Merge pull request #273 from CanDIG/develop

Update versioned AJCC to single AJCC in enum and synth data
CanDIG · Oct 16, 2024 · 8371d13 · 8371d13
2 parents 900dd3a + a7cec23
commit 8371d13
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Showing 9 changed files with 28 additions and 36 deletions.
diff --git a/...metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json b/...metadata_service/mohpackets/data/extra_small_dataset/synthetic_data/PrimaryDiagnosis.json
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
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
diff --git a/chord_metadata_service/mohpackets/data/small_dataset/synthetic_data/PrimaryDiagnosis.json b/chord_metadata_service/mohpackets/data/small_dataset/synthetic_data/PrimaryDiagnosis.json
diff --git 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
@@ -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
@@ -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
 <a id="tocstumourstagingsystemenum"></a>
 
 ```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
@@ -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
@@ -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"
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		fd2be0bb1831f72571095a6e231e4b74131e070c
		827f8485764cf524dee24e3835778864ea25dd27