From ad51926bbb062be0970064e4869327b41dea29f5 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Sat, 5 Apr 2025 15:44:43 +0200 Subject: [PATCH] chore: update to DNPM-Datamodel 2.1 preview --- src/lib.rs | 32 +- src/mtb.rs | 1887 ++++++++++++++++-------- tests/mv64e-mtb-fake-patient.json | 2244 ++++++++++++++++++++++++++++- 3 files changed, 3561 insertions(+), 602 deletions(-) diff --git a/src/lib.rs b/src/lib.rs index 492b0d2..46a31c6 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -58,37 +58,45 @@ impl Mtb { care_plans: None, claim_responses: None, claims: None, - diagnoses: None, + diagnoses: vec![], performance_status: None, - episode: None, - episodes_of_care: None, - genetic_counselling_requests: None, + episodes_of_care: vec![], histology_reports: None, guideline_therapies: None, - molecular_therapies: None, ngs_reports: None, ihc_reports: None, - patient: MtbPatient { - address: None, + patient: Patient { + address: Address { + municipality_code: String::new(), + }, age: None, birth_date: String::new(), date_of_death: None, gender: CodingGender { - code: Gender::Male, + code: GenderCode::Female, display: None, system: None, version: None, }, id: patient_id.to_string(), - health_insurance: None, + health_insurance: HealthInsurance { + health_insurance_type: CodingHealthInsurance { + code: CodingHealthInsuranceCode::Bei, + display: None, + system: None, + version: None, + }, + reference: None, + }, vital_status: None, + managing_site: None, }, - recommendations: None, responses: None, specimens: None, - study_inclusion_requests: None, guideline_procedures: None, - therapies: None, + follow_ups: None, + prior_diagnostic_reports: None, + systemic_therapies: None, } } } diff --git a/src/mtb.rs b/src/mtb.rs index 83b4a06..03166a3 100644 --- a/src/mtb.rs +++ b/src/mtb.rs @@ -13,23 +13,18 @@ pub struct Mtb { #[serde(skip_serializing_if = "Option::is_none")] pub claims: Option>, - #[serde(skip_serializing_if = "Option::is_none")] - pub diagnoses: Option>, + pub diagnoses: Vec, + + pub episodes_of_care: Vec, #[serde(skip_serializing_if = "Option::is_none")] - pub episode: Option, + pub follow_ups: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub episodes_of_care: Option>, + pub guideline_procedures: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub genetic_counselling_requests: Option>, - - #[serde(skip_serializing_if = "Option::is_none")] - pub guideline_procedures: Option>, - - #[serde(skip_serializing_if = "Option::is_none")] - pub guideline_therapies: Option>, + pub guideline_therapies: Option>, #[serde(skip_serializing_if = "Option::is_none")] pub histology_reports: Option>, @@ -38,18 +33,15 @@ pub struct Mtb { pub ihc_reports: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub molecular_therapies: Option>, + pub ngs_reports: Option>, - #[serde(skip_serializing_if = "Option::is_none")] - pub ngs_reports: Option>, - - pub patient: MtbPatient, + pub patient: Patient, #[serde(skip_serializing_if = "Option::is_none")] pub performance_status: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub recommendations: Option>, + pub prior_diagnostic_reports: Option>, #[serde(skip_serializing_if = "Option::is_none")] pub responses: Option>, @@ -58,10 +50,7 @@ pub struct Mtb { pub specimens: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub study_inclusion_requests: Option>, - - #[serde(skip_serializing_if = "Option::is_none")] - pub therapies: Option>, + pub systemic_therapies: Option>, } #[derive(Debug, Serialize, Deserialize)] @@ -69,35 +58,37 @@ pub struct Mtb { #[serde(rename_all = "camelCase")] pub struct MtbCarePlan { #[serde(skip_serializing_if = "Option::is_none")] - pub diagnosis: Option, + pub genetic_counseling_recommendation: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub genetic_counseling_recommendation: Option, + pub histology_reevaluation_requests: Option>, pub id: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub indication: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, + pub issued_on: String, #[serde(skip_serializing_if = "Option::is_none")] pub medication_recommendations: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub no_target_finding: Option, + pub notes: Option>, + + pub patient: Reference, #[serde(skip_serializing_if = "Option::is_none")] - pub notes: Option, - - pub patient: Patient, + pub procedure_recommendations: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub status_reason: Option, + pub reason: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub study_enrollment_recommendations: Option>, + pub rebiopsy_requests: Option>, + + #[serde(skip_serializing_if = "Option::is_none")] + pub status_reason: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub study_enrollment_recommendations: Option>, } #[derive(Debug, Serialize, Deserialize)] @@ -106,42 +97,11 @@ pub struct MtbCarePlan { pub struct GeneticCounselingRecommendation { pub id: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, + pub issued_on: String, - pub patient: Patient, + pub patient: Reference, - pub reason: Coding, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct Patient { - pub id: String, - - #[serde(rename = "type")] - pub patient_type: PatientType, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum PatientType { - Patient, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct Coding { - pub code: String, - - #[serde(skip_serializing_if = "Option::is_none")] - pub display: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub version: Option, + pub reason: CodingGeneticCounselingRecommendationReason, } #[derive(Debug, Serialize, Deserialize)] @@ -155,36 +115,122 @@ pub struct Reference { #[serde(rename = "type")] #[serde(skip_serializing_if = "Option::is_none")] pub reference_type: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingGeneticCounselingRecommendationReason { + pub code: ReasonCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum ReasonCode { + #[serde(rename = "family-anamnesis")] + FamilyAnamnesis, + + Other, + + #[serde(rename = "secondary-tumor")] + SecondaryTumor, + + #[serde(rename = "self-anamnesis")] + SelfAnamnesis, + + Unknown, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "camelCase")] +pub struct HistologyReevaluationRequest { + pub id: String, + + pub issued_on: String, + + pub patient: Reference, + + pub specimen: Reference, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct MtbMedicationRecommendation { + #[serde(skip_serializing_if = "Option::is_none")] + pub category: Option, + pub id: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub indication: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, + pub issued_on: String, #[serde(skip_serializing_if = "Option::is_none")] pub level_of_evidence: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub medication: Option>, + pub medication: Vec, + + pub patient: Reference, + + pub priority: CodingRecommendationPriority, #[serde(skip_serializing_if = "Option::is_none")] - pub ngs_report: Option, - - pub patient: Patient, + pub reason: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub priority: Option, + pub supporting_variants: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub supporting_variants: Option>, + pub use_type: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbMedicationRecommendationCategory { + pub code: CodingMtbMedicationRecommendationCategoryCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum CodingMtbMedicationRecommendationCategoryCode { + #[serde(rename = "CH")] + Ch, + + #[serde(rename = "HO")] + Ho, + + #[serde(rename = "IM")] + Im, + + #[serde(rename = "SO")] + So, + + #[serde(rename = "SZ")] + Sz, + + #[serde(rename = "ZS")] + Zs, } #[derive(Debug, Serialize, Deserialize)] @@ -196,7 +242,7 @@ pub struct LevelOfEvidence { pub grading: CodingLevelOfEvidenceGrading, #[serde(skip_serializing_if = "Option::is_none")] - pub publications: Option>, + pub publications: Option>, } #[derive(Debug, Serialize, Deserialize)] @@ -231,7 +277,7 @@ pub enum AddendumCode { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingLevelOfEvidenceGrading { - pub code: GradingCode, + pub code: LevelOfEvidenceCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, @@ -246,7 +292,7 @@ pub struct CodingLevelOfEvidenceGrading { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub enum GradingCode { +pub enum LevelOfEvidenceCode { #[serde(rename = "m1A")] M1A, @@ -274,78 +320,99 @@ pub enum GradingCode { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -#[serde(rename_all = "camelCase")] -pub struct ReferencePublication { +pub struct PublicationReference { #[serde(skip_serializing_if = "Option::is_none")] - pub ext_id: Option, + pub display: Option, + + pub id: String, #[serde(rename = "type")] #[serde(skip_serializing_if = "Option::is_none")] - pub reference_publication_type: Option, + pub publication_reference_type: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub uri: Option, + pub system: PublicationSystem, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct ExtId { - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, - - pub value: String, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum ExtIdSystem { - #[serde(rename = "https://pubmed.ncbi.nlm.nih.gov/")] +pub enum PublicationSystem { + #[serde(rename = "https://pubmed.ncbi.nlm.nih.gov")] HttpsPubmedNcbiNlmNihGov, + + #[serde(rename = "https://www.doi.org")] + HttpsWwwDoiOrg, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct CodingTherapyRecommendationPriority { - pub code: TherapyRecommendationPriority, +pub struct CodingAtcUnregisteredMedication { + pub code: String, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + pub system: RequestedMedicationSystem, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "snake_case")] +pub enum RequestedMedicationSystem { + #[serde(rename = "http://fhir.de/CodeSystem/bfarm/atc")] + HttpFhirDeCodeSystemBfarmAtc, + + Undefined, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingRecommendationPriority { + pub code: PriorityCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum TherapyRecommendationPriority { - #[serde(rename = "1")] - Prio1, - - #[serde(rename = "2")] - Prio2, - - #[serde(rename = "3")] - Prio3, - - #[serde(rename = "4")] - Prio4, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -#[serde(rename_all = "camelCase")] -pub struct NoTargetFinding { - pub diagnosis: String, #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, - - pub patient: Patient, + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct CodingCarePlanStatusReason { +pub enum PriorityCode { + #[serde(rename = "1")] + The1, + + #[serde(rename = "2")] + The2, + + #[serde(rename = "3")] + The3, + + #[serde(rename = "4")] + The4, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct GeneAlterationReference { + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub gene: Option, + + pub variant: Reference, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct Coding { pub code: String, #[serde(skip_serializing_if = "Option::is_none")] @@ -353,49 +420,222 @@ pub struct CodingCarePlanStatusReason { #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbMedicationRecommendationUseType { + pub code: UseTypeCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum UseTypeCode { + Compassionate, + + #[serde(rename = "in-label")] + InLabel, + + #[serde(rename = "off-label")] + OffLabel, + + #[serde(rename = "sec-preventive")] + SecPreventive, + + Unknown, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct StudyEnrollmentRecommendation { +pub struct ProcedureRecommendation { + pub code: CodingMtbProcedureRecommendationCategory, + pub id: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, + pub issued_on: String, #[serde(skip_serializing_if = "Option::is_none")] - pub level_of_evidence: Option, + pub level_of_evidence: Option, - pub patient: Patient, + pub patient: Reference, - pub reason: Reference, - - pub studies: Vec, + pub priority: CodingRecommendationPriority, #[serde(skip_serializing_if = "Option::is_none")] - pub supporting_variants: Option>, + pub reason: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub supporting_variants: Option>, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct Study { - pub system: String, +pub struct CodingMtbProcedureRecommendationCategory { + pub code: CodingMtbProcedureRecommendationCategoryCode, - pub value: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum CodingMtbProcedureRecommendationCategoryCode { + #[serde(rename = "AS")] + As, + + #[serde(rename = "OP")] + Op, + + #[serde(rename = "SO")] + So, + + #[serde(rename = "ST")] + St, + + #[serde(rename = "WS")] + Ws, + + #[serde(rename = "WW")] + Ww, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "camelCase")] +pub struct RebiopsyRequest { + pub id: String, + + pub issued_on: String, + + pub patient: Reference, + + pub tumor_entity: Reference, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbCarePlanStatusReason { + pub code: CodingMtbCarePlanStatusReasonCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum CodingMtbCarePlanStatusReasonCode { + #[serde(rename = "no-target")] + NoTarget, + + #[serde(rename = "non-genetic-cause")] + NonGeneticCause, + + #[serde(rename = "not-rare-disease")] + NotRareDisease, + + Other, + + Psychosomatic, + + #[serde(rename = "targeted-diagnostics-recommended")] + TargetedDiagnosticsRecommended, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "camelCase")] +pub struct MtbStudyEnrollmentRecommendation { + pub id: String, + + pub issued_on: