compressedfhir 1.0.3__tar.gz → 1.0.5__tar.gz

{compressedfhir-1.0.3 → compressedfhir-1.0.5}/Makefile

@@ -73,3 +73,21 @@ help: ## Show this help.
 pipenv-setup:devdocker ## Run pipenv-setup to update setup.py with latest dependencies
 	docker compose run --rm dev sh -c "pipenv run pipenv install --skip-lock --categories \"pipenvsetup\" && pipenv run pipenv-setup sync --pipfile" && \
 	make run-pre-commit
+
+.PHONY: coverage
+coverage: up ## Run code coverage and generate reports
+	mkdir -p reports
+	docker compose run --rm \
+        -v $(PWD)/reports:/reports \
+        --name compressedfhir_coverage \
+        dev pytest \
+        --cov=. \
+        --cov-report=term-missing \
+        --cov-report=xml:/reports/coverage.xml \
+        --cov-report=html:/reports/htmlcov \
+        --cov-fail-under=80 \
+        tests compressedfhir
+
+.PHONY: clean-coverage
+clean-coverage: ## Remove coverage reports
+	rm -rf reports/coverage.xml reports/htmlcov .coverage

{compressedfhir-1.0.3/compressedfhir.egg-info → compressedfhir-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: compressedfhir
-Version: 1.0.3
+Version: 1.0.5
 Summary: Stores FHIR JSON resources in compressed form in memory
 Home-page: https://github.com/icanbwell/compressed-fhir
 Author: Imran Qureshi

compressedfhir-1.0.5/VERSION

@@ -0,0 +1 @@
+1.0.5

{compressedfhir-1.0.3 → compressedfhir-1.0.5}/compressedfhir/fhir/fhir_resource.py

@@ -61,14 +61,10 @@ class FhirResource(CompressedDict[str, Any]):
             else None
         )
 
-    def json(self) -> str:
-        """Convert the resource to a JSON string."""
-        return json.dumps(obj=self.dict(), cls=FhirJSONEncoder)
-
     def __deepcopy__(self, memo: Dict[int, Any]) -> "FhirResource":
         """Create a copy of the resource."""
         return FhirResource(
-            initial_dict=super().dict(),
+            initial_dict=super().raw_dict(),
             storage_mode=self._storage_mode,
         )
 
@@ -84,29 +80,6 @@ class FhirResource(CompressedDict[str, Any]):
         """
         return copy.deepcopy(self)
 
-    @override
-    def dict(self, *, remove_nulls: bool = True) -> OrderedDict[str, Any]:
-        """
-        Converts the FhirResource object to a dictionary.
-
-        :param remove_nulls: If True, removes None values from the dictionary.
-        :return: A dictionary representation of the FhirResource object.
-        """
-        ordered_dict = super().dict()
-        result: OrderedDict[str, Any] = copy.deepcopy(ordered_dict)
-        if remove_nulls:
-            result = FhirClientJsonHelpers.remove_empty_elements_from_ordered_dict(
-                result
-            )
-
-        return result
-
-    def remove_nulls(self) -> None:
-        """
-        Removes None values from the resource dictionary.
-        """
-        self.replace(value=self.dict(remove_nulls=True))
-
     @property
     def id(self) -> Optional[str]:
         """Get the ID from the resource dictionary."""
@@ -171,3 +144,15 @@ class FhirResource(CompressedDict[str, Any]):
                 properties_to_cache=properties_to_cache,
             ),
         )
+
+    @override
+    def json(self) -> str:
+        """Convert the resource to a JSON string."""
+
+        # working_dict preserves the python types so create a fhir friendly version
+        raw_dict: OrderedDict[str, Any] = self.raw_dict()
+
+        raw_dict = FhirClientJsonHelpers.remove_empty_elements_from_ordered_dict(
+            raw_dict
+        )
+        return json.dumps(obj=raw_dict, cls=FhirJSONEncoder)

{compressedfhir-1.0.3 → compressedfhir-1.0.5}/compressedfhir/fhir/fhir_resource_map.py

