From c5162768715462f182dc6ea7030b62af32790606 Mon Sep 17 00:00:00 2001 From: Son Chau Date: Thu, 19 Sep 2024 09:11:33 -0700 Subject: [PATCH 1/4] add static folder path --- config/settings/base.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config/settings/base.py b/config/settings/base.py index 1b6c90fb7..5aa7b157d 100644 --- a/config/settings/base.py +++ b/config/settings/base.py @@ -130,6 +130,9 @@ STATIC_URL = "static/" STATIC_ROOT = BASE_DIR / "staticfiles" +STATICFILES_DIRS = [ + BASE_DIR / "chord_metadata_service/mohpackets/docs/schemas", +] # Default primary key field type # https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field From 5350ea8ec24572f3cf03c4ff6d0e077927f781c6 Mon Sep 17 00:00:00 2001 From: Son Chau Date: Thu, 19 Sep 2024 09:12:00 -0700 Subject: [PATCH 2/4] move schemas to its own folder --- chord_metadata_service/mohpackets/docs/{ => schemas}/schema.json | 0 chord_metadata_service/mohpackets/docs/{ => schemas}/schema.md | 0 chord_metadata_service/mohpackets/docs/{ => schemas}/schema.yml | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename chord_metadata_service/mohpackets/docs/{ => schemas}/schema.json (100%) rename chord_metadata_service/mohpackets/docs/{ => schemas}/schema.md (100%) rename chord_metadata_service/mohpackets/docs/{ => schemas}/schema.yml (100%) diff --git a/chord_metadata_service/mohpackets/docs/schema.json b/chord_metadata_service/mohpackets/docs/schemas/schema.json similarity index 100% rename from chord_metadata_service/mohpackets/docs/schema.json rename to chord_metadata_service/mohpackets/docs/schemas/schema.json diff --git a/chord_metadata_service/mohpackets/docs/schema.md b/chord_metadata_service/mohpackets/docs/schemas/schema.md similarity index 100% rename from chord_metadata_service/mohpackets/docs/schema.md rename to chord_metadata_service/mohpackets/docs/schemas/schema.md diff --git a/chord_metadata_service/mohpackets/docs/schema.yml b/chord_metadata_service/mohpackets/docs/schemas/schema.yml similarity index 100% rename from chord_metadata_service/mohpackets/docs/schema.yml rename to chord_metadata_service/mohpackets/docs/schemas/schema.yml From d3c10f1e9465e8e616b1f46ef1a5b28bf44d27aa Mon Sep 17 00:00:00 2001 From: Son Chau Date: Thu, 19 Sep 2024 09:12:04 -0700 Subject: [PATCH 3/4] Delete schema_v3.yml --- .../mohpackets/docs/schema_v3.yml | 6914 ----------------- 1 file changed, 6914 deletions(-) delete mode 100644 chord_metadata_service/mohpackets/docs/schema_v3.yml diff --git a/chord_metadata_service/mohpackets/docs/schema_v3.yml b/chord_metadata_service/mohpackets/docs/schema_v3.yml deleted file mode 100644 index c2ca8b3ba..000000000 --- a/chord_metadata_service/mohpackets/docs/schema_v3.yml +++ /dev/null @@ -1,6914 +0,0 @@ -openapi: 3.0.3 -info: - title: Katsu - version: 3.0.0 -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 - SystemicTherapyFilterSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: number - - type: 'null' - title: Actual Cumulative Drug Dose - drug_dose_units: - anyOf: - - type: string - - type: 'null' - title: 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: number - - type: 'null' - title: Prescribed Cumulative Drug Dose - systemic_therapy_type: - anyOf: - - 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 - - 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: SystemicTherapyFilterSchema - type: object - SystemicTherapyIngestSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: number - - type: 'null' - title: Actual Cumulative Drug Dose - 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: number - - type: 'null' - title: Prescribed Cumulative Drug Dose - systemic_therapy_type: - 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 - 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 - 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 - - systemic_therapy_type - title: SystemicTherapyIngestSchema - type: object - SystemicTherapyModelSchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: number - - type: 'null' - title: Actual Cumulative Drug Dose - 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: number - - type: 'null' - title: Prescribed Cumulative Drug Dose - systemic_therapy_type: - 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 - 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 - 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 - - systemic_therapy_type - title: SystemicTherapyModelSchema - 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: - systemic_therapy_drug_name: - items: - type: string - title: Systemic Therapy Drug Name - type: array - exclude_cohorts: - items: - type: string - title: Exclude Cohorts - type: array - treatment_type: - items: - type: string - 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: - 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 - 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' - 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' - 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 - 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 - 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 - 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 - 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 - HpvStrainEnum: - enum: - - HPV16 - - HPV18 - - HPV31 - - HPV33 - - HPV35 - - HPV39 - - HPV45 - - HPV51 - - HPV52 - - HPV56 - - HPV58 - - HPV59 - - HPV66 - - HPV68 - - HPV73 - title: HpvStrainEnum - type: string - 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 - - Not applicable - 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 - NestedSystemicTherapySchema: - properties: - actual_cumulative_drug_dose: - anyOf: - - type: number - - type: 'null' - title: Actual Cumulative Drug Dose - 