helix.fhir.client.sdk 4.2.10__tar.gz → 4.2.12__tar.gz

{helix_fhir_client_sdk-4.2.10/helix.fhir.client.sdk.egg-info → helix_fhir_client_sdk-4.2.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helix.fhir.client.sdk
-Version: 4.2.10
+Version: 4.2.12
 Summary: helix.fhir.client.sdk
 Home-page: https://github.com/icanbwell/helix.fhir.client.sdk
 Author: Imran Qureshi
@@ -19,7 +19,7 @@ Requires-Dist: chardet
 Requires-Dist: aiohttp
 Requires-Dist: async-timeout>=4.0.3
 Requires-Dist: python-dateutil
-Requires-Dist: compressedfhir>=1.0.13
+Requires-Dist: compressedfhir<3,>=1.0.13
 Requires-Dist: certifi>=2025.1.31
 Requires-Dist: opentelemetry-api>=1.39
 Requires-Dist: multidict>=6

helix_fhir_client_sdk-4.2.12/VERSION

@@ -0,0 +1 @@
+4.2.12

{helix_fhir_client_sdk-4.2.10 → helix_fhir_client_sdk-4.2.12/helix.fhir.client.sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helix.fhir.client.sdk
-Version: 4.2.10
+Version: 4.2.12
 Summary: helix.fhir.client.sdk
 Home-page: https://github.com/icanbwell/helix.fhir.client.sdk
 Author: Imran Qureshi
@@ -19,7 +19,7 @@ Requires-Dist: chardet
 Requires-Dist: aiohttp
 Requires-Dist: async-timeout>=4.0.3
 Requires-Dist: python-dateutil
-Requires-Dist: compressedfhir>=1.0.13
+Requires-Dist: compressedfhir<3,>=1.0.13
 Requires-Dist: certifi>=2025.1.31
 Requires-Dist: opentelemetry-api>=1.39
 Requires-Dist: multidict>=6

{helix_fhir_client_sdk-4.2.10 → helix_fhir_client_sdk-4.2.12}/helix.fhir.client.sdk.egg-info/SOURCES.txt

@@ -165,6 +165,7 @@ tests/async/test_async_fhir_client_patient_update.py
 tests/async/test_async_real_fhir_server_get_patients.py
 tests/async/test_async_real_fhir_server_get_patients_error.py
 tests/async/test_benchmark_compress.py
+tests/async/test_benchmark_merge.py
 tests/async/fhir_server/__init__.py
 tests/async/fhir_server/test_async_real_fhir_server_get_graph_large.py
 tests/async/fhir_server/test_async_real_fhir_server_get_patients_large.py

{helix_fhir_client_sdk-4.2.10 → helix_fhir_client_sdk-4.2.12}/helix.fhir.client.sdk.egg-info/requires.txt

@@ -5,7 +5,7 @@ chardet
 aiohttp
 async-timeout>=4.0.3
 python-dateutil
-compressedfhir>=1.0.13
+compressedfhir<3,>=1.0.13
 certifi>=2025.1.31
 opentelemetry-api>=1.39
 multidict>=6

{helix_fhir_client_sdk-4.2.10 → helix_fhir_client_sdk-4.2.12}/setup.py

@@ -40,7 +40,7 @@ setup(
         "aiohttp",
         "async-timeout>=4.0.3",
         "python-dateutil",
-        "compressedfhir>=1.0.13",
+        "compressedfhir>=1.0.13,<3",
         "certifi>=2025.1.31",
         "opentelemetry-api>=1.39",
         "multidict>=6",

