCoding category; + private MtbSystemicTherapyDosageDensityCoding dosage; private String id; - private CodingMtbTherapyIntent intent; - private List medication; + private MtbTherapyIntentCoding intent; + private List medication; private List notes; private Reference patient; private PeriodDate period; private Reference reason; - private CodingMtbSystemicTherapyRecommendationFulfillmentStatus recommendationFulfillmentStatus; + private MtbSystemicTherapyRecommendationFulfillmentStatusCoding recommendationFulfillmentStatus; private Date recordedOn; - private CodingTherapyStatus status; - private CodingMtbTherapyStatusReason statusReason; + private TherapyStatusCoding status; + private MtbTherapyStatusReasonCoding statusReason; private Long therapyLine; @JsonProperty("basedOn") @@ -26,9 +27,14 @@ public class MTBSystemicTherapy { public void setBasedOn(Reference value) { this.basedOn = value; } @JsonProperty("category") - public CodingMtbSystemicTherapyCategory getCategory() { return category; } + public MtbSystemicTherapyCategoryCoding getCategory() { return category; } @JsonProperty("category") - public void setCategory(CodingMtbSystemicTherapyCategory value) { this.category = value; } + public void setCategory(MtbSystemicTherapyCategoryCoding value) { this.category = value; } + + @JsonProperty("dosage") + public MtbSystemicTherapyDosageDensityCoding getDosage() { return dosage; } + @JsonProperty("dosage") + public void setDosage(MtbSystemicTherapyDosageDensityCoding value) { this.dosage = value; } @JsonProperty("id") public String getId() { return id; } @@ -36,14 +42,14 @@ public class MTBSystemicTherapy { public void setId(String value) { this.id = value; } @JsonProperty("intent") - public CodingMtbTherapyIntent getIntent() { return intent; } + public MtbTherapyIntentCoding getIntent() { return intent; } @JsonProperty("intent") - public void setIntent(CodingMtbTherapyIntent value) { this.intent = value; } + public void setIntent(MtbTherapyIntentCoding value) { this.intent = value; } @JsonProperty("medication") - public List getMedication() { return medication; } + public List getMedication() { return medication; } @JsonProperty("medication") - public void setMedication(List value) { this.medication = value; } + public void setMedication(List value) { this.medication = value; } @JsonProperty("notes") public List getNotes() { return notes; } @@ -66,9 +72,9 @@ public class MTBSystemicTherapy { public void setReason(Reference value) { this.reason = value; } @JsonProperty("recommendationFulfillmentStatus") - public CodingMtbSystemicTherapyRecommendationFulfillmentStatus getRecommendationFulfillmentStatus() { return recommendationFulfillmentStatus; } + public MtbSystemicTherapyRecommendationFulfillmentStatusCoding getRecommendationFulfillmentStatus() { return recommendationFulfillmentStatus; } @JsonProperty("recommendationFulfillmentStatus") - public void setRecommendationFulfillmentStatus(CodingMtbSystemicTherapyRecommendationFulfillmentStatus value) { this.recommendationFulfillmentStatus = value; } + public void setRecommendationFulfillmentStatus(MtbSystemicTherapyRecommendationFulfillmentStatusCoding value) { this.recommendationFulfillmentStatus = value; } @JsonProperty("recordedOn") @JsonFormat(pattern = "yyyy-MM-dd") @@ -78,14 +84,14 @@ public class MTBSystemicTherapy { public void setRecordedOn(Date value) { this.recordedOn = value; } @JsonProperty("status") - public CodingTherapyStatus getStatus() { return status; } + public TherapyStatusCoding getStatus() { return status; } @JsonProperty("status") - public void setStatus(CodingTherapyStatus value) { this.status = value; } + public void setStatus(TherapyStatusCoding value) { this.status = value; } @JsonProperty("statusReason") - public CodingMtbTherapyStatusReason getStatusReason() { return statusReason; } + public MtbTherapyStatusReasonCoding getStatusReason() { return statusReason; } @JsonProperty("statusReason") - public void setStatusReason(CodingMtbTherapyStatusReason value) { this.statusReason = value; } + public void setStatusReason(MtbTherapyStatusReasonCoding value) { this.statusReason = value; } @JsonProperty("therapyLine") public Long getTherapyLine() { return therapyLine; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCoding.java index 86c9303..2e4cdf9 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategory.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingMtbSystemicTherapyCategory { - private CodingMtbSystemicTherapyCategoryCode code; +public class MtbSystemicTherapyCategoryCoding { + private MtbSystemicTherapyCategoryCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingMtbSystemicTherapyCategoryCode getCode() { return code; } + public MtbSystemicTherapyCategoryCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbSystemicTherapyCategoryCode value) { this.code = value; } + public void setCode(MtbSystemicTherapyCategoryCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCodingCode.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCodingCode.java index 807246b..83200bf 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbSystemicTherapyCategoryCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyCategoryCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbSystemicTherapyCategoryCode { +public enum MtbSystemicTherapyCategoryCodingCode { A, I, N, O, S; @JsonValue @@ -19,12 +19,12 @@ public enum CodingMtbSystemicTherapyCategoryCode { } @JsonCreator - public static CodingMtbSystemicTherapyCategoryCode forValue(String value) throws IOException { + public static MtbSystemicTherapyCategoryCodingCode forValue(String value) throws IOException { if (value.equals("A")) return A; if (value.equals("I")) return I; if (value.equals("N")) return N; if (value.equals("O")) return O; if (value.equals("S")) return S; - throw new IOException("Cannot deserialize CodingMtbSystemicTherapyCategoryCode"); + throw new IOException("Cannot deserialize MtbSystemicTherapyCategoryCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCoding.java new file mode 100644 index 0000000..871d4e2 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class MtbSystemicTherapyDosageDensityCoding { + private MtbSystemicTherapyDosageDensityCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public MtbSystemicTherapyDosageDensityCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(MtbSystemicTherapyDosageDensityCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCodingCode.java new file mode 100644 index 0000000..19f4642 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyDosageDensityCodingCode.java @@ -0,0 +1,24 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum MtbSystemicTherapyDosageDensityCodingCode { + OVER_50, UNDER_50; + + @JsonValue + public String toValue() { + switch (this) { + case OVER_50: return "over-50%"; + case UNDER_50: return "under-50%"; + } + return null; + } + + @JsonCreator + public static MtbSystemicTherapyDosageDensityCodingCode forValue(String value) throws IOException { + if (value.equals("over-50%")) return OVER_50; + if (value.equals("under-50%")) return UNDER_50; + throw new IOException("Cannot deserialize MtbSystemicTherapyDosageDensityCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCoding.java new file mode 100644 index 0000000..fbc1c64 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class MtbSystemicTherapyRecommendationFulfillmentStatusCoding { + private MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.java similarity index 59% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.java index 3fc4269..48b3024 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationFulfillmentStatusCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum RecommendationFulfillmentStatusCode { +public enum MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode { COMPLETE, PARTIAL; @JsonValue @@ -16,9 +16,9 @@ public enum RecommendationFulfillmentStatusCode { } @JsonCreator - public static RecommendationFulfillmentStatusCode forValue(String value) throws IOException { + public static MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode forValue(String value) throws IOException { if (value.equals("complete")) return COMPLETE; if (value.equals("partial")) return PARTIAL; - throw new IOException("Cannot deserialize RecommendationFulfillmentStatusCode"); + throw new IOException("Cannot deserialize MtbSystemicTherapyRecommendationFulfillmentStatusCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCoding.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCoding.java index 2c55eba..5bae22f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGeneticCounselingRecommendationReason.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingGeneticCounselingRecommendationReason { - private ReasonCode code; +public class MtbTherapyIntentCoding { + private MtbTherapyIntentCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public ReasonCode getCode() { return code; } + public MtbTherapyIntentCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(ReasonCode value) { this.code = value; } + public void setCode(MtbTherapyIntentCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCodingCode.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCodingCode.java index 2fc318f..5239a43 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/IntentCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyIntentCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum IntentCode { +public enum MtbTherapyIntentCodingCode { K, P, S, X; @JsonValue @@ -18,11 +18,11 @@ public enum IntentCode { } @JsonCreator - public static IntentCode forValue(String value) throws IOException { + public static MtbTherapyIntentCodingCode forValue(String value) throws IOException { if (value.equals("K")) return K; if (value.equals("P")) return P; if (value.equals("S")) return S; if (value.equals("X")) return X; - throw new IOException("Cannot deserialize IntentCode"); + throw new IOException("Cannot deserialize MtbTherapyIntentCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCoding.java index e6826f5..a16c010 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorCellContentMethod { - private CodingTumorCellContentMethodCode code; +public class MtbTherapyStatusReasonCoding { + private MtbTherapyStatusReasonCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTumorCellContentMethodCode getCode() { return code; } + public MtbTherapyStatusReasonCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTumorCellContentMethodCode value) { this.code = value; } + public void setCode(MtbTherapyStatusReasonCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCodingCode.java similarity index 94% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCodingCode.java index c3fad95..12848b5 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbTherapyStatusReasonCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MtbTherapyStatusReasonCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbTherapyStatusReasonCode { +public enum MtbTherapyStatusReasonCodingCode { BEST_SUPPORTIVE_CARE, CHRONIC_REMISSION, DETERIORATION, LOST_TO_FU, MEDICAL_REASONS, NO_INDICATION, OTHER, OTHER_THERAPY_CHOSEN, PATIENT_DEATH, PATIENT_REFUSAL, PATIENT_WISH, PAYMENT_ENDED, PAYMENT_PENDING, PAYMENT_REFUSED, PROGRESSION, REGULAR_COMPLETION, REGULAR_COMPLETION_WITH_DOSAGE_REDUCTION, REGULAR_COMPLETION_WITH_SUBSTANCE_CHANGE, TOXICITY; @JsonValue @@ -33,7 +33,7 @@ public enum CodingMtbTherapyStatusReasonCode { } @JsonCreator - public static CodingMtbTherapyStatusReasonCode forValue(String value) throws IOException { + public static MtbTherapyStatusReasonCodingCode forValue(String value) throws IOException { if (value.equals("best-supportive-care")) return BEST_SUPPORTIVE_CARE; if (value.equals("chronic-remission")) return CHRONIC_REMISSION; if (value.equals("deterioration")) return DETERIORATION; @@ -53,6 +53,6 @@ public enum CodingMtbTherapyStatusReasonCode { if (value.equals("regular-completion-with-dosage-reduction")) return REGULAR_COMPLETION_WITH_DOSAGE_REDUCTION; if (value.equals("regular-completion-with-substance-change")) return REGULAR_COMPLETION_WITH_SUBSTANCE_CHANGE; if (value.equals("toxicity")) return TOXICITY; - throw new IOException("Cannot deserialize CodingMtbTherapyStatusReasonCode"); + throw new IOException("Cannot deserialize MtbTherapyStatusReasonCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhMetadata.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhMetadata.java new file mode 100644 index 0000000..39e7b89 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhMetadata.java @@ -0,0 +1,32 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.List; +import java.util.Map; + +public class MvhMetadata { + private ModelProjectConsent modelProjectConsent; + private List> researchConsents; + private String transferTan; + private MvhSubmissionType type; + + @JsonProperty("modelProjectConsent") + public ModelProjectConsent getModelProjectConsent() { return modelProjectConsent; } + @JsonProperty("modelProjectConsent") + public void setModelProjectConsent(ModelProjectConsent value) { this.modelProjectConsent = value; } + + @JsonProperty("researchConsents") + public List> getResearchConsents() { return researchConsents; } + @JsonProperty("researchConsents") + public void setResearchConsents(List> value) { this.researchConsents = value; } + + @JsonProperty("transferTAN") + public String getTransferTan() { return transferTan; } + @JsonProperty("transferTAN") + public void setTransferTan(String value) { this.transferTan = value; } + + @JsonProperty("type") + public MvhSubmissionType getType() { return type; } + @JsonProperty("type") + public void setType(MvhSubmissionType value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhSubmissionType.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhSubmissionType.java new file mode 100644 index 0000000..47733de --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/MvhSubmissionType.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum MvhSubmissionType { + ADDITION, CORRECTION, FOLLOWUP, INITIAL; + + @JsonValue + public String toValue() { + switch (this) { + case ADDITION: return "addition"; + case CORRECTION: return "correction"; + case FOLLOWUP: return "followup"; + case INITIAL: return "initial"; + } + return null; + } + + @JsonCreator + public static MvhSubmissionType forValue(String value) throws IOException { + if (value.equals("addition")) return ADDITION; + if (value.equals("correction")) return CORRECTION; + if (value.equals("followup")) return FOLLOWUP; + if (value.equals("initial")) return INITIAL; + throw new IOException("Cannot deserialize MvhSubmissionType"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCoding.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCoding.java index e4b0faa..d083713 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingNgsReport { - private CodingNgsReportCode code; +public class NgsReportCoding { + private NgsReportCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingNgsReportCode getCode() { return code; } + public NgsReportCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingNgsReportCode value) { this.code = value; } + public void setCode(NgsReportCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCodingCode.java similarity index 87% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCodingCode.java index 7e3f156..a86968c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingNgsReportCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingNgsReportCode { +public enum NgsReportCodingCode { ARRAY, EXOME, GENOME_LONG_READ, GENOME_SHORT_READ, KARYOTYPING, OTHER, PANEL, SINGLE; @JsonValue @@ -22,7 +22,7 @@ public enum CodingNgsReportCode { } @JsonCreator - public static CodingNgsReportCode forValue(String value) throws IOException { + public static NgsReportCodingCode forValue(String value) throws IOException { if (value.equals("array")) return ARRAY; if (value.equals("exome")) return EXOME; if (value.equals("genome-long-read")) return GENOME_LONG_READ; @@ -31,6 +31,6 @@ public enum CodingNgsReportCode { if (value.equals("other")) return OTHER; if (value.equals("panel")) return PANEL; if (value.equals("single")) return SINGLE; - throw new IOException("Cannot deserialize CodingNgsReportCode"); + throw new IOException("Cannot deserialize NgsReportCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportMetadata.java similarity index 97% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportMetadata.java index dab2b86..036fcc4 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Metadata.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportMetadata.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class Metadata { +public class NgsReportMetadata { private String kitManufacturer; private String kitType; private String pipeline; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java index 567aa4b..e5d8c4a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportResults.java @@ -4,20 +4,20 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class NgsReportResults { - private BRCAness brcaness; + private Brcaness brcaness; private List copyNumberVariants; - private List dnaFusions; - private HRDScore hrdScore; - private List rnaFusions; - private List rnaSeqs; + 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; } + public Brcaness getBrcaness() { return brcaness; } @JsonProperty("brcaness") - public void setBrcaness(BRCAness value) { this.brcaness = value; } + public void setBrcaness(Brcaness value) { this.brcaness = value; } @JsonProperty("copyNumberVariants") public List getCopyNumberVariants() { return copyNumberVariants; } @@ -25,24 +25,24 @@ public class NgsReportResults { public void setCopyNumberVariants(List value) { this.copyNumberVariants = value; } @JsonProperty("dnaFusions") - public List getDnaFusions() { return dnaFusions; } + public List getDnaFusions() { return dnaFusions; } @JsonProperty("dnaFusions") - public void setDnaFusions(List value) { this.dnaFusions = value; } + public void setDnaFusions(List value) { this.dnaFusions = value; } @JsonProperty("hrdScore") - public HRDScore getHrdScore() { return hrdScore; } + public HrdScore getHrdScore() { return hrdScore; } @JsonProperty("hrdScore") - public void setHrdScore(HRDScore value) { this.hrdScore = value; } + public void setHrdScore(HrdScore value) { this.hrdScore = value; } @JsonProperty("rnaFusions") - public List getRnaFusions() { return rnaFusions; } + public List getRnaFusions() { return rnaFusions; } @JsonProperty("rnaFusions") - public void setRnaFusions(List value) { this.rnaFusions = value; } + public void setRnaFusions(List value) { this.rnaFusions = value; } @JsonProperty("rnaSeqs") - public List getRnaSeqs() { return rnaSeqs; } + public List getRnaSeqs() { return rnaSeqs; } @JsonProperty("rnaSeqs") - public void setRnaSeqs(List value) { this.rnaSeqs = value; } + public void setRnaSeqs(List value) { this.rnaSeqs = value; } @JsonProperty("simpleVariants") public List getSimpleVariants() { return simpleVariants; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/NoSequencingPerformedReasonCode.java similarity index 67% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/NoSequencingPerformedReasonCode.java index 0e89c48..15f3915 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbCarePlanStatusReasonCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/NoSequencingPerformedReasonCode.java @@ -3,15 +3,14 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbCarePlanStatusReasonCode { - NON_GENETIC_CAUSE, NOT_RARE_DISEASE, NO_TARGET, OTHER, PSYCHOSOMATIC, TARGETED_DIAGNOSTICS_RECOMMENDED; +public enum NoSequencingPerformedReasonCode { + NON_GENETIC_CAUSE, NOT_RARE_DISEASE, OTHER, PSYCHOSOMATIC, TARGETED_DIAGNOSTICS_RECOMMENDED; @JsonValue public String toValue() { switch (this) { case NON_GENETIC_CAUSE: return "non-genetic-cause"; case NOT_RARE_DISEASE: return "not-rare-disease"; - case