String, + + #[serde(skip_serializing_if = "Option::is_none")] + pub level_of_evidence: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub medication: Option>, + + pub patient: Reference, + + pub priority: CodingRecommendationPriority, + + pub reason: Reference, + + pub study: Vec, + + #[serde(skip_serializing_if = "Option::is_none")] + pub supporting_variants: Option>, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct StudyReference { + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + pub id: String, + + #[serde(rename = "type")] + #[serde(skip_serializing_if = "Option::is_none")] + pub study_reference_type: Option, + + pub system: StudySystem, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum StudySystem { + #[serde(rename = "DRKS")] + Drks, + + #[serde(rename = "EUDAMED")] + Eudamed, + + #[serde(rename = "Eudra-CT")] + EudraCt, + + #[serde(rename = "NCT")] + Nct, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct ClaimResponse { - pub claim: ClaimResponseClaim, + pub claim: Reference, pub id: String, pub issued_on: String, - pub patient: Patient, + pub patient: Reference, pub status: CodingClaimResponseStatus, @@ -403,39 +643,25 @@ pub struct ClaimResponse { pub status_reason: Option, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct ClaimResponseClaim { - #[serde(rename = "type")] - #[serde(skip_serializing_if = "Option::is_none")] - pub claim_response_claim_type: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub id: Option, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum ClaimResponseClaimType { - Claim, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingClaimResponseStatus { - pub code: ClaimResponseStatus, + pub code: CodingClaimResponseStatusCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "snake_case")] -pub enum ClaimResponseStatus { +pub enum CodingClaimResponseStatusCode { Accepted, Rejected, @@ -446,19 +672,22 @@ pub enum ClaimResponseStatus { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingClaimResponseStatusReason { - pub code: ClaimResponseStatusReason, + pub code: CodingClaimResponseStatusReasonCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum ClaimResponseStatusReason { +pub enum CodingClaimResponseStatusReasonCode { #[serde(rename = "approval-revocation")] ApprovalRevocation, @@ -490,73 +719,20 @@ pub struct Claim { pub issued_on: String, - pub patient: Patient, + pub patient: Reference, + + pub recommendation: Reference, #[serde(skip_serializing_if = "Option::is_none")] - pub recommendation: Option, + pub requested_medication: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub stage: Option, + pub stage: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct Recommendation { - pub id: String, - - #[serde(rename = "type")] - pub recommendation_type: String, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -#[serde(rename_all = "camelCase")] -pub struct MtbDiagnosis { - pub code: Coding, - - #[serde(skip_serializing_if = "Option::is_none")] - pub guideline_treatment_status: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub histology_results: Option>, - - #[serde(skip_serializing_if = "Option::is_none")] - pub icd_o3_t: Option, - - pub id: String, - - pub patient: Patient, - - #[serde(skip_serializing_if = "Option::is_none")] - pub recorded_on: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub stage_history: Option>, - - #[serde(skip_serializing_if = "Option::is_none")] - pub topography: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub tumor_grade: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub who_grade: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub who_grading: Option, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct StageHistory { - pub date: String, - - pub stage: CodingTumorSpread, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingTumorSpread { +pub struct CodingClaimStage { pub code: StageCode, #[serde(skip_serializing_if = "Option::is_none")] @@ -564,32 +740,6 @@ pub struct CodingTumorSpread { #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -#[serde(rename_all = "kebab-case")] -pub enum StageCode { - Local, - - Metastasized, - - #[serde(rename = "tumor-free")] - TumorFree, - - Unknown, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingTumorGrade { - pub code: TumorGradeCode, - - #[serde(skip_serializing_if = "Option::is_none")] - pub display: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, #[serde(skip_serializing_if = "Option::is_none")] pub version: Option, @@ -597,32 +747,214 @@ pub struct CodingTumorGrade { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub enum TumorGradeCode { - G1, +#[serde(rename_all = "kebab-case")] +pub enum StageCode { + #[serde(rename = "follow-up-claim")] + FollowUpClaim, - G2, + #[serde(rename = "initial-claim")] + InitialClaim, - G3, + Revocation, - G4, - - #[serde(rename = "GX")] - Gx, + Unknown, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct MtbEpisode { +#[serde(rename_all = "camelCase")] +pub struct MtbDiagnosis { + pub code: Coding, + + #[serde(skip_serializing_if = "Option::is_none")] + pub germline_codes: Option>, + + #[serde(skip_serializing_if = "Option::is_none")] + pub grading: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub guideline_treatment_status: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub histology: Option>, + pub id: String, - pub patient: Patient, + #[serde(rename = "type")] + pub mtb_diagnosis_type: Type, - pub period: PeriodLocalDate, + #[serde(skip_serializing_if = "Option::is_none")] + pub notes: Option>, + + pub patient: Reference, + + #[serde(skip_serializing_if = "Option::is_none")] + pub recorded_on: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub staging: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub topography: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct PeriodLocalDate { +pub struct Grading { + pub history: Vec, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct TumorGrading { + pub codes: Vec, + + pub date: String, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbDiagnosisGuidelineTreatmentStatus { + pub code: GuidelineTreatmentStatusCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum GuidelineTreatmentStatusCode { + Exhausted, + + Impossible, + + #[serde(rename = "no-guidelines-available")] + NoGuidelinesAvailable, + + #[serde(rename = "non-exhausted")] + NonExhausted, + + Unknown, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct Type { + pub history: Vec, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct History { + pub date: String, + + pub value: CodingMtbDiagnosis, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbDiagnosis { + pub code: CodingMtbDiagnosisCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "snake_case")] +pub