helix_fhir_client_sdk-4.2.12/tests/async/test_benchmark_merge.py

@@ -0,0 +1,506 @@
+"""
+Benchmark tests for comparing compressed vs uncompressed FHIR client merge operations.
+
+These tests measure the performance of:
+- merge_async() with compress=True vs compress=False
+
+=============================================================================
+HOW TO RUN THESE TESTS
+=============================================================================
+
+1. Start services using docker-compose:
+   docker-compose up -d mock-server
+
+2. First time only - rebuild dev container to include pytest-benchmark:
+   docker-compose build dev
+
+   OR install pytest-benchmark in the running container:
+   docker-compose run --rm dev pip install pytest-benchmark
+
+3. Run benchmark tests inside docker container:
+   docker-compose run --rm dev pytest tests/async/test_benchmark_merge.py -v --benchmark-only
+
+4. Or run all benchmark variations:
+   docker-compose run --rm dev pytest tests/async/test_benchmark_merge.py -v --benchmark-only --benchmark-group-by=func
+
+5. Save benchmark results for comparison:
+   docker-compose run --rm dev pytest tests/async/test_benchmark_merge.py -v --benchmark-autosave
+
+6. Compare with previous runs:
+   docker-compose run --rm dev pytest tests/async/test_benchmark_merge.py -v --benchmark-compare
+
+7. Run with more iterations for accuracy:
+   docker-compose run --rm dev pytest tests/async/test_benchmark_merge.py -v --benchmark-min-rounds=10
+
+8. To stop mock-server:
+   docker-compose down mock-server
+
+=============================================================================
+"""
+
+import asyncio
+import json
+import socket
+from typing import Any
+
+import pytest
+from mockserver_client.mockserver_client import (
+    MockServerFriendlyClient,
+    mock_request,
+    mock_response,
+    times,
+)
+
+from helix_fhir_client_sdk.fhir_client import FhirClient
+from helix_fhir_client_sdk.responses.fhir_merge_response import FhirMergeResponse
+
+
+def is_mock_server_running(host: str = "mock-server", port: int = 1080) -> bool:
+    """Check if mock-server is reachable."""
+    try:
+        sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+        sock.settimeout(2)
+        result = sock.connect_ex((host, port))
+        sock.close()
+        return result == 0
+    except OSError:
+        return False
+
+
+# Skip all tests if the mock-server is not running
+pytestmark = pytest.mark.skipif(
+    not is_mock_server_running(), reason="Mock server not running. Start with: docker-compose up -d mock-server"
+)
+
+
+def generate_patient_resource(index: int) -> dict[str, Any]:
+    """Generate a realistic FHIR Patient resource."""
+    return {
+        "resourceType": "Patient",
+        "id": f"patient-{index}",
+        "meta": {
+            "versionId": "1",
+            "lastUpdated": "2025-01-15T10:30:00.000Z",
+            "source": "http://example.org/fhir",
+            "profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"],
+        },
+        "identifier": [
+            {
+                "use": "official",
+                "type": {
+                    "coding": [
+                        {
+                            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                            "code": "MR",
+                            "display": "Medical Record Number",
+                        }
+                    ]
+                },
+                "system": "http://hospital.example.org/mrn",
+                "value": f"MRN-{index:08d}",
+            },
+            {
+                "use": "official",
+                "type": {
+                    "coding": [
+                        {
+                            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                            "code": "SS",
+                            "display": "Social Security Number",
+                        }
+                    ]
+                },
+                "system": "http://hl7.org/fhir/sid/us-ssn",
+                "value": f"{100 + index:03d}-{50 + index:02d}-{1000 + index:04d}",
+            },
+        ],
+        "active": True,
+        "name": [
+            {
+                "use": "official",
+                "family": f"TestFamily{index}",
+                "given": [f"TestGiven{index}", f"MiddleName{index}"],
+                "prefix": ["Mr."],
+                "suffix": ["Jr."],
+            },
+            {
+                "use": "nickname",
+                "given": [f"Nick{index}"],
+            },
+        ],
+        "telecom": [
+            {"system": "phone", "value": f"555-{100 + index:03d}-{1000 + index:04d}", "use": "home"},
+            {"system": "phone", "value": f"555-{200 + index:03d}-{2000 + index:04d}", "use": "mobile"},
+            {"system": "email", "value": f"patient{index}@example.com", "use": "home"},
+        ],
+        "gender": "male" if index % 2 == 0 else "female",
+        "birthDate": f"{1950 + (index % 50)}-{(index % 12) + 1:02d}-{(index % 28) + 1:02d}",
+        "deceasedBoolean": False,
+        "address": [
+            {
+                "use": "home",
+                "type": "physical",
+                "line": [f"{100 + index} Main Street", f"Apt {index}"],
+                "city": "Boston",
+                "state": "MA",
+                "postalCode": f"02{100 + (index % 900):03d}",
+                "country": "USA",
+            },
+            {
+                "use": "work",
+                "type": "postal",
+                "line": [f"{200 + index} Business Ave"],
+                "city": "Cambridge",
+                "state": "MA",
+                "postalCode": f"02{200 + (index % 800):03d}",
+                "country": "USA",
+            },
+        ],
+        "maritalStatus": {
+            "coding": [
+                {
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+                    "code": "M" if index % 2 == 0 else "S",
+                    "display": "Married" if index % 2 == 0 else "Never Married",
+                }
+            ]
+        },
+        "communication": [
+            {
+                "language": {
+                    "coding": [
+                        {
+                            "system": "urn:ietf:bcp:47",
+                            "code": "en-US",
+                            "display": "English (United States)",
+                        }
+                    ]
+                },
+                "preferred": True,
+            }
+        ],
+        "generalPractitioner": [{"reference": f"Practitioner/practitioner-{index % 10}"}],
+        "managingOrganization": {"reference": "Organization/org-1"},
+    }
+
+
+def generate_patient_resources_list(count: int) -> list[dict[str, Any]]:
+    """Generate a list of FHIR Patient resources."""
+    return [generate_patient_resource(i) for i in range(count)]
+
+
+def generate_merge_response(count: int) -> list[dict[str, Any]]:
+    """Generate a merge response for the given count of resources."""
+    return [{"created": 1, "updated": 0} for _ in range(count)]
+
+
+@pytest.fixture(scope="module")
+def mock_server_url() -> str:
+    return "http://mock-server:1080"
+
+
+@pytest.fixture(scope="module")
+def mock_client(mock_server_url: str) -> MockServerFriendlyClient:
+    return MockServerFriendlyClient(base_url=mock_server_url)
+
+
+@pytest.fixture(scope="module")
+def setup_mock_merge_endpoints(mock_client: MockServerFriendlyClient, mock_server_url: str) -> str:
+    """Set up mock endpoints for merge operations with different payload sizes."""
+    test_name = "benchmark_merge"
+
+    mock_client.clear(f"/{test_name}/*.*")
+    mock_client.reset()
+
+    # Create payloads of different sizes for benchmarking
+    payload_sizes = {
+        "small": 10,  # 10 patients
+        "medium": 100,  # 100 patients
+        "large": 500,  # 500 patients
+    }
+
+    # Setup mock endpoints for each payload size - using regex to match any request body
+    for size, count in payload_sizes.items():
+        response_body = json.dumps(generate_merge_response(count))
+
+        # Endpoint for POST /Patient/1/$merge (single resource merge)
+        mock_client.expect(
+            request=mock_request(
+                path=f"/{test_name}/{size}/Patient/1/$merge",
+                method="POST",
+            ),
+            response=mock_response(body=response_body),
+            timing=times(10000),  # Allow many requests for benchmarking
+        )
+
+        # Endpoint for POST /Patient/$merge (batch merge)
+        mock_client.expect(
+            request=mock_request(
+                path=f"/{test_name}/{size}/Patient/$merge",
+                method="POST",
+            ),
+            response=mock_response(body=response_body),
+            timing=times(10000),
+        )
+
+    return f"{mock_server_url}/{test_name}"
+
+
+# ============================================================================
+# Benchmark Tests for merge_async() - Small Payload (10 patients)
+# ============================================================================
+
+
+def test_benchmark_merge_async_compress_false_small(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=False and small payload (10 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/small"
+    resources = generate_patient_resources_list(10)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_merge_async_compress_true_small(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=True and small payload (10 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/small"
+    resources = generate_patient_resources_list(10)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+# ============================================================================
+# Benchmark Tests for merge_async() - Medium Payload (100 patients)
+# ============================================================================
+
+
+def test_benchmark_merge_async_compress_false_medium(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=False and medium payload (100 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/medium"
+    resources = generate_patient_resources_list(100)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_merge_async_compress_true_medium(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=True and medium payload (100 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/medium"
+    resources = generate_patient_resources_list(100)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+# ============================================================================
+# Benchmark Tests for merge_async() - Large Payload (500 patients)
+# ============================================================================
+
+
+def test_benchmark_merge_async_compress_false_large(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=False and large payload (500 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/large"
+    resources = generate_patient_resources_list(500)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_merge_async_compress_true_large(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark merge_async with compress=True and large payload (500 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/large"
+    resources = generate_patient_resources_list(500)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(id_="1", json_data_list=json_data_list)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+# ============================================================================
+# Benchmark Tests for batch merge_async() - Multiple resources in single call
+# ============================================================================
+
+
+def test_benchmark_batch_merge_async_compress_false_small(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=False and small payload (10 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/small"
+    resources = generate_patient_resources_list(10)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=10)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_batch_merge_async_compress_true_small(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=True and small payload (10 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/small"
+    resources = generate_patient_resources_list(10)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=10)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_batch_merge_async_compress_false_medium(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=False and medium payload (100 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/medium"
+    resources = generate_patient_resources_list(100)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=50)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_batch_merge_async_compress_true_medium(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=True and medium payload (100 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/medium"
+    resources = generate_patient_resources_list(100)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=50)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_batch_merge_async_compress_false_large(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=False and large payload (500 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/large"
+    resources = generate_patient_resources_list(500)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(False)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=100)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None
+
+
+def test_benchmark_batch_merge_async_compress_true_large(benchmark: Any, setup_mock_merge_endpoints: str) -> None:
+    """Benchmark batch merge_async with compress=True and large payload (500 patients)."""
+    base_url = f"{setup_mock_merge_endpoints}/large"
+    resources = generate_patient_resources_list(500)
+    json_data_list = [json.dumps(r) for r in resources]
+
+    async def run_merge_async() -> FhirMergeResponse | None:
+        fhir_client = FhirClient().url(base_url).resource("Patient")
+        fhir_client = fhir_client.compress(True)
+        return await FhirMergeResponse.from_async_generator(
+            fhir_client.merge_async(json_data_list=json_data_list, batch_size=100)
+        )
+
+    def run_sync() -> FhirMergeResponse | None:
+        return asyncio.run(run_merge_async())
+
+    result = benchmark(run_sync)
+    assert result is not None

helix_fhir_client_sdk-4.2.10/VERSION

@@ -1 +0,0 @@
-4.2.10