NO_TARGET: return "no-target"; case OTHER: return "other"; case PSYCHOSOMATIC: return "psychosomatic"; case TARGETED_DIAGNOSTICS_RECOMMENDED: return "targeted-diagnostics-recommended"; @@ -20,13 +19,12 @@ public enum CodingMtbCarePlanStatusReasonCode { } @JsonCreator - public static CodingMtbCarePlanStatusReasonCode forValue(String value) throws IOException { + public static NoSequencingPerformedReasonCode forValue(String value) throws IOException { if (value.equals("non-genetic-cause")) return NON_GENETIC_CAUSE; if (value.equals("not-rare-disease")) return NOT_RARE_DISEASE; - if (value.equals("no-target")) return NO_TARGET; if (value.equals("other")) return OTHER; if (value.equals("psychosomatic")) return PSYCHOSOMATIC; if (value.equals("targeted-diagnostics-recommended")) return TARGETED_DIAGNOSTICS_RECOMMENDED; - throw new IOException("Cannot deserialize CodingMtbCarePlanStatusReasonCode"); + throw new IOException("Cannot deserialize NoSequencingPerformedReasonCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java index 8a8d037..1c0eeac 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedure.java @@ -6,16 +6,16 @@ import java.util.List; public class OncoProcedure { private Reference basedOn; - private CodingOncoProcedure code; + private OncoProcedureCoding code; private String id; - private CodingMtbTherapyIntent intent; + private MtbTherapyIntentCoding intent; private List notes; private Reference patient; private PeriodDate period; private Reference reason; private Date recordedOn; - private CodingTherapyStatus status; - private CodingMtbTherapyStatusReason statusReason; + private TherapyStatusCoding status; + private MtbTherapyStatusReasonCoding statusReason; private Long therapyLine; @JsonProperty("basedOn") @@ -24,9 +24,9 @@ public class OncoProcedure { public void setBasedOn(Reference value) { this.basedOn = value; } @JsonProperty("code") - public CodingOncoProcedure getCode() { return code; } + public OncoProcedureCoding getCode() { return code; } @JsonProperty("code") - public void setCode(CodingOncoProcedure value) { this.code = value; } + public void setCode(OncoProcedureCoding value) { this.code = value; } @JsonProperty("id") public String getId() { return id; } @@ -34,9 +34,9 @@ public class OncoProcedure { public void setId(String value) { this.id = value; } @JsonProperty("intent") - public CodingMtbTherapyIntent getIntent() { return intent; } + public MtbTherapyIntentCoding getIntent() { return intent; } @JsonProperty("intent") - public void setIntent(CodingMtbTherapyIntent value) { this.intent = value; } + public void setIntent(MtbTherapyIntentCoding value) { this.intent = value; } @JsonProperty("notes") public List getNotes() { return notes; } @@ -66,14 +66,14 @@ public class OncoProcedure { public void setRecordedOn(Date value) { this.recordedOn = value; } @JsonProperty("status") - public CodingTherapyStatus getStatus() { return status; } + public TherapyStatusCoding getStatus() { return status; } @JsonProperty("status") - public void setStatus(CodingTherapyStatus value) { this.status = value; } + public void setStatus(TherapyStatusCoding value) { this.status = value; } @JsonProperty("statusReason") - public CodingMtbTherapyStatusReason getStatusReason() { return statusReason; } + public MtbTherapyStatusReasonCoding getStatusReason() { return statusReason; } @JsonProperty("statusReason") - public void setStatusReason(CodingMtbTherapyStatusReason value) { this.statusReason = value; } + public void setStatusReason(MtbTherapyStatusReasonCoding value) { this.statusReason = value; } @JsonProperty("therapyLine") public Long getTherapyLine() { return therapyLine; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCoding.java index 4fea654..aca7471 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedure.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingOncoProcedure { - private CodingOncoProcedureCode code; +public class OncoProcedureCoding { + private OncoProcedureCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingOncoProcedureCode getCode() { return code; } + public OncoProcedureCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingOncoProcedureCode value) { this.code = value; } + public void setCode(OncoProcedureCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCodingCode.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCodingCode.java index 62eac67..81d781f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingOncoProcedureCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/OncoProcedureCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingOncoProcedureCode { +public enum OncoProcedureCodingCode { NUCLEAR_MEDICINE, RADIO_THERAPY, SURGERY; @JsonValue @@ -17,10 +17,10 @@ public enum CodingOncoProcedureCode { } @JsonCreator - public static CodingOncoProcedureCode forValue(String value) throws IOException { + public static OncoProcedureCodingCode forValue(String value) throws IOException { if (value.equals("nuclear-medicine")) return NUCLEAR_MEDICINE; if (value.equals("radio-therapy")) return RADIO_THERAPY; if (value.equals("surgery")) return SURGERY; - throw new IOException("Cannot deserialize CodingOncoProcedureCode"); + throw new IOException("Cannot deserialize OncoProcedureCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java index 0ee6d26..8532ab8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java @@ -8,11 +8,11 @@ public class Patient { private Age age; private Date birthDate; private Date dateOfDeath; - private CodingGender gender; + private GenderCoding gender; private HealthInsurance healthInsurance; private String id; private Coding managingSite; - private CodingVitalStatus vitalStatus; + private VitalStatusCoding vitalStatus; @JsonProperty("address") public Address getAddress() { return address; } @@ -37,9 +37,9 @@ public class Patient { public void setDateOfDeath(Date value) { this.dateOfDeath = value; } @JsonProperty("gender") - public CodingGender getGender() { return gender; } + public GenderCoding getGender() { return gender; } @JsonProperty("gender") - public void setGender(CodingGender value) { this.gender = value; } + public void setGender(GenderCoding value) { this.gender = value; } @JsonProperty("healthInsurance") public HealthInsurance getHealthInsurance() { return healthInsurance; } @@ -57,7 +57,7 @@ public class Patient { public void setManagingSite(Coding value) { this.managingSite = value; } @JsonProperty("vitalStatus") - public CodingVitalStatus getVitalStatus() { return vitalStatus; } + public VitalStatusCoding getVitalStatus() { return vitalStatus; } @JsonProperty("vitalStatus") - public void setVitalStatus(CodingVitalStatus value) { this.vitalStatus = value; } + public void setVitalStatus(VitalStatusCoding value) { this.vitalStatus = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java index c9d473e..921dc19 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java @@ -7,7 +7,7 @@ public class PerformanceStatus { private Date effectiveDate; private String id; private Reference patient; - private CodingEcog value; + private EcogCoding value; @JsonProperty("effectiveDate") @JsonFormat(pattern = "yyyy-MM-dd") @@ -27,7 +27,7 @@ public class PerformanceStatus { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("value") - public CodingEcog getValue() { return value; } + public EcogCoding getValue() { return value; } @JsonProperty("value") - public void setValue(CodingEcog value) { this.value = value; } + public void setValue(EcogCoding value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java index 6c74b87..88e34a1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorDiagnosticReport.java @@ -11,7 +11,7 @@ public class PriorDiagnosticReport { private Reference performer; private List results; private Reference specimen; - private CodingMolecularDiagnosticReport type; + private MolecularDiagnosticReportCoding type; @JsonProperty("id") public String getId() { return id; } @@ -46,7 +46,7 @@ public class PriorDiagnosticReport { public void setSpecimen(Reference value) { this.specimen = value; } @JsonProperty("type") - public CodingMolecularDiagnosticReport getType() { return type; } + public MolecularDiagnosticReportCoding getType() { return type; } @JsonProperty("type") - public void setType(CodingMolecularDiagnosticReport value) { this.type = value; } + public void setType(MolecularDiagnosticReportCoding value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java deleted file mode 100644 index 2775a5c..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PriorityCode.java +++ /dev/null @@ -1,28 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum PriorityCode { - THE_1, THE_2, THE_3, THE_4; - - @JsonValue - public String toValue() { - switch (this) { - case THE_1: return "1"; - case THE_2: return "2"; - case THE_3: return "3"; - case THE_4: return "4"; - } - return null; - } - - @JsonCreator - public static PriorityCode forValue(String value) throws IOException { - if (value.equals("1")) return THE_1; - if (value.equals("2")) return THE_2; - if (value.equals("3")) return THE_3; - if (value.equals("4")) return THE_4; - throw new IOException("Cannot deserialize PriorityCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java index aa88124..255648a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProcedureRecommendation.java @@ -5,19 +5,19 @@ import java.util.Date; import java.util.List; public class ProcedureRecommendation { - private CodingMtbProcedureRecommendationCategory code; + private MtbProcedureRecommendationCategoryCoding code; private String id; private Date issuedOn; private LevelOfEvidence levelOfEvidence; private Reference patient; - private CodingRecommendationPriority priority; + private RecommendationPriorityCoding priority; private Reference reason; private List supportingVariants; @JsonProperty("code") - public CodingMtbProcedureRecommendationCategory getCode() { return code; } + public MtbProcedureRecommendationCategoryCoding getCode() { return