From 119fee76a237de9cbb93330876c25a17486c0800 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 14:54:52 -0400 Subject: [PATCH 01/17] Copy over the schema to a new file --- .../mohpackets/docs/schema_manual.yml | 7806 +++++++++++++++++ 1 file changed, 7806 insertions(+) create mode 100644 chord_metadata_service/mohpackets/docs/schema_manual.yml diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml new file mode 100644 index 000000000..e26b3a3f2 --- /dev/null +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -0,0 +1,7806 @@ +components: + schemas: + BasisOfDiagnosisEnum: + enum: + - Clinical investigation + - Clinical + - Cytology + - Death certificate only + - Histology of a metastasis + - Histology of a primary tumour + - Specific tumour markers + - Unknown + title: BasisOfDiagnosisEnum + type: string + BiomarkerFilterSchema: + properties: + ca125: + anyOf: + - type: integer + - type: 'null' + title: Ca125 + cea: + anyOf: + - type: integer + - type: 'null' + title: Cea + er_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Er Percent Positive + er_status: + anyOf: + - type: string + - type: 'null' + title: Er Status + her2_ihc_status: + anyOf: + - type: string + - type: 'null' + title: Her2 Ihc Status + her2_ish_status: + anyOf: + - type: string + - type: 'null' + title: Her2 Ish Status + hpv_ihc_status: + anyOf: + - type: string + - type: 'null' + title: Hpv Ihc Status + hpv_pcr_status: + anyOf: + - type: string + - type: 'null' + title: Hpv Pcr Status + hpv_strain: + items: + type: string + q: hpv_strain__overlap + title: Hpv Strain + type: array + pr_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Pr Percent Positive + pr_status: + anyOf: + - type: string + - type: 'null' + title: Pr Status + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + psa_level: + anyOf: + - type: integer + - type: 'null' + title: Psa Level + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_follow_up_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Follow Up Id + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_specimen_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: BiomarkerFilterSchema + type: object + BiomarkerIngestSchema: + properties: + ca125: + anyOf: + - type: integer + - type: 'null' + title: Ca125 + cea: + anyOf: + - type: integer + - type: 'null' + title: Cea + er_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Er Percent Positive + er_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + her2_ihc_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + her2_ish_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + hpv_ihc_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_pcr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_strain: + anyOf: + - items: + $ref: '#/components/schemas/HpvStrainEnum' + type: array + - type: 'null' + title: Hpv Strain + pr_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Pr Percent Positive + pr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + program_id: + title: Program Id + type: string + psa_level: + anyOf: + - type: integer + - type: 'null' + title: Psa Level + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_follow_up_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Follow Up Id + submitter_primary_diagnosis_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Treatment Id + test_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + title: BiomarkerIngestSchema + type: object + BiomarkerModelSchema: + properties: + ca125: + anyOf: + - type: integer + - type: 'null' + title: Ca125 + cea: + anyOf: + - type: integer + - type: 'null' + title: Cea + er_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Er Percent Positive + er_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + her2_ihc_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + her2_ish_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + hpv_ihc_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_pcr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_strain: + anyOf: + - items: + $ref: '#/components/schemas/HpvStrainEnum' + type: array + - type: 'null' + title: Hpv Strain + pr_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Pr Percent Positive + pr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + program_id: + title: Program Id + type: string + psa_level: + anyOf: + - type: integer + - type: 'null' + title: Psa Level + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_follow_up_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Follow Up Id + submitter_primary_diagnosis_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Treatment Id + test_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + required: + - program_id + - submitter_donor_id + title: BiomarkerModelSchema + type: object + CauseOfDeathEnum: + enum: + - Died of cancer + - Died of other reasons + - Unknown + title: CauseOfDeathEnum + type: string + CellsMeasureMethodEnum: + enum: + - Genomics + - Image analysis + - Pathology estimate by percent nuclei + - Unknown + title: CellsMeasureMethodEnum + type: string + ChemotherapyFilterSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + chemotherapy_drug_dose_units: + anyOf: + - type: string + - type: 'null' + title: Chemotherapy Drug Dose Units + drug_name: + anyOf: + - type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + drug_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: ChemotherapyFilterSchema + type: object + ChemotherapyIngestSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + chemotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: ChemotherapyIngestSchema + type: object + ChemotherapyModelSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + chemotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: ChemotherapyModelSchema + type: object + ComorbidityFilterSchema: + properties: + age_at_comorbidity_diagnosis: + anyOf: + - type: integer + - type: 'null' + title: Age At Comorbidity Diagnosis + comorbidity_treatment: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Treatment + comorbidity_treatment_status: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Treatment Status + comorbidity_type_code: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Type Code + laterality_of_prior_malignancy: + anyOf: + - type: string + - type: 'null' + title: Laterality Of Prior Malignancy + prior_malignancy: + anyOf: + - type: string + - type: 'null' + title: Prior Malignancy + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + title: ComorbidityFilterSchema + type: object + ComorbidityIngestSchema: + properties: + age_at_comorbidity_diagnosis: + anyOf: + - type: integer + - type: 'null' + title: Age At Comorbidity Diagnosis + comorbidity_treatment: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Comorbidity Treatment + comorbidity_treatment_status: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + comorbidity_type_code: + anyOf: + - maxLength: 64 + pattern: ^[A-Z][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$ + type: string + - type: 'null' + title: Comorbidity Type Code + laterality_of_prior_malignancy: + anyOf: + - $ref: '#/components/schemas/MalignancyLateralityEnum' + - type: 'null' + prior_malignancy: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + title: ComorbidityIngestSchema + type: object + ComorbidityModelSchema: + properties: + age_at_comorbidity_diagnosis: + anyOf: + - type: integer + - type: 'null' + title: Age At Comorbidity Diagnosis + comorbidity_treatment: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Comorbidity Treatment + comorbidity_treatment_status: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + comorbidity_type_code: + anyOf: + - maxLength: 64 + pattern: ^[A-Z][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$ + type: string + - type: 'null' + title: Comorbidity Type Code + laterality_of_prior_malignancy: + anyOf: + - $ref: '#/components/schemas/MalignancyLateralityEnum' + - type: 'null' + prior_malignancy: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + required: + - program_id + - submitter_donor_id + title: ComorbidityModelSchema + type: object + ConfirmedDiagnosisTumourEnum: + enum: + - 'Yes' + - 'No' + - Not done + - Unknown + title: ConfirmedDiagnosisTumourEnum + type: string + DateInterval: + properties: + day_interval: + anyOf: + - type: integer + - type: 'null' + description: number of days since first diagnosis + title: Day Interval + month_interval: + description: number of months since first diagnosis + title: Month Interval + type: integer + required: + - month_interval + title: DateInterval + type: object + DiagnosisAgeCountSchema: + properties: + age_at_diagnosis: + title: Age At Diagnosis + type: string + age_count: + title: Age Count + type: string + required: + - age_at_diagnosis + - age_count + title: DiagnosisAgeCountSchema + type: object + DiscoveryDonorSchema: + properties: + donors_count: + title: Donors Count + type: string + program_id: + title: Program Id + type: string + required: + - program_id + - donors_count + title: DiscoveryDonorSchema + type: object + DiseaseStatusFollowupEnum: + enum: + - Complete remission + - Distant progression + - Loco-regional progression + - No evidence of disease + - Partial remission + - Progression not otherwise specified + - Relapse or recurrence + - Stable + title: DiseaseStatusFollowupEnum + type: string + DonorExplorerFilterSchema: + properties: + chemotherapy_drug_name: + items: + type: string + title: Chemotherapy Drug Name + type: array + exclude_cohorts: + items: + type: string + title: Exclude Cohorts + type: array + hormone_therapy_drug_name: + items: + type: string + title: Hormone Therapy Drug Name + type: array + immunotherapy_drug_name: + items: + type: string + title: Immunotherapy Drug Name + type: array + primary_site: + items: + type: string + q: primary_site__overlap + title: Primary Site + type: array + treatment_type: + items: + type: string + q: treatment_type__overlap + title: Treatment Type + type: array + title: DonorExplorerFilterSchema + type: object + DonorExplorerSchema: + properties: + age_at_diagnosis: + anyOf: + - type: string + - type: 'null' + title: Age At Diagnosis + primary_site: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Primary Site + program_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Program Id + type: string + submitter_donor_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Donor Id + type: string + submitter_sample_ids: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Submitter Sample Ids + treatment_type: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Treatment Type + required: + - program_id + - submitter_donor_id + - submitter_sample_ids + title: DonorExplorerSchema + type: object + DonorFilterSchema: + properties: + cause_of_death: + anyOf: + - type: string + - type: 'null' + title: Cause Of Death + gender: + anyOf: + - type: string + - type: 'null' + q: gender__icontains + title: Gender + is_deceased: + anyOf: + - type: boolean + - type: 'null' + title: Is Deceased + lost_to_followup_after_clinical_event_identifier: + anyOf: + - type: string + - type: 'null' + title: Lost To Followup After Clinical Event Identifier + lost_to_followup_reason: + anyOf: + - type: string + - type: 'null' + title: Lost To Followup Reason + primary_site: + items: + type: string + q: primary_site__overlap + title: Primary Site + type: array + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + sex_at_birth: + anyOf: + - type: string + - type: 'null' + title: Sex At Birth + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + title: DonorFilterSchema + type: object + DonorIngestSchema: + properties: + cause_of_death: + anyOf: + - $ref: '#/components/schemas/CauseOfDeathEnum' + - type: 'null' + date_alive_after_lost_to_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_birth: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_death: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_resolution: + anyOf: + - maxLength: 32 + type: string + - type: 'null' + title: Date Resolution + gender: + anyOf: + - $ref: '#/components/schemas/GenderEnum' + - type: 'null' + is_deceased: + anyOf: + - type: boolean + - type: 'null' + title: Is Deceased + lost_to_followup_after_clinical_event_identifier: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Lost To Followup After Clinical Event Identifier + lost_to_followup_reason: + anyOf: + - $ref: '#/components/schemas/LostToFollowupReasonEnum' + - type: 'null' + primary_site: + anyOf: + - items: + $ref: '#/components/schemas/PrimarySiteEnum' + type: array + - type: 'null' + title: Primary Site + program_id: + title: Program Id + type: string + sex_at_birth: + anyOf: + - $ref: '#/components/schemas/SexAtBirthEnum' + - type: 'null' + submitter_donor_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Donor Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_donor_id + - program_id + title: DonorIngestSchema + type: object + DonorModelSchema: + properties: + cause_of_death: + anyOf: + - $ref: '#/components/schemas/CauseOfDeathEnum' + - type: 'null' + date_alive_after_lost_to_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_birth: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_death: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_resolution: + anyOf: + - maxLength: 32 + type: string + - type: 'null' + title: Date Resolution + gender: + anyOf: + - $ref: '#/components/schemas/GenderEnum' + - type: 'null' + is_deceased: + anyOf: + - type: boolean + - type: 'null' + title: Is Deceased + lost_to_followup_after_clinical_event_identifier: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Lost To Followup After Clinical Event Identifier + lost_to_followup_reason: + anyOf: + - $ref: '#/components/schemas/LostToFollowupReasonEnum' + - type: 'null' + primary_site: + anyOf: + - items: + $ref: '#/components/schemas/PrimarySiteEnum' + type: array + - type: 'null' + title: Primary Site + program_id: + title: Program Id + type: string + sex_at_birth: + anyOf: + - $ref: '#/components/schemas/SexAtBirthEnum' + - type: 'null' + submitter_donor_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Donor Id + type: string + required: + - submitter_donor_id + - program_id + title: DonorModelSchema + type: object + DonorWithClinicalDataSchema: + properties: + biomarkers: + items: + $ref: '#/components/schemas/NestedBiomarkerSchema' + title: Biomarkers + type: array + cause_of_death: + anyOf: + - $ref: '#/components/schemas/CauseOfDeathEnum' + - type: 'null' + comorbidities: + items: + $ref: '#/components/schemas/NestedComorbiditySchema' + title: Comorbidities + type: array + date_alive_after_lost_to_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_birth: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_death: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_resolution: + anyOf: + - maxLength: 32 + type: string + - type: 'null' + title: Date Resolution + exposures: + items: + $ref: '#/components/schemas/NestedExposureSchema' + title: Exposures + type: array + followups: + items: + $ref: '#/components/schemas/NestedFollowUpSchema' + title: Followups + type: array + gender: + anyOf: + - $ref: '#/components/schemas/GenderEnum' + - type: 'null' + is_deceased: + anyOf: + - type: boolean + - type: 'null' + title: Is Deceased + lost_to_followup_after_clinical_event_identifier: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Lost To Followup After Clinical Event Identifier + lost_to_followup_reason: + anyOf: + - $ref: '#/components/schemas/LostToFollowupReasonEnum' + - type: 'null' + primary_diagnoses: + items: + $ref: '#/components/schemas/NestedPrimaryDiagnosisSchema' + title: Primary Diagnoses + type: array + primary_site: + anyOf: + - items: + $ref: '#/components/schemas/PrimarySiteEnum' + type: array + - type: 'null' + title: Primary Site + program_id: + title: Program Id + type: string + sex_at_birth: + anyOf: + - $ref: '#/components/schemas/SexAtBirthEnum' + - type: 'null' + submitter_donor_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Donor Id + type: string + required: + - submitter_donor_id + - program_id + title: DonorWithClinicalDataSchema + type: object + DosageUnitsEnum: + enum: + - mg/m2 + - IU/m2 + - IU/kg + - ug/m2 + - g/m2 + - mg/kg + - cells/kg + title: DosageUnitsEnum + type: string + DrugReferenceDbEnum: + enum: + - RxNorm + - PubChem + - NCI Thesaurus + title: DrugReferenceDbEnum + type: string + ErPrHpvStatusEnum: + enum: + - Cannot be determined + - Negative + - Not applicable + - Positive + - Unknown + title: ErPrHpvStatusEnum + type: string + ExposureFilterSchema: + properties: + pack_years_smoked: + anyOf: + - type: number + - type: 'null' + title: Pack Years Smoked + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + tobacco_smoking_status: + anyOf: + - type: string + - type: 'null' + title: Tobacco Smoking Status + tobacco_type: + items: + type: string + q: tobacco_type__overlap + title: Tobacco Type + type: array + title: ExposureFilterSchema + type: object + ExposureIngestSchema: + properties: + pack_years_smoked: + anyOf: + - type: number + - type: 'null' + title: Pack Years Smoked + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + tobacco_smoking_status: + anyOf: + - $ref: '#/components/schemas/SmokingStatusEnum' + - type: 'null' + tobacco_type: + anyOf: + - items: + $ref: '#/components/schemas/TobaccoTypeEnum' + type: array + - type: 'null' + title: Tobacco Type + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + title: ExposureIngestSchema + type: object + ExposureModelSchema: + properties: + pack_years_smoked: + anyOf: + - type: number + - type: 'null' + title: Pack Years Smoked + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + tobacco_smoking_status: + anyOf: + - $ref: '#/components/schemas/SmokingStatusEnum' + - type: 'null' + tobacco_type: + anyOf: + - items: + $ref: '#/components/schemas/TobaccoTypeEnum' + type: array + - type: 'null' + title: Tobacco Type + required: + - program_id + - submitter_donor_id + title: ExposureModelSchema + type: object + FollowUpFilterSchema: + properties: + anatomic_site_progression_or_recurrence: + items: + type: string + q: anatomic_site_progression_or_recurrence__overlap + title: Anatomic Site Progression Or Recurrence + type: array + disease_status_at_followup: + anyOf: + - type: string + - type: 'null' + title: Disease Status At Followup + method_of_progression_status: + items: + type: string + q: method_of_progression_status__overlap + title: Method Of Progression Status + type: array + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + recurrence_m_category: + anyOf: + - type: string + - type: 'null' + title: Recurrence M Category + recurrence_n_category: + anyOf: + - type: string + - type: 'null' + title: Recurrence N Category + recurrence_stage_group: + anyOf: + - type: string + - type: 'null' + title: Recurrence Stage Group + recurrence_t_category: + anyOf: + - type: string + - type: 'null' + title: Recurrence T Category + recurrence_tumour_staging_system: + anyOf: + - type: string + - type: 'null' + title: Recurrence Tumour Staging System + relapse_type: + anyOf: + - type: string + - type: 'null' + title: Relapse Type + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_follow_up_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Follow Up Id + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: FollowUpFilterSchema + type: object + FollowUpIngestSchema: + properties: + anatomic_site_progression_or_recurrence: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Anatomic Site Progression Or Recurrence + date_of_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_relapse: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + disease_status_at_followup: + anyOf: + - $ref: '#/components/schemas/DiseaseStatusFollowupEnum' + - type: 'null' + method_of_progression_status: + anyOf: + - items: + $ref: '#/components/schemas/ProgressionStatusMethodEnum' + type: array + - type: 'null' + title: Method Of Progression Status + program_id: + title: Program Id + type: string + recurrence_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + recurrence_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + recurrence_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + recurrence_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + recurrence_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + relapse_type: + anyOf: + - $ref: '#/components/schemas/RelapseTypeEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_follow_up_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Follow Up Id + type: string + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_follow_up_id + - program_id + - submitter_donor_id + title: FollowUpIngestSchema + type: object + FollowUpModelSchema: + properties: + anatomic_site_progression_or_recurrence: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Anatomic Site Progression Or Recurrence + date_of_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_relapse: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + disease_status_at_followup: + anyOf: + - $ref: '#/components/schemas/DiseaseStatusFollowupEnum' + - type: 'null' + method_of_progression_status: + anyOf: + - items: + $ref: '#/components/schemas/ProgressionStatusMethodEnum' + type: array + - type: 'null' + title: Method Of Progression Status + program_id: + title: Program Id + type: string + recurrence_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + recurrence_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + recurrence_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + recurrence_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + recurrence_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + relapse_type: + anyOf: + - $ref: '#/components/schemas/RelapseTypeEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_follow_up_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Follow Up Id + type: string + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + required: + - submitter_follow_up_id + - program_id + - submitter_donor_id + title: FollowUpModelSchema + type: object + GenderCountSchema: + properties: + gender: + anyOf: + - type: string + - type: 'null' + title: Gender + gender_count: + title: Gender Count + type: string + required: + - gender + - gender_count + title: GenderCountSchema + type: object + GenderEnum: + enum: + - Man + - Woman + - Non-binary + title: GenderEnum + type: string + Her2StatusEnum: + enum: + - Cannot be determined + - Equivocal + - Positive + - Negative + - Not applicable + - Unknown + title: Her2StatusEnum + type: string + HormoneTherapyFilterSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + drug_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + hormone_drug_dose_units: + anyOf: + - type: string + - type: 'null' + title: Hormone Drug Dose Units + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: HormoneTherapyFilterSchema + type: object + HormoneTherapyIngestSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + hormone_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: HormoneTherapyIngestSchema + type: object + HormoneTherapyModelSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + hormone_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: HormoneTherapyModelSchema + type: object + HpvStrainEnum: + enum: + - HPV16 + - HPV18 + - HPV31 + - HPV33 + - HPV35 + - HPV39 + - HPV45 + - HPV51 + - HPV52 + - HPV56 + - HPV58 + - HPV59 + - HPV66 + - HPV68 + - HPV73 + title: HpvStrainEnum + type: string + ImmunotherapyFilterSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + drug_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + immunotherapy_drug_dose_units: + anyOf: + - type: string + - type: 'null' + title: Immunotherapy Drug Dose Units + immunotherapy_type: + anyOf: + - type: string + - type: 'null' + title: Immunotherapy Type + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: ImmunotherapyFilterSchema + type: object + ImmunotherapyIngestSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + immunotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + immunotherapy_type: + anyOf: + - $ref: '#/components/schemas/ImmunotherapyTypeEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: ImmunotherapyIngestSchema + type: object + ImmunotherapyModelSchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + immunotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + immunotherapy_type: + anyOf: + - $ref: '#/components/schemas/ImmunotherapyTypeEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: ImmunotherapyModelSchema + type: object + ImmunotherapyTypeEnum: + enum: + - Cell-based + - Immune checkpoint inhibitors + - Monoclonal antibodies other than immune checkpoint inhibitors + - Other immunomodulatory substances + title: ImmunotherapyTypeEnum + type: string + Input: + properties: + page: + minimum: 1 + title: Page + type: integer + page_size: + minimum: 1 + title: Page Size + type: integer + title: Input + type: object + LostToFollowupReasonEnum: + enum: + - Completed study + - Discharged to palliative care + - Lost contact + - Not applicable + - Unknown + - Withdrew from study + title: LostToFollowupReasonEnum + type: string + LymphNodeMethodEnum: + enum: + - Imaging + - Lymph node dissection/pathological exam + - Physical palpation of patient + title: LymphNodeMethodEnum + type: string + LymphNodeStatusEnum: + enum: + - Cannot be determined + - 'No' + - No lymph nodes found in resected specimen + - Not applicable + - 'Yes' + title: LymphNodeStatusEnum + type: string + LymphovascularInvasionEnum: + enum: + - Absent + - Both lymphatic and small vessel and venous (large vessel) invasion + - Lymphatic and small vessel invasion only + - Not applicable + - Present + - Venous (large vessel) invasion only + - Unknown + title: LymphovascularInvasionEnum + type: string + MCategoryEnum: + enum: + - M0 + - M0(i+) + - M1 + - M1a + - M1a(0) + - M1a(1) + - M1b + - M1b(0) + - M1b(1) + - M1c + - M1c(0) + - M1c(1) + - M1d + - M1d(0) + - M1d(1) + - M1e + - MX + title: MCategoryEnum + type: string + MalignancyLateralityEnum: + enum: + - Bilateral + - Left + - Midline + - Not applicable + - Right + - Unilateral, Side not specified + - Unknown + title: MalignancyLateralityEnum + type: string + MarginTypesEnum: + enum: + - Circumferential resection margin + - Common bile duct margin + - Distal margin + - Not applicable + - Proximal margin + - Unknown + title: MarginTypesEnum + type: string + NCategoryEnum: + enum: + - N0 + - N0a + - N0a (biopsy) + - N0b + - N0b (no biopsy) + - N0(i+) + - N0(i-) + - N0(mol+) + - N0(mol-) + - N1 + - N1a + - N1a(sn) + - N1b + - N1c + - N1mi + - N2 + - N2a + - N2b + - N2c + - N2mi + - N3 + - N3a + - N3b + - N3c + - N4 + - NX + title: NCategoryEnum + type: string + NestedBiomarkerSchema: + properties: + ca125: + anyOf: + - type: integer + - type: 'null' + title: Ca125 + cea: + anyOf: + - type: integer + - type: 'null' + title: Cea + er_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Er Percent Positive + er_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + her2_ihc_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + her2_ish_status: + anyOf: + - $ref: '#/components/schemas/Her2StatusEnum' + - type: 'null' + hpv_ihc_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_pcr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + hpv_strain: + anyOf: + - items: + $ref: '#/components/schemas/HpvStrainEnum' + type: array + - type: 'null' + title: Hpv Strain + pr_percent_positive: + anyOf: + - type: number + - type: 'null' + title: Pr Percent Positive + pr_status: + anyOf: + - $ref: '#/components/schemas/ErPrHpvStatusEnum' + - type: 'null' + psa_level: + anyOf: + - type: integer + - type: 'null' + title: Psa Level + submitter_follow_up_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Follow Up Id + submitter_primary_diagnosis_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Treatment Id + test_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: NestedBiomarkerSchema + type: object + NestedChemotherapySchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + chemotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + title: NestedChemotherapySchema + type: object + NestedComorbiditySchema: + properties: + age_at_comorbidity_diagnosis: + anyOf: + - type: integer + - type: 'null' + title: Age At Comorbidity Diagnosis + comorbidity_treatment: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Comorbidity Treatment + comorbidity_treatment_status: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + comorbidity_type_code: + anyOf: + - maxLength: 64 + pattern: ^[A-Z][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$ + type: string + - type: 'null' + title: Comorbidity Type Code + laterality_of_prior_malignancy: + anyOf: + - $ref: '#/components/schemas/MalignancyLateralityEnum' + - type: 'null' + prior_malignancy: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + title: NestedComorbiditySchema + type: object + NestedExposureSchema: + properties: + pack_years_smoked: + anyOf: + - type: number + - type: 'null' + title: Pack Years Smoked + tobacco_smoking_status: + anyOf: + - $ref: '#/components/schemas/SmokingStatusEnum' + - type: 'null' + tobacco_type: + anyOf: + - items: + $ref: '#/components/schemas/TobaccoTypeEnum' + type: array + - type: 'null' + title: Tobacco Type + title: NestedExposureSchema + type: object + NestedFollowUpSchema: + properties: + anatomic_site_progression_or_recurrence: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Anatomic Site Progression Or Recurrence + date_of_followup: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + date_of_relapse: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + disease_status_at_followup: + anyOf: + - $ref: '#/components/schemas/DiseaseStatusFollowupEnum' + - type: 'null' + method_of_progression_status: + anyOf: + - items: + $ref: '#/components/schemas/ProgressionStatusMethodEnum' + type: array + - type: 'null' + title: Method Of Progression Status + recurrence_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + recurrence_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + recurrence_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + recurrence_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + recurrence_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + relapse_type: + anyOf: + - $ref: '#/components/schemas/RelapseTypeEnum' + - type: 'null' + submitter_follow_up_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Follow Up Id + type: string + required: + - submitter_follow_up_id + title: NestedFollowUpSchema + type: object + NestedHormoneTherapySchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + hormone_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + title: NestedHormoneTherapySchema + type: object + NestedImmunotherapySchema: + properties: + actual_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + drug_name: + anyOf: + - maxLength: 255 + type: string + - type: 'null' + title: Drug Name + drug_reference_database: + anyOf: + - $ref: '#/components/schemas/DrugReferenceDbEnum' + - type: 'null' + drug_reference_identifier: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Drug Reference Identifier + immunotherapy_drug_dose_units: + anyOf: + - $ref: '#/components/schemas/DosageUnitsEnum' + - type: 'null' + immunotherapy_type: + anyOf: + - $ref: '#/components/schemas/ImmunotherapyTypeEnum' + - type: 'null' + prescribed_cumulative_drug_dose: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + title: NestedImmunotherapySchema + type: object + NestedPrimaryDiagnosisSchema: + properties: + basis_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/BasisOfDiagnosisEnum' + - type: 'null' + cancer_type_code: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Cancer Type Code + clinical_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + clinical_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + clinical_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + clinical_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + clinical_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + date_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + followups: + items: + $ref: '#/components/schemas/NestedFollowUpSchema' + title: Followups + type: array + laterality: + anyOf: + - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' + - type: 'null' + lymph_nodes_examined_method: + anyOf: + - $ref: '#/components/schemas/LymphNodeMethodEnum' + - type: 'null' + lymph_nodes_examined_status: + anyOf: + - $ref: '#/components/schemas/LymphNodeStatusEnum' + - type: 'null' + number_lymph_nodes_positive: + anyOf: + - type: integer + - type: 'null' + title: Number Lymph Nodes Positive + specimens: + items: + $ref: '#/components/schemas/NestedSpecimenSchema' + title: Specimens + type: array + submitter_primary_diagnosis_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Primary Diagnosis Id + type: string + treatments: + items: + $ref: '#/components/schemas/NestedTreatmentSchema' + title: Treatments + type: array + required: + - submitter_primary_diagnosis_id + title: NestedPrimaryDiagnosisSchema + type: object + NestedRadiationSchema: + properties: + anatomical_site_irradiated: + anyOf: + - $ref: '#/components/schemas/RadiationAnatomicalSiteEnum' + - type: 'null' + radiation_boost: + anyOf: + - type: boolean + - type: 'null' + title: Radiation Boost + radiation_therapy_dosage: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Dosage + radiation_therapy_fractions: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Fractions + radiation_therapy_modality: + anyOf: + - $ref: '#/components/schemas/RadiationTherapyModalityEnum' + - type: 'null' + radiation_therapy_type: + anyOf: + - $ref: '#/components/schemas/TherapyTypeEnum' + - type: 'null' + reference_radiation_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Reference Radiation Treatment Id + title: NestedRadiationSchema + type: object + NestedSampleRegistrationSchema: + properties: + sample_type: + anyOf: + - $ref: '#/components/schemas/SampleTypeEnum' + - type: 'null' + specimen_tissue_source: + anyOf: + - $ref: '#/components/schemas/SpecimenTissueSourceEnum' + - type: 'null' + specimen_type: + anyOf: + - $ref: '#/components/schemas/SpecimenTypeEnum' + - type: 'null' + submitter_sample_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Sample Id + type: string + tumour_normal_designation: + anyOf: + - $ref: '#/components/schemas/TumourDesginationEnum' + - type: 'null' + required: + - submitter_sample_id + title: NestedSampleRegistrationSchema + type: object + NestedSpecimenSchema: + properties: + pathological_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + pathological_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + pathological_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + pathological_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + pathological_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + percent_tumour_cells_measurement_method: + anyOf: + - $ref: '#/components/schemas/CellsMeasureMethodEnum' + - type: 'null' + percent_tumour_cells_range: + anyOf: + - $ref: '#/components/schemas/PercentCellsRangeEnum' + - type: 'null' + reference_pathology_confirmed_diagnosis: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + reference_pathology_confirmed_tumour_presence: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + sample_registrations: + items: + $ref: '#/components/schemas/NestedSampleRegistrationSchema' + title: Sample Registrations + type: array + specimen_anatomic_location: + anyOf: + - maxLength: 32 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Specimen Anatomic Location + specimen_collection_date: + anyOf: + - type: object + - type: 'null' + title: Specimen Collection Date + specimen_laterality: + anyOf: + - $ref: '#/components/schemas/SpecimenLateralityEnum' + - type: 'null' + specimen_processing: + anyOf: + - $ref: '#/components/schemas/SpecimenProcessingEnum' + - type: 'null' + specimen_storage: + anyOf: + - $ref: '#/components/schemas/StorageEnum' + - type: 'null' + submitter_specimen_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Specimen Id + type: string + tumour_grade: + anyOf: + - $ref: '#/components/schemas/TumourGradeEnum' + - type: 'null' + tumour_grading_system: + anyOf: + - $ref: '#/components/schemas/TumourGradingSystemEnum' + - type: 'null' + tumour_histological_type: + anyOf: + - maxLength: 128 + pattern: ^[8,9]{1}[0-9]{3}/[0,1,2,3,6,9]{1}[1-9]{0,1}$ + type: string + - type: 'null' + title: Tumour Histological Type + required: + - submitter_specimen_id + title: NestedSpecimenSchema + type: object + NestedSurgerySchema: + properties: + greatest_dimension_tumour: + anyOf: + - type: integer + - type: 'null' + title: Greatest Dimension Tumour + lymphovascular_invasion: + anyOf: + - $ref: '#/components/schemas/LymphovascularInvasionEnum' + - type: 'null' + margin_types_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Involved + margin_types_not_assessed: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Assessed + margin_types_not_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Involved + perineural_invasion: + anyOf: + - $ref: '#/components/schemas/PerineuralInvasionEnum' + - type: 'null' + residual_tumour_classification: + anyOf: + - $ref: '#/components/schemas/TumourClassificationEnum' + - type: 'null' + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + surgery_location: + anyOf: + - $ref: '#/components/schemas/SurgeryLocationEnum' + - type: 'null' + surgery_site: + anyOf: + - maxLength: 255 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Surgery Site + surgery_type: + anyOf: + - $ref: '#/components/schemas/SurgeryTypeEnum' + - type: 'null' + tumour_focality: + anyOf: + - $ref: '#/components/schemas/TumourFocalityEnum' + - type: 'null' + tumour_length: + anyOf: + - type: integer + - type: 'null' + title: Tumour Length + tumour_width: + anyOf: + - type: integer + - type: 'null' + title: Tumour Width + title: NestedSurgerySchema + type: object + NestedTreatmentSchema: + properties: + chemotherapies: + items: + $ref: '#/components/schemas/NestedChemotherapySchema' + title: Chemotherapies + type: array + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + followups: + items: + $ref: '#/components/schemas/NestedFollowUpSchema' + title: Followups + type: array + hormone_therapies: + items: + $ref: '#/components/schemas/NestedHormoneTherapySchema' + title: Hormone Therapies + type: array + immunotherapies: + items: + $ref: '#/components/schemas/NestedImmunotherapySchema' + title: Immunotherapies + type: array + is_primary_treatment: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + line_of_treatment: + anyOf: + - type: integer + - type: 'null' + title: Line Of Treatment + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles + radiations: + items: + $ref: '#/components/schemas/NestedRadiationSchema' + title: Radiations + type: array + response_to_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseEnum' + - type: 'null' + response_to_treatment_criteria_method: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseMethodEnum' + - type: 'null' + status_of_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentStatusEnum' + - type: 'null' + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Treatment Id + type: string + surgeries: + items: + $ref: '#/components/schemas/NestedSurgerySchema' + title: Surgeries + type: array + treatment_end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_intent: + anyOf: + - $ref: '#/components/schemas/TreatmentIntentEnum' + - type: 'null' + treatment_setting: + anyOf: + - $ref: '#/components/schemas/TreatmentSettingEnum' + - type: 'null' + treatment_start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_type: + anyOf: + - items: + $ref: '#/components/schemas/TreatmentTypeEnum' + type: array + - type: 'null' + title: Treatment Type + required: + - submitter_treatment_id + title: NestedTreatmentSchema + type: object + PagedBiomarkerModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/BiomarkerModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedBiomarkerModelSchema + type: object + PagedChemotherapyModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/ChemotherapyModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedChemotherapyModelSchema + type: object + PagedComorbidityModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/ComorbidityModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedComorbidityModelSchema + type: object + PagedDonorModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/DonorModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedDonorModelSchema + type: object + PagedExposureModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/ExposureModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedExposureModelSchema + type: object + PagedFollowUpModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/FollowUpModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedFollowUpModelSchema + type: object + PagedHormoneTherapyModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/HormoneTherapyModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedHormoneTherapyModelSchema + type: object + PagedImmunotherapyModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/ImmunotherapyModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedImmunotherapyModelSchema + type: object + PagedPrimaryDiagnosisModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/PrimaryDiagnosisModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedPrimaryDiagnosisModelSchema + type: object + PagedProgramModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/ProgramModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedProgramModelSchema + type: object + PagedRadiationModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/RadiationModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedRadiationModelSchema + type: object + PagedSampleRegistrationModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/SampleRegistrationModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedSampleRegistrationModelSchema + type: object + PagedSpecimenModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/SpecimenModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedSpecimenModelSchema + type: object + PagedSurgeryModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/SurgeryModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedSurgeryModelSchema + type: object + PagedTreatmentModelSchema: + properties: + count: + anyOf: + - type: integer + - type: 'null' + title: Count + items: + items: + $ref: '#/components/schemas/TreatmentModelSchema' + title: Items + type: array + next_page: + anyOf: + - type: integer + - type: 'null' + title: Next Page + previous_page: + anyOf: + - type: integer + - type: 'null' + title: Previous Page + required: + - items + - count + - next_page + - previous_page + title: PagedTreatmentModelSchema + type: object + PatientPerCohortSchema: + properties: + patients_count: + title: Patients Count + type: string + program_id: + title: Program Id + type: string + required: + - program_id + - patients_count + title: PatientPerCohortSchema + type: object + PercentCellsRangeEnum: + enum: + - 0-19% + - 20-50% + - 51-100% + title: PercentCellsRangeEnum + type: string + PerineuralInvasionEnum: + enum: + - Absent + - Cannot be assessed + - Not applicable + - Present + - Unknown + title: PerineuralInvasionEnum + type: string + PrimaryDiagnosisFilterSchema: + properties: + basis_of_diagnosis: + anyOf: + - type: string + - type: 'null' + title: Basis Of Diagnosis + cancer_type_code: + anyOf: + - type: string + - type: 'null' + title: Cancer Type Code + clinical_m_category: + anyOf: + - type: string + - type: 'null' + title: Clinical M Category + clinical_n_category: + anyOf: + - type: string + - type: 'null' + title: Clinical N Category + clinical_stage_group: + anyOf: + - type: string + - type: 'null' + title: Clinical Stage Group + clinical_t_category: + anyOf: + - type: string + - type: 'null' + title: Clinical T Category + clinical_tumour_staging_system: + anyOf: + - type: string + - type: 'null' + title: Clinical Tumour Staging System + laterality: + anyOf: + - type: string + - type: 'null' + title: Laterality + lymph_nodes_examined_method: + anyOf: + - type: string + - type: 'null' + title: Lymph Nodes Examined Method + lymph_nodes_examined_status: + anyOf: + - type: string + - type: 'null' + title: Lymph Nodes Examined Status + number_lymph_nodes_positive: + anyOf: + - type: integer + - type: 'null' + title: Number Lymph Nodes Positive + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + title: PrimaryDiagnosisFilterSchema + type: object + PrimaryDiagnosisIngestSchema: + properties: + basis_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/BasisOfDiagnosisEnum' + - type: 'null' + cancer_type_code: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Cancer Type Code + clinical_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + clinical_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + clinical_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + clinical_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + clinical_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + date_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + laterality: + anyOf: + - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' + - type: 