Added smoking related fields in medical_history module. Fix#1565

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

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 +79,38 @@
             "user_friendly": "Treatments",
             "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer"
         }
+    },
+    "if": {
+        "properties": { 
+            "smoking_status": {
+                 "const": "active" 
+            } 
+        }
+    },
+    "then": {
+        "properties": {
+            "years_since_smoking_cessation": { 
+                "maximum": 0 
+            }
+        }
+    },
+    "else": {
+        "if": {
+            "properties": { 
+                "smoking_status": { 
+                    "const": "never" 
+                } 
+            }
+        },
+        "then": {
+            "properties": {
+                "years_since_smoking_cessation": { 
+                    "type": "null" 
+                },
+                "smoking_pack_years": { 
+                    "maximum": 0 
+                }
+            }
+        }
     }
 }

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",

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/biomaterial/medical_history,minor,"Added optional smoking related fields in medical_history module. Fix #1565",,
+module/biomaterial/medical_history,major,"Removed smoking_history in medical_history module. Fix #1565",,