@@ -43,7 +43,7 @@ class FhirResourceMap:
         """
         result: OrderedDict[str, Any] = OrderedDict[str, Any]()
         for key, value in self._resource_map.items():
-            result[key] = [resource.dict(remove_nulls=True) for resource in value]
+            result[key] = [resource.dict() for resource in value]
         return result
 
     def get(self, *, resource_type: str) -> Optional[FhirResourceList]:

compressedfhir-1.0.5/compressedfhir/fhir/test/test_fhir_resource.py

@@ -0,0 +1,104 @@
+import json
+from typing import Dict, Any
+
+from compressedfhir.fhir.fhir_resource import FhirResource
+from compressedfhir.utilities.compressed_dict.v1.compressed_dict_storage_mode import (
+    CompressedDictStorageMode,
+)
+
+
+class TestFhirResource:
+    def test_init_empty(self) -> None:
+        """Test initializing FhirResource with no initial dictionary."""
+        resource = FhirResource(storage_mode=CompressedDictStorageMode())
+        assert len(resource) == 0
+        assert resource.resource_type is None
+        assert resource.id is None
+        assert resource.resource_type_and_id is None
+
+    def test_init_with_data(self) -> None:
+        """Test initializing FhirResource with a dictionary."""
+        initial_data: Dict[str, Any] = {
+            "resourceType": "Patient",
+            "id": "123",
+            "name": [{"given": ["John"]}],
+        }
+        resource = FhirResource(
+            initial_dict=initial_data, storage_mode=CompressedDictStorageMode()
+        )
+
+        with resource.transaction():
+            assert resource.resource_type == "Patient"
+            assert resource.id == "123"
+            assert resource.resource_type_and_id == "Patient/123"
+            assert resource["name"][0]["given"][0] == "John"
+
+    def test_resource_type_and_id_property(self) -> None:
+        """Test resource_type_and_id property with various scenarios."""
+        # Scenario 1: Both resource type and id present
+        resource1 = FhirResource(
+            initial_dict={"resourceType": "Observation", "id": "456"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        assert resource1.resource_type_and_id == "Observation/456"
+
+        # Scenario 2: Missing resource type
+        resource2 = FhirResource(
+            initial_dict={"id": "789"}, storage_mode=CompressedDictStorageMode()
+        )
+        assert resource2.resource_type_and_id is None
+
+        # Scenario 3: Missing id
+        resource3 = FhirResource(
+            initial_dict={"resourceType": "Patient"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        assert resource3.resource_type_and_id is None
+
+    def test_equality(self) -> None:
+        """Test equality comparison between FhirResource instances."""
+        # Scenario 1: Equal resources
+        resource1 = FhirResource(
+            initial_dict={"resourceType": "Patient", "id": "123"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        resource2 = FhirResource(
+            initial_dict={"resourceType": "Patient", "id": "123"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        assert resource1 == resource2
+
+        # Scenario 2: Different resource types
+        resource3 = FhirResource(
+            initial_dict={"resourceType": "Observation", "id": "123"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        assert resource1 != resource3
+
+        # Scenario 3: Different ids
+        resource4 = FhirResource(
+            initial_dict={"resourceType": "Patient", "id": "456"},
+            storage_mode=CompressedDictStorageMode(),
+        )
+        assert resource1 != resource4
+
+        # Scenario 4: Comparing with non-FhirResource
+        assert resource1 != "Not a FhirResource"
+
+    def test_to_json(self) -> None:
+        """Test JSON serialization of FhirResource."""
+        initial_data: Dict[str, Any] = {
+            "resourceType": "Patient",
+            "id": "123",
+            "name": [{"given": ["John"]}],
+        }
+        resource = FhirResource(
+            initial_dict=initial_data, storage_mode=CompressedDictStorageMode()
+        )
+
+        json_str = resource.json()
+        parsed_json = json.loads(json_str)
+
+        assert parsed_json == initial_data
+        assert "resourceType" in parsed_json
+        assert "id" in parsed_json

{compressedfhir-1.0.3 → compressedfhir-1.0.5}/compressedfhir/utilities/compressed_dict/v1/compressed_dict.py

@@ -1,4 +1,5 @@
 import copy
+import json
 from collections.abc import KeysView, ValuesView, ItemsView, MutableMapping
 from contextlib import contextmanager
 from typing import Dict, Optional, Iterator, cast, List, Any, overload, OrderedDict
@@ -13,6 +14,7 @@ from compressedfhir.utilities.compressed_dict.v1.compressed_dict_storage_mode im
     CompressedDictStorageMode,
     CompressedDictStorageType,
 )
+from compressedfhir.utilities.fhir_json_encoder import FhirJSONEncoder
 from compressedfhir.utilities.json_serializers.type_preservation_serializer import (
     TypePreservationSerializer,
 )
@@ -176,9 +178,7 @@ class CompressedDict[K, V](MutableMapping[K, V]):
         assert isinstance(dictionary, OrderedDict)
         if storage_type == "compressed":
             # Serialize to JSON and compress with zlib
-            json_str = TypePreservationSerializer.serialize(
-                dictionary, separators=(",", ":")
-            )
+            json_str = TypePreservationSerializer.serialize(dictionary)
             return zlib.compress(
                 json_str.encode("utf-8"), level=zlib.Z_BEST_COMPRESSION
             )
@@ -219,9 +219,7 @@ class CompressedDict[K, V](MutableMapping[K, V]):
             decompressed_bytes: bytes = zlib.decompress(serialized_dict_bytes)
             decoded_text: str = decompressed_bytes.decode("utf-8")
             # noinspection PyTypeChecker
-            decompressed_dict = TypePreservationSerializer.deserialize(
-                decoded_text, object_pairs_hook=OrderedDict
-            )
+            decompressed_dict = TypePreservationSerializer.deserialize(decoded_text)
             assert isinstance(decompressed_dict, OrderedDict)
             return cast(OrderedDict[K, V], decompressed_dict)
 
