Merge pull request #1580 from HumanCellAtlas/staging

Release from staging to master 2024-09-16
HumanCellAtlas · Sep 16, 2024 · 3b5ec14 · 3b5ec14
2 parents b53b325 + cee678b
commit 3b5ec14
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diff --git a/changelog.md b/changelog.md
@@ -9,6 +9,19 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
+
+### [module/biomaterial/medical_history.json - v5.3.0] - 2024-09-16
+### Added
+Added optional smoking related fields in medical_history module. Fix #1565
+
+### [module/biomaterial/medical_history.json - v6.0.0] - 2024-09-16
+### Removed
+Removed smoking_history in medical_history module. Fix #1565
+
+### [type/biomaterial/donor_organism.json - v16.2.0] - 2024-09-16
+### Added
+Added optional smoking related fields in medical_history module. Fix #1565
+
 ### [module/ontology/file_content_ontology.json - v2.0.0] - 2024-08-28
 ### Fixed
 Fixed class from data:0006 to EDAM:0006. Fixes #1571

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
@@ -507,7 +507,9 @@ Property name | Description | Type | Required? | Object reference? | User friend
 --- | --- | --- | --- | --- | --- | --- | --- 
 alcohol_history | Estimated amount of alcohol consumed per day. | string | no |  | Alcohol history |  | 3-6 alcohol units/day; 1 drink per day
 medication | Medications the individual was taking at time of biomaterial collection. | string | no |  | Medications |  | Naproxen 500mg/day; Citalopram 20mg/day
-smoking_history | Estimated number of cigarettes smoked per day. | string | no |  | Smoking history |  | 20 cigarettes/day for 25 years, stopped 2000
+smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no |  | Smoking status | active, former, never | Should be one of: active, former, never.
+smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no |  | Smoking pack years |  | 4.55
+years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no |  | Years since smoking cessation |  | 12
 nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no |  | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed.
 test_results | Results from medical tests performed on the individual. | string | no |  | Test results |  | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative
 treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no |  | Treatments |  | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer

diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json
@@ -31,12 +31,30 @@
             "example": "Naproxen 500mg/day; Citalopram 20mg/day",
             "guidelines": "Enter the medication and dosage. Separate multiple medications with commas."
         },
-        "smoking_history": {
-            "description": "Estimated number of cigarettes smoked per day.",
+        "smoking_status": {
+            "description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.",
             "type": "string",
-            "user_friendly": "Smoking history",
-            "example": "20 cigarettes/day for 25 years, stopped 2000",
-            "guidelines": "Enter an estimated number of cigarettes smoked per day and for how many years."
+            "enum": [
+                "active",
+                "former",
+                "never"
+            ],
+            "user_friendly": "Smoking status",
+            "example": "Should be one of: active, former, never."
+        },
+        "smoking_pack_years": {
+            "description": "Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking.",
+            "type": "number",
+            "user_friendly": "Smoking pack years",
+            "minimum": 0,
+            "example": 4.55
+        },
+        "years_since_smoking_cessation": {
+            "description": "If smoking status is 'former', specify the number of years since smoking cessation.",
+            "type": "integer",
+            "user_friendly": "Years since smoking cessation",
+            "minimum": 0,
+            "example": 12
         },
         "nutritional_state": {
             "description": "Nutritional state of individual at time of biomaterial collection.",
@@ -61,5 +79,43 @@
             "user_friendly": "Treatments",
             "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer"
         }
-    }
+    },
+    "allOf": 
+        [
+            {
+                "if": {
+                    "properties": { 
+                        "smoking_status": {
+                            "const": "active" 
+                        } 
+                    }
+                },
+                "then": {
+                    "properties": {
+                        "years_since_smoking_cessation": { 
+                            "maximum": 0 
+                        }
+                    }
+                }
+            },
+            {
+                "if": {
+                    "properties": { 
+                        "smoking_status": { 
+                            "const": "never" 
+                        } 
+                    }
+                },
+                "then": {
+                    "properties": {
+                        "years_since_smoking_cessation": { 
+                            "type": "null" 
+                        },
+                        "smoking_pack_years": { 
+                            "maximum": 0 
+                        }
+                    }
+                }
+            }
+        ]
 }
diff --git a/json_schema/property_migrations.json b/json_schema/property_migrations.json
@@ -1,5 +1,12 @@
 {
     "migrations": [
+        {
+            "source_schema": "medical_history",
+            "property": "smoking_history",
+            "effective_from": "6.0.0",
+            "reason": "Field standardization",
+            "type": "deprecated property"
+        },
         {
             "source_schema": "project",
             "property": "data_use_restriction",

diff --git a/json_schema/versions.json b/json_schema/versions.json
@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2024-08-28T14:24:32Z",
+    "last_update_date": "2024-09-16T14:52:03Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -25,7 +25,7 @@
                 "familial_relationship": "6.0.3",
                 "growth_conditions": "6.4.2",
                 "human_specific": "1.0.11",
-                "medical_history": "5.2.8",
+                "medical_history": "6.0.0",
                 "medical_tests": "1.0.0",
                 "mouse_specific": "1.0.8",
                 "preservation_storage": "6.1.1",
@@ -92,7 +92,7 @@
             "biomaterial": {
                 "cell_line": "16.0.0",
                 "cell_suspension": "14.0.0",
-                "donor_organism": "16.1.0",
+                "donor_organism": "16.2.0",
                 "imaged_specimen": "3.5.0",
                 "organoid": "11.5.0",
                 "specimen_from_organism": "10.9.0"