enum CodingMtbDiagnosisCode { + Main, + + Metachronous, + + Secondary, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct Staging { + pub history: Vec, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "camelCase")] +pub struct TumorStaging { + pub date: String, + + pub method: CodingTumorStagingMethod, + + #[serde(skip_serializing_if = "Option::is_none")] + pub other_classifications: Option>, + + #[serde(skip_serializing_if = "Option::is_none")] + pub tnm_classification: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingTumorStagingMethod { + pub code: CodingTumorStagingMethodCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "snake_case")] +pub enum CodingTumorStagingMethodCode { + Clinical, + + Pathologic, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct TnmClassification { + pub metastasis: Coding, + + pub nodes: Coding, + + pub tumor: Coding, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct MtbEpisodeOfCare { + #[serde(skip_serializing_if = "Option::is_none")] + pub diagnoses: Option>, + + pub id: String, + + pub patient: Reference, + + pub period: PeriodDate, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct PeriodDate { #[serde(skip_serializing_if = "Option::is_none")] pub end: Option, @@ -631,51 +963,68 @@ pub struct PeriodLocalDate { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct EpisodeOfCare { +#[serde(rename_all = "camelCase")] +pub struct FollowUp { + pub date: String, + #[serde(skip_serializing_if = "Option::is_none")] - pub diagnoses: Option>, + pub patient_status: Option, +} - pub id: String, +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingFollowUpPatientStatus { + pub code: PatientStatusCode, - pub patient: Reference, + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, - pub period: PeriodLocalDate, + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum PatientStatusCode { + #[serde(rename = "lost-to-fu")] + LostToFu, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct OncoProdecure { +pub struct OncoProcedure { #[serde(skip_serializing_if = "Option::is_none")] - pub based_on: Option, + pub based_on: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub code: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub diagnosis: Option, + pub code: CodingOncoProcedure, pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub indication: Option, + pub intent: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub notes: Option, + pub notes: Option>, - pub patient: Patient, + pub patient: Reference, #[serde(skip_serializing_if = "Option::is_none")] - pub period: Option, + pub period: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub recorded_on: Option, + pub reason: Option, + + pub recorded_on: String, + + pub status: CodingTherapyStatus, #[serde(skip_serializing_if = "Option::is_none")] - pub status: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub status_reason: Option, + pub status_reason: Option, #[serde(skip_serializing_if = "Option::is_none")] pub therapy_line: Option, @@ -683,20 +1032,78 @@ pub struct OncoProdecure { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct CodingTherapyStatus { - pub code: TherapyStatus, +pub struct CodingOncoProcedure { + pub code: CodingOncoProcedureCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum TherapyStatus { +pub enum CodingOncoProcedureCode { + #[serde(rename = "nuclear-medicine")] + NuclearMedicine, + + #[serde(rename = "radio-therapy")] + RadioTherapy, + + Surgery, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbTherapyIntent { + pub code: IntentCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum IntentCode { + K, + + P, + + S, + + X, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingTherapyStatus { + pub code: CodingTherapyStatusCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum CodingTherapyStatusCode { Completed, #[serde(rename = "not-done")] @@ -712,8 +1119,8 @@ pub enum TherapyStatus { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct CodingTherapyStatusReason { - pub code: StatusReasonCode, +pub struct CodingMtbTherapyStatusReason { + pub code: CodingMtbTherapyStatusReasonCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, @@ -728,20 +1135,20 @@ pub struct CodingTherapyStatusReason { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum StatusReasonCode { +pub enum CodingMtbTherapyStatusReasonCode { + #[serde(rename = "best-supportive-care")] + BestSupportiveCare, + #[serde(rename = "chronic-remission")] ChronicRemission, - #[serde(rename = "continued-externally")] - ContinuedExternally, - Deterioration, #[serde(rename = "lost-to-fu")] LostToFu, - #[serde(rename = "medical-reason")] - MedicalReason, + #[serde(rename = "medical-reasons")] + MedicalReasons, #[serde(rename = "no-indication")] NoIndication, @@ -771,50 +1178,114 @@ pub enum StatusReasonCode { Progression, - Toxicity, + #[serde(rename = "regular-completion")] + RegularCompletion, - Unknown, + #[serde(rename = "regular-completion-with-dosage-reduction")] + RegularCompletionWithDosageReduction, + + #[serde(rename = "regular-completion-with-substance-change")] + RegularCompletionWithSubstanceChange, + + Toxicity, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct MtbMedicationTherapy { +pub struct MtbSystemicTherapy { #[serde(skip_serializing_if = "Option::is_none")] pub based_on: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub diagnosis: Option, + pub category: Option, pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub indication: Option, + pub intent: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub medication: Option>, + pub medication: Option>, #[serde(skip_serializing_if = "Option::is_none")] - pub notes: Option, + pub notes: Option>, - pub patient: Patient, + pub patient: Reference, #[serde(skip_serializing_if = "Option::is_none")] - pub period: Option, + pub period: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub recorded_on: Option, + pub reason: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub status: Option, + pub recommendation_fulfillment_status: Option, + + pub recorded_on: String, + + pub status: CodingTherapyStatus, #[serde(skip_serializing_if = "Option::is_none")] - pub status_reason: Option, + pub status_reason: Option, #[serde(skip_serializing_if = "Option::is_none")] pub therapy_line: Option, } +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbSystemicTherapyCategory { + pub code: CodingMtbSystemicTherapyCategoryCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum CodingMtbSystemicTherapyCategoryCode { + A, + + I, + + N, + + O, + + S, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMtbSystemicTherapyRecommendationFulfillmentStatus { + pub code: RecommendationFulfillmentStatusCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "snake_case")] +pub