code; } @JsonProperty("code") - public void setCode(CodingMtbProcedureRecommendationCategory value) { this.code = value; } + public void setCode(MtbProcedureRecommendationCategoryCoding value) { this.code = value; } @JsonProperty("id") public String getId() { return id; } @@ -42,9 +42,9 @@ public class ProcedureRecommendation { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("priority") - public CodingRecommendationPriority getPriority() { return priority; } + public RecommendationPriorityCoding getPriority() { return priority; } @JsonProperty("priority") - public void setPriority(CodingRecommendationPriority value) { this.priority = value; } + public void setPriority(RecommendationPriorityCoding value) { this.priority = value; } @JsonProperty("reason") public Reference getReason() { return reason; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java index 64b9b46..092251c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpression.java @@ -3,18 +3,18 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; public class ProteinExpression { - private CodingProteinExpressionIcScore icScore; + private ProteinExpressionIcScoreCoding icScore; private String id; private Reference patient; private Coding protein; - private CodingProteinExpressionTcScore tcScore; + private ProteinExpressionTcScoreCoding tcScore; private Long tpsScore; - private CodingProteinExpressionResult value; + private ProteinExpressionResultCoding value; @JsonProperty("icScore") - public CodingProteinExpressionIcScore getIcScore() { return icScore; } + public ProteinExpressionIcScoreCoding getIcScore() { return icScore; } @JsonProperty("icScore") - public void setIcScore(CodingProteinExpressionIcScore value) { this.icScore = value; } + public void setIcScore(ProteinExpressionIcScoreCoding value) { this.icScore = value; } @JsonProperty("id") public String getId() { return id; } @@ -32,9 +32,9 @@ public class ProteinExpression { public void setProtein(Coding value) { this.protein = value; } @JsonProperty("tcScore") - public CodingProteinExpressionTcScore getTcScore() { return tcScore; } + public ProteinExpressionTcScoreCoding getTcScore() { return tcScore; } @JsonProperty("tcScore") - public void setTcScore(CodingProteinExpressionTcScore value) { this.tcScore = value; } + public void setTcScore(ProteinExpressionTcScoreCoding value) { this.tcScore = value; } @JsonProperty("tpsScore") public Long getTpsScore() { return tpsScore; } @@ -42,7 +42,7 @@ public class ProteinExpression { public void setTpsScore(Long value) { this.tpsScore = value; } @JsonProperty("value") - public CodingProteinExpressionResult getValue() { return value; } + public ProteinExpressionResultCoding getValue() { return value; } @JsonProperty("value") - public void setValue(CodingProteinExpressionResult value) { this.value = value; } + public void setValue(ProteinExpressionResultCoding value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCoding.java new file mode 100644 index 0000000..7d01df1 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class ProteinExpressionIcScoreCoding { + private ProteinExpressionIcScoreCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public ProteinExpressionIcScoreCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(ProteinExpressionIcScoreCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCodingCode.java new file mode 100644 index 0000000..3a08d05 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionIcScoreCodingCode.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ProteinExpressionIcScoreCodingCode { + CODE_0, CODE_1, CODE_2, CODE_3; + + @JsonValue + public String toValue() { + switch (this) { + case CODE_0: return "0"; + case CODE_1: return "1"; + case CODE_2: return "2"; + case CODE_3: return "3"; + } + return null; + } + + @JsonCreator + public static ProteinExpressionIcScoreCodingCode forValue(String value) throws IOException { + if (value.equals("0")) return CODE_0; + if (value.equals("1")) return CODE_1; + if (value.equals("2")) return CODE_2; + if (value.equals("3")) return CODE_3; + throw new IOException("Cannot deserialize ProteinExpressionIcScoreCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCoding.java similarity index 77% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCoding.java index 26d9c4f..31fd787 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingBaseVariantLocalization.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingBaseVariantLocalization { - private CodingBaseVariantLocalizationCode code; +public class ProteinExpressionResultCoding { + private ProteinExpressionResultCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingBaseVariantLocalizationCode getCode() { return code; } + public ProteinExpressionResultCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingBaseVariantLocalizationCode value) { this.code = value; } + public void setCode(ProteinExpressionResultCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCodingCode.java similarity index 50% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCodingCode.java index 96889dc..06478dd 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResultCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCodingCode.java @@ -3,30 +3,30 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingProteinExpressionResultCode { - EXP, NOT_EXP, THE_1, THE_2, THE_3, UNKNOWN; +public enum ProteinExpressionResultCodingCode { + EXP, NOT_EXP, CODE_1PLUS, CODE_2PLUS, CODE_3PLUS, UNKNOWN; @JsonValue public String toValue() { switch (this) { case EXP: return "exp"; case NOT_EXP: return "not-exp"; - case THE_1: return "1+"; - case THE_2: return "2+"; - case THE_3: return "3+"; + case CODE_1PLUS: return "1+"; + case CODE_2PLUS: return "2+"; + case CODE_3PLUS: return "3+"; case UNKNOWN: return "unknown"; } return null; } @JsonCreator - public static CodingProteinExpressionResultCode forValue(String value) throws IOException { + public static ProteinExpressionResultCodingCode forValue(String value) throws IOException { if (value.equals("exp")) return EXP; if (value.equals("not-exp")) return NOT_EXP; - if (value.equals("1+")) return THE_1; - if (value.equals("2+")) return THE_2; - if (value.equals("3+")) return THE_3; + if (value.equals("1+")) return CODE_1PLUS; + if (value.equals("2+")) return CODE_2PLUS; + if (value.equals("3+")) return CODE_3PLUS; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingProteinExpressionResultCode"); + throw new IOException("Cannot deserialize ProteinExpressionResultCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCoding.java new file mode 100644 index 0000000..54c110c --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class ProteinExpressionTcScoreCoding { + private ProteinExpressionTcScoreCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public ProteinExpressionTcScoreCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(ProteinExpressionTcScoreCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCodingCode.java new file mode 100644 index 0000000..f0740f4 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionTcScoreCodingCode.java @@ -0,0 +1,34 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum ProteinExpressionTcScoreCodingCode { + CODE_0, CODE_1, CODE_2, CODE_3, CODE_4, CODE_5, CODE_6; + + @JsonValue + public String toValue() { + switch (this) { + case CODE_0: return "0"; + case CODE_1: return "1"; + case CODE_2: return "2"; + case CODE_3: return "3"; + case CODE_4: return "4"; + case CODE_5: return "5"; + case CODE_6: return "6"; + } + return null; + } + + @JsonCreator + public static ProteinExpressionTcScoreCodingCode forValue(String value) throws IOException { + if (value.equals("0")) return CODE_0; + if (value.equals("1")) return CODE_1; + if (value.equals("2")) return CODE_2; + if (value.equals("3")) return CODE_3; + if (value.equals("4")) return CODE_4; + if (value.equals("5")) return CODE_5; + if (value.equals("6")) return CODE_6; + throw new IOException("Cannot deserialize ProteinExpressionTcScoreCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Provision.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Provision.java new file mode 100644 index 0000000..f5c9c26 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Provision.java @@ -0,0 +1,27 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; +import java.util.Date; + +public class Provision { + private Date date; + private ModelProjectConsentPurpose purpose; + private ConsentProvision type; + + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public Date getDate() { return date; } + @JsonProperty("date") + @JsonFormat(pattern = "yyyy-MM-dd") + public void setDate(Date value) { this.date = value; } + + @JsonProperty("purpose") + public ModelProjectConsentPurpose getPurpose() { return purpose; } + @JsonProperty("purpose") + public void setPurpose(ModelProjectConsentPurpose value) { this.purpose = value; } + + @JsonProperty("type") + public ConsentProvision getType() { return type; } + @JsonProperty("type") + public void setType(ConsentProvision value) { this.type = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java index fcfc0ec..34bb2aa 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/PublicationSystem.java @@ -4,21 +4,21 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum PublicationSystem { - HTTPS_PUBMED_NCBI_NLM_NIH_GOV, HTTPS_Www_DOI_ORG; + PUBMED_NCBI_NLM_NIH_GOV, DOI_ORG; @JsonValue public String toValue() { switch (this) { - case HTTPS_PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov"; - case HTTPS_Www_DOI_ORG: return "https://www.doi.org"; + case PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov"; + case DOI_ORG: return "https://www.doi.org"; } return null; } @JsonCreator public static PublicationSystem forValue(String value) throws IOException { - if (value.equals("https://pubmed.ncbi.nlm.nih.gov")) return HTTPS_PUBMED_NCBI_NLM_NIH_GOV; - if (value.equals("https://www.doi.org")) return HTTPS_Www_DOI_ORG; + if (value.equals("https://pubmed.ncbi.nlm.nih.gov")) return PUBMED_NCBI_NLM_NIH_GOV; + if (value.equals("https://www.doi.org")) return DOI_ORG; throw new IOException("Cannot deserialize PublicationSystem"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCoding.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCoding.java index bc4a36e..7ba1a8a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingClaimResponseStatus { - private StickyCode code; +public class RecistCoding { + private RecistCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public StickyCode getCode() { return code; } + public RecistCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(StickyCode value) { this.code = value; } + public void setCode(RecistCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCodingCode.java similarity index 82% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCodingCode.java index 5b5ba47..9df7135 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecistCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingRecistCode { +public enum RecistCodingCode { CR, MR, NA, PD, PR, SD; @JsonValue @@ -20,13 +20,13 @@ public enum CodingRecistCode { } @JsonCreator - public static CodingRecistCode forValue(String value) throws IOException { + public static RecistCodingCode forValue(String value) throws IOException { if (value.equals("CR")) return CR; if (value.equals("MR")) return MR; if (value.equals("NA")) return NA; if (value.equals("PD")) return PD; if (value.equals("PR")) return PR; if (value.equals("SD")) return SD; - throw new IOException("Cannot deserialize CodingRecistCode"); + throw new IOException("Cannot deserialize RecistCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCoding.java new file mode 100644 index 0000000..0df4de6 --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class RecommendationPriorityCoding { + private RecommendationPriorityCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public RecommendationPriorityCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(RecommendationPriorityCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCodingCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCodingCode.java new file mode 100644 index 0000000..dccf9ab --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RecommendationPriorityCodingCode.java @@ -0,0 +1,28 @@ +package dev.pcvolkmer.mv64e.mtb; + +import java.io.IOException; +import com.fasterxml.jackson.annotation.*; + +public enum RecommendationPriorityCodingCode { + CODE_1, CODE_2, CODE_3, CODE_4; + + @JsonValue + public String toValue() { + switch (this) { + case CODE_1: return "1"; + case CODE_2: return "2"; + case CODE_3: return "3"; + case CODE_4: return "4"; + } + return null; + } + + @JsonCreator + public static RecommendationPriorityCodingCode forValue(String value) throws IOException { + if (value.equals("1")) return CODE_1; + if (value.equals("2")) return CODE_2; + if (value.equals("3")) return CODE_3; + if (value.equals("4")) return CODE_4; + throw new IOException("Cannot deserialize RecommendationPriorityCodingCode"); + } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java index a1b5992..d62d678 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RequestedMedicationSystem.java @@ -4,12 +4,12 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum RequestedMedicationSystem { - HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC, UNDEFINED; + FHIR_DE_CODE_SYSTEM_BFARM_ATC, UNDEFINED; @JsonValue public String toValue() { switch (this) { - case HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC: return "http://fhir.de/CodeSystem/bfarm/atc"; + case FHIR_DE_CODE_SYSTEM_BFARM_ATC: return "http://fhir.de/CodeSystem/bfarm/atc"; case UNDEFINED: return "undefined"; } return null; @@ -17,7 +17,7 @@ public enum RequestedMedicationSystem { @JsonCreator public static RequestedMedicationSystem forValue(String value) throws IOException { - if (value.equals("http://fhir.de/CodeSystem/bfarm/atc")) return HTTP_FHIR_DE_CODE_SYSTEM_BFARM_ATC; + if (value.equals("http://fhir.de/CodeSystem/bfarm/atc")) return FHIR_DE_CODE_SYSTEM_BFARM_ATC; if (value.equals("undefined")) return UNDEFINED; throw new IOException("Cannot deserialize RequestedMedicationSystem"); } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java index d4bf8cb..d03077a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java @@ -6,10 +6,10 @@ import java.util.Date; public class Response { private Date effectiveDate; private String id; - private CodingResponseMethod method; + private ResponseMethodCoding method; private Reference patient; private Reference therapy; - private CodingRecist value; + private RecistCoding value; @JsonProperty("effectiveDate") @JsonFormat(pattern = "yyyy-MM-dd") @@ -24,9 +24,9 @@ public class Response { public void setId(String value) { this.id = value; } @JsonProperty("method") - public CodingResponseMethod getMethod() { return method; } + public ResponseMethodCoding getMethod() { return method; } @JsonProperty("method") - public void setMethod(CodingResponseMethod value) { this.method = value; } + public void setMethod(ResponseMethodCoding value) { this.method = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -39,7 +39,7 @@ public class Response { public void setTherapy(Reference value) { this.therapy = value; } @JsonProperty("value") - public CodingRecist getValue() { return value; } + public RecistCoding getValue() { return value; } @JsonProperty("value") - public void setValue(CodingRecist value) { this.value = value; } + public void setValue(RecistCoding value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCoding.java index 2446beb..04f7e98 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingResponseMethod { - private CodingResponseMethodCode code; +public class ResponseMethodCoding { + private ResponseMethodCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingResponseMethodCode getCode() { return code; } + public ResponseMethodCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingResponseMethodCode value) { this.code = value; } + public void setCode(ResponseMethodCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCodingCode.java similarity index 71% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCodingCode.java index 68a5de5..08707b0 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingResponseMethodCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseMethodCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingResponseMethodCode { +public enum ResponseMethodCodingCode { RANO, RECIST; @JsonValue @@ -16,9 +16,9 @@ public enum CodingResponseMethodCode { } @JsonCreator - public static CodingResponseMethodCode forValue(String value) throws IOException { + public static ResponseMethodCodingCode forValue(String value) throws IOException { if (value.equals("RANO")) return RANO; if (value.equals("RECIST")) return RECIST; - throw new IOException("Cannot deserialize CodingResponseMethodCode"); + throw new IOException("Cannot deserialize ResponseMethodCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java similarity index 88% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java index 11494ee..f2f097f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusion.java @@ -3,13 +3,13 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.List; -public class RNAFusion { +public class RnaFusion { private String effect; private List externalIds; private RnaFusionFusionPartner3Prime fusionPartner3Prime; private RnaFusionFusionPartner5Prime fusionPartner5Prime; private String id; - private List localization; + private List localization; private Reference patient; private long reportedNumReads; @@ -39,9 +39,9 @@ public class RNAFusion { public void setId(String value) { this.id = value; } @JsonProperty("localization") - public List getLocalization() { return localization; } + public List getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(List value) { this.localization = value; } + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java index 777886d..947b9f2 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java @@ -6,7 +6,7 @@ public class RnaFusionFusionPartner3Prime { private String exonId; private Coding gene; private double position; - private RNAFusionStrand strand; + private RnaFusionStrand strand; private TranscriptId transcriptId; @JsonProperty("exonId") @@ -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 TranscriptId 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 bf1767d..7a76c87 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java @@ -6,7 +6,7 @@ public class RnaFusionFusionPartner5Prime { private String exonId; private Coding gene; private double position; - private RNAFusionStrand strand; + private RnaFusionStrand strand; private TranscriptId transcriptId; @JsonProperty("exonId") @@ -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 TranscriptId getTranscriptId() { return transcriptId; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java similarity index 75% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusionStrand.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java index 8de16d9..e749cd0 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 @@ -16,9 +16,9 @@ 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"); + 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 91% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java index 73b09b7..ab7b6a8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/RNASeq.