'null' + lymph_nodes_examined_method: + anyOf: + - $ref: '#/components/schemas/LymphNodeMethodEnum' + - type: 'null' + lymph_nodes_examined_status: + anyOf: + - $ref: '#/components/schemas/LymphNodeStatusEnum' + - type: 'null' + number_lymph_nodes_positive: + anyOf: + - type: integer + - type: 'null' + title: Number Lymph Nodes Positive + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Primary Diagnosis Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_primary_diagnosis_id + - program_id + - submitter_donor_id + title: PrimaryDiagnosisIngestSchema + type: object + PrimaryDiagnosisLateralityEnum: + enum: + - Bilateral + - Left + - Midline + - Not a paired site + - Right + - Unilateral, side not specified + - Unknown + title: PrimaryDiagnosisLateralityEnum + type: string + PrimaryDiagnosisModelSchema: + properties: + basis_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/BasisOfDiagnosisEnum' + - type: 'null' + cancer_type_code: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Cancer Type Code + clinical_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + clinical_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + clinical_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + clinical_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + clinical_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + date_of_diagnosis: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + laterality: + anyOf: + - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' + - type: 'null' + lymph_nodes_examined_method: + anyOf: + - $ref: '#/components/schemas/LymphNodeMethodEnum' + - type: 'null' + lymph_nodes_examined_status: + anyOf: + - $ref: '#/components/schemas/LymphNodeStatusEnum' + - type: 'null' + number_lymph_nodes_positive: + anyOf: + - type: integer + - type: 'null' + title: Number Lymph Nodes Positive + program_id: + title: Program Id + type: string + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Primary Diagnosis Id + type: string + required: + - submitter_primary_diagnosis_id + - program_id + - submitter_donor_id + title: PrimaryDiagnosisModelSchema + type: object + PrimarySiteCountSchema: + properties: + primary_site_count: + title: Primary Site Count + type: string + primary_site_name: + title: Primary Site Name + type: string + required: + - primary_site_name + - primary_site_count + title: PrimarySiteCountSchema + type: object + PrimarySiteEnum: + enum: + - Accessory sinuses + - Adrenal gland + - Anus and anal canal + - Base of tongue + - Bladder + - Bones, joints and articular cartilage of limbs + - Bones, joints and articular cartilage of other and unspecified sites + - Brain + - Breast + - Bronchus and lung + - Cervix uteri + - Colon + - Connective, subcutaneous and other soft tissues + - Corpus uteri + - Esophagus + - Eye and adnexa + - Floor of mouth + - Gallbladder + - Gum + - Heart, mediastinum, and pleura + - Hematopoietic and reticuloendothelial systems + - Hypopharynx + - Kidney + - Larynx + - Lip + - Liver and intrahepatic bile ducts + - Lymph nodes + - Meninges + - Nasal cavity and middle ear + - Nasopharynx + - Oropharynx + - Other and ill-defined digestive organs + - Other and ill-defined sites + - Other and ill-defined sites in lip, oral cavity and pharynx + - Other and ill-defined sites within respiratory system and intrathoracic organs + - Other and unspecified female genital organs + - Other and unspecified major salivary glands + - Other and unspecified male genital organs + - Other and unspecified parts of biliary tract + - Other and unspecified parts of mouth + - Other and unspecified parts of tongue + - Other and unspecified urinary organs + - Other endocrine glands and related structures + - Ovary + - Palate + - Pancreas + - Parotid gland + - Penis + - Peripheral nerves and autonomic nervous system + - Placenta + - Prostate gland + - Pyriform sinus + - Rectosigmoid junction + - Rectum + - Renal pelvis + - Retroperitoneum and peritoneum + - Skin + - Small intestine + - Spinal cord, cranial nerves, and other parts of central nervous system + - Stomach + - Testis + - Thymus + - Thyroid gland + - Tonsil + - Trachea + - Ureter + - Uterus, NOS + - Vagina + - Vulva + - Unknown primary site + title: PrimarySiteEnum + type: string + ProgramDiscoverySchema: + properties: + metadata: + title: Metadata + program_id: + title: Program Id + type: string + required: + - program_id + - metadata + title: ProgramDiscoverySchema + type: object + ProgramFilterSchema: + properties: + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + title: ProgramFilterSchema + type: object + ProgramIngestSchema: + properties: + created: + format: date-time + title: Created + type: string + metadata: + anyOf: + - type: object + - type: 'null' + title: Metadata + program_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Program Id + type: string + updated: + format: date-time + title: Updated + type: string + required: + - program_id + title: ProgramIngestSchema + type: object + ProgramModelSchema: + properties: + created: + format: date-time + title: Created + type: string + metadata: + anyOf: + - type: object + - type: 'null' + title: Metadata + program_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Program Id + type: string + updated: + format: date-time + title: Updated + type: string + required: + - program_id + title: ProgramModelSchema + type: object + ProgressionStatusMethodEnum: + enum: + - Imaging (procedure) + - Histopathology test (procedure) + - Assessment of symptom control (procedure) + - Physical examination procedure (procedure) + - Tumor marker measurement (procedure) + - Laboratory data interpretation (procedure) + title: ProgressionStatusMethodEnum + type: string + RadiationAnatomicalSiteEnum: + enum: + - Left Abdomen + - Whole Abdomen + - Right Abdomen + - Lower Abdomen + - Left Lower Abdomen + - Right Lower Abdomen + - Upper Abdomen + - Left Upper Abdomen + - Right Upper Abdomen + - Left Adrenal + - Right Adrenal + - Bilateral Ankle + - Left Ankle + - Right Ankle + - Bilateral Antrum (Bull's Eye) + - Left Antrum + - Right Antrum + - Anus + - Lower Left Arm + - Lower Right Arm + - Bilateral Arms + - Left Arm + - Right Arm + - Upper Left Arm + - Upper Right Arm + - Left Axilla + - Right Axilla + - Skin or Soft Tissue of Back + - Bile Duct + - Bladder + - Lower Body + - Middle Body + - Upper Body + - Whole Body + - Boost - Area Previously Treated + - Brain + - Left Breast Boost + - Right Breast Boost + - Bilateral Breast + - Left Breast + - Right Breast + - Bilateral Breasts with Nodes + - Left Breast with Nodes + - Right Breast with Nodes + - Bilateral Buttocks + - Left Buttock + - Right Buttock + - Inner Canthus + - Outer Canthus + - Cervix + - Bilateral Chest Lung & Area Involve + - Left Chest + - Right Chest + - Chin + - Left Cheek + - Right Cheek + - Bilateral Chest Wall (W/o Breast) + - Left Chest Wall + - Right Chest Wall + - Bilateral Clavicle + - Left Clavicle + - Right Clavicle + - Coccyx + - Colon + - Whole C.N.S. (Medulla Techinque) + - Csf Spine (Medull Tech 2 Diff Machi + - Left Chestwall Boost + - Right Chestwall Boost + - Bilateral Chestwall with Nodes + - Left Chestwall with Nodes + - Right Chestwall with Nodes + - Left Ear + - Right Ear + - Epigastrium + - Lower Esophagus + - Middle Esophagus + - Upper Esophagus + - Entire Esophagus + - Ethmoid Sinus + - Bilateral Eyes + - Left Eye + - Right Eye + - Bilateral Face + - Left Face + - Right Face + - Left Fallopian Tubes + - Right Fallopian Tubes + - Bilateral Femur + - Left Femur + - Right Femur + - Left Fibula + - Right Fibula + - Finger (Including Thumbs) + - Floor of Mouth (Boosts) + - Bilateral Feet + - Left Foot + - Right Foot + - Forehead + - Posterior Fossa + - Gall Bladder + - Gingiva + - Bilateral Hand + - Left Hand + - Right Hand + - Head + - Bilateral Heel + - Left Heel + - Right Heel + - Left Hemimantle + - Right Hemimantle + - Heart + - Bilateral Hip + - Left Hip + - Right Hip + - Left Humerus + - Right Humerus + - Hypopharynx + - Bilateral Internal Mammary Chain + - Bilateral Inguinal Nodes + - Left Inguinal Nodes + - Right Inguinal Nodes + - Inverted 'Y' (Dog-Leg,Hockey-Stick) + - Left Kidney + - Right Kidney + - Bilateral Knee + - Left Knee + - Right Knee + - Bilateral Lacrimal Gland + - Left Lacrimal Gland + - Right Lacrimal Gland + - Larygopharynx + - Larynx + - Bilateral Leg + - Left Leg + - Right Leg + - Lower Bilateral Leg + - Lower Left Leg + - Lower Right Leg + - Upper Bilateral Leg + - Upper Left Leg + - Upper Right Leg + - Both Eyelid(s) + - Left Eyelid + - Right Eyelid + - Both Lip(s) + - Lower Lip + - Upper Lip + - Liver + - Bilateral Lung + - Left Lung + - Right Lung + - Bilateral Mandible + - Left Mandible + - Right Mandible + - Mantle + - Bilateral Maxilla + - Left Maxilla + - Right Maxilla + - Mediastinum + - Multiple Skin + - Nasal Fossa + - Nasopharynx + - Bilateral Neck Includes Nodes + - Left Neck Includes Nodes + - Right Neck Includes Nodes + - Neck - Skin + - Nose + - Oral Cavity / Buccal Mucosa + - Bilateral Orbit + - Left Orbit + - Right Orbit + - Oropharynx + - Bilateral Ovary + - Left Ovary + - Right Ovary + - Hard Palate + - Soft Palate + - Palate Unspecified + - Pancreas + - Para-Aortic Nodes + - Left Parotid + - Right Parotid + - Bilateral Pelvis + - Left Pelvis + - Right Pelvis + - Penis + - Perineum + - Pituitary + - Left Pleura (As in Mesothelioma) + - Right Pleura + - Prostate + - Pubis + - Pyriform Fossa (Sinuses) + - Left Radius + - Right Radius + - Rectum (Includes Sigmoid) + - Left Ribs + - Right Ribs + - Sacrum + - Left Salivary Gland + - Right Salivary Gland + - Bilateral Scapula + - Left Scapula + - Right Scapula + - Bilateral Supraclavicular Nodes + - Left Supraclavicular Nodes + - Right Supraclavicular Nodes + - Bilateral Scalp + - Left Scalp + - Right Scalp + - Scrotum + - Bilateral Shoulder + - Left Shoulder + - Right Shoulder + - Whole Body - Skin + - Skull + - Cervical & Thoracic Spine + - Sphenoid Sinus + - Cervical Spine + - Lumbar Spine + - Thoracic Spine + - Whole Spine + - Spleen + - Lumbo-Sacral Spine + - Thoracic & Lumbar Spine + - Sternum + - Stomach + - Submandibular Glands + - Left Temple + - Right Temple + - Bilateral Testis + - Left Testis + - Right Testis + - Thyroid + - Left Tibia + - Right Tibia + - Left Toes + - Right Toes + - Tongue + - Tonsil + - Trachea + - Left Ulna + - Right Ulna + - Left Ureter + - Right Ureter + - Urethra + - Uterus + - Uvula + - Vagina + - Vulva + - Abdomen + - Body + - Chest + - Lower Limb + - Neck + - Other + - Pelvis + - Skin + - Spine + - Upper Limb + title: RadiationAnatomicalSiteEnum + type: string + RadiationFilterSchema: + properties: + anatomical_site_irradiated: + anyOf: + - type: string + - type: 'null' + title: Anatomical Site Irradiated + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + radiation_boost: + anyOf: + - type: boolean + - type: 'null' + title: Radiation Boost + radiation_therapy_dosage: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Dosage + radiation_therapy_fractions: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Fractions + radiation_therapy_modality: + anyOf: + - type: string + - type: 'null' + title: Radiation Therapy Modality + radiation_therapy_type: + anyOf: + - type: string + - type: 'null' + title: Radiation Therapy Type + reference_radiation_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Reference Radiation Treatment Id + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + title: RadiationFilterSchema + type: object + RadiationIngestSchema: + properties: + anatomical_site_irradiated: + anyOf: + - $ref: '#/components/schemas/RadiationAnatomicalSiteEnum' + - type: 'null' + program_id: + title: Program Id + type: string + radiation_boost: + anyOf: + - type: boolean + - type: 'null' + title: Radiation Boost + radiation_therapy_dosage: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Dosage + radiation_therapy_fractions: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Fractions + radiation_therapy_modality: + anyOf: + - $ref: '#/components/schemas/RadiationTherapyModalityEnum' + - type: 'null' + radiation_therapy_type: + anyOf: + - $ref: '#/components/schemas/TherapyTypeEnum' + - type: 'null' + reference_radiation_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Reference Radiation Treatment Id + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: RadiationIngestSchema + type: object + RadiationModelSchema: + properties: + anatomical_site_irradiated: + anyOf: + - $ref: '#/components/schemas/RadiationAnatomicalSiteEnum' + - type: 'null' + program_id: + title: Program Id + type: string + radiation_boost: + anyOf: + - type: boolean + - type: 'null' + title: Radiation Boost + radiation_therapy_dosage: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Dosage + radiation_therapy_fractions: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Fractions + radiation_therapy_modality: + anyOf: + - $ref: '#/components/schemas/RadiationTherapyModalityEnum' + - type: 'null' + radiation_therapy_type: + anyOf: + - $ref: '#/components/schemas/TherapyTypeEnum' + - type: 'null' + reference_radiation_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Reference Radiation Treatment Id + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: RadiationModelSchema + type: object + RadiationTherapyModalityEnum: + enum: + - Megavoltage radiation therapy using photons (procedure) + - Radiopharmaceutical + - Teleradiotherapy using electrons (procedure) + - Teleradiotherapy protons (procedure) + - Teleradiotherapy neutrons (procedure) + - Brachytherapy (procedure) + - Other + title: RadiationTherapyModalityEnum + type: string + RelapseTypeEnum: + enum: + - Distant recurrence/metastasis + - Local recurrence + - Local recurrence and distant metastasis + - Progression (liquid tumours) + - Biochemical progression + title: RelapseTypeEnum + type: string + SampleRegistrationFilterSchema: + properties: + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + sample_type: + anyOf: + - type: string + - type: 'null' + title: Sample Type + specimen_tissue_source: + anyOf: + - type: string + - type: 'null' + title: Specimen Tissue Source + specimen_type: + anyOf: + - type: string + - type: 'null' + title: Specimen Type + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_sample_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Sample Id + submitter_specimen_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + tumour_normal_designation: + anyOf: + - type: string + - type: 'null' + title: Tumour Normal Designation + title: SampleRegistrationFilterSchema + type: object + SampleRegistrationIngestSchema: + properties: + program_id: + title: Program Id + type: string + sample_type: + anyOf: + - $ref: '#/components/schemas/SampleTypeEnum' + - type: 'null' + specimen_tissue_source: + anyOf: + - $ref: '#/components/schemas/SpecimenTissueSourceEnum' + - type: 'null' + specimen_type: + anyOf: + - $ref: '#/components/schemas/SpecimenTypeEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_sample_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Sample Id + type: string + submitter_specimen_id: + title: Submitter Specimen Id + type: string + tumour_normal_designation: + anyOf: + - $ref: '#/components/schemas/TumourDesginationEnum' + - type: 'null' + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_sample_id + - program_id + - submitter_donor_id + - submitter_specimen_id + title: SampleRegistrationIngestSchema + type: object + SampleRegistrationModelSchema: + properties: + program_id: + title: Program Id + type: string + sample_type: + anyOf: + - $ref: '#/components/schemas/SampleTypeEnum' + - type: 'null' + specimen_tissue_source: + anyOf: + - $ref: '#/components/schemas/SpecimenTissueSourceEnum' + - type: 'null' + specimen_type: + anyOf: + - $ref: '#/components/schemas/SpecimenTypeEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_sample_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Sample Id + type: string + submitter_specimen_id: + title: Submitter Specimen Id + type: string + tumour_normal_designation: + anyOf: + - $ref: '#/components/schemas/TumourDesginationEnum' + - type: 'null' + required: + - submitter_sample_id + - program_id + - submitter_donor_id + - submitter_specimen_id + title: SampleRegistrationModelSchema + type: object + SampleTypeEnum: + enum: + - Amplified DNA + - ctDNA + - Other DNA enrichments + - Other RNA fractions + - polyA+ RNA + - Protein + - rRNA-depleted RNA + - Total DNA + - Total RNA + title: SampleTypeEnum + type: string + SexAtBirthEnum: + enum: + - Male + - Female + - Other + - Unknown + title: SexAtBirthEnum + type: string + SmokingStatusEnum: + enum: + - Current reformed smoker for <= 15 years + - Current reformed smoker for > 15 years + - Current reformed smoker, duration not specified + - Current smoker + - Lifelong non-smoker (<100 cigarettes smoked in lifetime) + - Not applicable + - Smoking history not documented + title: SmokingStatusEnum + type: string + SpecimenFilterSchema: + properties: + pathological_m_category: + anyOf: + - type: string + - type: 'null' + title: Pathological M Category + pathological_n_category: + anyOf: + - type: string + - type: 'null' + title: Pathological N Category + pathological_stage_group: + anyOf: + - type: string + - type: 'null' + title: Pathological Stage Group + pathological_t_category: + anyOf: + - type: string + - type: 'null' + title: Pathological T Category + pathological_tumour_staging_system: + anyOf: + - type: string + - type: 'null' + title: Pathological Tumour Staging System + percent_tumour_cells_measurement_method: + anyOf: + - type: string + - type: 'null' + title: Percent Tumour Cells Measurement Method + percent_tumour_cells_range: + anyOf: + - type: string + - type: 'null' + title: Percent Tumour Cells Range + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + reference_pathology_confirmed_diagnosis: + anyOf: + - type: string + - type: 'null' + title: Reference Pathology Confirmed Diagnosis + reference_pathology_confirmed_tumour_presence: + anyOf: + - type: string + - type: 'null' + title: Reference Pathology Confirmed Tumour Presence + specimen_anatomic_location: + anyOf: + - type: string + - type: 'null' + title: Specimen Anatomic Location + specimen_laterality: + anyOf: + - type: string + - type: 'null' + title: Specimen Laterality + specimen_processing: + anyOf: + - type: string + - type: 'null' + title: Specimen Processing + specimen_storage: + anyOf: + - type: string + - type: 'null' + title: Specimen Storage + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_specimen_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + tumour_grade: + anyOf: + - type: string + - type: 'null' + title: Tumour Grade + tumour_grading_system: + anyOf: + - type: string + - type: 'null' + title: Tumour Grading System + tumour_histological_type: + anyOf: + - type: string + - type: 'null' + title: Tumour Histological Type + title: SpecimenFilterSchema + type: object + SpecimenIngestSchema: + properties: + pathological_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + pathological_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + pathological_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + pathological_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + pathological_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + percent_tumour_cells_measurement_method: + anyOf: + - $ref: '#/components/schemas/CellsMeasureMethodEnum' + - type: 'null' + percent_tumour_cells_range: + anyOf: + - $ref: '#/components/schemas/PercentCellsRangeEnum' + - type: 'null' + program_id: + title: Program Id + type: string + reference_pathology_confirmed_diagnosis: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + reference_pathology_confirmed_tumour_presence: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + specimen_anatomic_location: + anyOf: + - maxLength: 32 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Specimen Anatomic Location + specimen_collection_date: + anyOf: + - type: object + - type: 'null' + title: Specimen Collection Date + specimen_laterality: + anyOf: + - $ref: '#/components/schemas/SpecimenLateralityEnum' + - type: 'null' + specimen_processing: + anyOf: + - $ref: '#/components/schemas/SpecimenProcessingEnum' + - type: 'null' + specimen_storage: + anyOf: + - $ref: '#/components/schemas/StorageEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + title: Submitter Primary Diagnosis Id + type: string + submitter_specimen_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Specimen Id + type: string + tumour_grade: + anyOf: + - $ref: '#/components/schemas/TumourGradeEnum' + - type: 'null' + tumour_grading_system: + anyOf: + - $ref: '#/components/schemas/TumourGradingSystemEnum' + - type: 'null' + tumour_histological_type: + anyOf: + - maxLength: 128 + pattern: ^[8,9]{1}[0-9]{3}/[0,1,2,3,6,9]{1}[1-9]{0,1}$ + type: string + - type: 'null' + title: Tumour Histological Type + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_specimen_id + - program_id + - submitter_donor_id + - submitter_primary_diagnosis_id + title: SpecimenIngestSchema + type: object + SpecimenLateralityEnum: + enum: + - Left + - Not applicable + - Right + - Unknown + title: SpecimenLateralityEnum + type: string + SpecimenModelSchema: + properties: + pathological_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + pathological_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + pathological_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + pathological_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + pathological_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' + percent_tumour_cells_measurement_method: + anyOf: + - $ref: '#/components/schemas/CellsMeasureMethodEnum' + - type: 'null' + percent_tumour_cells_range: + anyOf: + - $ref: '#/components/schemas/PercentCellsRangeEnum' + - type: 'null' + program_id: + title: Program Id + type: string + reference_pathology_confirmed_diagnosis: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + reference_pathology_confirmed_tumour_presence: + anyOf: + - $ref: '#/components/schemas/ConfirmedDiagnosisTumourEnum' + - type: 'null' + specimen_anatomic_location: + anyOf: + - maxLength: 32 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Specimen Anatomic Location + specimen_collection_date: + anyOf: + - type: object + - type: 'null' + title: Specimen Collection Date + specimen_laterality: + anyOf: + - $ref: '#/components/schemas/SpecimenLateralityEnum' + - type: 'null' + specimen_processing: + anyOf: + - $ref: '#/components/schemas/SpecimenProcessingEnum' + - type: 'null' + specimen_storage: + anyOf: + - $ref: '#/components/schemas/StorageEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + title: Submitter Primary Diagnosis Id + type: string + submitter_specimen_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Specimen Id + type: string + tumour_grade: + anyOf: + - $ref: '#/components/schemas/TumourGradeEnum' + - type: 'null' + tumour_grading_system: + anyOf: + - $ref: '#/components/schemas/TumourGradingSystemEnum' + - type: 'null' + tumour_histological_type: + anyOf: + - maxLength: 128 + pattern: ^[8,9]{1}[0-9]{3}/[0,1,2,3,6,9]{1}[1-9]{0,1}$ + type: string + - type: 'null' + title: Tumour Histological Type + required: + - submitter_specimen_id + - program_id + - submitter_donor_id + - submitter_primary_diagnosis_id + title: SpecimenModelSchema + type: object + SpecimenProcessingEnum: + enum: + - Cryopreservation in liquid nitrogen (dead tissue) + - Cryopreservation in dry ice (dead tissue) + - Cryopreservation of live cells in liquid nitrogen + - Cryopreservation - other + - Formalin fixed & paraffin embedded + - Formalin fixed - buffered + - Formalin fixed - unbuffered + - Fresh + - Other + - Unknown + title: SpecimenProcessingEnum + type: string + SpecimenTissueSourceEnum: + enum: + - Abdominal fluid + - Amniotic fluid + - Arterial blood + - Bile + - Blood derived - bone marrow + - Blood derived - peripheral blood + - Bone marrow fluid + - Bone marrow derived mononuclear cells + - Buccal cell + - Buffy coat + - Cerebrospinal fluid + - Cervical mucus + - Convalescent plasma + - Cord blood + - Duodenal fluid + - Female genital fluid + - Fetal blood + - Hydrocele fluid + - Male genital fluid + - Pancreatic fluid + - Pericardial effusion + - Pleural fluid + - Renal cyst fluid + - Saliva + - Seminal fluid + - Serum + - Solid tissue + - Sputum + - Synovial fluid + - Urine + - Venous blood + - Vitreous fluid + - Whole blood + - Wound + title: SpecimenTissueSourceEnum + type: string + SpecimenTypeEnum: + enum: + - Cell line - derived from normal + - Cell line - derived from primary tumour + - Cell line - derived from metastatic tumour + - Cell line - derived from xenograft tumour + - Metastatic tumour - additional metastatic + - Metastatic tumour - metastasis local to lymph node + - Metastatic tumour - metastasis to distant location + - Metastatic tumour + - Normal - tissue adjacent to primary tumour + - Normal + - Primary tumour - additional new primary + - Primary tumour - adjacent to normal + - Primary tumour + - Recurrent tumour + - Tumour - unknown if derived from primary or metastatic tumour + - Xenograft - derived from primary tumour + - Xenograft - derived from metastatic tumour + - Xenograft - derived from tumour cell line + title: SpecimenTypeEnum + type: string + StageGroupEnum: + enum: + - Stage 0 + - Stage 0a + - Stage 0is + - Stage 1 + - Stage 1A + - Stage 1B + - Stage A + - Stage B + - Stage C + - Stage I + - Stage IA + - Stage IA1 + - Stage IA2 + - Stage IA3 + - Stage IAB + - Stage IAE + - Stage IAES + - Stage IAS + - Stage IB + - Stage IB1 + - Stage IB2 + - Stage IBE + - Stage IBES + - Stage IBS + - Stage IC + - Stage IE + - Stage IEA + - Stage IEB + - Stage IES + - Stage II + - Stage II bulky + - Stage IIA + - Stage IIA1 + - Stage IIA2 + - Stage IIAE + - Stage IIAES + - Stage IIAS + - Stage IIB + - Stage IIBE + - Stage IIBES + - Stage IIBS + - Stage IIC + - Stage IIE + - Stage IIEA + - Stage IIEB + - Stage IIES + - Stage III + - Stage IIIA + - Stage IIIA1 + - Stage IIIA2 + - Stage IIIAE + - Stage IIIAES + - Stage IIIAS + - Stage IIIB + - Stage IIIBE + - Stage IIIBES + - Stage IIIBS + - Stage IIIC + - Stage IIIC1 + - Stage IIIC2 + - Stage IIID + - Stage IIIE + - Stage IIIES + - Stage IIIS + - Stage IIS + - Stage IS + - Stage IV + - Stage IVA + - Stage IVA1 + - Stage IVA2 + - Stage IVAE + - Stage IVAES + - Stage IVAS + - Stage IVB + - Stage IVBE + - Stage IVBES + - Stage IVBS + - Stage IVC + - Stage IVE + - Stage IVES + - Stage IVS + - In situ + - Localized + - Regionalized + - Distant + - Stage L1 + - Stage L2 + - Stage M + - Stage Ms + - Stage 2A + - Stage 2B + - Stage 3 + - Stage 4 + - Stage 4S + - Occult Carcinoma + title: StageGroupEnum + type: string + StorageEnum: + enum: + - Cut slide + - Frozen in -70 freezer + - Frozen in liquid nitrogen + - Frozen in vapour phase + - Not Applicable + - Other + - Paraffin block + - RNA later frozen + - Unknown + title: StorageEnum + type: string + SurgeryFilterSchema: + properties: + greatest_dimension_tumour: + anyOf: + - type: integer + - type: 'null' + title: Greatest Dimension Tumour + lymphovascular_invasion: + anyOf: + - type: string + - type: 'null' + title: Lymphovascular Invasion + margin_types_involved: + items: + type: string + q: margin_types_involved__overlap + title: Margin Types Involved + type: array + margin_types_not_assessed: + items: + type: string + q: margin_types_not_assessed__overlap + title: Margin Types Not Assessed + type: array + margin_types_not_involved: + items: + type: string + q: margin_types_not_involved__overlap + title: Margin Types Not Involved + type: array + perineural_invasion: + anyOf: + - type: string + - type: 'null' + title: Perineural Invasion + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + residual_tumour_classification: + anyOf: + - type: string + - type: 'null' + title: Residual Tumour Classification + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_specimen_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + surgery_location: + anyOf: + - type: string + - type: 'null' + title: Surgery Location + surgery_site: + anyOf: + - type: string + - type: 'null' + title: Surgery Site + surgery_type: + anyOf: + - type: string + - type: 'null' + title: Surgery Type + tumour_focality: + anyOf: + - type: string + - type: 'null' + title: Tumour Focality + tumour_length: + anyOf: + - type: integer + - type: 'null' + title: Tumour Length + tumour_width: + anyOf: + - type: integer + - type: 'null' + title: Tumour Width + title: SurgeryFilterSchema + type: object + SurgeryIngestSchema: + properties: + greatest_dimension_tumour: + anyOf: + - type: integer + - type: 'null' + title: Greatest Dimension Tumour + lymphovascular_invasion: + anyOf: + - $ref: '#/components/schemas/LymphovascularInvasionEnum' + - type: 'null' + margin_types_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Involved + margin_types_not_assessed: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Assessed + margin_types_not_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Involved + perineural_invasion: + anyOf: + - $ref: '#/components/schemas/PerineuralInvasionEnum' + - type: 'null' + program_id: + title: Program Id + type: string + residual_tumour_classification: + anyOf: + - $ref: '#/components/schemas/TumourClassificationEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + title: Submitter Treatment Id + type: string + surgery_location: + anyOf: + - $ref: '#/components/schemas/SurgeryLocationEnum' + - type: 'null' + surgery_site: + anyOf: + - maxLength: 255 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Surgery Site + surgery_type: + anyOf: + - $ref: '#/components/schemas/SurgeryTypeEnum' + - type: 'null' + tumour_focality: + anyOf: + - $ref: '#/components/schemas/TumourFocalityEnum' + - type: 'null' + tumour_length: + anyOf: + - type: integer + - type: 'null' + title: Tumour Length + tumour_width: + anyOf: + - type: integer + - type: 'null' + title: Tumour Width + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: SurgeryIngestSchema + type: object + SurgeryLocationEnum: + enum: + - Local recurrence + - Metastatic + - Primary + title: SurgeryLocationEnum + type: string + SurgeryModelSchema: + properties: + greatest_dimension_tumour: + anyOf: + - type: integer + - type: 'null' + title: Greatest Dimension Tumour + lymphovascular_invasion: + anyOf: + - $ref: '#/components/schemas/LymphovascularInvasionEnum' + - type: 'null' + margin_types_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Involved + margin_types_not_assessed: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Assessed + margin_types_not_involved: + anyOf: + - items: + $ref: '#/components/schemas/MarginTypesEnum' + type: array + - type: 'null' + title: Margin Types Not Involved + perineural_invasion: + anyOf: + - $ref: '#/components/schemas/PerineuralInvasionEnum' + - type: 'null' + program_id: + title: Program Id + type: string + residual_tumour_classification: + anyOf: + - $ref: '#/components/schemas/TumourClassificationEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_specimen_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Specimen Id + submitter_treatment_id: + title: Submitter Treatment Id + type: string + surgery_location: + anyOf: + - $ref: '#/components/schemas/SurgeryLocationEnum' + - type: 'null' + surgery_site: + anyOf: + - maxLength: 255 + pattern: ^[C][0-9]{2}(.[0-9]{1})?$ + type: string + - type: 'null' + title: Surgery Site + surgery_type: + anyOf: + - $ref: '#/components/schemas/SurgeryTypeEnum' + - type: 'null' + tumour_focality: + anyOf: + - $ref: '#/components/schemas/TumourFocalityEnum' + - type: 'null' + tumour_length: + anyOf: + - type: integer + - type: 'null' + title: Tumour Length + tumour_width: + anyOf: + - type: integer + - type: 'null' + title: Tumour Width + required: + - program_id + - submitter_donor_id + - submitter_treatment_id + title: SurgeryModelSchema + type: object + SurgeryTypeEnum: + enum: + - Ablation + - Axillary Clearance + - Axillary lymph nodes sampling + - Bilateral complete salpingo-oophorectomy + - Biopsy + - Bypass Gastrojejunostomy + - Cholecystectomy + - Cholecystojejunostomy + - Completion Gastrectomy + - Debridement of pancreatic and peripancreatic necrosis + - Distal subtotal pancreatectomy + - Drainage of abscess + - Duodenal preserving pancreatic head resection + - Endoscopic biopsy + - Endoscopic brushings of gastrointestinal tract + - Enucleation + - Esophageal bypass surgery/jejunostomy only + - Exploratory laparotomy + - Fine needle aspiration biopsy + - Gastric Antrectomy + - Glossectomy + - Hepatojejunostomy + - Hysterectomy + - Incision of thorax + - Ivor Lewis subtotal esophagectomy + - Laparotomy + - Left thoracoabdominal incision + - Lobectomy + - Mammoplasty + - Mastectomy + - McKeown esophagectomy + - Merendino procedure + - Minimally invasive esophagectomy + - Omentectomy + - Ovariectomy + - Pancreaticoduodenectomy (Whipple procedure) + - Pancreaticojejunostomy, side-to-side anastomosis + - Partial pancreatectomy + - Pneumonectomy + - Prostatectomy + - Proximal subtotal gastrectomy + - Pylorus-sparing Whipple operation + - Radical pancreaticoduodenectomy + - Radical prostatectomy + - Reexcision + - Segmentectomy + - Sentinal Lymph Node Biopsy + - Spleen preserving distal pancreatectomy + - Splenectomy + - Total gastrectomy + - Total gastrectomy with extended lymphadenectomy + - Total pancreatectomy + - Transhiatal esophagectomy + - Triple bypass of pancreas + - Tumor Debulking + - Wedge/localised gastric resection + - Wide Local Excision + title: SurgeryTypeEnum + type: string + TCategoryEnum: + enum: + - T0 + - T1 + - T1a + - T1a1 + - T1a2 + - T1a(s) + - T1a(m) + - T1b + - T1b1 + - T1b2 + - T1b(s) + - T1b(m) + - T1c + - T1d + - T1mi + - T2 + - T2(s) + - T2(m) + - T2a + - T2a1 + - T2a2 + - T2b + - T2c + - T2d + - T3 + - T3(s) + - T3(m) + - T3a + - T3b + - T3c + - T3d + - T3e + - T4 + - T4a + - T4a(s) + - T4a(m) + - T4b + - T4b(s) + - T4b(m) + - T4c + - T4d + - T4e + - Ta + - Tis + - Tis(DCIS) + - Tis(LAMN) + - Tis(LCIS) + - Tis(Paget) + - Tis(Paget's) + - Tis pu + - Tis pd + - TX + title: TCategoryEnum + type: string + TherapyTypeEnum: + enum: + - External + - Internal + title: TherapyTypeEnum + type: string + TobaccoTypeEnum: + enum: + - Chewing Tobacco + - Cigar + - Cigarettes + - Electronic cigarettes + - Not applicable + - Pipe + - Roll-ups + - Snuff + - Unknown + - Waterpipe + title: TobaccoTypeEnum + type: string + TreatmentFilterSchema: + properties: + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + is_primary_treatment: + anyOf: + - type: string + - type: 'null' + title: Is Primary Treatment + line_of_treatment: + anyOf: + - type: integer + - type: 'null' + title: Line Of Treatment + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles + program_id: + anyOf: + - type: string + - type: 'null' + title: Program Id + response_to_treatment: + anyOf: + - type: string + - type: 'null' + title: Response To Treatment + response_to_treatment_criteria_method: + anyOf: + - type: string + - type: 'null' + title: Response To Treatment Criteria Method + status_of_treatment: + anyOf: + - type: string + - type: 'null' + title: Status Of Treatment + submitter_donor_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + submitter_primary_diagnosis_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + treatment_intent: + anyOf: + - type: string + - type: 'null' + title: Treatment Intent + treatment_setting: + anyOf: + - type: string + - type: 'null' + title: Treatment Setting + treatment_type: + items: + type: string + q: treatment_type__overlap + title: Treatment Type + type: array + title: TreatmentFilterSchema + type: object + TreatmentIngestSchema: + properties: + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + is_primary_treatment: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + line_of_treatment: + anyOf: + - type: integer + - type: 'null' + title: Line Of Treatment + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles + program_id: + title: Program Id + type: string + response_to_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseEnum' + - type: 'null' + response_to_treatment_criteria_method: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseMethodEnum' + - type: 'null' + status_of_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentStatusEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + title: Submitter Primary Diagnosis Id + type: string + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Treatment Id + type: string + treatment_end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_intent: + anyOf: + - $ref: '#/components/schemas/TreatmentIntentEnum' + - type: 'null' + treatment_setting: + anyOf: + - $ref: '#/components/schemas/TreatmentSettingEnum' + - type: 'null' + treatment_start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_type: + anyOf: + - items: + $ref: '#/components/schemas/TreatmentTypeEnum' + type: array + - type: 'null' + title: Treatment Type + uuid: + anyOf: + - type: string + - type: 'null' + title: Uuid + required: + - submitter_treatment_id + - program_id + - submitter_donor_id + - submitter_primary_diagnosis_id + title: TreatmentIngestSchema + type: object + TreatmentIntentEnum: + enum: + - Curative + - Palliative + - Supportive + - Diagnostic + - Preventive + - Guidance + - Screening + - Forensic + title: TreatmentIntentEnum + type: string + TreatmentModelSchema: + properties: + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + is_primary_treatment: + anyOf: + - $ref: '#/components/schemas/uBooleanEnum' + - type: 'null' + line_of_treatment: + anyOf: + - type: integer + - type: 'null' + title: Line Of Treatment + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles + program_id: + title: Program Id + type: string + response_to_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseEnum' + - type: 'null' + response_to_treatment_criteria_method: + anyOf: + - $ref: '#/components/schemas/TreatmentResponseMethodEnum' + - type: 'null' + status_of_treatment: + anyOf: + - $ref: '#/components/schemas/TreatmentStatusEnum' + - type: 'null' + submitter_donor_id: + title: Submitter Donor Id + type: string + submitter_primary_diagnosis_id: + title: Submitter Primary Diagnosis Id + type: string + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Treatment Id + type: string + treatment_end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_intent: + anyOf: + - $ref: '#/components/schemas/TreatmentIntentEnum' + - type: 'null' + treatment_setting: + anyOf: + - $ref: '#/components/schemas/TreatmentSettingEnum' + - type: 'null' + treatment_start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + treatment_type: + anyOf: + - items: + $ref: '#/components/schemas/TreatmentTypeEnum' + type: array + - type: 'null' + title: Treatment Type + required: + - submitter_treatment_id + - program_id + - submitter_donor_id + - submitter_primary_diagnosis_id + title: TreatmentModelSchema + type: object + TreatmentResponseEnum: + enum: + - Complete response + - Partial response + - Progressive disease + - Stable disease + - Immune complete response (iCR) + - Immune partial response (iPR) + - Immune uncomfirmed progressive disease (iUPD) + - Immune confirmed progressive disease (iCPD) + - Immune stable disease (iSD) + - Complete remission + - Partial remission + - Minor response + - Complete remission without measurable residual disease (CR MRD-) + - Complete remission with incomplete hematologic recovery (CRi) + - Morphologic leukemia-free state + - Primary refractory disease + - Hematologic relapse (after CR MRD-, CR, CRi) + - Molecular relapse (after CR MRD-) + - Physician assessed complete response + - Physician assessed partial response + - Physician assessed stable disease + - No evidence of disease (NED) + - Major response + title: TreatmentResponseEnum + type: string + TreatmentResponseMethodEnum: + enum: + - RECIST 1.1 + - iRECIST + - Cheson CLL 2012 Oncology Response Criteria + - Response Assessment in Neuro-Oncology (RANO) + - AML Response Criteria + - Physician Assessed Response Criteria + - Blazer score + title: TreatmentResponseMethodEnum + type: string + TreatmentSettingEnum: + enum: + - Adjuvant + - Advanced/Metastatic + - Neoadjuvant + - Conditioning + - Induction + - Locally advanced + - Maintenance + - Mobilization + - Preventative + - Radiosensitization + - Salvage + title: TreatmentSettingEnum + type: string + TreatmentStatusEnum: + enum: + - Treatment completed as prescribed + - Treatment incomplete due to technical or organizational problems + - Treatment incomplete because patient died + - Patient choice (stopped or interrupted treatment) + - Physician decision (stopped or interrupted treatment) + - Treatment stopped due to lack of efficacy (disease progression) + - Treatment stopped due to acute toxicity + - Other + - Not applicable + - Unknown + title: TreatmentStatusEnum + type: string + TreatmentTypeCountSchema: + properties: + treatment_type_count: + title: Treatment Type Count + type: string + treatment_type_name: + title: Treatment Type Name + type: string + required: + - treatment_type_name + - treatment_type_count + title: TreatmentTypeCountSchema + type: object + TreatmentTypeEnum: + enum: + - Bone marrow transplant + - Chemotherapy + - Hormonal therapy + - Immunotherapy + - No treatment + - Other targeting molecular therapy + - Photodynamic therapy + - Radiation therapy + - Stem cell transplant + - Surgery + title: TreatmentTypeEnum + type: string + TumourClassificationEnum: + enum: + - Not applicable + - RX + - R0 + - R1 + - R2 + - Unknown + title: TumourClassificationEnum + type: string + TumourDesginationEnum: + enum: + - Normal + - Tumour + title: TumourDesginationEnum + type: string + TumourFocalityEnum: + enum: + - Cannot be assessed + - Multifocal + - Not applicable + - Unifocal + - Unknown + title: TumourFocalityEnum + type: string + TumourGradeEnum: + enum: + - Low grade + - High grade + - GX + - G1 + - G2 + - G3 + - G4 + - Low + - High + - Grade 1 + - Grade 2 + - Grade 3 + - Grade 4 + - Grade I + - Grade II + - Grade III + - Grade IV + - Grade Group 1 + - Grade Group 2 + - Grade Group 3 + - Grade Group 4 + - Grade Group 5 + title: TumourGradeEnum + type: string + TumourGradingSystemEnum: + enum: + - FNCLCC grading system + - Four-tier grading system + - Gleason grade group system + - Grading system for GISTs + - Grading system for GNETs + - IASLC grading system + - ISUP grading system + - Nottingham grading system + - Nuclear grading system for DCIS + - Scarff-Bloom-Richardson grading system + - Three-tier grading system + - Two-tier grading system + - WHO grading system for CNS tumours + title: TumourGradingSystemEnum + type: string + TumourStagingSystemEnum: + enum: + - AJCC 8th edition + - AJCC 7th edition + - AJCC 6th edition + - Ann Arbor staging system + - Binet staging system + - Durie-Salmon staging system + - FIGO staging system + - International Neuroblastoma Risk Group Staging System + - International Neuroblastoma Staging System + - Lugano staging system + - Rai staging system + - Revised International staging system (RISS) + - SEER staging system + - St Jude staging system + title: TumourStagingSystemEnum + type: string + uBooleanEnum: + enum: + - 'Yes' + - 'No' + - Unknown + title: uBooleanEnum + type: string + securitySchemes: + LoginAuth: + scheme: bearer + type: http + ServiceTokenAuth: + in: header + name: X-Service-Token + type: apiKey +info: + description: This is the RESTful API for the MoH Service. + title: MoH Service API + version: 4.4.0 +openapi: 3.1.0 +paths: + /v2/authorized/biomarkers/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_biomarkers + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_specimen_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + - in: query + name: submitter_primary_diagnosis_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: submitter_follow_up_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Follow Up Id + - in: query + name: psa_level + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Psa Level + - in: query + name: ca125 + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Ca125 + - in: query + name: cea + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Cea + - in: query + name: er_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Er Status + - in: query + name: er_percent_positive + required: false + schema: + anyOf: + - type: number + - type: 'null' + title: Er Percent Positive + - in: query + name: pr_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pr Status + - in: query + name: pr_percent_positive + required: false + schema: + anyOf: + - type: number + - type: 'null' + title: Pr Percent Positive + - in: query + name: her2_ihc_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Her2 Ihc Status + - in: query + name: her2_ish_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Her2 Ish Status + - in: query + name: hpv_ihc_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Hpv Ihc Status + - in: query + name: hpv_pcr_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Hpv Pcr Status + - in: query + name: hpv_strain + required: false + schema: + items: + type: string + q: hpv_strain__overlap + title: Hpv Strain + type: array + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedBiomarkerModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Biomarkers + tags: + - authorized + /v2/authorized/chemotherapies/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_chemotherapies + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: drug_reference_database + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + - in: query + name: drug_name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Name + - in: query + name: drug_reference_identifier + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + - in: query + name: chemotherapy_drug_dose_units + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Chemotherapy Drug Dose Units + - in: query + name: prescribed_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + - in: query + name: actual_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedChemotherapyModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Chemotherapies + tags: + - authorized + /v2/authorized/comorbidities/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_comorbidities + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: prior_malignancy + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Prior Malignancy + - in: query + name: laterality_of_prior_malignancy + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Laterality Of Prior Malignancy + - in: query + name: age_at_comorbidity_diagnosis + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Age At Comorbidity Diagnosis + - in: query + name: comorbidity_type_code + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Type Code + - in: query + name: comorbidity_treatment_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Treatment Status + - in: query + name: comorbidity_treatment + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Comorbidity Treatment + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedComorbidityModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Comorbidities + tags: + - authorized + /v2/authorized/donor_with_clinical_data/program/{program_id}/donor/{donor_id}: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_get_donor_with_clinical_data + parameters: + - in: path + name: program_id + required: true + schema: + title: Program Id + type: string + - in: path + name: donor_id + required: true + schema: + title: Donor Id + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DonorWithClinicalDataSchema' + description: OK + '404': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response + type: object + description: Not Found + security: + - LoginAuth: [] + summary: Get Donor With Clinical Data + tags: + - authorized + /v2/authorized/donors/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_donors + parameters: + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: gender + required: false + schema: + anyOf: + - type: string + - type: 'null' + q: gender__icontains + title: Gender + - in: query + name: sex_at_birth + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Sex At Birth + - in: query + name: is_deceased + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Is Deceased + - in: query + name: lost_to_followup_after_clinical_event_identifier + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Lost To Followup After Clinical Event Identifier + - in: query + name: lost_to_followup_reason + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Lost To Followup Reason + - in: query + name: cause_of_death + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Cause Of Death + - in: query + name: primary_site + required: false + schema: + items: + type: string + q: primary_site__overlap + title: Primary Site + type: array + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedDonorModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Donors + tags: + - authorized + /v2/authorized/exposures/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_exposures + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: tobacco_smoking_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tobacco Smoking Status + - in: query + name: tobacco_type + required: false + schema: + items: + type: string + q: tobacco_type__overlap + title: Tobacco Type + type: array + - in: query + name: pack_years_smoked + required: false + schema: + anyOf: + - type: number + - type: 'null' + title: Pack Years Smoked + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedExposureModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Exposures + tags: + - authorized + /v2/authorized/follow_ups/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_follow_ups + parameters: + - in: query + name: submitter_follow_up_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Follow Up Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_primary_diagnosis_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: disease_status_at_followup + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Disease Status At Followup + - in: query + name: relapse_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Relapse Type + - in: query + name: method_of_progression_status + required: false + schema: + items: + type: string + q: method_of_progression_status__overlap + title: Method Of Progression Status + type: array + - in: query + name: anatomic_site_progression_or_recurrence + required: false + schema: + items: + type: string + q: anatomic_site_progression_or_recurrence__overlap + title: Anatomic Site Progression Or Recurrence + type: array + - in: query + name: recurrence_tumour_staging_system + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Recurrence Tumour Staging System + - in: query + name: recurrence_t_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Recurrence T Category + - in: query + name: recurrence_n_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Recurrence N Category + - in: query + name: recurrence_m_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Recurrence M Category + - in: query + name: recurrence_stage_group + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Recurrence Stage Group + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedFollowUpModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Follow Ups + tags: + - authorized + /v2/authorized/hormone_therapies/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_hormone_therapies + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: drug_reference_database + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + - in: query + name: drug_name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Name + - in: query + name: drug_reference_identifier + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + - in: query + name: hormone_drug_dose_units + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Hormone Drug Dose Units + - in: query + name: prescribed_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + - in: query + name: actual_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedHormoneTherapyModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Hormone Therapies + tags: + - authorized + /v2/authorized/immunotherapies/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_immunotherapies + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: drug_reference_database + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Database + - in: query + name: immunotherapy_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Immunotherapy Type + - in: query + name: drug_name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Name + - in: query + name: drug_reference_identifier + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Drug Reference Identifier + - in: query + name: immunotherapy_drug_dose_units + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Immunotherapy Drug Dose Units + - in: query + name: prescribed_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Prescribed Cumulative Drug Dose + - in: query + name: actual_cumulative_drug_dose + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Actual Cumulative Drug Dose + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedImmunotherapyModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Immunotherapies + tags: + - authorized + /v2/authorized/primary_diagnoses/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_primary_diagnoses + parameters: + - in: query + name: submitter_primary_diagnosis_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: cancer_type_code + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Cancer Type Code + - in: query + name: basis_of_diagnosis + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Basis Of Diagnosis + - in: query + name: laterality + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Laterality + - in: query + name: lymph_nodes_examined_status + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Lymph Nodes Examined Status + - in: query + name: lymph_nodes_examined_method + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Lymph Nodes Examined Method + - in: query + name: number_lymph_nodes_positive + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Number Lymph Nodes Positive + - in: query + name: clinical_tumour_staging_system + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Clinical Tumour Staging System + - in: query + name: clinical_t_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Clinical T Category + - in: query + name: clinical_n_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Clinical N Category + - in: query + name: clinical_m_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Clinical M Category + - in: query + name: clinical_stage_group + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Clinical Stage Group + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedPrimaryDiagnosisModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Primary Diagnoses + tags: + - authorized + /v2/authorized/program/{program_id}/: + delete: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_delete_program + parameters: + - in: path + name: program_id + required: true + schema: + title: Program Id + type: string + responses: + '204': + description: No Content + '404': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response + type: object + description: Not Found + security: + - LoginAuth: [] + summary: Delete Program + tags: + - authorized + /v2/authorized/programs/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_programs + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedProgramModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Programs + tags: + - authorized + /v2/authorized/radiations/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_radiations + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: radiation_therapy_modality + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Radiation Therapy Modality + - in: query + name: radiation_therapy_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Radiation Therapy Type + - in: query + name: radiation_therapy_fractions + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Fractions + - in: query + name: radiation_therapy_dosage + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Radiation Therapy Dosage + - in: query + name: anatomical_site_irradiated + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Anatomical Site Irradiated + - in: query + name: radiation_boost + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Radiation Boost + - in: query + name: reference_radiation_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Reference Radiation Treatment Id + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedRadiationModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Radiations + tags: + - authorized + /v2/authorized/sample_registrations/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_sample_registrations + parameters: + - in: query + name: submitter_sample_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Sample Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_specimen_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + - in: query + name: specimen_tissue_source + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Tissue Source + - in: query + name: tumour_normal_designation + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tumour Normal Designation + - in: query + name: specimen_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Type + - in: query + name: sample_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Sample Type + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedSampleRegistrationModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Sample Registrations + tags: + - authorized + /v2/authorized/specimens/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_specimens + parameters: + - in: query + name: submitter_specimen_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_primary_diagnosis_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + - in: query + name: pathological_tumour_staging_system + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pathological Tumour Staging System + - in: query + name: pathological_t_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pathological T Category + - in: query + name: pathological_n_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pathological N Category + - in: query + name: pathological_m_category + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pathological M Category + - in: query + name: pathological_stage_group + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Pathological Stage Group + - in: query + name: specimen_storage + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Storage + - in: query + name: specimen_processing + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Processing + - in: query + name: tumour_histological_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tumour Histological Type + - in: query + name: specimen_anatomic_location + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Anatomic Location + - in: query + name: specimen_laterality + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Specimen Laterality + - in: query + name: reference_pathology_confirmed_diagnosis + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Reference Pathology Confirmed Diagnosis + - in: query + name: reference_pathology_confirmed_tumour_presence + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Reference Pathology Confirmed Tumour Presence + - in: query + name: tumour_grading_system + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tumour Grading System + - in: query + name: tumour_grade + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tumour Grade + - in: query + name: percent_tumour_cells_range + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Percent Tumour Cells Range + - in: query + name: percent_tumour_cells_measurement_method + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Percent Tumour Cells Measurement Method + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedSpecimenModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Specimens + tags: + - authorized + /v2/authorized/surgeries/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_surgeries + parameters: + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: submitter_specimen_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Specimen Id + - in: query + name: surgery_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Surgery Type + - in: query + name: surgery_site + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Surgery Site + - in: query + name: surgery_location + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Surgery Location + - in: query + name: tumour_length + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Tumour Length + - in: query + name: tumour_width + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Tumour Width + - in: query + name: greatest_dimension_tumour + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Greatest Dimension Tumour + - in: query + name: tumour_focality + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tumour Focality + - in: query + name: residual_tumour_classification + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Residual Tumour Classification + - in: query + name: margin_types_involved + required: false + schema: + items: + type: string + q: margin_types_involved__overlap + title: Margin Types Involved + type: array + - in: query + name: margin_types_not_involved + required: false + schema: + items: + type: string + q: margin_types_not_involved__overlap + title: Margin Types Not Involved + type: array + - in: query + name: margin_types_not_assessed + required: false + schema: + items: + type: string + q: margin_types_not_assessed__overlap + title: Margin Types Not Assessed + type: array + - in: query + name: lymphovascular_invasion + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Lymphovascular Invasion + - in: query + name: perineural_invasion + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Perineural Invasion + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedSurgeryModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Surgeries + tags: + - authorized + /v2/authorized/treatments/: + get: + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_treatments + parameters: + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id + - in: query + name: program_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Program Id + - in: query + name: submitter_donor_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Donor Id + - in: query + name: submitter_primary_diagnosis_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Primary Diagnosis Id + - in: query + name: treatment_type + required: false + schema: + items: + type: string + q: treatment_type__overlap + title: Treatment Type + type: array + - in: query + name: is_primary_treatment + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Is Primary Treatment + - in: query + name: line_of_treatment + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Line Of Treatment + - in: query + name: treatment_setting + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Treatment Setting + - in: query + name: treatment_intent + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Treatment Intent + - in: query + name: days_per_cycle + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + - in: query + name: number_of_cycles + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles + - in: query + name: response_to_treatment_criteria_method + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Response To Treatment Criteria Method + - in: query + name: response_to_treatment + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Response To Treatment + - in: query + name: status_of_treatment + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Status Of Treatment + - in: query + name: page + required: false + schema: + minimum: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + minimum: 1 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PagedTreatmentModelSchema' + description: OK + security: + - LoginAuth: [] + summary: List Treatments + tags: + - authorized + /v2/discovery/donors/: + get: + description: 'Return the number of donors per cohort in the database. + + Note: This function is identical to `discover_patients_per_cohort` + + and is here because the frontend ingest uses it. It''s probably best + + to clean up later.' + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_donors + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/DiscoveryDonorSchema' + title: Response + type: array + description: OK + summary: Discover Donors + tags: + - discovery + /v2/discovery/overview/cohort_count/: + get: + description: Return the number of cohorts in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_cohort_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: integer + title: Response + type: object + description: OK + summary: Discover Cohort Count + tags: + - overview + /v2/discovery/overview/diagnosis_age_count/: + get: + description: Return the count for age of diagnosis by calculating the date of + birth interval. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_diagnosis_age_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/DiagnosisAgeCountSchema' + title: Response + type: array + description: OK + summary: Discover Diagnosis Age Count + tags: + - overview + /v2/discovery/overview/gender_count/: + get: + description: Return the count for every gender in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_gender_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/GenderCountSchema' + title: Response + type: array + description: OK + summary: Discover Gender Count + tags: + - overview + /v2/discovery/overview/individual_count/: + get: + description: Return the number of individuals in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_individual_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response + type: object + description: OK + summary: Discover Individual Count + tags: + - overview + /v2/discovery/overview/patients_per_cohort/: + get: + description: Return the number of patients per cohort in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_patients_per_cohort + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/PatientPerCohortSchema' + title: Response + type: array + description: OK + summary: Discover Patients Per Cohort + tags: + - overview + /v2/discovery/overview/primary_site_count/: + get: + description: Return the count for every cancer type in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_primary_site_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/PrimarySiteCountSchema' + title: Response + type: array + description: OK + summary: Discover Primary Site Count + tags: + - overview + /v2/discovery/overview/treatment_type_count/: + get: + description: Return the count for every treatment type in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_treatment_type_count + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/TreatmentTypeCountSchema' + title: Response + type: array + description: OK + summary: Discover Treatment Type Count + tags: + - overview + /v2/discovery/programs/: + get: + description: Return all the programs in the database. + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_programs + parameters: [] + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/ProgramDiscoverySchema' + title: Response + type: array + description: OK + summary: Discover Programs + tags: + - discovery + /v2/discovery/sidebar_list/: + get: + description: Retrieve the list of drug names and treatment for frontend usage + operationId: chord_metadata_service_mohpackets_apis_discovery_discover_sidebar_list + parameters: [] + responses: + '200': + content: + application/json: + schema: + title: Response + type: object + description: OK + summary: Discover Sidebar List + tags: + - discovery + /v2/explorer/donors/: + get: + operationId: chord_metadata_service_mohpackets_apis_explorer_explorer_donor + parameters: + - in: query + name: treatment_type + required: false + schema: + items: + type: string + q: treatment_type__overlap + title: Treatment Type + type: array + - in: query + name: primary_site + required: false + schema: + items: + type: string + q: primary_site__overlap + title: Primary Site + type: array + - in: query + name: chemotherapy_drug_name + required: false + schema: + items: + type: string + title: Chemotherapy Drug Name + type: array + - in: query + name: immunotherapy_drug_name + required: false + schema: + items: + type: string + title: Immunotherapy Drug Name + type: array + - in: query + name: hormone_therapy_drug_name + required: false + schema: + items: + type: string + title: Hormone Therapy Drug Name + type: array + - in: query + name: exclude_cohorts + required: false + schema: + items: + type: string + title: Exclude Cohorts + type: array + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/DonorExplorerSchema' + title: Response + type: array + description: OK + security: + - ServiceTokenAuth: [] + summary: Explorer Donor + tags: + - explorer + /v2/ingest/biomarker/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_biomarker + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/BiomarkerIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Biomarker + tags: + - ingest + /v2/ingest/chemotherapy/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_chemotherapy + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ChemotherapyIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Chemotherapy + tags: + - ingest + /v2/ingest/comorbidity/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_comorbidity + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ComorbidityIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Comorbidity + tags: + - ingest + /v2/ingest/donor/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_donor + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/DonorIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Donor + tags: + - ingest + /v2/ingest/exposure/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_exposure + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ExposureIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Exposure + tags: + - ingest + /v2/ingest/follow_up/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_follow_up + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/FollowUpIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Follow Up + tags: + - ingest + /v2/ingest/hormone_therapy/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_hormone_therapy + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/HormoneTherapyIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Hormone Therapy + tags: + - ingest + /v2/ingest/immunotherapy/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_immunotherapy + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ImmunotherapyIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Immunotherapy + tags: + - ingest + /v2/ingest/primary_diagnosis/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_primary_diagnosis + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/PrimaryDiagnosisIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Primary Diagnosis + tags: + - ingest + /v2/ingest/program/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_program + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ProgramIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Program + tags: + - ingest + /v2/ingest/radiation/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_radiation + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/RadiationIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Radiation + tags: + - ingest + /v2/ingest/sample_registration/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_sample_registration + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SampleRegistrationIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Sample Registration + tags: + - ingest + /v2/ingest/specimen/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_specimen + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SpecimenIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Specimen + tags: + - ingest + /v2/ingest/surgery/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_surgery + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SurgeryIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Surgery + tags: + - ingest + /v2/ingest/treatment/: + post: + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_treatment + parameters: [] + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/TreatmentIngestSchema' + required: true + responses: + '200': + description: OK + security: + - LoginAuth: [] + summary: Create Treatment + tags: + - ingest + /v2/service-info: + get: + operationId: chord_metadata_service_mohpackets_apis_core_service_info + parameters: [] + responses: + '200': + description: OK + summary: Service Info +servers: [] + From a5cacf689592cfa2bcf75d2d0ea4a0379a1b9890 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 14:55:36 -0400 Subject: [PATCH 02/17] Working on a new schema (written manually) to cover changes to v3 of the data model MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This has the following work done so far: 1. Move required field “primary_site” from Donor to Primary Diagnosis 2. Add optional “submitter_treatment_id” if the specimen was resected during surgery 3. Moved the conditional fields [“pathological_tumour_staging_system, “pathological_stage_group”, “pathological_t_category”, “pathological_n_category”, “pathological_m_category”] from Specimen to Primary Diagnosis --- .../mohpackets/docs/schema_manual.yml | 298 +++++++----------- 1 file changed, 119 insertions(+), 179 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index e26b3a3f2..aa1db507c 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -688,12 +688,6 @@ components: type: string title: Immunotherapy Drug Name type: array - primary_site: - items: - type: string - q: primary_site__overlap - title: Primary Site - type: array treatment_type: items: type: string @@ -840,13 +834,6 @@ components: anyOf: - $ref: '#/components/schemas/LostToFollowupReasonEnum' - type: 'null' - primary_site: - anyOf: - - items: - $ref: '#/components/schemas/PrimarySiteEnum' - type: array - - type: 'null' - title: Primary Site program_id: title: Program Id type: string @@ -912,13 +899,6 @@ components: anyOf: - $ref: '#/components/schemas/LostToFollowupReasonEnum' - type: 'null' - primary_site: - anyOf: - - items: - $ref: '#/components/schemas/PrimarySiteEnum' - type: array - - type: 'null' - title: Primary Site program_id: title: Program Id type: string @@ -2187,6 +2167,31 @@ components: type: object NestedPrimaryDiagnosisSchema: properties: + pathological_m_category: + anyOf: + - type: string + - type: 'null' + title: Pathological M Category + pathological_n_category: + anyOf: + - type: string + - type: 'null' + title: Pathological N Category + pathological_stage_group: + anyOf: + - type: string + - type: 'null' + title: Pathological Stage Group + pathological_t_category: + anyOf: + - type: string + - type: 'null' + title: Pathological T Category + pathological_tumour_staging_system: + anyOf: + - type: string + - type: 'null' + title: Pathological Tumour Staging System basis_of_diagnosis: anyOf: - $ref: '#/components/schemas/BasisOfDiagnosisEnum' @@ -2230,19 +2235,6 @@ components: anyOf: - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' - type: 'null' - lymph_nodes_examined_method: - anyOf: - - $ref: '#/components/schemas/LymphNodeMethodEnum' - - type: 'null' - lymph_nodes_examined_status: - anyOf: - - $ref: '#/components/schemas/LymphNodeStatusEnum' - - type: 'null' - number_lymph_nodes_positive: - anyOf: - - type: integer - - type: 'null' - title: Number Lymph Nodes Positive specimens: items: $ref: '#/components/schemas/NestedSpecimenSchema' @@ -2328,26 +2320,6 @@ components: type: object NestedSpecimenSchema: properties: - pathological_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - pathological_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - pathological_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - pathological_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - pathological_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' percent_tumour_cells_measurement_method: anyOf: - $ref: '#/components/schemas/CellsMeasureMethodEnum' @@ -2398,6 +2370,11 @@ components: pattern: ^[A-Za-z0-9\-\._]{1,64} title: Submitter Specimen Id type: string + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Treatment Id + type: string tumour_grade: anyOf: - $ref: '#/components/schemas/TumourGradeEnum' @@ -2463,6 +2440,12 @@ components: type: string - type: 'null' title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - maxLength: 64 + type: string + - type: 'null' + title: Submitter Treatment Id surgery_location: anyOf: - $ref: '#/components/schemas/SurgeryLocationEnum' @@ -3095,21 +3078,6 @@ components: - type: string - type: 'null' title: Laterality - lymph_nodes_examined_method: - anyOf: - - type: string - - type: 'null' - title: Lymph Nodes Examined Method - lymph_nodes_examined_status: - anyOf: - - type: string - - type: 'null' - title: Lymph Nodes Examined Status - number_lymph_nodes_positive: - anyOf: - - type: integer - - type: 'null' - title: Number Lymph Nodes Positive program_id: anyOf: - type: string @@ -3129,6 +3097,26 @@ components: type: object PrimaryDiagnosisIngestSchema: properties: + pathological_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + pathological_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + pathological_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + pathological_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + pathological_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' basis_of_diagnosis: anyOf: - $ref: '#/components/schemas/BasisOfDiagnosisEnum' @@ -3167,19 +3155,9 @@ components: anyOf: - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' - type: 'null' - lymph_nodes_examined_method: - anyOf: - - $ref: '#/components/schemas/LymphNodeMethodEnum' - - type: 'null' - lymph_nodes_examined_status: - anyOf: - - $ref: '#/components/schemas/LymphNodeStatusEnum' - - type: 'null' - number_lymph_nodes_positive: - anyOf: - - type: integer - - type: 'null' - title: Number Lymph Nodes Positive + primary_site: + type: string + title: Primary Site program_id: title: Program Id type: string @@ -3215,6 +3193,26 @@ components: type: string PrimaryDiagnosisModelSchema: properties: + pathological_m_category: + anyOf: + - $ref: '#/components/schemas/MCategoryEnum' + - type: 'null' + pathological_n_category: + anyOf: + - $ref: '#/components/schemas/NCategoryEnum' + - type: 'null' + pathological_stage_group: + anyOf: + - $ref: '#/components/schemas/StageGroupEnum' + - type: 'null' + pathological_t_category: + anyOf: + - $ref: '#/components/schemas/TCategoryEnum' + - type: 'null' + pathological_tumour_staging_system: + anyOf: + - $ref: '#/components/schemas/TumourStagingSystemEnum' + - type: 'null' basis_of_diagnosis: anyOf: - $ref: '#/components/schemas/BasisOfDiagnosisEnum' @@ -3253,19 +3251,13 @@ components: anyOf: - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' - type: 'null' - lymph_nodes_examined_method: - anyOf: - - $ref: '#/components/schemas/LymphNodeMethodEnum' - - type: 'null' lymph_nodes_examined_status: anyOf: - $ref: '#/components/schemas/LymphNodeStatusEnum' - type: 'null' - number_lymph_nodes_positive: - anyOf: - - type: integer - - type: 'null' - title: Number Lymph Nodes Positive + primary_site: + title: Primary Site + type: string program_id: title: Program Id type: string @@ -3964,6 +3956,9 @@ components: submitter_specimen_id: title: Submitter Specimen Id type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string tumour_normal_designation: anyOf: - $ref: '#/components/schemas/TumourDesginationEnum' @@ -4008,6 +4003,9 @@ components: submitter_specimen_id: title: Submitter Specimen Id type: string + submitter_treatment_id: + title: Submitter Treatment Id + type: string tumour_normal_designation: anyOf: - $ref: '#/components/schemas/TumourDesginationEnum' @@ -4053,31 +4051,6 @@ components: type: string SpecimenFilterSchema: properties: - pathological_m_category: - anyOf: - - type: string - - type: 'null' - title: Pathological M Category - pathological_n_category: - anyOf: - - type: string - - type: 'null' - title: Pathological N Category - pathological_stage_group: - anyOf: - - type: string - - type: 'null' - title: Pathological Stage Group - pathological_t_category: - anyOf: - - type: string - - type: 'null' - title: Pathological T Category - pathological_tumour_staging_system: - anyOf: - - type: string - - type: 'null' - title: Pathological Tumour Staging System percent_tumour_cells_measurement_method: anyOf: - type: string @@ -4138,6 +4111,11 @@ components: - type: string - type: 'null' title: Submitter Specimen Id + submitter_treatment_id: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id tumour_grade: anyOf: - type: string @@ -4157,26 +4135,6 @@ components: type: object SpecimenIngestSchema: properties: - pathological_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - pathological_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - pathological_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - pathological_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - pathological_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' percent_tumour_cells_measurement_method: anyOf: - $ref: '#/components/schemas/CellsMeasureMethodEnum' @@ -4231,6 +4189,11 @@ components: pattern: ^[A-Za-z0-9\-\._]{1,64} title: Submitter Specimen Id type: string + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Specimen Id + type: string tumour_grade: anyOf: - $ref: '#/components/schemas/TumourGradeEnum' @@ -4268,26 +4231,6 @@ components: type: string SpecimenModelSchema: properties: - pathological_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - pathological_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - pathological_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - pathological_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - pathological_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' percent_tumour_cells_measurement_method: anyOf: - $ref: '#/components/schemas/CellsMeasureMethodEnum' @@ -4342,6 +4285,11 @@ components: pattern: ^[A-Za-z0-9\-\._]{1,64} title: Submitter Specimen Id type: string + submitter_treatment_id: + maxLength: 64 + pattern: ^[A-Za-z0-9\-\._]{1,64} + title: Submitter Specimen Id + type: string tumour_grade: anyOf: - $ref: '#/components/schemas/TumourGradeEnum' @@ -6409,30 +6357,6 @@ paths: - type: string - type: 'null' title: Laterality - - in: query - name: lymph_nodes_examined_status - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Lymph Nodes Examined Status - - in: query - name: lymph_nodes_examined_method - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Lymph Nodes Examined Method - - in: query - name: number_lymph_nodes_positive - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Number Lymph Nodes Positive - in: query name: clinical_tumour_staging_system required: false @@ -6710,6 +6634,14 @@ paths: - type: string - type: 'null' title: Submitter Specimen Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id - in: query name: specimen_tissue_source required: false @@ -6780,6 +6712,14 @@ paths: - type: string - type: 'null' title: Submitter Specimen Id + - in: query + name: submitter_treatment_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id - in: query name: program_id required: false From 8f5db3940595d06b8bab3a717de2e49e30d26756 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 13:13:39 -0400 Subject: [PATCH 03/17] =?UTF-8?q?Remove=20fields=20[=E2=80=9Clymph=5Fnodes?= =?UTF-8?q?=5Fexamined=5Fstatus=E2=80=9D,=20=E2=80=9Clymph=5Fnodes=5Fexami?= =?UTF-8?q?ned=5Fmethod=E2=80=9D,=20=E2=80=9Cnumber=5Flymph=5Fnodes=5Fposi?= =?UTF-8?q?tive=E2=80=9D]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- chord_metadata_service/mohpackets/docs/schema_manual.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index aa1db507c..a64a2d3f6 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -3251,10 +3251,6 @@ components: anyOf: - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' - type: 'null' - lymph_nodes_examined_status: - anyOf: - - $ref: '#/components/schemas/LymphNodeStatusEnum' - - type: 'null' primary_site: title: Primary Site type: string From 8ae059f8766aed7087a7b7bdef02dca54ee1db4e Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 13:16:56 -0400 Subject: [PATCH 04/17] =?UTF-8?q?Surgery=20remove=20the=20optional=20field?= =?UTF-8?q?=20=E2=80=9Csubmitter=5Fspecimen=5Fid=E2=80=9D?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../mohpackets/docs/schema_manual.yml | 29 +------------------ 1 file changed, 1 insertion(+), 28 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index a64a2d3f6..61aae3245 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -2434,12 +2434,6 @@ components: anyOf: - $ref: '#/components/schemas/TumourClassificationEnum' - type: 'null' - submitter_specimen_id: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Submitter Specimen Id submitter_treatment_id: anyOf: - maxLength: 64 @@ -4544,11 +4538,6 @@ components: - type: string - type: 'null' title: Submitter Donor Id - submitter_specimen_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Specimen Id submitter_treatment_id: anyOf: - type: string @@ -4632,13 +4621,11 @@ components: submitter_donor_id: title: Submitter Donor Id type: string - submitter_specimen_id: + submitter_treatment_id: anyOf: - maxLength: 64 type: string - type: 'null' - title: Submitter Specimen Id - submitter_treatment_id: title: Submitter Treatment Id type: string surgery_location: @@ -4734,12 +4721,6 @@ components: submitter_donor_id: title: Submitter Donor Id type: string - submitter_specimen_id: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Submitter Specimen Id submitter_treatment_id: title: Submitter Treatment Id type: string @@ -6922,14 +6903,6 @@ paths: - type: string - type: 'null' title: Submitter Treatment Id - - in: query - name: submitter_specimen_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Specimen Id - in: query name: surgery_type required: false From e773686a706b2ad9a5660c5ea79cc1f165294194 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 13:36:01 -0400 Subject: [PATCH 05/17] =?UTF-8?q?Added=20required=20fields=20[=E2=80=9Csur?= =?UTF-8?q?gery=5Freference=5Fdatabase=E2=80=9D,=20=E2=80=9Csurgery=5Frefe?= =?UTF-8?q?rence=5Fidentifier=E2=80=9D]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Assuming there's no 64 character limit on the surgery_reference_identifier yet --- .../mohpackets/docs/schema_manual.yml | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 61aae3245..503315c86 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -2440,6 +2440,15 @@ components: type: string - type: 'null' title: Submitter Treatment Id + surgery_reference_database: + anyOf: + - $ref: '#/components/schemas/SurgeryReferenceDatabaseEnum' + - type: 'null' + surgery_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id surgery_location: anyOf: - $ref: '#/components/schemas/SurgeryLocationEnum' @@ -4543,6 +4552,15 @@ components: - type: string - type: 'null' title: Submitter Treatment Id + surgery_reference_database: + anyOf: + - $ref: '#/components/schemas/SurgeryReferenceDatabaseEnum' + - type: 'null' + surgery_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Submitter Treatment Id surgery_location: anyOf: - type: string @@ -4628,6 +4646,18 @@ components: - type: 'null' title: Submitter Treatment Id type: string + surgery_reference_database: + anyOf: + - $ref: '#/components/schemas/SurgeryReferenceDatabaseEnum' + - type: 'null' + title: Surgery Reference Database + type: string + surgery_reference_identifier: + anyOf: + - type: string + - type: 'null' + title: Surgery Reference Identifier + type: string surgery_location: anyOf: - $ref: '#/components/schemas/SurgeryLocationEnum' @@ -4724,6 +4754,12 @@ components: submitter_treatment_id: title: Submitter Treatment Id type: string + surgery_reference_database: + title: Surgery Reference Database + type: string + surgery_reference_identifier: + title: Surgery Reference Identifier + type: string surgery_location: anyOf: - $ref: '#/components/schemas/SurgeryLocationEnum' @@ -4820,6 +4856,13 @@ components: - Wide Local Excision title: SurgeryTypeEnum type: string + SurgeryReferenceDatabaseEnum: + enum: + - SNOMED + - NCIt + - UMLS + title: SurgeryReferenceDatabaseEnum + type: string TCategoryEnum: enum: - T0 @@ -6903,6 +6946,22 @@ paths: - type: string - type: 'null' title: Submitter Treatment Id + - in: query + name: surgery_reference_database + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Surgery Reference Database + - in: query + name: surgery_reference_identifier + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Surgery Reference Identifier - in: query name: surgery_type required: false From 0552691f71ba87f65e1ffd524a29bb3e0279f2ef Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 13:42:15 -0400 Subject: [PATCH 06/17] Remove follow-up optional fields MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [“recurrence_tumour_staging_system”, “recurrence_stage_group”, “recurrence_t_category”, “recurrence_n_category”, “recurrence_m_category”] --- .../mohpackets/docs/schema_manual.yml | 125 ------------------ 1 file changed, 125 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 503315c86..d4d6b9c37 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -1152,31 +1152,6 @@ components: - type: string - type: 'null' title: Program Id - recurrence_m_category: - anyOf: - - type: string - - type: 'null' - title: Recurrence M Category - recurrence_n_category: - anyOf: - - type: string - - type: 'null' - title: Recurrence N Category - recurrence_stage_group: - anyOf: - - type: string - - type: 'null' - title: Recurrence Stage Group - recurrence_t_category: - anyOf: - - type: string - - type: 'null' - title: Recurrence T Category - recurrence_tumour_staging_system: - anyOf: - - type: string - - type: 'null' - title: Recurrence Tumour Staging System relapse_type: anyOf: - type: string @@ -1235,26 +1210,6 @@ components: program_id: title: Program Id type: string - recurrence_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - recurrence_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - recurrence_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - recurrence_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - recurrence_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' relapse_type: anyOf: - $ref: '#/components/schemas/RelapseTypeEnum' @@ -1319,26 +1274,6 @@ components: program_id: title: Program Id type: string - recurrence_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - recurrence_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - recurrence_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - recurrence_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - recurrence_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' relapse_type: anyOf: - $ref: '#/components/schemas/RelapseTypeEnum' @@ -2060,26 +1995,6 @@ components: type: array - type: 'null' title: Method Of Progression Status - recurrence_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - recurrence_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - recurrence_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - recurrence_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - type: 'null' - recurrence_tumour_staging_system: - anyOf: - - $ref: '#/components/schemas/TumourStagingSystemEnum' - - type: 'null' relapse_type: anyOf: - $ref: '#/components/schemas/RelapseTypeEnum' @@ -6047,46 +5962,6 @@ paths: q: anatomic_site_progression_or_recurrence__overlap title: Anatomic Site Progression Or Recurrence type: array - - in: query - name: recurrence_tumour_staging_system - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Recurrence Tumour Staging System - - in: query - name: recurrence_t_category - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Recurrence T Category - - in: query - name: recurrence_n_category - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Recurrence N Category - - in: query - name: recurrence_m_category - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Recurrence M Category - - in: query - name: recurrence_stage_group - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Recurrence Stage Group - in: query name: page required: false From 823dc094d4f27a41fc749788dcde298882376da5 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 13:59:21 -0400 Subject: [PATCH 07/17] Add new Systemic Therapy table, remove old chemo/immuno/hormone therapy tables --- .../mohpackets/docs/schema_manual.yml | 836 ++---------------- 1 file changed, 73 insertions(+), 763 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index d4d6b9c37..2c2d6428c 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -321,18 +321,18 @@ components: - Unknown title: CellsMeasureMethodEnum type: string - ChemotherapyFilterSchema: + SystemicTherapyFilterSchema: properties: actual_cumulative_drug_dose: anyOf: - type: integer - type: 'null' title: Actual Cumulative Drug Dose - chemotherapy_drug_dose_units: + drug_dose_units: anyOf: - type: string - type: 'null' - title: Chemotherapy Drug Dose Units + title: Drug Dose Units drug_name: anyOf: - type: string @@ -353,6 +353,11 @@ components: - type: integer - type: 'null' title: Prescribed Cumulative Drug Dose + systemic_therapy_type: + anyOf: + - type: string + - type: 'null' + title: Systemic Therapy Type program_id: anyOf: - type: string @@ -368,16 +373,16 @@ components: - type: string - type: 'null' title: Submitter Treatment Id - title: ChemotherapyFilterSchema + title: SystemicTherapyFilterSchema type: object - ChemotherapyIngestSchema: + SystemicTherapyIngestSchema: properties: actual_cumulative_drug_dose: anyOf: - type: integer - type: 'null' title: Actual Cumulative Drug Dose - chemotherapy_drug_dose_units: + drug_dose_units: anyOf: - $ref: '#/components/schemas/DosageUnitsEnum' - type: 'null' @@ -402,6 +407,11 @@ components: - type: integer - type: 'null' title: Prescribed Cumulative Drug Dose + systemic_therapy_type: + anyOf: + - $ref: '#/components/schemas/SystemicTherapyTypeEnum' + - type: 'null' + title: Systemic Therapy Type program_id: title: Program Id type: string @@ -420,16 +430,16 @@ components: - program_id - submitter_donor_id - submitter_treatment_id - title: ChemotherapyIngestSchema + title: SystemicTherapyIngestSchema type: object - ChemotherapyModelSchema: + SystemicTherapyModelSchema: properties: actual_cumulative_drug_dose: anyOf: - type: integer - type: 'null' title: Actual Cumulative Drug Dose - chemotherapy_drug_dose_units: + drug_dose_units: anyOf: - $ref: '#/components/schemas/DosageUnitsEnum' - type: 'null' @@ -454,6 +464,10 @@ components: - type: integer - type: 'null' title: Prescribed Cumulative Drug Dose + systemic_therapy_type: + anyOf: + - $ref: '#/components/schemas/SystemicTherapyTypeEnum' + - type: 'null' program_id: title: Program Id type: string @@ -467,7 +481,7 @@ components: - program_id - submitter_donor_id - submitter_treatment_id - title: ChemotherapyModelSchema + title: SystemicTherapyModelSchema type: object ComorbidityFilterSchema: properties: @@ -668,26 +682,16 @@ components: type: string DonorExplorerFilterSchema: properties: - chemotherapy_drug_name: + systemic_therapy_drug_name: items: type: string - title: Chemotherapy Drug Name + title: Systemic Therapy Drug Name type: array exclude_cohorts: items: type: string title: Exclude Cohorts type: array - hormone_therapy_drug_name: - items: - type: string - title: Hormone Therapy Drug Name - type: array - immunotherapy_drug_name: - items: - type: string - title: Immunotherapy Drug Name - type: array treatment_type: items: type: string @@ -1334,154 +1338,6 @@ components: - Unknown title: Her2StatusEnum type: string - HormoneTherapyFilterSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Database - drug_reference_identifier: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Identifier - hormone_drug_dose_units: - anyOf: - - type: string - - type: 'null' - title: Hormone Drug Dose Units - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - anyOf: - - type: string - - type: 'null' - title: Program Id - submitter_donor_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Donor Id - submitter_treatment_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment Id - title: HormoneTherapyFilterSchema - type: object - HormoneTherapyIngestSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - hormone_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - title: Program Id - type: string - submitter_donor_id: - title: Submitter Donor Id - type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string - uuid: - anyOf: - - type: string - - type: 'null' - title: Uuid - required: - - program_id - - submitter_donor_id - - submitter_treatment_id - title: HormoneTherapyIngestSchema - type: object - HormoneTherapyModelSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - hormone_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - title: Program Id - type: string - submitter_donor_id: - title: Submitter Donor Id - type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string - required: - - program_id - - submitter_donor_id - - submitter_treatment_id - title: HormoneTherapyModelSchema - type: object HpvStrainEnum: enum: - HPV16 @@ -1501,167 +1357,6 @@ components: - HPV73 title: HpvStrainEnum type: string - ImmunotherapyFilterSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Database - drug_reference_identifier: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Identifier - immunotherapy_drug_dose_units: - anyOf: - - type: string - - type: 'null' - title: Immunotherapy Drug Dose Units - immunotherapy_type: - anyOf: - - type: string - - type: 'null' - title: Immunotherapy Type - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - anyOf: - - type: string - - type: 'null' - title: Program Id - submitter_donor_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Donor Id - submitter_treatment_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment Id - title: ImmunotherapyFilterSchema - type: object - ImmunotherapyIngestSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - immunotherapy_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - immunotherapy_type: - anyOf: - - $ref: '#/components/schemas/ImmunotherapyTypeEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - title: Program Id - type: string - submitter_donor_id: - title: Submitter Donor Id - type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string - uuid: - anyOf: - - type: string - - type: 'null' - title: Uuid - required: - - program_id - - submitter_donor_id - - submitter_treatment_id - title: ImmunotherapyIngestSchema - type: object - ImmunotherapyModelSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - immunotherapy_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - immunotherapy_type: - anyOf: - - $ref: '#/components/schemas/ImmunotherapyTypeEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - program_id: - title: Program Id - type: string - submitter_donor_id: - title: Submitter Donor Id - type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string - required: - - program_id - - submitter_donor_id - - submitter_treatment_id - title: ImmunotherapyModelSchema - type: object ImmunotherapyTypeEnum: enum: - Cell-based @@ -1879,14 +1574,14 @@ components: - type: 'null' title: NestedBiomarkerSchema type: object - NestedChemotherapySchema: + NestedSystemicTherapySchema: properties: actual_cumulative_drug_dose: anyOf: - type: integer - type: 'null' title: Actual Cumulative Drug Dose - chemotherapy_drug_dose_units: + drug_dose_units: anyOf: - $ref: '#/components/schemas/DosageUnitsEnum' - type: 'null' @@ -1911,7 +1606,11 @@ components: - type: integer - type: 'null' title: Prescribed Cumulative Drug Dose - title: NestedChemotherapySchema + systemic_therapy_type: + anyOf: + - $ref: '#/components/schemas/SystemicTherapyTypeEnum' + - type: 'null' + title: NestedSystemicTherapySchema type: object NestedComorbiditySchema: properties: @@ -2008,78 +1707,6 @@ components: - submitter_follow_up_id title: NestedFollowUpSchema type: object - NestedHormoneTherapySchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - hormone_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - title: NestedHormoneTherapySchema - type: object - NestedImmunotherapySchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - drug_name: - anyOf: - - maxLength: 255 - type: string - - type: 'null' - title: Drug Name - drug_reference_database: - anyOf: - - $ref: '#/components/schemas/DrugReferenceDbEnum' - - type: 'null' - drug_reference_identifier: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Drug Reference Identifier - immunotherapy_drug_dose_units: - anyOf: - - $ref: '#/components/schemas/DosageUnitsEnum' - - type: 'null' - immunotherapy_type: - anyOf: - - $ref: '#/components/schemas/ImmunotherapyTypeEnum' - - type: 'null' - prescribed_cumulative_drug_dose: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - title: NestedImmunotherapySchema - type: object NestedPrimaryDiagnosisSchema: properties: pathological_m_category: @@ -2397,10 +2024,10 @@ components: type: object NestedTreatmentSchema: properties: - chemotherapies: + systemic_therapies: items: - $ref: '#/components/schemas/NestedChemotherapySchema' - title: Chemotherapies + $ref: '#/components/schemas/NestedSystemicTherapySchema' + title: Systemic Therapies type: array days_per_cycle: anyOf: @@ -2412,16 +2039,6 @@ components: $ref: '#/components/schemas/NestedFollowUpSchema' title: Followups type: array - hormone_therapies: - items: - $ref: '#/components/schemas/NestedHormoneTherapySchema' - title: Hormone Therapies - type: array - immunotherapies: - items: - $ref: '#/components/schemas/NestedImmunotherapySchema' - title: Immunotherapies - type: array is_primary_treatment: anyOf: - $ref: '#/components/schemas/uBooleanEnum' @@ -2519,7 +2136,7 @@ components: - previous_page title: PagedBiomarkerModelSchema type: object - PagedChemotherapyModelSchema: + PagedSystemicTherapyModelSchema: properties: count: anyOf: @@ -2528,7 +2145,7 @@ components: title: Count items: items: - $ref: '#/components/schemas/ChemotherapyModelSchema' + $ref: '#/components/schemas/SystemicTherapyModelSchema' title: Items type: array next_page: @@ -2546,7 +2163,7 @@ components: - count - next_page - previous_page - title: PagedChemotherapyModelSchema + title: PagedSystemicTherapyModelSchema type: object PagedComorbidityModelSchema: properties: @@ -2604,67 +2221,9 @@ components: - count - next_page - previous_page - title: PagedDonorModelSchema - type: object - PagedExposureModelSchema: - properties: - count: - anyOf: - - type: integer - - type: 'null' - title: Count - items: - items: - $ref: '#/components/schemas/ExposureModelSchema' - title: Items - type: array - next_page: - anyOf: - - type: integer - - type: 'null' - title: Next Page - previous_page: - anyOf: - - type: integer - - type: 'null' - title: Previous Page - required: - - items - - count - - next_page - - previous_page - title: PagedExposureModelSchema - type: object - PagedFollowUpModelSchema: - properties: - count: - anyOf: - - type: integer - - type: 'null' - title: Count - items: - items: - $ref: '#/components/schemas/FollowUpModelSchema' - title: Items - type: array - next_page: - anyOf: - - type: integer - - type: 'null' - title: Next Page - previous_page: - anyOf: - - type: integer - - type: 'null' - title: Previous Page - required: - - items - - count - - next_page - - previous_page - title: PagedFollowUpModelSchema + title: PagedDonorModelSchema type: object - PagedHormoneTherapyModelSchema: + PagedExposureModelSchema: properties: count: anyOf: @@ -2673,7 +2232,7 @@ components: title: Count items: items: - $ref: '#/components/schemas/HormoneTherapyModelSchema' + $ref: '#/components/schemas/ExposureModelSchema' title: Items type: array next_page: @@ -2691,9 +2250,9 @@ components: - count - next_page - previous_page - title: PagedHormoneTherapyModelSchema + title: PagedExposureModelSchema type: object - PagedImmunotherapyModelSchema: + PagedFollowUpModelSchema: properties: count: anyOf: @@ -2702,7 +2261,7 @@ components: title: Count items: items: - $ref: '#/components/schemas/ImmunotherapyModelSchema' + $ref: '#/components/schemas/FollowUpModelSchema' title: Items type: array next_page: @@ -2720,7 +2279,7 @@ components: - count - next_page - previous_page - title: PagedImmunotherapyModelSchema + title: PagedFollowUpModelSchema type: object PagedPrimaryDiagnosisModelSchema: properties: @@ -4778,6 +4337,13 @@ components: - UMLS title: SurgeryReferenceDatabaseEnum type: string + SystemicTherapyTypeEnum: + enum: + - Chemotherapy + - Hormone Therapy + - Immunotherapy + title: SystemicTherapyTypeEnum + type: string TCategoryEnum: enum: - T0 @@ -5476,9 +5042,9 @@ paths: summary: List Biomarkers tags: - authorized - /v2/authorized/chemotherapies/: + /v2/authorized/systemic_therapies/: get: - operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_chemotherapies + operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_systemic_therapies parameters: - in: query name: program_id @@ -5529,13 +5095,13 @@ paths: - type: 'null' title: Drug Reference Identifier - in: query - name: chemotherapy_drug_dose_units + name: drug_dose_units required: false schema: anyOf: - type: string - type: 'null' - title: Chemotherapy Drug Dose Units + title: Drug Dose Units - in: query name: prescribed_cumulative_drug_dose required: false @@ -5552,6 +5118,14 @@ paths: - type: integer - type: 'null' title: Actual Cumulative Drug Dose + - in: query + name: systemic_therapy_type + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Systemic Therapy Type - in: query name: page required: false @@ -5571,11 +5145,11 @@ paths: content: application/json: schema: - $ref: '#/components/schemas/PagedChemotherapyModelSchema' + $ref: '#/components/schemas/PagedSystemicTherapyModelSchema' description: OK security: - LoginAuth: [] - summary: List Chemotherapies + summary: List Systemic Therapies tags: - authorized /v2/authorized/comorbidities/: @@ -5988,218 +5562,6 @@ paths: summary: List Follow Ups tags: - authorized - /v2/authorized/hormone_therapies/: - get: - operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_hormone_therapies - parameters: - - in: query - name: program_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Program Id - - in: query - name: submitter_donor_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Donor Id - - in: query - name: submitter_treatment_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment Id - - in: query - name: drug_reference_database - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Database - - in: query - name: drug_name - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Name - - in: query - name: drug_reference_identifier - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Identifier - - in: query - name: hormone_drug_dose_units - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Hormone Drug Dose Units - - in: query - name: prescribed_cumulative_drug_dose - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - - in: query - name: actual_cumulative_drug_dose - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - - in: query - name: page - required: false - schema: - minimum: 1 - title: Page - type: integer - - in: query - name: page_size - required: false - schema: - minimum: 1 - title: Page Size - type: integer - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/PagedHormoneTherapyModelSchema' - description: OK - security: - - LoginAuth: [] - summary: List Hormone Therapies - tags: - - authorized - /v2/authorized/immunotherapies/: - get: - operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_immunotherapies - parameters: - - in: query - name: program_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Program Id - - in: query - name: submitter_donor_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Donor Id - - in: query - name: submitter_treatment_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment Id - - in: query - name: drug_reference_database - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Database - - in: query - name: immunotherapy_type - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Immunotherapy Type - - in: query - name: drug_name - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Name - - in: query - name: drug_reference_identifier - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Reference Identifier - - in: query - name: immunotherapy_drug_dose_units - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Immunotherapy Drug Dose Units - - in: query - name: prescribed_cumulative_drug_dose - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Prescribed Cumulative Drug Dose - - in: query - name: actual_cumulative_drug_dose - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Actual Cumulative Drug Dose - - in: query - name: page - required: false - schema: - minimum: 1 - title: Page - type: integer - - in: query - name: page_size - required: false - schema: - minimum: 1 - title: Page Size - type: integer - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/PagedImmunotherapyModelSchema' - description: OK - security: - - LoginAuth: [] - summary: List Immunotherapies - tags: - - authorized /v2/authorized/primary_diagnoses/: get: operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_primary_diagnoses @@ -7321,28 +6683,12 @@ paths: title: Primary Site type: array - in: query - name: chemotherapy_drug_name - required: false - schema: - items: - type: string - title: Chemotherapy Drug Name - type: array - - in: query - name: immunotherapy_drug_name - required: false - schema: - items: - type: string - title: Immunotherapy Drug Name - type: array - - in: query - name: hormone_therapy_drug_name + name: systemic_therapy_drug_name required: false schema: items: type: string - title: Hormone Therapy Drug Name + title: Systemic Therapy Drug Name type: array - in: query name: exclude_cohorts @@ -7385,22 +6731,22 @@ paths: summary: Create Biomarker tags: - ingest - /v2/ingest/chemotherapy/: + /v2/ingest/systemic_therapy/: post: - operationId: chord_metadata_service_mohpackets_apis_ingestion_create_chemotherapy + operationId: chord_metadata_service_mohpackets_apis_ingestion_create_systemic_therapy parameters: [] requestBody: content: application/json: schema: - $ref: '#/components/schemas/ChemotherapyIngestSchema' + $ref: '#/components/schemas/SystemicTherapyIngestSchema' required: true responses: '200': description: OK security: - LoginAuth: [] - summary: Create Chemotherapy + summary: Create Systemic Therapy tags: - ingest /v2/ingest/comorbidity/: @@ -7475,42 +6821,6 @@ paths: summary: Create Follow Up tags: - ingest - /v2/ingest/hormone_therapy/: - post: - operationId: chord_metadata_service_mohpackets_apis_ingestion_create_hormone_therapy - parameters: [] - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/HormoneTherapyIngestSchema' - required: true - responses: - '200': - description: OK - security: - - LoginAuth: [] - summary: Create Hormone Therapy - tags: - - ingest - /v2/ingest/immunotherapy/: - post: - operationId: chord_metadata_service_mohpackets_apis_ingestion_create_immunotherapy - parameters: [] - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ImmunotherapyIngestSchema' - required: true - responses: - '200': - description: OK - security: - - LoginAuth: [] - summary: Create Immunotherapy - tags: - - ingest /v2/ingest/primary_diagnosis/: post: operationId: chord_metadata_service_mohpackets_apis_ingestion_create_primary_diagnosis From ffab3824e28a435c3e5cf9e023013d85b0c15310 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 14:05:59 -0400 Subject: [PATCH 08/17] Add start/end dates to the systemic therapy schemas --- .../mohpackets/docs/schema_manual.yml | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 2c2d6428c..f89636077 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -412,6 +412,16 @@ components: - $ref: '#/components/schemas/SystemicTherapyTypeEnum' - type: 'null' title: Systemic Therapy Type + start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: Start date + end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: End date program_id: title: Program Id type: string @@ -468,6 +478,17 @@ components: anyOf: - $ref: '#/components/schemas/SystemicTherapyTypeEnum' - type: 'null' + title: Systemic Therapy Type + start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: Start date + end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: End date program_id: title: Program Id type: string @@ -1610,6 +1631,17 @@ components: anyOf: - $ref: '#/components/schemas/SystemicTherapyTypeEnum' - type: 'null' + title: Systemic Therapy Type + start_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: Start date + end_date: + anyOf: + - $ref: '#/components/schemas/DateInterval' + - type: 'null' + title: End date title: NestedSystemicTherapySchema type: object NestedComorbiditySchema: From 71d28c052be47fb2fc6d029de4a2209cb86543c1 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 14:51:33 -0400 Subject: [PATCH 09/17] Cleanup: Make systemic_therapy_type required, remove submitter_treatment_id from the SampleRegistrations I accidentally added it to --- .../mohpackets/docs/schema_manual.yml | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index f89636077..0bea30580 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -440,6 +440,7 @@ components: - program_id - submitter_donor_id - submitter_treatment_id + - systemic_therapy_type title: SystemicTherapyIngestSchema type: object SystemicTherapyModelSchema: @@ -502,6 +503,7 @@ components: - program_id - submitter_donor_id - submitter_treatment_id + - systemic_therapy_type title: SystemicTherapyModelSchema type: object ComorbidityFilterSchema: @@ -2008,12 +2010,6 @@ components: anyOf: - $ref: '#/components/schemas/TumourClassificationEnum' - type: 'null' - submitter_treatment_id: - anyOf: - - maxLength: 64 - type: string - - type: 'null' - title: Submitter Treatment Id surgery_reference_database: anyOf: - $ref: '#/components/schemas/SurgeryReferenceDatabaseEnum' @@ -3461,9 +3457,6 @@ components: submitter_specimen_id: title: Submitter Specimen Id type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string tumour_normal_designation: anyOf: - $ref: '#/components/schemas/TumourDesginationEnum' @@ -3508,9 +3501,6 @@ components: submitter_specimen_id: title: Submitter Specimen Id type: string - submitter_treatment_id: - title: Submitter Treatment Id - type: string tumour_normal_designation: anyOf: - $ref: '#/components/schemas/TumourDesginationEnum' From 5ad658463af54ed3a69b32a2b08c80677efecdb7 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 15:00:50 -0400 Subject: [PATCH 10/17] =?UTF-8?q?Moved=20optional=20fields=20[=E2=80=9Cday?