Add pathogenStatus to the day zero schema #2714

globaldothealth · Jul 27, 2022 · d0bb66a · d0bb66a
1 parent aa4a32a
commit d0bb66a
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Showing 5 changed files with 22 additions and 6 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
@@ -18,6 +18,17 @@
             "omit_error"
         ]
     },
+    {
+        "key": "pathogenStatus",
+        "type": "string",
+        "data_dictionary_text": "Whether the infection occured in an endemic, or non-endemic region.",
+        "required": "true",
+        "values": [
+            "endemic",
+            "emerging",
+            "unknown"
+        ]
+    },
     {
         "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
@@ -7,5 +7,6 @@
         "date": "2022-06-01T01:23:45.678Z",
         "note": "Excluded upon this day, for reasons"
     },
-    "caseStatus": "omit_error"
+    "caseStatus": "omit_error",
+    "pathogenStatus": "endemic"
 }
diff --git a/data-serving/reusable-data-service/tests/data/case.minimal.json b/data-serving/reusable-data-service/tests/data/case.minimal.json
@@ -3,5 +3,6 @@
     "caseReference": {
         "sourceId": "fedc09876543210987654321"
     },
-    "caseStatus": "probable"
+    "caseStatus": "probable",
+    "pathogenStatus": "emerging"
 }
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
@@ -16,5 +16,6 @@
             "country": "IND"
         }
     },
-    "caseStatus": "probable"
+    "caseStatus": "probable",
+    "pathogenStatus": "unknown"
 }
diff --git a/data-serving/reusable-data-service/tests/test_case_model.py b/data-serving/reusable-data-service/tests/test_case_model.py
@@ -31,7 +31,7 @@ def test_csv_header():
     header_line = Case.csv_header()
     assert (
         header_line
-        == "_id,caseStatus,confirmationDate,caseReference.sourceId,location.country,location.latitude,location.longitude,location.admin1,location.admin2,location.admin3\r\n"
+        == "_id,caseStatus,pathogenStatus,confirmationDate,caseReference.sourceId,location.country,location.latitude,location.longitude,location.admin1,location.admin2,location.admin3\r\n"
     )
 
 
@@ -44,8 +44,9 @@ def test_csv_row_with_no_id():
     case.confirmationDate = date(2022, 6, 13)
     case.caseReference = ref
     case.caseStatus = "probable"
+    case.pathogenStatus = "emerging"
     csv = case.to_csv()
-    assert csv == ",probable,2022-06-13,abcd12903478565647382910,,,,,,\r\n"
+    assert csv == ",probable,emerging,2022-06-13,abcd12903478565647382910,,,,,,\r\n"
 
 
 def test_csv_row_with_id():
@@ -59,8 +60,9 @@ def test_csv_row_with_id():
     case.confirmationDate = date(2022, 6, 13)
     case.caseReference = ref
     case.caseStatus = "probable"
+    case.pathogenStatus = "unknown"
     csv = case.to_csv()
-    assert csv == f"{id1},probable,2022-06-13,{id2},,,,,,\r\n"
+    assert csv == f"{id1},probable,unknown,2022-06-13,{id2},,,,,,\r\n"
 
 
 def test_apply_update_to_case():