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java @@ -3,13 +3,13 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; import java.util.List; -public class RNASeq { +public class RnaSeq { private Long cohortRanking; private List externalIds; private Coding gene; private String id; private Long librarySize; - private List localization; + private List localization; private Reference patient; private long rawCounts; private Boolean tissueCorrectedExpression; @@ -43,9 +43,9 @@ public class RNASeq { public void setLibrarySize(Long value) { this.librarySize = value; } @JsonProperty("localization") - public List getLocalization() { return localization; } + public List getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(List value) { this.localization = value; } + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java index 733c8b8..a0a7058 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java @@ -7,16 +7,16 @@ public class Snv { private double allelicFrequency; private String altAllele; private Chromosome chromosome; - private Coding dnaChange; + private String dnaChange; private String exonId; private List externalIds; private Coding gene; private String id; - private CodingClinVar interpretation; - private List localization; + private ClinVarCoding interpretation; + private List localization; private Reference patient; private Position position; - private Coding proteinChange; + private String proteinChange; private long readDepth; private String refAllele; private TranscriptId transcriptId; @@ -37,9 +37,9 @@ public class Snv { public void setChromosome(Chromosome value) { this.chromosome = value; } @JsonProperty("dnaChange") - public Coding getDnaChange() { return dnaChange; } + public String getDnaChange() { return dnaChange; } @JsonProperty("dnaChange") - public void setDnaChange(Coding value) { this.dnaChange = value; } + public void setDnaChange(String value) { this.dnaChange = value; } @JsonProperty("exonId") public String getExonId() { return exonId; } @@ -62,14 +62,14 @@ public class Snv { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public CodingClinVar getInterpretation() { return interpretation; } + public ClinVarCoding getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(CodingClinVar value) { this.interpretation = value; } + public void setInterpretation(ClinVarCoding value) { this.interpretation = value; } @JsonProperty("localization") - public List getLocalization() { return localization; } + public List getLocalization() { return localization; } @JsonProperty("localization") - public void setLocalization(List value) { this.localization = value; } + public void setLocalization(List value) { this.localization = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -82,9 +82,9 @@ public class Snv { public void setPosition(Position value) { this.position = value; } @JsonProperty("proteinChange") - public Coding getProteinChange() { return proteinChange; } + public String getProteinChange() { return proteinChange; } @JsonProperty("proteinChange") - public void setProteinChange(Coding value) { this.proteinChange = value; } + public void setProteinChange(String value) { this.proteinChange = value; } @JsonProperty("readDepth") public long getReadDepth() { return readDepth; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java index 3ec147b..7c6156a 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReportMetadata.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java @@ -4,14 +4,14 @@ import com.fasterxml.jackson.annotation.*; import java.util.Date; import java.util.List; -public class SomaticNgsReportMetadata { +public class SomaticNgsReport { private String id; private Date issuedOn; - private List metadata; + private List metadata; private Reference patient; private NgsReportResults results; private Reference specimen; - private CodingNgsReport type; + private NgsReportCoding type; @JsonProperty("id") public String getId() { return id; } @@ -26,9 +26,9 @@ public class SomaticNgsReportMetadata { public void setIssuedOn(Date value) { this.issuedOn = value; } @JsonProperty("metadata") - public List getMetadata() { return metadata; } + public List getMetadata() { return metadata; } @JsonProperty("metadata") - public void setMetadata(List value) { this.metadata = value; } + public void setMetadata(List value) { this.metadata = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -46,7 +46,7 @@ public class SomaticNgsReportMetadata { public void setSpecimen(Reference value) { this.specimen = value; } @JsonProperty("type") - public CodingNgsReport getType() { return type; } + public NgsReportCoding getType() { return type; } @JsonProperty("type") - public void setType(CodingNgsReport value) { this.type = value; } + public void setType(NgsReportCoding value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java index 4447e0a..6098479 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/StudySystem.java @@ -4,14 +4,14 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum StudySystem { - DRKS, EUDAMED, EUDRA_Ct, NCT; + DRKS, EUDAMED, EUDRA_CT, NCT; @JsonValue public String toValue() { switch (this) { case DRKS: return "DRKS"; case EUDAMED: return "EUDAMED"; - case EUDRA_Ct: return "Eudra-CT"; + case EUDRA_CT: return "Eudra-CT"; case NCT: return "NCT"; } return null; @@ -21,7 +21,7 @@ public enum StudySystem { public static StudySystem forValue(String value) throws IOException { if (value.equals("DRKS")) return DRKS; if (value.equals("EUDAMED")) return EUDAMED; - if (value.equals("Eudra-CT")) return EUDRA_Ct; + if (value.equals("Eudra-CT")) return EUDRA_CT; if (value.equals("NCT")) return NCT; throw new IOException("Cannot deserialize StudySystem"); } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java index ac7441a..3abd517 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/SystemicTherapy.java @@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*; import java.util.List; public class SystemicTherapy { - 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/TcScoreCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java deleted file mode 100644 index 833bac4..0000000 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java +++ /dev/null @@ -1,34 +0,0 @@ -package dev.pcvolkmer.mv64e.mtb; - -import java.io.IOException; -import com.fasterxml.jackson.annotation.*; - -public enum TcScoreCode { - THE_0, THE_1, THE_2, THE_3, THE_4, THE_5, THE_6; - - @JsonValue - public String toValue() { - switch (this) { - case THE_0: return "0"; - case THE_1: return "1"; - case THE_2: return "2"; - case THE_3: return "3"; - case THE_4: return "4"; - case THE_5: return "5"; - case THE_6: return "6"; - } - return null; - } - - @JsonCreator - public static TcScoreCode forValue(String value) throws IOException { - if (value.equals("0")) return THE_0; - if (value.equals("1")) return THE_1; - if (value.equals("2")) return THE_2; - if (value.equals("3")) return THE_3; - if (value.equals("4")) return THE_4; - if (value.equals("5")) return THE_5; - if (value.equals("6")) return THE_6; - throw new IOException("Cannot deserialize TcScoreCode"); - } -} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCoding.java index 76c8a40..7c6fc48 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatus.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTherapyStatus { - private CodingTherapyStatusCode code; +public class TherapyStatusCoding { + private TherapyStatusCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTherapyStatusCode getCode() { return code; } + public TherapyStatusCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTherapyStatusCode value) { this.code = value; } + public void setCode(TherapyStatusCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCodingCode.java similarity index 81% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCodingCode.java index 8388a6f..8d3c5ee 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTherapyStatusCode { +public enum TherapyStatusCodingCode { COMPLETED, NOT_DONE, ON_GOING, STOPPED, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum CodingTherapyStatusCode { } @JsonCreator - public static CodingTherapyStatusCode forValue(String value) throws IOException { + public static TherapyStatusCodingCode forValue(String value) throws IOException { if (value.equals("completed")) return COMPLETED; if (value.equals("not-done")) return NOT_DONE; if (value.equals("on-going")) return ON_GOING; if (value.equals("stopped")) return STOPPED; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingTherapyStatusCode"); + throw new IOException("Cannot deserialize TherapyStatusCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java index 605cefd..83bf7d8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/Tmb.java @@ -4,10 +4,10 @@ import com.fasterxml.jackson.annotation.*; public class Tmb { private String id; - private CodingTmbInterpretation interpretation; + private TmbInterpretationCoding interpretation; private Reference patient; private Reference specimen; - private TMBResult value; + private TmbResult value; @JsonProperty("id") public String getId() { return id; } @@ -15,9 +15,9 @@ public class Tmb { public void setId(String value) { this.id = value; } @JsonProperty("interpretation") - public CodingTmbInterpretation getInterpretation() { return interpretation; } + public TmbInterpretationCoding getInterpretation() { return interpretation; } @JsonProperty("interpretation") - public void setInterpretation(CodingTmbInterpretation value) { this.interpretation = value; } + public void setInterpretation(TmbInterpretationCoding value) { this.interpretation = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } @@ -30,7 +30,7 @@ public class Tmb { public void setSpecimen(Reference value) { this.specimen = value; } @JsonProperty("value") - public TMBResult getValue() { return value; } + public TmbResult getValue() { return value; } @JsonProperty("value") - public void setValue(TMBResult value) { this.value = value; } + public void setValue(TmbResult value) { this.value = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TmbInterpretationCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TmbInterpretationCoding.java new file mode 100644 index 0000000..a61f27f --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TmbInterpretationCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class TmbInterpretationCoding { + private InterpretationCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public InterpretationCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(InterpretationCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TmbResult.java similarity index 94% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TmbResult.java index e49ae10..f2b0a54 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TMBResult.