@@ -427,19 +425,43 @@ class CompressedDict[K, V](MutableMapping[K, V]):
         """
         return self._get_dict().items()
 
-    def dict(self, *, remove_nulls: bool = True) -> OrderedDict[K, V]:
+    def raw_dict(self) -> OrderedDict[K, V]:
         """
-        Convert to a standard dictionary
+        Returns the raw dictionary.  Deserializes if necessary.
+        Note that this dictionary preserves the python types so it is not FHIR friendly.
+        Use dict() if you want a FHIR friendly version.
 
         Returns:
-            Standard dictionary with all values
+            raw dictionary
         """
         if self._working_dict:
             return self._working_dict
         else:
-            # if the working dict is None, return it but don't store it in the self._working_dict to keep memory low
+            # if the working dict is not None, return it but don't store it in the self._working_dict to keep memory low
             return self.create_working_dict()
 
+    def dict(self) -> OrderedDict[K, V]:
+        """
+        Convert to a FHIR friendly dictionary where the python types like datetime are converted to string versions
+
+        Returns:
+            FHIR friendly dictionary
+        """
+        return cast(
+            OrderedDict[K, V],
+            json.loads(
+                self.json(),
+                object_pairs_hook=lambda pairs: OrderedDict(pairs),
+            ),
+        )
+
+    def json(self) -> str:
+        """Convert the resource to a JSON string."""
+
+        raw_dict: OrderedDict[K, V] = self.raw_dict()
+
+        return json.dumps(obj=raw_dict, cls=FhirJSONEncoder)
+
     def __repr__(self) -> str:
         """
         String representation of the dictionary
@@ -563,7 +585,7 @@ class CompressedDict[K, V](MutableMapping[K, V]):
         """
         # Create a new instance with the same storage mode
         new_instance = CompressedDict(
-            initial_dict=copy.deepcopy(self.dict()),
+            initial_dict=copy.deepcopy(self.raw_dict()),
             storage_mode=self._storage_mode,
             properties_to_cache=self._properties_to_cache,
         )
@@ -637,7 +659,7 @@ class CompressedDict[K, V](MutableMapping[K, V]):
         Returns:
             Plain dictionary
         """
-        return OrderedDictToDictConverter.convert(self.dict())
+        return OrderedDictToDictConverter.convert(self.raw_dict())
 
     @classmethod
     def from_json(cls, json_str: str) -> "CompressedDict[K, V]":

{compressedfhir-1.0.3 → compressedfhir-1.0.5}/compressedfhir/utilities/compressed_dict/v1/test/test_compressed_dict.py

@@ -1,3 +1,5 @@
+from datetime import datetime
+
 import pytest
 from typing import Any, cast
 
@@ -232,7 +234,7 @@ def test_transaction_basic_raw_storage() -> None:
 
     # After transaction
     assert compressed_dict._transaction_depth == 0
-    assert compressed_dict.dict() == {
+    assert compressed_dict.raw_dict() == {
         "key1": "value1",
         "key2": "value2",
         "key3": "value3",
@@ -260,7 +262,7 @@ def test_transaction_nested_context() -> None:
         assert compressed_dict._transaction_depth == 1
 
     assert compressed_dict._transaction_depth == 0
-    assert compressed_dict.dict() == {"key1": "value1", "key2": "value2"}
+    assert compressed_dict.raw_dict() == {"key1": "value1", "key2": "value2"}
 
 
 def test_transaction_access_error() -> None:
@@ -309,7 +311,7 @@ def test_transaction_different_storage_modes() -> None:
         with compressed_dict.transaction() as d:
             d["key2"] = "value2"
 
-        assert compressed_dict.dict() == {"key1": "value1", "key2": "value2"}
+        assert compressed_dict.raw_dict() == {"key1": "value1", "key2": "value2"}
 
 
 def test_transaction_with_properties_to_cache() -> None:
@@ -328,7 +330,7 @@ def test_transaction_with_properties_to_cache() -> None:
     with compressed_dict.transaction() as d:
         d["key2"] = "value2"
 
