From 1cefda4bbaf3913e17f722f2e5b5fa261765bb33 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Fri, 30 May 2025 16:28:22 +0200 Subject: [PATCH] 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": "http://fhir.de/CodeSystem/bfarm/icd-10-gm", + "version": "2025" + }, + "topography": { + "code": "C57.0", + "display": "Eileiter", + "system": "urn:oid:2.16.840.1.113883.6.43.1", + "version": "Zweite Revision" + }, + "grading": { + "history": [ + { + "date": "2022-09-01", + "codes": [ + { + "code": "4", + "display": "4 = undifferenziert", + "system": "https://www.basisdatensatz.de/feld/161/grading" + }, + { + "code": "1", + "display": "Pilocytic astrocytoma", + "system": "dnpm-dip/mtb/who-grading-cns-tumors", + "version": "2021" + } + ] + } + ] + }, + "staging": { + "history": [ + { + "date": "2022-09-01", + "method": { + "code": "clinical", + "display": "Klinisch", + "system": "dnpm-dip/mtb/tumor-staging/method" + }, + "tnmClassification": { + "tumor": { + "code": "T1", + "system": "UICC" + }, + "nodes": { + "code": "N3", + "system": "UICC" + }, + "metastasis": { + "code": "M0", + "system": "UICC" + } + }, + "otherClassifications": [ + { + "code": "local", + "display": "Lokal", + "system": "dnpm-dip/mtb/diagnosis/kds-tumor-spread" + } + ] + } + ] + }, + "guidelineTreatmentStatus": { + "code": "no-guidelines-available", + "display": "Keine Leitlinien vorhanden", + "system": "dnpm-dip/mtb/diagnosis/guideline-treatment-status" + }, + "notes": [ + "Notes on the tumor diagnosis..." + ] + } + ], + "guidelineTherapies": [ + { + "id": "b63bcd3e-1bbb-425d-bd4f-03820036e249", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "therapyLine": 8, + "intent": { + "code": "X", + "display": "Keine Angabe", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "S", + "display": "Sonstiges", + "system": "dnpm-dip/therapy/category" + }, + "recordedOn": "2025-05-30", + "status": { + "code": "stopped", + "display": "Abgebrochen", + "system": "dnpm-dip/therapy/status" + }, + "statusReason": { + "code": "progression", + "display": "Progression", + "system": "dnpm-dip/therapy/status-reason" + }, + "period": { + "start": "2024-05-30", + "end": "2024-08-22" + }, + "medication": [ + { + "code": "L01XX57", + "display": "Plitidepsin", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] }, - "period" : { - "start" : "2024-10-03" - }, - "diagnoses" : [ { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "type" : "MTBDiagnosis" - } ] - } ], - "diagnoses" : [ { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "recordedOn" : "2004-01-25", - "type" : { - "history" : [ { - "value" : { - "code" : "main", - "display" : "Hauptdiagnose", - "system" : "dnpm-dip/mtb/diagnosis/type" + { + "id": "d7de61c1-a5cc-429b-9c6f-e47765828f90", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": 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