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: number - - type: 'null' - title: Prescribed Cumulative Drug Dose - systemic_therapy_type: - 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 - 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: - 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 - 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 - NestedPrimaryDiagnosisSchema: - properties: - pathological_m_category: - anyOf: - - $ref: '#/components/schemas/MCategoryEnum' - - type: 'null' - title: Pathological M Category - pathological_n_category: - anyOf: - - $ref: '#/components/schemas/NCategoryEnum' - - type: 'null' - title: Pathological N Category - pathological_stage_group: - anyOf: - - $ref: '#/components/schemas/StageGroupEnum' - - type: 'null' - title: Pathological Stage Group - pathological_t_category: - anyOf: - - $ref: '#/components/schemas/TCategoryEnum' - - 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' - - 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' - 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 - primary_site: - anyOf: - - $ref: '#/components/schemas/PrimarySiteEnum' - - type: 'null' - title: Primary Site - 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: - 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 - 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' - - 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' - 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: - - $ref: '#/components/schemas/SurgeryLocationEnum' - - type: 'null' - surgery_site: - anyOf: - - maxLength: 255 - pattern: ^[C][0-9]{2}(.[0-9]{1})?$ - 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: - systemic_therapies: - items: - $ref: '#/components/schemas/NestedSystemicTherapySchema' - title: Systemic Therapies - type: array - followups: - items: - $ref: '#/components/schemas/NestedFollowUpSchema' - title: Followups - type: array - is_primary_treatment: - anyOf: - - $ref: '#/components/schemas/uBooleanEnum' - - type: 'null' - 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_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 - PagedSystemicTherapyModelSchema: - properties: - count: - anyOf: - - type: integer - - type: 'null' - title: Count - items: - items: - $ref: '#/components/schemas/SystemicTherapyModelSchema' - 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: PagedSystemicTherapyModelSchema - 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 - 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 - primary_site: - anyOf: - - type: string - - type: 'null' - title: Primary Site - 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: - 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' - - 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' - primary_site: - type: string - title: Primary Site - 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: - 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' - - 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' - primary_site: - anyOf: - - $ref: '#/components/schemas/PrimarySiteEnum' - - type: 'null' - title: Primary Site - 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: - 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 - submitter_treatment_id: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment 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: - 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 - 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' - - 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: - 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 - 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' - - 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_treatment_id: - anyOf: - - 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 - - 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_treatment_id: - anyOf: - - maxLength: 64 - type: string - - 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: - - $ref: '#/components/schemas/SurgeryLocationEnum' - - type: 'null' - surgery_site: - anyOf: - - maxLength: 255 - pattern: ^[C][0-9]{2}(.[0-9]{1})?$ - 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_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: - - $ref: '#/components/schemas/SurgeryLocationEnum' - - type: 'null' - surgery_site: - anyOf: - - maxLength: 255 - pattern: ^[C][0-9]{2}(.[0-9]{1})?$ - 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 - SurgeryReferenceDatabaseEnum: - enum: - - SNOMED - - NCIt - - UMLS - title: SurgeryReferenceDatabaseEnum - type: string - SystemicTherapyTypeEnum: - enum: - - Chemotherapy - - Hormone therapy - - Immunotherapy - title: SystemicTherapyTypeEnum - 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: - is_primary_treatment: - anyOf: - - type: string - - type: 'null' - title: Is Primary Treatment - 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_type: - items: - type: string - q: treatment_type__overlap - title: Treatment Type - type: array - title: TreatmentFilterSchema - type: object - TreatmentIngestSchema: - properties: - is_primary_treatment: - anyOf: - - $ref: '#/components/schemas/uBooleanEnum' - - type: 'null' - 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_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: - is_primary_treatment: - anyOf: - - $ref: '#/components/schemas/uBooleanEnum' - - type: 'null' - 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_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 - 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/systemic_therapies/: - get: - operationId: chord_metadata_service_mohpackets_apis_clinical_data_list_systemic_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: drug_dose_units - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Drug Dose Units - - in: query - name: prescribed_cumulative_drug_dose - required: false - schema: - anyOf: - - type: number - - type: 'null' - title: Prescribed Cumulative Drug Dose - - in: query - name: actual_cumulative_drug_dose - required: false - schema: - anyOf: - - type: number - - 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: 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 - 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/PagedSystemicTherapyModelSchema' - description: OK - security: - - LoginAuth: [] - summary: List Systemic Therapies - 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: 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: 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/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: 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: submitter_treatment_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Submitter Treatment 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: 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: 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: 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 - 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: treatment_intent - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Treatment Intent - - 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: systemic_therapy_drug_name - required: false - schema: - items: - type: string - title: Systemic 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/systemic_therapy/: - post: - operationId: chord_metadata_service_mohpackets_apis_ingestion_create_systemic_therapy - parameters: [] - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/SystemicTherapyIngestSchema' - required: true - responses: - '200': - description: OK - security: - - LoginAuth: [] - summary: Create Systemic Therapy - 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/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 71bd3343f09de95e20b569b2e4c6a0c5aabdcc1e Mon Sep 17 00:00:00 2001 From: Son Chau Date: Thu, 19 Sep 2024 09:12:13 -0700 Subject: [PATCH 4/4] modify the path --- .github/workflows/update-schema.yaml | 10 +++++----- chord_metadata_service/mohpackets/docs/README.MD | 9 +++------ 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/.github/workflows/update-schema.yaml b/.github/workflows/update-schema.yaml index 096b46cdd..1ceb1ff1c 100644 --- a/.github/workflows/update-schema.yaml +++ b/.github/workflows/update-schema.yaml @@ -36,30 +36,30 @@ jobs: export DJANGO_SETTINGS_MODULE=config.settings.base echo "CACHE_DURATION = 0" >> config/settings/base.py echo "AGGREGATE_COUNT_THRESHOLD = 5" >> config/settings/base.py - 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/schemas/schema.json - name: Install widdershins run: npm install -g widdershins - name: Convert schema to OpenAPI documentation run: | - npx 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 + npx widdershins ./chord_metadata_service/mohpackets/docs/schemas/schema.json -o ./chord_metadata_service/mohpackets/docs/schemas/schema.md -u ./chord_metadata_service/mohpackets/docs/widdershins/templates/openapi3 -c true --omitHeader true - name: Install PyYAML run: pip install PyYAML - name: Convert schema.json to schema.yml - run: python -c 'import json, yaml; json.load(open("chord_metadata_service/mohpackets/docs/schema.json")); print(yaml.dump(json.load(open("chord_metadata_service/mohpackets/docs/schema.json"))))' > chord_metadata_service/mohpackets/docs/schema.yml + run: python -c 'import json, yaml; json.load(open("chord_metadata_service/mohpackets/docs/schemas/schema.json")); print(yaml.dump(json.load(open("chord_metadata_service/mohpackets/docs/schemas/schema.json"))))' > chord_metadata_service/mohpackets/docs/schemas/schema.yml - name: Update schemas uses: stefanzweifel/git-auto-commit-action@v5 with: commit_message: Update schemas - file_pattern: "chord_metadata_service/mohpackets/docs/schema.json chord_metadata_service/mohpackets/docs/schema.md chord_metadata_service/mohpackets/docs/schema.yml" + file_pattern: "chord_metadata_service/mohpackets/docs/schemas/schema.json chord_metadata_service/mohpackets/docs/schemas/schema.md chord_metadata_service/mohpackets/docs/schemas/schema.yml" - name: Get SHA commit of schema.json id: get-sha - run: echo "SHA=$(git log -1 --format=%H chord_metadata_service/mohpackets/docs/schema.json)" >> $GITHUB_ENV + run: echo "SHA=$(git log -1 --format=%H chord_metadata_service/mohpackets/docs/schemas/schema.json)" >> $GITHUB_ENV - name: Write SHA to schema_version.txt run: echo ${{ env.SHA }} > chord_metadata_service/mohpackets/docs/schema_version.txt diff --git a/chord_metadata_service/mohpackets/docs/README.MD b/chord_metadata_service/mohpackets/docs/README.MD index 0c5c99bff..cb3ff1333 100644 --- a/chord_metadata_service/mohpackets/docs/README.MD +++ b/chord_metadata_service/mohpackets/docs/README.MD @@ -4,21 +4,18 @@ 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/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). - -> [!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 view the API documentation, simply open [schemas/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/schemas/schema.json). 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.json +python manage.py export_openapi_schema --api chord_metadata_service.mohpackets.apis.core.api | python -m json.tool > chord_metadata_service/mohpackets/docs/schemas/schema.json ``` 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.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/schemas/schema.json -o ./chord_metadata_service/mohpackets/docs/schemas/schema.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.