-    assert compressed_dict.dict() == {
+    assert compressed_dict.raw_dict() == {
         "key1": "value1",
         "important_prop": "cached_value",
         "key2": "value2",
@@ -358,3 +360,108 @@ def test_transaction_error_handling() -> None:
         # Verify the dictionary state remains unchanged
         with compressed_dict.transaction() as d:
             assert d.dict() == {"key1": "value1", "key2": "value2"}
+
+
+def test_nested_dict_with_datetime() -> None:
+    nested_dict = {
+        "beneficiary": {"reference": "Patient/1234567890123456703", "type": "Patient"},
+        "class": [
+            {
+                "name": "Aetna Plan",
+                "type": {
+                    "coding": [
+                        {
+                            "code": "plan",
+                            "display": "Plan",
+                            "system": "http://terminology.hl7.org/CodeSystem/coverage-class",
+                        }
+                    ]
+                },
+                "value": "AE303",
+            }
+        ],
+        "costToBeneficiary": [
+            {
+                "type": {"text": "Annual Physical Exams NMC - In Network"},
+                "valueQuantity": {
+                    "system": "http://aetna.com/Medicare/CostToBeneficiary/ValueQuantity/code",
+                    "unit": "$",
+                    "value": 50.0,
+                },
+            }
+        ],
+        "id": "3456789012345670304",
+        "identifier": [
+            {
+                "system": "https://sources.aetna.com/coverage/identifier/membershipid/59",
+                "type": {
+                    "coding": [
+                        {
+                            "code": "SN",
+                            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                        }
+                    ]
+                },
+                "value": "435679010300+AE303+2021-01-01",
+            },
+            {
+                "id": "uuid",
+                "system": "https://www.icanbwell.com/uuid",
+                "value": "92266603-aa8b-58c6-99bd-326fd1da1896",
+            },
+        ],
+        "meta": {
+            "security": [
+                {"code": "aetna", "system": "https://www.icanbwell.com/owner"},
+                {"code": "aetna", "system": "https://www.icanbwell.com/access"},
+                {"code": "aetna", "system": "https://www.icanbwell.com/vendor"},
+                {"code": "proa", "system": "https://www.icanbwell.com/connectionType"},
+            ],
+            "source": "http://mock-server:1080/test_patient_access_transformer/source/4_0_0/Coverage/3456789012345670304",
+        },
+        "network": "Medicare - MA/NY/NJ - Full Reciprocity",
+        "payor": [
+            {
+                "display": "Aetna",
+                "reference": "Organization/6667778889990000015",
+                "type": "Organization",
+            }
+        ],
+        "period": {
+            "end": datetime.fromisoformat("2021-12-31").date(),
+            "start": datetime.fromisoformat("2021-01-01").date(),
+        },
+        "policyHolder": {"reference": "Patient/1234567890123456703", "type": "Patient"},
+        "relationship": {
+            "coding": [
+                {
+                    "code": "self",
+                    "system": "http://terminology.hl7.org/CodeSystem/subscriber-relationship",
+                }
+            ]
+        },
+        "resourceType": "Coverage",
+        "status": "active",
+        "subscriber": {"reference": "Patient/1234567890123456703", "type": "Patient"},
+        "subscriberId": "435679010300",
+        "type": {
+            "coding": [
+                {
+                    "code": "PPO",
+                    "display": "preferred provider organization policy",
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+                }
+            ]
+        },
+    }
+
+    compressed_dict = CompressedDict(
+        initial_dict=nested_dict,
+        storage_mode=CompressedDictStorageMode.compressed(),
+        properties_to_cache=[],
+    )
+
+    plain_dict = compressed_dict.to_plain_dict()
+
+    assert plain_dict["period"]["start"] == nested_dict["period"]["start"]  # type: ignore[index]
+    assert plain_dict == nested_dict

compressedfhir-1.0.5/compressedfhir/utilities/json_serializers/test/test_type_preservation_decoder.py

