diff --git a/chord_metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json b/chord_metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json index 8ce6350e8..c09007d3e 100644 --- a/chord_metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json +++ b/chord_metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json @@ -1 +1 @@ -[{"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0001", "submitter_donor_id": "DONOR_0001", "primary_site": "Breast", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "D05", "basis_of_diagnosis": "Histology of a metastasis", "laterality": null, "clinical_tumour_staging_system": "International Neuroblastoma Risk Group Staging System", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage IIBES", "pathological_tumour_staging_system": "Lugano staging system", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": "Stage IB"}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0002", "submitter_donor_id": "DONOR_0002", "primary_site": "Bronchus and lung", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C45", "basis_of_diagnosis": null, "laterality": null, "clinical_tumour_staging_system": null, "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage IE", "pathological_tumour_staging_system": "AJCC 8th edition", "pathological_t_category": null, "pathological_n_category": "N2b", "pathological_m_category": null, "pathological_stage_group": null}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0003", "submitter_donor_id": "DONOR_0003", "primary_site": "Colon", "date_of_diagnosis": 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"pathological_stage_group": "Stage IIIAES"}, {"program_id": "SYNTH_02", "submitter_primary_diagnosis_id": "DIAG_0009", "submitter_donor_id": "DONOR_0009", "primary_site": "Skin", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C14", "basis_of_diagnosis": "Death certificate only", "laterality": "Unilateral, side not specified", "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T1b(s)", "clinical_n_category": "N1a(sn)", "clinical_m_category": "M1b(0)", "clinical_stage_group": "Stage Ms", "pathological_tumour_staging_system": "Rai staging system", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": "Stage 0"}, {"program_id": "SYNTH_02", "submitter_primary_diagnosis_id": "DIAG_0010", "submitter_donor_id": "DONOR_0010", "primary_site": null, "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": null, 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"pathological_stage_group": null}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_ALL_0001", "submitter_donor_id": "DONOR_ALL_0001", "primary_site": "Floor of mouth", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C06.9", "basis_of_diagnosis": null, "laterality": null, "clinical_tumour_staging_system": "Ann Arbor staging system", "clinical_t_category": "T4d", "clinical_n_category": "N3b", "clinical_m_category": "M1e", "clinical_stage_group": "Stage C", "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T1a(m)", "pathological_n_category": "N0(i+)", "pathological_m_category": null, "pathological_stage_group": "Stage IVC"}] \ No newline at end of file diff --git a/chord_metadata_service/mohpackets/data/large_dataset/synthetic_data/PrimaryDiagnosis.json b/chord_metadata_service/mohpackets/data/large_dataset/synthetic_data/PrimaryDiagnosis.json index e87f14aef..1ca677178 100644 --- a/chord_metadata_service/mohpackets/data/large_dataset/synthetic_data/PrimaryDiagnosis.json +++ b/chord_metadata_service/mohpackets/data/large_dataset/synthetic_data/PrimaryDiagnosis.json @@ -1 +1 @@ -[{"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0001", "submitter_donor_id": "DONOR_0001", "primary_site": "Breast", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C16", "basis_of_diagnosis": "Clinical investigation", "laterality": "Not available", "clinical_tumour_staging_system": "Not available", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": null, "pathological_tumour_staging_system": "International Neuroblastoma Risk Group Staging System", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": "Stage IIIAES"}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0002", 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diff --git a/chord_metadata_service/mohpackets/data/medium_dataset/synthetic_data/PrimaryDiagnosis.json b/chord_metadata_service/mohpackets/data/medium_dataset/synthetic_data/PrimaryDiagnosis.json index 4821ed887..8b0c25a45 100644 --- a/chord_metadata_service/mohpackets/data/medium_dataset/synthetic_data/PrimaryDiagnosis.json +++ b/chord_metadata_service/mohpackets/data/medium_dataset/synthetic_data/PrimaryDiagnosis.json @@ -1 +1 @@ -[{"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_0001", "submitter_donor_id": "DONOR_0001", "primary_site": "Breast", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C23", "basis_of_diagnosis": "Clinical investigation", "laterality": "Not a paired site", "clinical_tumour_staging_system": "Binet staging system", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage B", "pathological_tumour_staging_system": "Durie-Salmon staging system", 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"pathological_stage_group": "Stage IA"}, {"program_id": "SYNTH_04", "submitter_primary_diagnosis_id": "DIAG_0077", "submitter_donor_id": "DONOR_0077", "primary_site": "Bronchus and lung", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C93", "basis_of_diagnosis": "Clinical", "laterality": "Bilateral", "clinical_tumour_staging_system": "SEER staging system", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage 1A", "pathological_tumour_staging_system": "Lugano staging system", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": "Stage IIIA1"}, {"program_id": "SYNTH_04", "submitter_primary_diagnosis_id": "DIAG_0078", "submitter_donor_id": "DONOR_0078", "primary_site": "Colon", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "D04", "basis_of_diagnosis": "Clinical", "laterality": "Bilateral", "clinical_tumour_staging_system": "International Neuroblastoma Risk Group Staging System", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage IIES", "pathological_tumour_staging_system": "International Neuroblastoma Staging System", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": "Stage IB"}, {"program_id": "SYNTH_04", "submitter_primary_diagnosis_id": "DIAG_0079", "submitter_donor_id": "DONOR_0079", "primary_site": "Skin", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "D00", "basis_of_diagnosis": null, "laterality": "Not a paired site", "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T1a2", "clinical_n_category": "N3b", "clinical_m_category": null, "clinical_stage_group": "Stage IVA", "pathological_tumour_staging_system": "International Neuroblastoma Staging System", "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": null}, {"program_id": "SYNTH_04", "submitter_primary_diagnosis_id": "DIAG_0080", "submitter_donor_id": "DONOR_0080", "primary_site": null, "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "D42", "basis_of_diagnosis": null, "laterality": "Not available", "clinical_tumour_staging_system": "St Jude staging system", "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": "Stage III", "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T1a", "pathological_n_category": "N2c", "pathological_m_category": "M1d(0)", "pathological_stage_group": "Stage IVB"}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_NULL_0001", "submitter_donor_id": "DONOR_NULL_0001", "primary_site": null, "date_of_diagnosis": null, "cancer_type_code": null, "basis_of_diagnosis": null, "laterality": null, "clinical_tumour_staging_system": null, "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": null, "pathological_tumour_staging_system": null, "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": null}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_NULL_0002", "submitter_donor_id": "DONOR_NULL_0002", "primary_site": null, "date_of_diagnosis": null, "cancer_type_code": null, "basis_of_diagnosis": null, "laterality": null, "clinical_tumour_staging_system": null, "clinical_t_category": null, "clinical_n_category": null, "clinical_m_category": null, "clinical_stage_group": null, "pathological_tumour_staging_system": null, "pathological_t_category": null, "pathological_n_category": null, "pathological_m_category": null, "pathological_stage_group": null}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_ALL_0001", "submitter_donor_id": "DONOR_ALL_0001", "primary_site": "Floor of mouth", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C06.9", "basis_of_diagnosis": "Clinical", "laterality": "Bilateral", "clinical_tumour_staging_system": "Rai staging system", "clinical_t_category": "Tis(Paget)", "clinical_n_category": "N2a", "clinical_m_category": "M1a(1)", "clinical_stage_group": "Stage 1", "pathological_tumour_staging_system": "Binet staging system", "pathological_t_category": "T1a(m)", "pathological_n_category": "N3b", "pathological_m_category": "M1b(0)", "pathological_stage_group": "Stage IVC"}, {"program_id": "SYNTH_01", "submitter_primary_diagnosis_id": "DIAG_ALL_0002", "submitter_donor_id": "DONOR_ALL_0002", "primary_site": "Floor of mouth", "date_of_diagnosis": {"month_interval": 0, "day_interval": 0}, "cancer_type_code": "C06.9", "basis_of_diagnosis": "Cytology", "laterality": null, "clinical_tumour_staging_system": "Revised International staging system (R-ISS)", "clinical_t_category": "T1d", "clinical_n_category": "N0(i+)", "clinical_m_category": "M0(i+)", "clinical_stage_group": "Stage A", "pathological_tumour_staging_system": "Binet staging system", "pathological_t_category": "T3(m)", "pathological_n_category": "N0(mol-)", "pathological_m_category": "MX", "pathological_stage_group": "Stage IVB"}] \ No newline at end of file diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt index 818b74da1..2dc8b3e67 100644 --- a/chord_metadata_service/mohpackets/docs/schema_version.txt +++ b/chord_metadata_service/mohpackets/docs/schema_version.txt @@ -1 +1 @@ -fd2be0bb1831f72571095a6e231e4b74131e070c +827f8485764cf524dee24e3835778864ea25dd27 diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.json b/chord_metadata_service/mohpackets/docs/schemas/schema.json index 6b263928a..d232eae0f 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.json +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.json @@ -5652,9 +5652,7 @@ }, "TumourStagingSystemEnum": { "enum": [ - "AJCC 8th edition", - "AJCC 7th edition", - "AJCC 6th edition", + "AJCC cancer staging system", "Ann Arbor staging system", "Binet staging system", "Durie-Salmon staging system", @@ -5663,7 +5661,7 @@ "International Neuroblastoma Staging System", "Lugano staging system", "Rai staging system", - "Revised International staging system (RISS)", + "Revised International staging system (R-ISS)", "SEER staging system", "St Jude staging system", "Not available" diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.md b/chord_metadata_service/mohpackets/docs/schemas/schema.md index e19f39901..38ecb8602 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.md +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.md @@ -525,12 +525,12 @@ Retrieves a single donor along with all related clinical data, organized in a ne "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -975,12 +975,12 @@ Used by the query service to return donors along with their sample IDs, treatmen "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -3896,12 +3896,12 @@ NCategoryEnum "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -4540,7 +4540,7 @@ TCategoryEnum ```json -"AJCC 8th edition" +"AJCC cancer staging system" ``` @@ -4556,9 +4556,7 @@ TumourStagingSystemEnum |Property|Value| |---|---| -|TumourStagingSystemEnum|AJCC 8th edition| -|TumourStagingSystemEnum|AJCC 7th edition| -|TumourStagingSystemEnum|AJCC 6th edition| +|TumourStagingSystemEnum|AJCC cancer staging system| |TumourStagingSystemEnum|Ann Arbor staging system| |TumourStagingSystemEnum|Binet staging system| |TumourStagingSystemEnum|Durie-Salmon staging system| @@ -4567,7 +4565,7 @@ TumourStagingSystemEnum |TumourStagingSystemEnum|International Neuroblastoma Staging System| |TumourStagingSystemEnum|Lugano staging system| |TumourStagingSystemEnum|Rai staging system| -|TumourStagingSystemEnum|Revised International staging system (RISS)| +|TumourStagingSystemEnum|Revised International staging system (R-ISS)| |TumourStagingSystemEnum|SEER staging system| |TumourStagingSystemEnum|St Jude staging system| |TumourStagingSystemEnum|Not available| @@ -6917,12 +6915,12 @@ TreatmentTypeEnum "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -8074,12 +8072,12 @@ or "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -11313,12 +11311,12 @@ or "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", @@ -11409,12 +11407,12 @@ or "cancer_type_code": "string", "basis_of_diagnosis": "Clinical investigation", "laterality": "Bilateral", - "clinical_tumour_staging_system": "AJCC 8th edition", + "clinical_tumour_staging_system": "AJCC cancer staging system", "clinical_t_category": "T0", "clinical_n_category": "N0", "clinical_m_category": "M0", "clinical_stage_group": "Stage 0", - "pathological_tumour_staging_system": "AJCC 8th edition", + "pathological_tumour_staging_system": "AJCC cancer staging system", "pathological_t_category": "T0", "pathological_n_category": "N0", "pathological_m_category": "M0", diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.yml b/chord_metadata_service/mohpackets/docs/schemas/schema.yml index c3907d442..751e9e00b 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.yml +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.yml @@ -5058,9 +5058,7 @@ components: type: string TumourStagingSystemEnum: enum: - - AJCC 8th edition - - AJCC 7th edition - - AJCC 6th edition + - AJCC cancer staging system - Ann Arbor staging system - Binet staging system - Durie-Salmon staging system @@ -5069,7 +5067,7 @@ components: - International Neuroblastoma Staging System - Lugano staging system - Rai staging system - - Revised International staging system (RISS) + - Revised International staging system (R-ISS) - SEER staging system - St Jude staging system - Not available diff --git a/chord_metadata_service/mohpackets/permissible_values.py b/chord_metadata_service/mohpackets/permissible_values.py index 29e202dc7..30532348e 100644 --- a/chord_metadata_service/mohpackets/permissible_values.py +++ b/chord_metadata_service/mohpackets/permissible_values.py @@ -94,9 +94,7 @@ ] TUMOUR_STAGING_SYSTEM = [ - "AJCC 8th edition", - "AJCC 7th edition", - "AJCC 6th edition", + "AJCC cancer staging system", "Ann Arbor staging system", "Binet staging system", "Durie-Salmon staging system", @@ -105,7 +103,7 @@ "International Neuroblastoma Staging System", "Lugano staging system", "Rai staging system", - "Revised International staging system (RISS)", + "Revised International staging system (R-ISS)", "SEER staging system", "St Jude staging system", "Not available"