Add sexAtBirth field #2714

globaldothealth · Jul 27, 2022 · 208a551 · 208a551
1 parent 83e335d
commit 208a551
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Showing 5 changed files with 48 additions and 56 deletions.
diff --git a/data-serving/reusable-data-service/data_service/day_zero_fields.json b/data-serving/reusable-data-service/data_service/day_zero_fields.json
@@ -41,6 +41,18 @@
         "data_dictionary_text": "Age of the individual, specified as a range, either open-ended (<n, >n) or as a range delimited by a hyphen following 5-year age increments (m-n)",
         "required": false
     },
+    {
+        "key": "sexAtBirth",
+        "type": "string",
+        "data_dictionary_text": "Sex at birth of an individual.",
+        "required": true,
+        "values": [
+            "Male",
+            "Female",
+            "Unknown",
+            "other"
+        ]
+    },
     {
         "key": "confirmationDate",
         "type": "date",

diff --git a/data-serving/reusable-data-service/tests/data/case.excluded.json b/data-serving/reusable-data-service/tests/data/case.excluded.json
@@ -8,5 +8,6 @@
         "note": "Excluded upon this day, for reasons"
     },
     "caseStatus": "omit_error",
-    "pathogenStatus": "endemic"
+    "pathogenStatus": "endemic",
+    "sexAtBirth": "Female"
 }
diff --git a/data-serving/reusable-data-service/tests/data/case.minimal.json b/data-serving/reusable-data-service/tests/data/case.minimal.json
@@ -4,5 +4,6 @@
         "sourceId": "fedc09876543210987654321"
     },
     "caseStatus": "probable",
-    "pathogenStatus": "emerging"
+    "pathogenStatus": "emerging",
+    "sexAtBirth": "Female"
 }
diff --git a/data-serving/reusable-data-service/tests/data/case.with_location.json b/data-serving/reusable-data-service/tests/data/case.with_location.json
@@ -17,5 +17,6 @@
         }
     },
     "caseStatus": "probable",
-    "pathogenStatus": "unknown"
+    "pathogenStatus": "unknown",
+    "sexAtBirth": "Female"
 }
diff --git a/data-serving/reusable-data-service/tests/test_case_schema_integration.py b/data-serving/reusable-data-service/tests/test_case_schema_integration.py
@@ -1,10 +1,13 @@
 import csv
 import io
+import json
 
 from tests.end_to_end_fixture import client_with_patched_mongo
 
 
 def test_adding_field_then_downloading_case(client_with_patched_mongo):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/schema",
         json={
@@ -14,17 +17,12 @@ def test_adding_field_then_downloading_case(client_with_patched_mongo):
         },
     )
     assert response.status_code == 201
+
+    case_doc["mySymptoms"] = "coughs, sneezles"
+
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-            "mySymptoms": "coughs, sneezles",
-        },
+        json=case_doc,
     )
     assert response.status_code == 201
     response = client_with_patched_mongo.get("/api/cases")
@@ -36,6 +34,8 @@ def test_adding_field_then_downloading_case(client_with_patched_mongo):
 
 
 def test_adding_field_then_downloading_csv(client_with_patched_mongo):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/schema",
         json={
@@ -45,17 +45,11 @@ def test_adding_field_then_downloading_csv(client_with_patched_mongo):
         },
     )
     assert response.status_code == 201
+
+    case_doc["someField"] = "well, what have we here"
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-            "someField": "well, what have we here",
-        },
+        json=case_doc,
     )
     assert response.status_code == 201
     response = client_with_patched_mongo.post(
@@ -73,16 +67,11 @@ def test_adding_field_then_downloading_csv(client_with_patched_mongo):
 def test_required_field_default_value_spread_to_existing_cases(
     client_with_patched_mongo,
 ):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-        },
+        json=case_doc,
     )
     assert response.status_code == 201
     response = client_with_patched_mongo.post(
@@ -105,6 +94,8 @@ def test_required_field_default_value_spread_to_existing_cases(
 
 
 def test_required_field_becomes_required_in_validation(client_with_patched_mongo):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/schema",
         json={
@@ -118,21 +109,16 @@ def test_required_field_becomes_required_in_validation(client_with_patched_mongo
     assert response.status_code == 201
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-        },
+        json=case_doc,
     )
     assert response.status_code == 422
 
 
 def test_field_enumerating_allowed_values_forbids_other_value(
     client_with_patched_mongo,
 ):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/schema",
         json={
@@ -144,22 +130,19 @@ def test_field_enumerating_allowed_values_forbids_other_value(
         },
     )
     assert response.status_code == 201
+
+    case_doc["customPathogenStatus"] = "Something Else"
+
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-            "customPathogenStatus": "Something Else",
-        },
+        json=case_doc,
     )
     assert response.status_code == 422
 
 
 def test_adding_enumerated_field_with_other_value(client_with_patched_mongo):
+    with open("./tests/data/case.minimal.json") as json_file:
+        case_doc = json.load(json_file)
     response = client_with_patched_mongo.post(
         "/api/schema",
         json={
@@ -171,18 +154,12 @@ def test_adding_enumerated_field_with_other_value(client_with_patched_mongo):
         },
     )
     assert response.status_code == 201
+
+    case_doc["customPathogenStatus"] = "other"
+    case_doc["customPathogenStatus_other"] = "Neopanspermia"
     response = client_with_patched_mongo.post(
         "/api/cases",
-        json={
-            "confirmationDate": "2022-06-01T00:00:00.000Z",
-            "caseReference": {
-                "status": "UNVERIFIED",
-                "sourceId": "24680135792468013579fedc",
-            },
-            "caseStatus": "probable",
-            "customPathogenStatus": "other",
-            "customPathogenStatus_other": "Neopanspermia",
-        },
+        json=case_doc,
     )
     assert response.status_code == 201
     response = client_with_patched_mongo.post(