@@ -0,0 +1,150 @@
+from datetime import datetime, date
+from decimal import Decimal
+from typing import Type, Any, Dict, Optional
+import pytest
+
+from compressedfhir.utilities.json_serializers.type_preservation_decoder import (
+    TypePreservationDecoder,
+)
+
+
+class TestCustomObject:
+    def __init__(
+        self,
+        name: str,
+        value: int,
+        created_at: Optional[datetime] = None,
+        nested_data: Optional[Dict[str, Any]] = None,
+    ):
+        self.name: str = name
+        self.value: int = value
+        self.created_at: Optional[datetime] = created_at
+        self.nested_data: Optional[Dict[str, Any]] = nested_data
+
+    def __eq__(self, other: Any) -> bool:
+        if not isinstance(other, TestCustomObject):
+            return False
+        return (
+            self.name == other.name
+            and self.value == other.value
+            and self.created_at == other.created_at
+            and self.nested_data == other.nested_data
+        )
+
+
+@pytest.mark.parametrize(
+    "input_type, input_dict, expected_type",
+    [
+        (
+            "datetime",
+            {"__type__": "datetime", "iso": "2023-01-01T00:00:00+00:00"},
+            datetime,
+        ),
+        ("date", {"__type__": "date", "iso": "2023-01-01"}, date),
+        ("decimal", {"__type__": "decimal", "value": "3.14"}, Decimal),
+        ("complex", {"__type__": "complex", "real": 3, "imag": 4}, complex),
+        ("bytes", {"__type__": "bytes", "value": "test"}, bytes),
+        ("set", {"__type__": "set", "values": [1, 2, 3]}, set),
+    ],
+)
+def test_complex_type_decoding(
+    input_type: str, input_dict: Dict[str, Any], expected_type: Type[Any]
+) -> None:
+    """
+    Test decoding of various complex types
+    """
+    decoded = TypePreservationDecoder.decode(input_dict)
+    assert isinstance(decoded, expected_type)
+
+
+def test_custom_object_decoding() -> None:
+    """
+    Test decoding of custom objects
+    """
+    custom_obj_dict = {
+        "__type__": "TestCustomObject",
+        "__module__": __name__,
+        "attributes": {"name": "test", "value": 42},
+    }
+    decoded = TypePreservationDecoder.decode(custom_obj_dict)
+    assert isinstance(decoded, TestCustomObject)
+    assert decoded.name == "test"
+    assert decoded.value == 42
+
+
+def test_custom_decoder() -> None:
+    """
+    Test custom decoder functionality
+    """
+
+    def custom_decoder(data: Dict[str, Any]) -> Any:
+        if data.get("__type__") == "special_type":
+            return f"Decoded: {data['value']}"
+        return data
+
+    special_dict = {"__type__": "special_type", "value": "test"}
+    decoded = TypePreservationDecoder.decode(
+        special_dict, custom_decoders={"special_type": custom_decoder}
+    )
+    assert decoded == "Decoded: test"
+
+
+def test_nested_datetime_decoding() -> None:
+    """
+    Test decoding of nested datetime fields
+    """
+    nested_datetime_dict = {
+        "__type__": "TestCustomObject",
+        "__module__": __name__,
+        "attributes": {
+            "name": "test",
+            "value": 42,
+            "created_at": {"__type__": "datetime", "iso": "2023-06-15T10:30:00"},
+            "nested_data": {
+                "timestamp": {"__type__": "datetime", "iso": "2023-06-16T15:45:00"}
+            },
+        },
+    }
+
+    decoded: TestCustomObject = TypePreservationDecoder.decode(nested_datetime_dict)
+
+    assert isinstance(decoded, TestCustomObject)
+    assert decoded.name == "test"
+    assert decoded.value == 42
+
+    # Check nested datetime fields
+    assert hasattr(decoded, "created_at")
+    assert isinstance(decoded.created_at, datetime)
+    assert decoded.created_at.year == 2023
+    assert decoded.created_at.month == 6
+    assert decoded.created_at.day == 15
+
+    assert hasattr(decoded, "nested_data")
+    assert isinstance(decoded.nested_data, dict)
+    assert "timestamp" in decoded.nested_data
+    assert isinstance(decoded.nested_data["timestamp"], datetime)
+    assert decoded.nested_data["timestamp"].year == 2023
+    assert decoded.nested_data["timestamp"].month == 6
+    assert decoded.nested_data["timestamp"].day == 16
+
+
+def test_direct_value_decoding() -> None:
+    """
+    Test decoding of direct values without type markers
+    """
+    # Test datetime direct string
+    datetime_str = "2023-01-01T00:00:00"
+    decoded_datetime = TypePreservationDecoder.decode(datetime_str)
+    assert decoded_datetime == datetime_str
+
+    # Test list with mixed types
+    mixed_list = [
+        {"__type__": "datetime", "iso": "2023-06-15T10:30:00"},
+        42,
+        "plain string",
+    ]
+    decoded_list = TypePreservationDecoder.decode(mixed_list)
+    assert len(decoded_list) == 3
+    assert isinstance(decoded_list[0], datetime)
+    assert decoded_list[1] == 42
+    assert decoded_list[2] == "plain string"