enum RecommendationFulfillmentStatusCode { + Complete, + + Partial, +} + #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] @@ -823,18 +1294,19 @@ pub struct HistologyReport { pub issued_on: String, - pub patient: Patient, + pub patient: Reference, pub results: HistologyReportResults, - pub specimen: HistologyReportSpecimen, + pub specimen: Reference, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct HistologyReportResults { - pub tumor_cell_content: TumorCellContent, + #[serde(skip_serializing_if = "Option::is_none")] + pub tumor_cell_content: Option, pub tumor_morphology: TumorMorphology, } @@ -846,10 +1318,9 @@ pub struct TumorCellContent { pub method: CodingTumorCellContentMethod, - #[serde(skip_serializing_if = "Option::is_none")] - pub patient: Option, + pub patient: Reference, - pub specimen: TumorCellContentSpecimen, + pub specimen: Reference, pub value: f64, } @@ -857,40 +1328,27 @@ pub struct TumorCellContent { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingTumorCellContentMethod { - pub code: TumorCellContentMethod, + pub code: CodingTumorCellContentMethodCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "snake_case")] -pub enum TumorCellContentMethod { +pub enum CodingTumorCellContentMethodCode { Bioinformatic, Histologic, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct TumorCellContentSpecimen { - pub id: String, - - #[serde(rename = "type")] - pub specimen_type: SpecimenType, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum SpecimenType { - #[serde(rename = "TumorSpecimen")] - TumorSpecimen, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct TumorMorphology { @@ -899,65 +1357,45 @@ pub struct TumorMorphology { #[serde(skip_serializing_if = "Option::is_none")] pub notes: Option, - pub patient: Patient, + pub patient: Reference, - pub specimen: TumorMorphologySpecimen, + pub specimen: Reference, pub value: Coding, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct TumorMorphologySpecimen { - pub id: String, - - #[serde(rename = "type")] - pub specimen_type: SpecimenType, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct HistologyReportSpecimen { - pub id: String, - - #[serde(rename = "type")] - pub specimen_type: SpecimenType, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct IhcReport { - pub block_id: ExternalId, - - pub date: String, + pub block_ids: Vec, pub id: String, - pub journal_id: ExternalId, + pub issued_on: String, - pub msi_mmr_results: Vec, + pub journal_id: String, pub patient: Reference, - pub protein_expression_results: Vec, + pub results: IhcReportResults, pub specimen: Reference, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct ExternalId { - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, +#[serde(rename_all = "camelCase")] +pub struct IhcReportResults { + pub msi_mmr: Vec, - pub value: String, + pub protein_expression: Vec, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct MsiMmrResult { +pub struct MsiMmr { #[serde(skip_serializing_if = "Option::is_none")] pub ic_score: Option, @@ -995,16 +1433,16 @@ pub struct CodingProteinExpressionIcScore { #[serde(deny_unknown_fields)] pub enum IcScoreCode { #[serde(rename = "0")] - Code0, + The0, #[serde(rename = "1")] - Code1, + The1, #[serde(rename = "2")] - Code2, + The2, #[serde(rename = "3")] - Code3, + The3, } #[derive(Debug, Serialize, Deserialize)] @@ -1026,25 +1464,25 @@ pub struct CodingProteinExpressionTcScore { #[serde(deny_unknown_fields)] pub enum TcScoreCode { #[serde(rename = "0")] - Code0, + The0, #[serde(rename = "1")] - Code1, + The1, #[serde(rename = "2")] - Code2, + The2, #[serde(rename = "3")] - Code3, + The3, #[serde(rename = "4")] - Code4, + The4, #[serde(rename = "5")] - Code5, + The5, #[serde(rename = "6")] - Code6, + The6, } #[derive(Debug, Serialize, Deserialize)] @@ -1072,13 +1510,13 @@ pub enum ProteinExpressionResultCode { NotExp, #[serde(rename = "1+")] - Code1Plus, + The1, #[serde(rename = "2+")] - Code2Plus, + The2, #[serde(rename = "3+")] - Code3Plus, + The3, Unknown, } @@ -1086,7 +1524,7 @@ pub enum ProteinExpressionResultCode { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct ProteinExpressionResult { +pub struct ProteinExpression { #[serde(skip_serializing_if = "Option::is_none")] pub ic_score: Option, @@ -1105,40 +1543,30 @@ pub struct ProteinExpressionResult { pub value: CodingProteinExpressionResult, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct MolecularTherapy { - pub history: Vec, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct SomaticNgsReport { +pub struct SomaticNgsReportMetadata { pub id: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub issued_on: Option, + pub issued_on: String, - pub metadata: Vec, + pub metadata: Vec, - #[serde(skip_serializing_if = "Option::is_none")] - pub msi: Option, + pub patient: Reference, - pub patient: Patient, + pub results: NgsReportResults, - #[serde(skip_serializing_if = "Option::is_none")] - pub results: Option, + #[serde(rename = "type")] + pub somatic_ngs_report_metadata_type: CodingNgsReport, - pub sequencing_type: Coding, - - pub specimen: NgsReportSpecimen, + pub specimen: Reference, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct Metadatum { +pub struct Metadata { pub kit_manufacturer: String, pub kit_type: String, @@ -1157,23 +1585,18 @@ pub struct NgsReportResults { #[serde(skip_serializing_if = "Option::is_none")] pub brcaness: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub copy_number_variants: Option>, + pub copy_number_variants: Vec, - #[serde(skip_serializing_if = "Option::is_none")] - pub dna_fusions: Option>, + pub dna_fusions: Vec, #[serde(skip_serializing_if = "Option::is_none")] pub hrd_score: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub rna_fusions: Option>, + pub rna_fusions: Vec, - #[serde(skip_serializing_if = "Option::is_none")] - pub rna_seqs: Option>, + pub rna_seqs: Vec, - #[serde(skip_serializing_if = "Option::is_none")] - pub simple_variants: Option>, + pub simple_variants: Vec, #[serde(skip_serializing_if = "Option::is_none")] pub tmb: Option, @@ -1209,7 +1632,7 @@ pub struct ConfidenceRange { #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct Cnv { - pub chromosome: CodingChromosome, + pub chromosome: Chromosome, #[serde(skip_serializing_if = "Option::is_none")] pub cn_a: Option, @@ -1218,52 +1641,44 @@ pub struct Cnv { pub cn_b: Option, #[serde(rename = "type")] - pub cnv_type: CodingCnvType, + pub cnv_type: CodingCnv, #[serde(skip_serializing_if = "Option::is_none")] - pub copy_number_neutral_lo_h: Option>, + pub copy_number_neutral_lo_h: Option>, - pub end_range: EndRange, + #[serde(skip_serializing_if = "Option::is_none")] + pub end_range: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub external_ids: Option>, pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub indication: Option, + pub localization: Option>, - #[serde(skip_serializing_if = "Option::is_none")] - pub patient: Option, + pub patient: Reference, #[serde(skip_serializing_if = "Option::is_none")] pub relative_copy_number: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub reported_affected_genes: Option>, + pub reported_affected_genes: Option>, #[serde(skip_serializing_if = "Option::is_none")] pub reported_focality: Option, - pub start_range: StartRange, + #[serde(skip_serializing_if = "Option::is_none")] + pub start_range: Option, #[serde(skip_serializing_if = "Option::is_none")] pub total_copy_number: Option, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingChromosome { - pub code: ChromosomeCode, - - #[serde(skip_serializing_if = "Option::is_none")] - pub display: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub enum ChromosomeCode { +pub enum Chromosome { Chr1, Chr10, @@ -1317,27 +1732,23 @@ pub enum ChromosomeCode { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -#[serde(rename_all = "snake_case")] -pub enum ChromosomeSystem { - Chromosome, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingCnvType { - pub code: CnvType, +pub struct CodingCnv { + pub code: CodingCnvCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum CnvType { +pub enum CodingCnvCode { #[serde(rename = "high-level-gain")] HighLevelGain, @@ -1347,25 +1758,6 @@ pub enum CnvType { LowLevelGain, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingGene { - pub code: String, - - #[serde(skip_serializing_if = "Option::is_none")] - pub display: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub system: Option, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum GeneSystem { - #[serde(rename = "https://www.genenames.org/")] - HttpsWwwGenenamesOrg, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct EndRange { @@ -1375,6 +1767,63 @@ pub struct EndRange { pub start: f64, } +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct VariantExternalId { + pub system: ExternalIdSystem, + + pub value: String, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum ExternalIdSystem { + #[serde(rename = "https://cancer.sanger.ac.uk/cosmic")] + HttpsCancerSangerAcUkCosmic, + + #[serde(rename = "https://www.ensembl.org")] + HttpsWwwEnsemblOrg, + + #[serde(rename = "https://www.ncbi.nlm.nih.gov/entrez")] + HttpsWwwNcbiNlmNihGovEntrez, + + #[serde(rename = "https://www.ncbi.nlm.nih.gov/snp")] + HttpsWwwNcbiNlmNihGovSnp, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingBaseVariantLocalization { + pub code: CodingBaseVariantLocalizationCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum CodingBaseVariantLocalizationCode { + #[serde(rename = "coding-region")] + CodingRegion, + + Intergenic, + + Intronic, + + #[serde(rename = "regulatory-region")] + RegulatoryRegion, + + #[serde(rename = "splicing-region")] + SplicingRegion, +} + #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct StartRange { @@ -1388,6 +1837,9 @@ pub struct StartRange { #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct DnaFusion { + #[serde(skip_serializing_if = "Option::is_none")] + pub external_ids: Option>, + #[serde(rename = "fusionPartner3prime")] pub fusion_partner3_prime: DnaFusionFusionPartner3Prime, @@ -1396,15 +1848,20 @@ pub struct DnaFusion { pub id: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub localization: Option>, + + pub patient: Reference, + pub reported_num_reads: i64, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct DnaFusionFusionPartner3Prime { - pub chromosome: CodingChromosome, + pub chromosome: Chromosome, - pub gene: CodingGene, + pub gene: Coding, pub position: f64, } @@ -1412,24 +1869,13 @@ pub struct DnaFusionFusionPartner3Prime { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct DnaFusionFusionPartner5Prime { - pub chromosome: CodingChromosome, + pub chromosome: Chromosome, - pub gene: Gene, + pub gene: Coding, pub position: f64, } -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -#[serde(rename_all = "camelCase")] -pub struct Gene { - #[serde(skip_serializing_if = "Option::is_none")] - pub ensembl_id: Option, - - #[serde(skip_serializing_if = "Option::is_none")] - pub hgnc_id: Option, -} - #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct HrdScore { @@ -1438,7 +1884,7 @@ pub struct HrdScore { pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub interpretation: Option, + pub interpretation: Option, pub patient: Reference, @@ -1457,15 +1903,41 @@ pub struct Components { pub tai: f64, } +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingHrdScoreInterpretation { + pub code: CodingHrdScoreInterpretationCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "snake_case")] +pub enum CodingHrdScoreInterpretationCode { + High, + + Intermediate, + + Low, +} + #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct RnaFusion { #[serde(skip_serializing_if = "Option::is_none")] - pub cosmic_id: Option, + pub effect: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub effect: Option, + pub external_ids: Option>, #[serde(rename = "fusionPartner3prime")] pub fusion_partner3_prime: RnaFusionFusionPartner3Prime, @@ -1475,6 +1947,11 @@ pub struct RnaFusion { pub id: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub localization: Option>, + + pub patient: Reference, + pub reported_num_reads: i64, } @@ -1482,15 +1959,15 @@ pub struct RnaFusion { #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct RnaFusionFusionPartner3Prime { - pub exon: String, + pub exon_id: String, - pub gene: CodingGene, + pub gene: Coding, pub position: f64, pub strand: RnaFusionStrand, - pub transcript_id: String, + pub transcript_id: TranscriptId, } #[derive(Debug, Serialize, Deserialize)] @@ -1503,19 +1980,37 @@ pub enum RnaFusionStrand { RnaFusionStrand, } +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct TranscriptId { + pub system: TranscriptIdSystem, + + pub value: String, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum TranscriptIdSystem { + #[serde(rename = "https://www.ensembl.org")] + HttpsWwwEnsemblOrg, + + #[serde(rename = "https://www.ncbi.nlm.nih.gov/refseq")] + HttpsWwwNcbiNlmNihGovRefseq, +} + #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] pub struct RnaFusionFusionPartner5Prime { - pub exon: String, + pub exon_id: String, - pub gene: CodingGene, + pub gene: Coding, pub position: f64, pub strand: RnaFusionStrand, - pub transcript_id: String, + pub transcript_id: TranscriptId, } #[derive(Debug, Serialize, Deserialize)] @@ -1525,26 +2020,33 @@ pub struct RnaSeq { #[serde(skip_serializing_if = "Option::is_none")] pub cohort_ranking: Option, - pub ensembl_id: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub external_ids: Option>, - pub entrez_id: String, - - pub fragments_per_kilobase_million: f64, - - #[serde(rename = "fromNGS")] - pub from_ngs: bool, - - pub gene: CodingGene, + #[serde(skip_serializing_if = "Option::is_none")] + pub gene: Option, pub id: String, - pub library_size: i64, + #[serde(skip_serializing_if = "Option::is_none")] + pub library_size: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub localization: Option>, + + pub patient: Reference, pub raw_counts: i64, - pub tissue_corrected_expression: bool, + #[serde(skip_serializing_if = "Option::is_none")] + pub tissue_corrected_expression: Option, - pub transcript_id: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub transcript_id: Option, + + pub transcripts_per_million: f64, + + pub variant: Reference, } #[derive(Debug, Serialize, Deserialize)] @@ -1555,33 +2057,29 @@ pub struct Snv { pub alt_allele: String, - #[serde(skip_serializing_if = "Option::is_none")] - pub amino_acid_change: Option, - - pub chromosome: CodingChromosome, - - #[serde(skip_serializing_if = "Option::is_none")] - pub cosmic_id: Option, - - #[serde(rename = "dbSNPId")] - #[serde(skip_serializing_if = "Option::is_none")] - pub db_snp_id: Option, + pub chromosome: Chromosome, #[serde(skip_serializing_if = "Option::is_none")] pub dna_change: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub external_ids: Option>, + pub exon_id: Option, #[serde(skip_serializing_if = "Option::is_none")] - pub gene: Option, + pub external_ids: Option>, + + #[serde(skip_serializing_if = "Option::is_none")] + pub gene: Option, pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub interpretation: Option, + pub interpretation: Option, - pub patient: Patient, + #[serde(skip_serializing_if = "Option::is_none")] + pub localization: Option>, + + pub patient: Reference, pub position: Position, @@ -1592,8 +2090,41 @@ pub struct Snv { pub ref_allele: String, + pub transcript_id: TranscriptId, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingClinVar { + pub code: CodingClinVarCode, + #[serde(skip_serializing_if = "Option::is_none")] - pub transcript_id: Option, + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum CodingClinVarCode { + #[serde(rename = "1")] + The1, + + #[serde(rename = "2")] + The2, + + #[serde(rename = "3")] + The3, + + #[serde(rename = "4")] + The4, + + #[serde(rename = "5")] + The5, } #[derive(Debug, Serialize, Deserialize)] @@ -1611,41 +2142,85 @@ pub struct Tmb { pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub interpretation: Option, + pub interpretation: Option, pub patient: Reference, pub specimen: Reference, - pub value: Value, + pub value: TmbResult, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct Value { - pub unit: String, +pub struct CodingTmbInterpretation { + pub code: CodingHrdScoreInterpretationCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct TmbResult { + #[serde(skip_serializing_if = "Option::is_none")] + pub unit: Option, pub value: f64, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct NgsReportSpecimen { - pub id: String, +pub struct CodingNgsReport { + pub code: CodingNgsReportCode, - #[serde(rename = "type")] - pub specimen_type: SpecimenType, + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum CodingNgsReportCode { + Array, + + Exome, + + #[serde(rename = "genome-long-read")] + GenomeLongRead, + + #[serde(rename = "genome-short-read")] + GenomeShortRead, + + Karyotyping, + + Other, + + Panel, + + Single, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "camelCase")] -pub struct MtbPatient { - #[serde(skip_serializing_if = "Option::is_none")] - pub address: Option
, +pub struct Patient { + pub address: Address, #[serde(skip_serializing_if = "Option::is_none")] - pub age: Option, + pub age: Option, pub birth_date: String, @@ -1654,13 +2229,15 @@ pub struct MtbPatient { pub gender: CodingGender, - #[serde(skip_serializing_if = "Option::is_none")] - pub health_insurance: Option, + pub health_insurance: HealthInsurance, pub id: String, #[serde(skip_serializing_if = "Option::is_none")] - pub vital_status: Option, + pub managing_site: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub vital_status: Option, } #[derive(Debug, Serialize, Deserialize)] @@ -1672,7 +2249,7 @@ pub struct Address { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct ValueWithUnit { +pub struct Age { pub unit: Unit, pub value: f64, @@ -1681,13 +2258,15 @@ pub struct ValueWithUnit { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub enum Unit { + Months, + Years, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingGender { - pub code: Gender, + pub code: GenderCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, @@ -1702,7 +2281,7 @@ pub struct CodingGender { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "snake_case")] -pub enum Gender { +pub enum GenderCode { Female, Male, @@ -1714,27 +2293,63 @@ pub enum Gender { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -#[serde(rename_all = "camelCase")] pub struct HealthInsurance { + #[serde(rename = "type")] + pub health_insurance_type: CodingHealthInsurance, + + #[serde(skip_serializing_if = "Option::is_none")] + pub reference: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingHealthInsurance { + pub code: CodingHealthInsuranceCode, + #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, - pub ext_id: ExternalId, - - #[serde(rename = "type")] #[serde(skip_serializing_if = "Option::is_none")] - pub health_insurance_type: Option, + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub enum Type { - Organization, +pub enum CodingHealthInsuranceCode { + #[serde(rename = "BEI")] + Bei, + + #[serde(rename = "BG")] + Bg, + + #[serde(rename = "GKV")] + Gkv, + + #[serde(rename = "GPV")] + Gpv, + + #[serde(rename = "PKV")] + Pkv, + + #[serde(rename = "PPV")] + Ppv, + + #[serde(rename = "SEL")] + Sel, + + #[serde(rename = "SOZ")] + Soz, + + #[serde(rename = "UNK")] + Unk, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct VitalStatus { +pub struct CodingVitalStatus { pub code: VitalStatusCode, #[serde(skip_serializing_if = "Option::is_none")] @@ -1742,6 +2357,9 @@ pub struct VitalStatus { #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] @@ -1761,7 +2379,7 @@ pub struct PerformanceStatus { pub id: String, - pub patient: Patient, + pub patient: Reference, pub value: CodingEcog, } @@ -1769,7 +2387,7 @@ pub struct PerformanceStatus { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingEcog { - pub code: EcogCode, + pub code: CodingEcogCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, @@ -1783,21 +2401,96 @@ pub struct CodingEcog { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub enum EcogCode { +pub enum CodingEcogCode { #[serde(rename = "0")] - Code0, + The0, #[serde(rename = "1")] - Code1, + The1, #[serde(rename = "2")] - Code2, + The2, #[serde(rename = "3")] - Code3, + The3, #[serde(rename = "4")] - Code4, + The4, + + #[serde(rename = "5")] + The5, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "camelCase")] +pub struct PriorDiagnosticReport { + pub id: String, + + pub issued_on: String, + + pub patient: Reference, + + #[serde(skip_serializing_if = "Option::is_none")] + pub performer: Option, + + #[serde(rename = "type")] + pub prior_diagnostic_report_type: CodingMolecularDiagnosticReport, + + #[serde(skip_serializing_if = "Option::is_none")] + pub results: Option>, + + pub specimen: Reference, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingMolecularDiagnosticReport { + pub code: CodingMolecularDiagnosticReportCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +#[serde(rename_all = "kebab-case")] +pub enum CodingMolecularDiagnosticReportCode { + Array, + + Exome, + + #[serde(rename = "FISH")] + Fish, + + #[serde(rename = "fusion-panel")] + FusionPanel, + + #[serde(rename = "gene-panel")] + GenePanel, + + #[serde(rename = "genome-long-read")] + GenomeLongRead, + + #[serde(rename = "genome-short-read")] + GenomeShortRead, + + Karyotyping, + + Other, + + Panel, + + #[serde(rename = "PCR")] + Pcr, + + Single, } #[derive(Debug, Serialize, Deserialize)] @@ -1808,33 +2501,19 @@ pub struct Response { pub id: String, - pub patient: Patient, + pub method: CodingResponseMethod, - pub therapy: ResponseTherapy, + pub patient: Reference, + + pub therapy: Reference, pub value: CodingRecist, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct ResponseTherapy { - pub id: String, - - #[serde(rename = "type")] - pub response_therapy_type: ResponseTherapyType, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub enum ResponseTherapyType { - #[serde(rename = "MTBMedicationTherapy")] - MtbMedicationTherapy, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingRecist { - pub code: RecistCode, +pub struct CodingResponseMethod { + pub code: CodingResponseMethodCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, @@ -1848,7 +2527,32 @@ pub struct CodingRecist { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub enum RecistCode { +pub enum CodingResponseMethodCode { + #[serde(rename = "RANO")] + Rano, + + #[serde(rename = "RECIST")] + Recist, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub struct CodingRecist { + pub code: CodingRecistCode, + + #[serde(skip_serializing_if = "Option::is_none")] + pub display: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, +} + +#[derive(Debug, Serialize, Deserialize)] +#[serde(deny_unknown_fields)] +pub enum CodingRecistCode { #[serde(rename = "CR")] Cr, @@ -1858,9 +2562,6 @@ pub enum RecistCode { #[serde(rename = "NA")] Na, - #[serde(rename = "NYA")] - Nya, - #[serde(rename = "PD")] Pd, @@ -1877,22 +2578,21 @@ pub struct TumorSpecimen { #[serde(skip_serializing_if = "Option::is_none")] pub collection: Option, - #[serde(skip_serializing_if = "Option::is_none")] - pub diagnosis: Option, + pub diagnosis: Reference, pub id: String, - pub patient: Patient, + pub patient: Reference, #[serde(rename = "type")] - #[serde(skip_serializing_if = "Option::is_none")] - pub tumor_specimen_type: Option, + pub tumor_specimen_type: CodingTumorSpecimen, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct Collection { - pub date: String, + #[serde(skip_serializing_if = "Option::is_none")] + pub date: Option, pub localization: CodingTumorSpecimenCollectionLocalization, @@ -1902,43 +2602,58 @@ pub struct Collection { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingTumorSpecimenCollectionLocalization { - pub code: TumorSpecimenCollectionLocalization, + pub code: CodingTumorSpecimenCollectionLocalizationCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum TumorSpecimenCollectionLocalization { +pub enum CodingTumorSpecimenCollectionLocalizationCode { + #[serde(rename = "cellfree-dna")] + CellfreeDna, + + #[serde(rename = "local-recurrence")] + LocalRecurrence, + Metastasis, #[serde(rename = "primary-tumor")] PrimaryTumor, + #[serde(rename = "regional-lymph-nodes")] + RegionalLymphNodes, + Unknown, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] pub struct CodingTumorSpecimenCollectionMethod { - pub code: TumorSpecimenCollectionMethod, + pub code: CodingTumorSpecimenCollectionMethodCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum TumorSpecimenCollectionMethod { +pub enum CodingTumorSpecimenCollectionMethodCode { Biopsy, Cytology, @@ -1953,29 +2668,23 @@ pub enum TumorSpecimenCollectionMethod { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct Diagnosis { - #[serde(rename = "type")] - pub diagnosis_type: String, - - pub id: String, -} - -#[derive(Debug, Serialize, Deserialize)] -#[serde(deny_unknown_fields)] -pub struct CodingTumorSpecimenType { - pub code: TumorSpecimenType, +pub struct CodingTumorSpecimen { + pub code: CodingTumorSpecimenCode, #[serde(skip_serializing_if = "Option::is_none")] pub display: Option, #[serde(skip_serializing_if = "Option::is_none")] pub system: Option, + + #[serde(skip_serializing_if = "Option::is_none")] + pub version: Option, } #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] #[serde(rename_all = "kebab-case")] -pub enum TumorSpecimenType { +pub enum CodingTumorSpecimenCode { #[serde(rename = "cryo-frozen")] CryoFrozen, @@ -1993,6 +2702,6 @@ pub enum TumorSpecimenType { #[derive(Debug, Serialize, Deserialize)] #[serde(deny_unknown_fields)] -pub struct Therapy { - pub history: Vec, +pub struct SystemicTherapy { + pub history: Vec, } diff --git a/tests/mv64e-mtb-fake-patient.json b/tests/mv64e-mtb-fake-patient.json index 94ec8ad..c82d951 100644 --- a/tests/mv64e-mtb-fake-patient.json +++ b/tests/mv64e-mtb-fake-patient.json @@ -1 +1,2243 @@ -{"patient":{"id":"b944f6b0-d65f-432c-9e6f-e6d3a4ea79f2","gender":{"code":"male","display":"Männlich","system":"Gender"},"birthDate":"1982-12-20","dateOfDeath":"2016-12-20","healthInsurance":{"extId":{"value":"aok-ik","system":"IK"},"display":"AOK","type":"Organization"},"age":{"value":34,"unit":"Years"},"vitalStatus":{"code":"deceased","display":"Verstorben","system":"dnpm-dip/patient/vital-status"}},"episodesOfCare":[{"id":"0a9c7aa4-2d50-4798-9903-a3e378e4cf47","patient":{"id":"b944f6b0-d65f-432c-9e6f-e6d3a4ea79f2","type":"Patient"},"period":{"start":"2024-06-05"},"diagnoses":[{"id":"78d5b572-c3fa-4d26-8a07-302a28956b80","type":"MTBDiagnosis"}]}],"diagnoses":[{"id":"78d5b572-c3fa-4d26-8a07-302a28956b80","patient":{"id":"b944f6b0-d65f-432c-9e6f-e6d3a4ea79f2","type":"Patient"},"recordedOn":"2013-07-20","code":{"code":"C72.8","display":"Bösartige Neubildung: Gehirn und andere Teile des Zentralnervensystems, mehrere Teilbereiche 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