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TmbResult.java @@ -2,7 +2,7 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class TMBResult { +public class TmbResult { private String unit; private double value; diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java index f6041ca..24ef392 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TranscriptIdSystem.java @@ -4,21 +4,21 @@ import java.io.IOException; import com.fasterxml.jackson.annotation.*; public enum TranscriptIdSystem { - HTTPS_Www_ENSEMBL_ORG, HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ; + ENSEMBL_ORG, NCBI_NLM_NIH_GOV_REFSEQ; @JsonValue public String toValue() { switch (this) { - case HTTPS_Www_ENSEMBL_ORG: return "https://www.ensembl.org"; - case HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ: return "https://www.ncbi.nlm.nih.gov/refseq"; + case ENSEMBL_ORG: return "https://www.ensembl.org"; + case NCBI_NLM_NIH_GOV_REFSEQ: return "https://www.ncbi.nlm.nih.gov/refseq"; } return null; } @JsonCreator public static TranscriptIdSystem forValue(String value) throws IOException { - if (value.equals("https://www.ensembl.org")) return HTTPS_Www_ENSEMBL_ORG; - if (value.equals("https://www.ncbi.nlm.nih.gov/refseq")) return HTTPS_Www_NCBI_NLM_NIH_GOV_REFSEQ; + if (value.equals("https://www.ensembl.org")) return ENSEMBL_ORG; + if (value.equals("https://www.ncbi.nlm.nih.gov/refseq")) return NCBI_NLM_NIH_GOV_REFSEQ; throw new IOException("Cannot deserialize TranscriptIdSystem"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java index 3b4f970..9013408 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; public class TumorCellContent { private String id; - private CodingTumorCellContentMethod method; + private TumorCellContentMethodCoding method; private Reference patient; private Reference specimen; private double value; @@ -15,9 +15,9 @@ public class TumorCellContent { public void setId(String value) { this.id = value; } @JsonProperty("method") - public CodingTumorCellContentMethod getMethod() { return method; } + public TumorCellContentMethodCoding getMethod() { return method; } @JsonProperty("method") - public void setMethod(CodingTumorCellContentMethod value) { this.method = value; } + public void setMethod(TumorCellContentMethodCoding value) { this.method = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCoding.java new file mode 100644 index 0000000..18858ba --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class TumorCellContentMethodCoding { + private TumorCellContentMethodCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public TumorCellContentMethodCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(TumorCellContentMethodCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCodingCode.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCodingCode.java index bac8a5f..7d3e963 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorCellContentMethodCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethodCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTumorCellContentMethodCode { +public enum TumorCellContentMethodCodingCode { BIOINFORMATIC, HISTOLOGIC; @JsonValue @@ -16,9 +16,9 @@ public enum CodingTumorCellContentMethodCode { } @JsonCreator - public static CodingTumorCellContentMethodCode forValue(String value) throws IOException { + public static TumorCellContentMethodCodingCode forValue(String value) throws IOException { if (value.equals("bioinformatic")) return BIOINFORMATIC; if (value.equals("histologic")) return HISTOLOGIC; - throw new IOException("Cannot deserialize CodingTumorCellContentMethodCode"); + throw new IOException("Cannot deserialize TumorCellContentMethodCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java index 24aac0f..3e5ec8c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java @@ -4,7 +4,7 @@ import com.fasterxml.jackson.annotation.*; public class TumorMorphology { private String id; - private String notes; + private String note; private Reference patient; private Reference specimen; private Coding value; @@ -14,10 +14,10 @@ public class TumorMorphology { @JsonProperty("id") public void setId(String value) { this.id = value; } - @JsonProperty("notes") - public String getNotes() { return notes; } - @JsonProperty("notes") - public void setNotes(String value) { this.notes = value; } + @JsonProperty("note") + public String getNote() { return note; } + @JsonProperty("note") + public void setNote(String value) { this.note = value; } @JsonProperty("patient") public Reference getPatient() { return patient; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java index c971e19..097c26e 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java @@ -7,7 +7,7 @@ public class TumorSpecimen { private Reference diagnosis; private String id; private Reference patient; - private CodingTumorSpecimen type; + private TumorSpecimenCoding type; @JsonProperty("collection") public Collection getCollection() { return collection; } @@ -30,7 +30,7 @@ public class TumorSpecimen { public void setPatient(Reference value) { this.patient = value; } @JsonProperty("type") - public CodingTumorSpecimen getType() { return type; } + public TumorSpecimenCoding getType() { return type; } @JsonProperty("type") - public void setType(CodingTumorSpecimen value) { this.type = value; } + public void setType(TumorSpecimenCoding value) { this.type = value; } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCoding.java index 0f2431f..40db539 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimen.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorSpecimen { - private CodingTumorSpecimenCode code; +public class TumorSpecimenCoding { + private TumorSpecimenCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTumorSpecimenCode getCode() { return code; } + public TumorSpecimenCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTumorSpecimenCode value) { this.code = value; } + public void setCode(TumorSpecimenCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCodingCode.java similarity index 82% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCodingCode.java index d1afbd9..f8ff478 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTumorSpecimenCode { +public enum TumorSpecimenCodingCode { CRYO_FROZEN, FFPE, FRESH_TISSUE, LIQUID_BIOPSY, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum CodingTumorSpecimenCode { } @JsonCreator - public static CodingTumorSpecimenCode forValue(String value) throws IOException { + public static TumorSpecimenCodingCode forValue(String value) throws IOException { if (value.equals("cryo-frozen")) return CRYO_FROZEN; if (value.equals("FFPE")) return FFPE; if (value.equals("fresh-tissue")) return FRESH_TISSUE; if (value.equals("liquid-biopsy")) return LIQUID_BIOPSY; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingTumorSpecimenCode"); + throw new IOException("Cannot deserialize TumorSpecimenCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCoding.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCoding.java index ee99f7c..e7827f9 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorSpecimenCollectionLocalization { - private CodingTumorSpecimenCollectionLocalizationCode code; +public class TumorSpecimenCollectionLocalizationCoding { + private TumorSpecimenCollectionLocalizationCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTumorSpecimenCollectionLocalizationCode getCode() { return code; } + public TumorSpecimenCollectionLocalizationCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTumorSpecimenCollectionLocalizationCode value) { this.code = value; } + public void setCode(TumorSpecimenCollectionLocalizationCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCodingCode.java similarity index 83% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCodingCode.java index ad5e4e6..c35658f 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalizationCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalizationCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTumorSpecimenCollectionLocalizationCode { +public enum TumorSpecimenCollectionLocalizationCodingCode { CELLFREE_DNA, LOCAL_RECURRENCE, METASTASIS, PRIMARY_TUMOR, REGIONAL_LYMPH_NODES, UNKNOWN; @JsonValue @@ -20,13 +20,13 @@ public enum CodingTumorSpecimenCollectionLocalizationCode { } @JsonCreator - public static CodingTumorSpecimenCollectionLocalizationCode forValue(String value) throws IOException { + public static TumorSpecimenCollectionLocalizationCodingCode forValue(String value) throws IOException { if (value.equals("cellfree-dna")) return CELLFREE_DNA; if (value.equals("local-recurrence")) return LOCAL_RECURRENCE; if (value.equals("metastasis")) return METASTASIS; if (value.equals("primary-tumor")) return PRIMARY_TUMOR; if (value.equals("regional-lymph-nodes")) return REGIONAL_LYMPH_NODES; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingTumorSpecimenCollectionLocalizationCode"); + throw new IOException("Cannot deserialize TumorSpecimenCollectionLocalizationCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCoding.java similarity index 76% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCoding.java index 69563b3..99c9515 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorSpecimenCollectionMethod { - private CodingTumorSpecimenCollectionMethodCode code; +public class TumorSpecimenCollectionMethodCoding { + private TumorSpecimenCollectionMethodCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTumorSpecimenCollectionMethodCode getCode() { return code; } + public TumorSpecimenCollectionMethodCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTumorSpecimenCollectionMethodCode value) { this.code = value; } + public void setCode(TumorSpecimenCollectionMethodCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCodingCode.java similarity index 80% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCodingCode.java index 49f859d..e514d62 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethodCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionMethodCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTumorSpecimenCollectionMethodCode { +public enum TumorSpecimenCollectionMethodCodingCode { BIOPSY, CYTOLOGY, LIQUID_BIOPSY, RESECTION, UNKNOWN; @JsonValue @@ -19,12 +19,12 @@ public enum CodingTumorSpecimenCollectionMethodCode { } @JsonCreator - public static CodingTumorSpecimenCollectionMethodCode forValue(String value) throws IOException { + public static TumorSpecimenCollectionMethodCodingCode forValue(String value) throws IOException { if (value.equals("biopsy")) return BIOPSY; if (value.equals("cytology")) return CYTOLOGY; if (value.equals("liquid-biopsy")) return LIQUID_BIOPSY; if (value.equals("resection")) return RESECTION; if (value.equals("unknown")) return UNKNOWN; - throw new IOException("Cannot deserialize CodingTumorSpecimenCollectionMethodCode"); + throw new IOException("Cannot deserialize TumorSpecimenCollectionMethodCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java index 72dd26a..d22f7f8 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStaging.java @@ -6,7 +6,7 @@ import java.util.List; public class TumorStaging { private Date date; - private CodingTumorStagingMethod method; + private TumorStagingMethodCoding method; private List otherClassifications; private TnmClassification tnmClassification; @@ -18,9 +18,9 @@ public class TumorStaging { public void setDate(Date value) { this.date = value; } @JsonProperty("method") - public CodingTumorStagingMethod getMethod() { return method; } + public TumorStagingMethodCoding getMethod() { return method; } @JsonProperty("method") - public void setMethod(CodingTumorStagingMethod value) { this.method = value; } + public void setMethod(TumorStagingMethodCoding value) { this.method = value; } @JsonProperty("otherClassifications") public List getOtherClassifications() { return otherClassifications; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCoding.java similarity index 78% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCoding.java index d49812f..64507e0 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethod.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCoding.java @@ -2,16 +2,16 @@ package dev.pcvolkmer.mv64e.mtb; import com.fasterxml.jackson.annotation.*; -public class CodingTumorStagingMethod { - private CodingTumorStagingMethodCode code; +public class TumorStagingMethodCoding { + private TumorStagingMethodCodingCode code; private String display; private String system; private String version; @JsonProperty("code") - public CodingTumorStagingMethodCode getCode() { return code; } + public TumorStagingMethodCodingCode getCode() { return code; } @JsonProperty("code") - public void setCode(CodingTumorStagingMethodCode value) { this.code = value; } + public void setCode(TumorStagingMethodCodingCode value) { this.code = value; } @JsonProperty("display") public String getDisplay() { return display; } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCodingCode.java similarity index 72% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCodingCode.java index 9f48c71..0b01f8c 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorStagingMethodCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/TumorStagingMethodCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingTumorStagingMethodCode { +public enum TumorStagingMethodCodingCode { CLINICAL, PATHOLOGIC; @JsonValue @@ -16,9 +16,9 @@ public enum CodingTumorStagingMethodCode { } @JsonCreator - public static CodingTumorStagingMethodCode forValue(String value) throws IOException { + public static TumorStagingMethodCodingCode forValue(String value) throws IOException { if (value.equals("clinical")) return CLINICAL; if (value.equals("pathologic")) return PATHOLOGIC; - throw new IOException("Cannot deserialize CodingTumorStagingMethodCode"); + throw new IOException("Cannot deserialize TumorStagingMethodCodingCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueCode.java similarity index 74% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/ValueCode.java index db0afd2..847bc49 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/CodingMtbDiagnosisCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/ValueCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum CodingMtbDiagnosisCode { +public enum ValueCode { MAIN, METACHRONOUS, SECONDARY; @JsonValue @@ -17,10 +17,10 @@ public enum CodingMtbDiagnosisCode { } @JsonCreator - public static CodingMtbDiagnosisCode forValue(String value) throws IOException { + public static ValueCode forValue(String value) throws IOException { if (value.equals("main")) return MAIN; if (value.equals("metachronous")) return METACHRONOUS; if (value.equals("secondary")) return SECONDARY; - throw new IOException("Cannot deserialize CodingMtbDiagnosisCode"); + throw new IOException("Cannot deserialize ValueCode"); } } diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCoding.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCoding.java new file mode 100644 index 0000000..1d9c95a --- /dev/null +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCoding.java @@ -0,0 +1,30 @@ +package dev.pcvolkmer.mv64e.mtb; + +import com.fasterxml.jackson.annotation.*; + +public class VitalStatusCoding { + private VitalStatusCodingCode code; + private String display; + private String system; + private String version; + + @JsonProperty("code") + public VitalStatusCodingCode getCode() { return code; } + @JsonProperty("code") + public void setCode(VitalStatusCodingCode value) { this.code = value; } + + @JsonProperty("display") + public String getDisplay() { return display; } + @JsonProperty("display") + public void setDisplay(String value) { this.display = value; } + + @JsonProperty("system") + public String getSystem() { return system; } + @JsonProperty("system") + public void setSystem(String value) { this.system = value; } + + @JsonProperty("version") + public String getVersion() { return version; } + @JsonProperty("version") + public void setVersion(String value) { this.version = value; } +} diff --git a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCodingCode.java similarity index 79% rename from src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java rename to src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCodingCode.java index 1bd604f..24a25c1 100644 --- a/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCode.java +++ b/src/main/java/dev/pcvolkmer/mv64e/mtb/VitalStatusCodingCode.java @@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb; import java.io.IOException; import com.fasterxml.jackson.annotation.*; -public enum VitalStatusCode { +public enum VitalStatusCodingCode { ALIVE, DECEASED; @JsonValue @@ -16,9 +16,9 @@ public enum VitalStatusCode { } @JsonCreator - public static VitalStatusCode forValue(String value) throws IOException { + public static VitalStatusCodingCode forValue(String value) throws IOException { if (value.equals("alive")) return ALIVE; if (value.equals("deceased")) return DECEASED; - throw new IOException("Cannot deserialize VitalStatusCode"); + throw new IOException("Cannot deserialize VitalStatusCodingCode"); } } diff --git a/src/test/resources/mv64e-mtb-fake-patient.json b/src/test/resources/mv64e-mtb-fake-patient.json index c82d951..5895be5 100644 --- a/src/test/resources/mv64e-mtb-fake-patient.json +++ b/src/test/resources/mv64e-mtb-fake-patient.json @@ -1,2243 +1,2606 @@ { - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "gender" : { - "code" : "female", - "display" : "Weiblich", - "system" : "Gender" + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "gender": { + "code": "male", + "display": "Männlich", + "system": "Gender" }, - "birthDate" : "1956-02-25", - "dateOfDeath" : "2007-02-25", - "healthInsurance" : { - "type" : { - "code" : "GKV", - "display" : "gesetzliche Krankenversicherung", - "system" : "http://fhir.de/CodeSystem/versicherungsart-de-basis" + "birthDate": "1993-08-01", + "healthInsurance": { + "type": { + "code": "GKV", + "display": "gesetzliche Krankenversicherung", + "system": "http://fhir.de/CodeSystem/versicherungsart-de-basis" }, - "reference" : { - "id" : "1234567890", - "system" : "https://www.dguv.de/arge-ik", - "display" : "AOK", - "type" : "HealthInsurance" + "reference": { + "id": "1234567890", + "system": "https://www.dguv.de/arge-ik", + "display": "AOK", + "type": "HealthInsurance" } }, - "address" : { - "municipalityCode" : "12345" + "address": { + "municipalityCode": "12345" }, - "age" : { - "value" : 51, - "unit" : "Years" + "age": { + "value": 31, + "unit": "Years" }, - "vitalStatus" : { - "code" : "deceased", - "display" : "Verstorben", - "system" : "dnpm-dip/patient/vital-status" + "vitalStatus": { + "code": "alive", + "display": "Lebend", + "system": "dnpm-dip/patient/vital-status" } }, - "episodesOfCare" : [ { - "id" : "a95f44a6-5dbb-4acd-9d52-05db10f8410b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" + "episodesOfCare": [ + { + "id": "dc4d1b2c-7468-4a4a-8fbd-1b0bb645c082", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "period": { + "start": "2024-11-30" + }, + "diagnoses": [ + { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "type": "MTBDiagnosis" + } + ] + } + ], + "diagnoses": [ + { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "recordedOn": "2022-09-01", + "type": { + "history": [ + { + "value": { + "code": "main", + "display": "Hauptdiagnose", + "system": "dnpm-dip/mtb/diagnosis/type" + }, + "date": "2022-09-01" + } + ] + }, + "code": { + "code": "C57.0", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "system": 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