2714 integrate schema case controllers

data-serving/reusable-data-service/data_service/controller/case_controller.py

@@ -4,7 +4,7 @@
 from datetime import date
 from typing import List, Optional
 
-from data_service.model.case import Case
+from data_service.model.case import observe_case_class
 from data_service.model.case_exclusion_metadata import CaseExclusionMetadata
 from data_service.model.case_page import CasePage
 from data_service.model.case_reference import CaseReference
@@ -24,6 +24,13 @@
     ValidationError,
 )
 
+Case = None
+
+
+def case_observer(cls):
+    global Case
+    Case = cls
+
 
 class CaseController:
     """Implements CRUD operations on cases. Uses an external store
@@ -36,6 +43,7 @@ def __init__(self, store, outbreak_date: date):
         outbreak_date is the earliest date on which this instance should accept cases."""
         self.store = store
         self.outbreak_date = outbreak_date
+        observe_case_class(case_observer)
 
     def get_case(self, id: str):
         """Implements get /cases/:id. Interpretation of ID is dependent

data-serving/reusable-data-service/data_service/model/document.py

@@ -1,6 +1,8 @@
 import copy
+import csv
 import dataclasses
 import datetime
+import io
 import operator
 
 from data_service.model.document_update import DocumentUpdate
@@ -108,7 +110,10 @@ def include_dataclass_fields(aType: type):
 
     def delimiter_separated_values(self, sep: str) -> str:
         """Create a line listing all of the fields in me and my member dataclasses."""
-        return sep.join(self.field_values()) + "\n"
+        f = io.StringIO()
+        csv_writer = csv.writer(f, delimiter=sep)
+        csv_writer.writerow(self.field_values())
+        return f.getvalue()
 
     def to_tsv(self) -> str:
         """Generate a row in a CSV file representing myself."""

data-serving/reusable-data-service/data_service/stores/mongo_store.py

@@ -1,7 +1,7 @@
 import datetime
 import os
 import pymongo
-from data_service.model.case import Case
+from data_service.model.case import observe_case_class
 from data_service.model.case_exclusion_metadata import CaseExclusionMetadata
 from data_service.model.document_update import DocumentUpdate
 from data_service.model.field import Field
@@ -19,6 +19,14 @@
 from typing import List, Tuple
 
 
+Case = None
+
+
+def case_observer(cls):
+    global Case
+    Case = cls
+
+
 class MongoStore:
     """A line list store backed by mongodb."""
 
@@ -33,6 +41,7 @@ def __init__(
         self.database_name = database_name
         self.case_collection_name = case_collection_name
         self.schema_collection_name = schema_collection_name
+        observe_case_class(case_observer)
 
     def get_client(self):
         return self.client

data-serving/reusable-data-service/tests/test_case_model.py

@@ -35,7 +35,7 @@ def test_csv_row_with_no_id():
     case.confirmationDate = date(2022, 6, 13)
     case.caseReference = ref
     csv = case.to_csv()
-    assert csv == ",2022-06-13,abcd12903478565647382910,UNVERIFIED\n"
+    assert csv == ",2022-06-13,abcd12903478565647382910,UNVERIFIED\r\n"
 
 
 def test_csv_row_with_id():
@@ -49,7 +49,7 @@ def test_csv_row_with_id():
     case.confirmationDate = date(2022, 6, 13)
     case.caseReference = ref
     csv = case.to_csv()
-    assert csv == f"{id1},2022-06-13,{id2},UNVERIFIED\n"
+    assert csv == f"{id1},2022-06-13,{id2},UNVERIFIED\r\n"
 
 
 def test_apply_update_to_case():

data-serving/reusable-data-service/tests/test_case_reference.py

@@ -10,7 +10,7 @@ def test_csv_row_unexcluded():
     ref = CaseReference()
     ref.sourceId = oid
     csv = ref.to_csv()
-    assert csv == "abcd12903478565647382910,UNVERIFIED\n"
+    assert csv == "abcd12903478565647382910,UNVERIFIED\r\n"
 
 
 def test_csv_row_excluded():
@@ -20,7 +20,7 @@ def test_csv_row_excluded():
     ref.sourceId = oid
     ref.status = "EXCLUDED"
     csv = ref.to_csv()
-    assert csv == "abcd12903478565647382910,EXCLUDED\n"
+    assert csv == "abcd12903478565647382910,EXCLUDED\r\n"
 
 
 def test_reference_must_have_valid_status():

data-serving/reusable-data-service/tests/test_case_schema_integration.py

@@ -0,0 +1,68 @@
+import csv
+import io
+
+from tests.end_to_end_fixture import client_with_patched_mongo
+
+
+def test_adding_field_then_downloading_case(client_with_patched_mongo):
+    response = client_with_patched_mongo.post(
+        "/api/schema",
+        json={
+            "name": "mySymptoms",
+            "type": "string",
+            "description": "A custom, comma-separated list of symptoms",
+        },
+    )
+    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",
+            },
+            "mySymptoms": "coughs, sneezles",
+        },
+    )
+    assert response.status_code == 201
+    response = client_with_patched_mongo.get("/api/cases")
+    assert response.status_code == 200
+    case_list = response.get_json()
+    assert case_list["total"] == 1
+    assert len(case_list["cases"]) == 1
+    assert case_list["cases"][0]["mySymptoms"] == "coughs, sneezles"
+
+
+def test_adding_field_then_downloading_csv(client_with_patched_mongo):
+    response = client_with_patched_mongo.post(
+        "/api/schema",
+        json={
+            "name": "someField",
+            "type": "string",
+            "description": "Another custom field",
+        },
+    )
+    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",
+            },
+            "someField": "well, what have we here",
+        },
+    )
+    assert response.status_code == 201
+    response = client_with_patched_mongo.post(
+        "/api/cases/download", json={"format": "csv"}
+    )
+    assert response.status_code == 200
+    csv_file = io.StringIO(response.get_data().decode("utf-8"))
+    csv_reader = csv.DictReader(csv_file)
+    cases = [c for c in csv_reader]
+    assert len(cases) == 1
+    case = cases[0]
+    assert case["someField"] == "well, what have we here"