dose sequence addressed comments and added unit tests

Author: robertnovac1

delta_backend/src/ConversionLayout.py

@@ -1,8 +1,5 @@
-
 # This file holds the schema/base layout that maps FHIR fields to flat JSON fields
 # Each entry tells the converter how to extract and transform a specific value
-from utils import is_integer_like
-
 EXTENSION_URL_VACCINATION_PRODEDURE = "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-VaccinationProcedure"
 EXTENSION_URL_SCT_DESC_DISPLAY = "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-CodingSCTDescDisplay"
 
@@ -99,13 +96,13 @@ def _extract_route_of_vaccination_term(immunization) -> str:
 # - requirements: If element doseNumberPositiveInt exists and is < 10 then populate as received, else null 
 # - path : protocolApplied.doseNumber[x]
 def _extract_dose_sequence(immunization) -> str: 
-    protocol_applied = immunization.get("protocolApplied")
-    dose_number_positive_int = protocol_applied.get("doseNumberPositiveInt", "")
-    
-    return dose_number_positive_int if is_integer_like(dose_number_positive_int) else ""
-    
+    protocol_applied = immunization.get("protocolApplied", [])
 
-
+    if protocol_applied:   
+        dose = protocol_applied[0].get("doseNumberPositiveInt", None)
+        return str(dose) if dose else ""
+    return ""
+        
 ConvertLayout = {
   "id": "7d78e9a6-d859-45d3-bb05-df9c405acbdb",
   "schemaName": "JSON Base",
@@ -279,7 +276,7 @@ def _extract_dose_sequence(immunization) -> str:
       "fieldNameFlat": "DOSE_SEQUENCE",
       "expression": {
         "expressionName": "Not Empty",
-        "expressionType": "DOSESEQUENCE",
+        "expressionType": "NORMAL",
         "expressionRule": _extract_dose_sequence
       }
     },

delta_backend/src/utils.py

@@ -1,6 +1,5 @@
 
 from stdnum.verhoeff import validate
-from decimal import Decimal
 
 def is_valid_simple_snomed(simple_snomed: str) -> bool:
     """
@@ -19,12 +18,3 @@ def is_valid_simple_snomed(simple_snomed: str) -> bool:
         )
     except:
         return False
-
-def is_integer_like(val):
-    if isinstance(val, Decimal):
-        return val == int(val)
-    try:
-        int(val)
-        return True
-    except (ValueError, TypeError):
-        return False

delta_backend/tests/test_convert_dose_sequence.py

@@ -0,0 +1,37 @@
+import copy
+import json
+import unittest
+from tests.utils_for_converter_tests import ValuesForTests
+from Converter import Converter
+
+
+class TestDoseSequenceToFlatJson(unittest.TestCase):
+    
+    def setUp(self):
+        self.request_json_data = copy.deepcopy(ValuesForTests.json_data)
+    
+    def _run_test(self, expected_result):
+        """Helper function to run the test"""
+        self.converter = Converter(json.dumps(self.request_json_data))
+        flat_json = self.converter.runConversion(self.request_json_data, False, True)
+        self.assertEqual(flat_json["DOSE_SEQUENCE"], expected_result)
+        
+    def test_dose_sequence_present_int(self):
+        self.request_json_data["protocolApplied"] = [
+            {
+                "doseNumberPositiveInt": 2
+            }
+        ]
+        self._run_test(expected_result="2")
+
+    def test_dose_sequence_missing(self):
+        self.request_json_data["protocolApplied"] = [{}]
+        self._run_test(expected_result="")
+
+    def test_dose_sequence_protocol_applied_empty(self):
+        self.request_json_data["protocolApplied"] = []
+        self._run_test(expected_result="")
+
+    def test_dose_sequence_protocol_applied_absent(self):
+        self.request_json_data.pop("protocolApplied", None)
+        self._run_test(expected_result="")

delta_backend/tests/utils_for_converter_tests.py

@@ -196,7 +196,7 @@ def get_expected_imms(expected_action_flag):
                 "PRIMARY_SOURCE": True,
                 "VACCINATION_PROCEDURE_CODE": "13246814444444",
                 "VACCINATION_PROCEDURE_TERM": "Test Value string 123456 COVID19 vaccination",
-                "DOSE_SEQUENCE": Decimal('1'),
+                "DOSE_SEQUENCE": "1",
                 "VACCINE_PRODUCT_CODE": "39114911000001105",
                 "VACCINE_PRODUCT_TERM": "COVID-19 Vaccine Vaxzevria (ChAdOx1 S [recombinant]) not less than 2.5x100,000,000 infectious units/0.5ml dose suspension for injection multidose vials (AstraZeneca UK Ltd) (product)",
                 "VACCINE_MANUFACTURER": "AstraZeneca Ltd",
@@ -272,7 +272,7 @@ def get_expected_imms(expected_action_flag):
             "PRIMARY_SOURCE": True,
             "VACCINATION_PROCEDURE_CODE": "13246814444444",
             "VACCINATION_PROCEDURE_TERM": "Test Value string 123456 COVID19 vaccination",
-            "DOSE_SEQUENCE": 1,
+            "DOSE_SEQUENCE": "1",
             "VACCINE_PRODUCT_CODE": "39114911000001105",
             "VACCINE_PRODUCT_TERM": "COVID-19 Vaccine Vaxzevria (ChAdOx1 S [recombinant]) not less than 2.5x100,000,000 infectious units/0.5ml dose suspension for injection multidose vials (AstraZeneca UK Ltd) (product)",
             "VACCINE_MANUFACTURER": "AstraZeneca Ltd",