= =?UTF-8?q?s=5Fper=5Fcycle=E2=80=9D,=20=E2=80=9Cnumber=5Fof=5Fcycles?= =?UTF-8?q?=E2=80=9D]=20to=20Systemic=20Therapy?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../mohpackets/docs/schema_manual.yml | 112 +++++++++--------- 1 file changed, 56 insertions(+), 56 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 0bea30580..6bd26c156 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -358,6 +358,16 @@ components: - type: string - type: 'null' title: Systemic Therapy Type + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles program_id: anyOf: - type: string @@ -422,6 +432,16 @@ components: - $ref: '#/components/schemas/DateInterval' - type: 'null' title: End date + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles program_id: title: Program Id type: string @@ -490,6 +510,16 @@ components: - $ref: '#/components/schemas/DateInterval' - type: 'null' title: End date + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles program_id: title: Program Id type: string @@ -1644,6 +1674,16 @@ components: - $ref: '#/components/schemas/DateInterval' - type: 'null' title: End date + days_per_cycle: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + number_of_cycles: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles title: NestedSystemicTherapySchema type: object NestedComorbiditySchema: @@ -2057,11 +2097,6 @@ components: $ref: '#/components/schemas/NestedSystemicTherapySchema' title: Systemic Therapies type: array - days_per_cycle: - anyOf: - - type: integer - - type: 'null' - title: Days Per Cycle followups: items: $ref: '#/components/schemas/NestedFollowUpSchema' @@ -2076,11 +2111,6 @@ components: - type: integer - type: 'null' title: Line Of Treatment - number_of_cycles: - anyOf: - - type: integer - - type: 'null' - title: Number Of Cycles radiations: items: $ref: '#/components/schemas/NestedRadiationSchema' @@ -4444,11 +4474,6 @@ components: type: string TreatmentFilterSchema: properties: - days_per_cycle: - anyOf: - - type: integer - - type: 'null' - title: Days Per Cycle is_primary_treatment: anyOf: - type: string @@ -4459,11 +4484,6 @@ components: - type: integer - type: 'null' title: Line Of Treatment - number_of_cycles: - anyOf: - - type: integer - - type: 'null' - title: Number Of Cycles program_id: anyOf: - type: string @@ -4519,11 +4539,6 @@ components: type: object TreatmentIngestSchema: properties: - days_per_cycle: - anyOf: - - type: integer - - type: 'null' - title: Days Per Cycle is_primary_treatment: anyOf: - $ref: '#/components/schemas/uBooleanEnum' @@ -4533,11 +4548,6 @@ components: - type: integer - type: 'null' title: Line Of Treatment - number_of_cycles: - anyOf: - - type: integer - - type: 'null' - title: Number Of Cycles program_id: title: Program Id type: string @@ -4613,11 +4623,6 @@ components: type: string TreatmentModelSchema: properties: - days_per_cycle: - anyOf: - - type: integer - - type: 'null' - title: Days Per Cycle is_primary_treatment: anyOf: - $ref: '#/components/schemas/uBooleanEnum' @@ -4627,11 +4632,6 @@ components: - type: integer - type: 'null' title: Line Of Treatment - number_of_cycles: - anyOf: - - type: integer - - type: 'null' - title: Number Of Cycles program_id: title: Program Id type: string @@ -5148,6 +5148,22 @@ paths: - type: string - type: 'null' title: Systemic Therapy Type + - in: query + name: days_per_cycle + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Days Per Cycle + - in: query + name: number_of_cycles + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Number Of Cycles - in: query name: page required: false @@ -6431,22 +6447,6 @@ paths: - type: string - type: 'null' title: Treatment Intent - - in: query - name: days_per_cycle - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Days Per Cycle - - in: query - name: number_of_cycles - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Number Of Cycles - in: query name: response_to_treatment_criteria_method required: false From 69d9c0b06bc7876de6b2677ad131912b98988965 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Tue, 2 Jul 2024 15:03:36 -0400 Subject: [PATCH 11/17] Remove line_of_treatment and treatment_setting --- .../mohpackets/docs/schema_manual.yml | 68 ------------------- 1 file changed, 68 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 6bd26c156..43b3a62da 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -2106,11 +2106,6 @@ components: anyOf: - $ref: '#/components/schemas/uBooleanEnum' - type: 'null' - line_of_treatment: - anyOf: - - type: integer - - type: 'null' - title: Line Of Treatment radiations: items: $ref: '#/components/schemas/NestedRadiationSchema' @@ -2146,10 +2141,6 @@ components: anyOf: - $ref: '#/components/schemas/TreatmentIntentEnum' - type: 'null' - treatment_setting: - anyOf: - - $ref: '#/components/schemas/TreatmentSettingEnum' - - type: 'null' treatment_start_date: anyOf: - $ref: '#/components/schemas/DateInterval' @@ -4479,11 +4470,6 @@ components: - type: string - type: 'null' title: Is Primary Treatment - line_of_treatment: - anyOf: - - type: integer - - type: 'null' - title: Line Of Treatment program_id: anyOf: - type: string @@ -4524,11 +4510,6 @@ components: - type: string - type: 'null' title: Treatment Intent - treatment_setting: - anyOf: - - type: string - - type: 'null' - title: Treatment Setting treatment_type: items: type: string @@ -4543,11 +4524,6 @@ components: anyOf: - $ref: '#/components/schemas/uBooleanEnum' - type: 'null' - line_of_treatment: - anyOf: - - type: integer - - type: 'null' - title: Line Of Treatment program_id: title: Program Id type: string @@ -4582,10 +4558,6 @@ components: anyOf: - $ref: '#/components/schemas/TreatmentIntentEnum' - type: 'null' - treatment_setting: - anyOf: - - $ref: '#/components/schemas/TreatmentSettingEnum' - - type: 'null' treatment_start_date: anyOf: - $ref: '#/components/schemas/DateInterval' @@ -4627,11 +4599,6 @@ components: anyOf: - $ref: '#/components/schemas/uBooleanEnum' - type: 'null' - line_of_treatment: - anyOf: - - type: integer - - type: 'null' - title: Line Of Treatment program_id: title: Program Id type: string @@ -4666,10 +4633,6 @@ components: anyOf: - $ref: '#/components/schemas/TreatmentIntentEnum' - type: 'null' - treatment_setting: - anyOf: - - $ref: '#/components/schemas/TreatmentSettingEnum' - - type: 'null' treatment_start_date: anyOf: - $ref: '#/components/schemas/DateInterval' @@ -4726,21 +4689,6 @@ components: - Blazer score title: TreatmentResponseMethodEnum type: string - TreatmentSettingEnum: - enum: - - Adjuvant - - Advanced/Metastatic - - Neoadjuvant - - Conditioning - - Induction - - Locally advanced - - Maintenance - - Mobilization - - Preventative - - Radiosensitization - - Salvage - title: TreatmentSettingEnum - type: string TreatmentStatusEnum: enum: - Treatment completed as prescribed @@ -6423,22 +6371,6 @@ paths: - type: string - type: 'null' title: Is Primary Treatment - - in: query - name: line_of_treatment - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Line Of Treatment - - in: query - name: treatment_setting - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Treatment Setting - in: query name: treatment_intent required: false From 7bc8591e540c7c7f45ac4fd1294d90cef6852483 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Wed, 3 Jul 2024 14:05:39 -0400 Subject: [PATCH 12/17] Fixes from the data portal meeting --- .../mohpackets/docs/schema_manual.yml | 35 ++++++++++--------- 1 file changed, 19 insertions(+), 16 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index 43b3a62da..fcd38aac3 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -751,6 +751,12 @@ components: q: treatment_type__overlap title: Treatment Type type: array + primary_site: + items: + type: string + q: primary_site__overlap + title: Primary Site + type: array title: DonorExplorerFilterSchema type: object DonorExplorerSchema: @@ -825,12 +831,6 @@ components: - type: string - type: 'null' title: Lost To Followup Reason - primary_site: - items: - type: string - q: primary_site__overlap - title: Primary Site - type: array program_id: anyOf: - type: string @@ -1861,6 +1861,11 @@ components: pattern: ^[A-Za-z0-9\-\._]{1,64} title: Submitter Primary Diagnosis Id type: string + primary_site: + anyOf: + - $ref: '#/components/schemas/PrimarySiteEnum' + - type: 'null' + title: Primary Site treatments: items: $ref: '#/components/schemas/NestedTreatmentSchema' @@ -2604,6 +2609,11 @@ components: - type: string - type: 'null' title: Laterality + primary_site: + anyOf: + - type: string + - type: 'null' + title: Primary Site program_id: anyOf: - type: string @@ -2778,8 +2788,10 @@ components: - $ref: '#/components/schemas/PrimaryDiagnosisLateralityEnum' - type: 'null' primary_site: + anyOf: + - $ref: '#/components/schemas/PrimarySiteEnum' + - type: 'null' title: Primary Site - type: string program_id: title: Program Id type: string @@ -5338,15 +5350,6 @@ paths: - type: string - type: 'null' title: Cause Of Death - - in: query - name: primary_site - required: false - schema: - items: - type: string - q: primary_site__overlap - title: Primary Site - type: array - in: query name: page required: false From 084acca37987fae47d6a667e73fe6e50aa1ec29a Mon Sep 17 00:00:00 2001 From: fnguyen Date: Thu, 4 Jul 2024 09:44:20 -0400 Subject: [PATCH 13/17] Apply suggestions by @mshadbolt - Switch pathological categories to be an enum - Switch actual/perscribed_cumulative_drug_dose to numbers --- .../mohpackets/docs/schema_manual.yml | 31 ++++++++++--------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index fcd38aac3..bc551cf05 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -325,7 +325,7 @@ components: properties: actual_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Actual Cumulative Drug Dose drug_dose_units: @@ -350,7 +350,7 @@ components: title: Drug Reference Identifier prescribed_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Prescribed Cumulative Drug Dose systemic_therapy_type: @@ -389,7 +389,7 @@ components: properties: actual_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Actual Cumulative Drug Dose drug_dose_units: @@ -414,7 +414,7 @@ components: title: Drug Reference Identifier prescribed_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Prescribed Cumulative Drug Dose systemic_therapy_type: @@ -467,7 +467,7 @@ components: properties: actual_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Actual Cumulative Drug Dose drug_dose_units: @@ -492,7 +492,7 @@ components: title: Drug Reference Identifier prescribed_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Prescribed Cumulative Drug Dose systemic_therapy_type: @@ -1486,6 +1486,7 @@ components: - M1d(1) - M1e - MX + - Not applicable title: MCategoryEnum type: string MalignancyLateralityEnum: @@ -1631,7 +1632,7 @@ components: properties: actual_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Actual Cumulative Drug Dose drug_dose_units: @@ -1656,7 +1657,7 @@ components: title: Drug Reference Identifier prescribed_cumulative_drug_dose: anyOf: - - type: integer + - type: number - type: 'null' title: Prescribed Cumulative Drug Dose systemic_therapy_type: @@ -1785,22 +1786,22 @@ components: properties: pathological_m_category: anyOf: - - type: string + - $ref: '#/components/schemas/MCategoryEnum' - type: 'null' title: Pathological M Category pathological_n_category: anyOf: - - type: string + - $ref: '#/components/schemas/NCategoryEnum' - type: 'null' title: Pathological N Category pathological_stage_group: anyOf: - - type: string + - $ref: '#/components/schemas/StageGroupEnum' - type: 'null' title: Pathological Stage Group pathological_t_category: anyOf: - - type: string + - $ref: '#/components/schemas/TCategoryEnum' - type: 'null' title: Pathological T Category pathological_tumour_staging_system: @@ -4395,7 +4396,7 @@ components: SystemicTherapyTypeEnum: enum: - Chemotherapy - - Hormone Therapy + - Hormone therapy - Immunotherapy title: SystemicTherapyTypeEnum type: string @@ -5089,7 +5090,7 @@ paths: required: false schema: anyOf: - - type: integer + - type: number - type: 'null' title: Prescribed Cumulative Drug Dose - in: query @@ -5097,7 +5098,7 @@ paths: required: false schema: anyOf: - - type: integer + - type: number - type: 'null' title: Actual Cumulative Drug Dose - in: query From 4d553ebe22d4f4704a25fbdbb5a419827124b828 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Fri, 5 Jul 2024 14:25:22 -0400 Subject: [PATCH 14/17] Remove primary site from the DonorWithClinicalData schema? --- chord_metadata_service/mohpackets/docs/schema_manual.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_manual.yml index bc551cf05..124b04f82 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_manual.yml @@ -1041,13 +1041,6 @@ components: $ref: '#/components/schemas/NestedPrimaryDiagnosisSchema' title: Primary Diagnoses type: array - primary_site: - anyOf: - - items: - $ref: '#/components/schemas/PrimarySiteEnum' - type: array - - type: 'null' - title: Primary Site program_id: title: Program Id type: string From ed7311f059bf3296de477356eb2afe33c5240f90 Mon Sep 17 00:00:00 2001 From: fnguyen Date: Fri, 5 Jul 2024 16:46:12 -0400 Subject: [PATCH 15/17] Move schema_v3 -> schema_manual and add stuff to the README? --- chord_metadata_service/mohpackets/docs/README.MD | 16 +++++++++------- .../docs/{schema_manual.yml => schema_v3.yml} | 4 ++++ 2 files changed, 13 insertions(+), 7 deletions(-) rename chord_metadata_service/mohpackets/docs/{schema_manual.yml => schema_v3.yml} (99%) diff --git a/chord_metadata_service/mohpackets/docs/README.MD b/chord_metadata_service/mohpackets/docs/README.MD index 0340c170d..56e771d7c 100644 --- a/chord_metadata_service/mohpackets/docs/README.MD +++ b/chord_metadata_service/mohpackets/docs/README.MD @@ -4,33 +4,35 @@ This folder contains the schema and documentation for **MoH models** ## Katsu API Documentation -To view the API documentation, simply open [schema.md](schema.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/develop/chord_metadata_service/mohpackets/docs/schema.json). +To view the API documentation, simply open [schema_v3.md](schema_v3.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). -To generate the `schema.json` file, run the following command: +To generate the `schema_v3.json` file, run the following command: ```bash -python manage.py export_openapi_schema --api chord_metadata_service.mohpackets.apis.core.api | python -m json.tool > chord_metadata_service/mohpackets/docs/schema.json +python manage.py export_openapi_schema --api chord_metadata_service.mohpackets.apis.core.api | python -m json.tool > chord_metadata_service/mohpackets/docs/schema_v3.json ``` -To generate the `schema.md` file, install [widdershins](https://github.com/Mermade/widdershins) and then run the following command: +To generate the `schema_v3.md` file, install [widdershins](https://github.com/Mermade/widdershins) and then run the following command: ```bash -widdershins ./chord_metadata_service/mohpackets/docs/schema.json -o ./chord_metadata_service/mohpackets/docs/schema.md -u ./chord_metadata_service/mohpackets/docs/widdershins/templates/openapi3 -c true --omitHeader true +widdershins ./chord_metadata_service/mohpackets/docs/schema_v3.json -o ./chord_metadata_service/mohpackets/docs/schema_v3.md -u ./chord_metadata_service/mohpackets/docs/widdershins/templates/openapi3 -c true --omitHeader true ``` -This will create the schema.md file with the updated documentation. +This will create the schema_v3.md file with the updated documentation. ## Katsu MoH data model Documentation -To regenerate the `er_diagram.md` file, run the following from the commandline in the current directory: +To regenerate the `er_diagram.md` file, run the following from the commandline in the current directory: To update the model classes: + ```bash pip install pylint pyreverse -o mmd ../models.py ``` To update the markdown file + ```bash python make_er_diagram.py ``` diff --git a/chord_metadata_service/mohpackets/docs/schema_manual.yml b/chord_metadata_service/mohpackets/docs/schema_v3.yml similarity index 99% rename from chord_metadata_service/mohpackets/docs/schema_manual.yml rename to chord_metadata_service/mohpackets/docs/schema_v3.yml index 124b04f82..c2ca8b3ba 100644 --- a/chord_metadata_service/mohpackets/docs/schema_manual.yml +++ b/chord_metadata_service/mohpackets/docs/schema_v3.yml @@ -1,3 +1,7 @@ +openapi: 3.0.3 +info: + title: Katsu + version: 3.0.0 components: schemas: BasisOfDiagnosisEnum: From 6091ca1daf1590d1dcaf968dc75ed5e165d5ca0d Mon Sep 17 00:00:00 2001 From: Marion Date: Mon, 8 Jul 2024 13:51:09 -0700 Subject: [PATCH 16/17] revert and add note --- chord_metadata_service/mohpackets/docs/README.MD | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/README.MD b/chord_metadata_service/mohpackets/docs/README.MD index 56e771d7c..fd3db20c5 100644 --- a/chord_metadata_service/mohpackets/docs/README.MD +++ b/chord_metadata_service/mohpackets/docs/README.MD @@ -4,21 +4,24 @@ This folder contains the schema and documentation for **MoH models** ## Katsu API Documentation -To view the API documentation, simply open [schema_v3.md](schema_v3.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). +To view the API documentation, simply open [schema.md](schema.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). -To generate the `schema_v3.json` file, run the following command: +> [!WARNING] +> Katsu is currently being transitioned to the MoH clinical data model v3.0.0. There is a manually created v3.0.0 of the OpenAPI schema at [schema_v3.yml](schema_v3.yml) that can be used as a reference in the interim period. This file will be replaced by the automatically generated schema documentaion files once katsu is fully transitions to model v3.0.0 + +To generate the `schema.json` file, run the following command: ```bash -python manage.py export_openapi_schema --api chord_metadata_service.mohpackets.apis.core.api | python -m json.tool > chord_metadata_service/mohpackets/docs/schema_v3.json +python manage.py export_openapi_schema --api chord_metadata_service.mohpackets.apis.core.api | python -m json.tool > chord_metadata_service/mohpackets/docs/schema.json ``` -To generate the `schema_v3.md` file, install [widdershins](https://github.com/Mermade/widdershins) and then run the following command: +To generate the `schema.md` file, install [widdershins](https://github.com/Mermade/widdershins) and then run the following command: ```bash -widdershins ./chord_metadata_service/mohpackets/docs/schema_v3.json -o ./chord_metadata_service/mohpackets/docs/schema_v3.md -u ./chord_metadata_service/mohpackets/docs/widdershins/templates/openapi3 -c true --omitHeader true +widdershins ./chord_metadata_service/mohpackets/docs/schema.json -o ./chord_metadata_service/mohpackets/docs/schema.md -u ./chord_metadata_service/mohpackets/docs/widdershins/templates/openapi3 -c true --omitHeader true ``` -This will create the schema_v3.md file with the updated documentation. +This will create the schema.md file with the updated documentation. ## Katsu MoH data model Documentation From 665386074621d5ee5d5bfd97fb76351419ca6b5b Mon Sep 17 00:00:00 2001 From: Marion Date: Mon, 8 Jul 2024 13:52:44 -0700 Subject: [PATCH 17/17] typo --- chord_metadata_service/mohpackets/docs/README.MD | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/chord_metadata_service/mohpackets/docs/README.MD b/chord_metadata_service/mohpackets/docs/README.MD index fd3db20c5..0c5c99bff 100644 --- a/chord_metadata_service/mohpackets/docs/README.MD +++ b/chord_metadata_service/mohpackets/docs/README.MD @@ -6,8 +6,8 @@ This folder contains the schema and documentation for **MoH models** To view the API documentation, simply open [schema.md](schema.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). -> [!WARNING] -> Katsu is currently being transitioned to the MoH clinical data model v3.0.0. There is a manually created v3.0.0 of the OpenAPI schema at [schema_v3.yml](schema_v3.yml) that can be used as a reference in the interim period. This file will be replaced by the automatically generated schema documentaion files once katsu is fully transitions to model v3.0.0 +> [!IMPORTANT] +> Katsu is currently being transitioned to MoH clinical data model v3.0.0. There is a manually created v3.0.0 of the OpenAPI schema at [schema_v3.yml](schema_v3.yml) that can be used as a reference in the interim period. This file will be replaced by the automatically generated schema documentaion files once katsu is fully transitioned to model v3.0.0. To generate the `schema.json` file, run the following command: