FHIR support

CHANGELOG.md

@@ -5,6 +5,83 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.7.0] - 2026-04-14
+
+### Added
+
+- **FHIR type interoperability** (`client.fhir.*`): The resolver now
+  accepts any Coding-like input via duck typing, so pipelines that
+  already parse FHIR with `fhir.resources` or `fhirpy` can pass those
+  objects directly - no manual conversion.
+  - New `coding=` kwarg on `Fhir.resolve` / `AsyncFhir.resolve`. Accepts
+    a plain dict, the `omophub.types.fhir.Coding` TypedDict, or any
+    object exposing `.system` / `.code` / `.display` attributes (e.g.
+    `fhir.resources.Coding`, `fhirpy` codings).
+  - `Fhir.resolve_batch` / `AsyncFhir.resolve_batch` now accept a
+    mixed list of dicts and Coding-like objects; each item is
+    normalized to the wire format automatically.
+  - `Fhir.resolve_codeable_concept` / async counterpart now accept
+    either a list of Coding-likes (existing) or a full
+    CodeableConcept-like object exposing `.coding` and `.text`
+    (new); explicit `text=` kwarg still wins when both are passed.
+  - Explicit `system` / `code` kwargs override the corresponding
+    fields on a `coding=` input - handy for last-mile overrides.
+- **New FHIR type definitions** in `omophub.types.fhir`:
+  - `Coding` and `CodeableConcept` lightweight TypedDicts
+  - `CodingLike` and `CodeableConceptLike` runtime-checkable
+    `Protocol`s for structural matching against external libraries.
+- **FHIR client interop helpers** (`omophub.fhir_interop`): Thin
+  helpers for configuring an external FHIR client library against
+  the OMOPHub FHIR Terminology Service.
+  - `get_fhir_server_url(version)` returns the FHIR base URL for
+    `"r4"` (default), `"r4b"`, `"r5"`, or `"r6"`.
+  - `get_fhirpy_client(api_key, version)` and
+    `get_async_fhirpy_client(api_key, version)` return `fhirpy`
+    clients pre-wired with the right URL and `Authorization: Bearer`
+    header. `fhirpy` is imported lazily, so it is never a required
+    dependency; a helpful `ImportError` with install instructions is
+    raised only when you actually call the helper.
+  - All three helpers are re-exported from the top-level `omophub`
+    namespace.
+- **`OMOPHub.fhir_server_url` / `AsyncOMOPHub.fhir_server_url`**:
+  Convenience read-only property returning the R4 FHIR endpoint for
+  drop-in use with external FHIR clients (`httpx`, `fhirpy`,
+  `fhir.resources`).
+- **Optional extras** in `pyproject.toml`:
+  - `pip install omophub[fhirpy]` pulls in `fhirpy>=1.4.0`.
+  - `pip install omophub[fhir-resources]` pulls in
+    `fhir.resources>=7.0.0`.
+  Both are purely optional; duck typing means neither is required
+  for core SDK use.
+
+### Changed
+
+- `Fhir.resolve_batch` signature broadened from
+  `codings: list[dict[str, str | None]]` to
+  `codings: list[CodingInput]` where `CodingInput` is the union of
+  dict, `Coding` TypedDict, and `CodingLike` protocol. Existing
+  call sites keep working unchanged.
+- `Fhir.resolve_codeable_concept` signature broadened from
+  `coding: list[dict[str, str]]` to
+  `coding: list[CodingInput] | CodeableConceptInput`, accepting
+  either the legacy list-of-codings shape or a full
+  CodeableConcept-like object.
+
+### Tests
+
+- 16 new unit tests covering `_extract_coding`, `_coding_to_dict`,
+  and duck-typed inputs across `resolve`, `resolve_batch`, and
+  `resolve_codeable_concept` on the sync client. Explicit-kwargs-win
+  precedence is covered.
+- New `tests/unit/test_fhir_interop.py` with 10 cases: URL builder
+  for all four FHIR versions, `fhirpy` lazy import with stubbed
+  success and missing-module failure paths, and the
+  `fhir_server_url` property on both sync and async clients.
+- 5 new integration tests in `tests/integration/test_fhir.py`
+  exercising the new `coding=` kwarg, mixed dict + duck-typed batch
+  inputs, CodeableConcept-like object resolution, and the
+  `fhir_server_url` property against the live API.
+
 ## [1.6.0] - 2026-04-10
 
 ### Added

README.md

@@ -32,6 +32,10 @@ Working with OHDSI ATHENA vocabularies traditionally requires downloading multi-
 
 ```bash
 pip install omophub
+
+# Optional extras for FHIR client interop
+pip install omophub[fhirpy]          # Pre-wired fhirpy client
+pip install omophub[fhir-resources]  # Install marker for fhir.resources
 ```
 
 ## Quick Start
@@ -98,6 +102,70 @@ result = client.fhir.resolve_codeable_concept(
 print(result["best_match"]["resolution"]["source_concept"]["vocabulary_id"])  # "SNOMED"
 ```
 
+### Type Interoperability
+
+The resolver accepts any Coding-like input via duck typing - a plain dict, omophub's lightweight `Coding` TypedDict, or any object with `.system` / `.code` attributes (e.g. `fhir.resources.Coding`, `fhirpy` codings).
+
+```python
+from omophub.types.fhir import Coding
+
+# omophub's TypedDict - IDE autocomplete, no extra deps
+coding: Coding = {"system": "http://snomed.info/sct", "code": "44054006"}
+result = client.fhir.resolve(coding=coding)
+
+# fhir.resources objects work via duck typing - no conversion needed
+from fhir.resources.R4B.coding import Coding as FhirCoding
+fhir_coding = FhirCoding(system="http://snomed.info/sct", code="44054006")
+result = client.fhir.resolve(coding=fhir_coding)
+
+# Mixed shapes in a single batch call
+result = client.fhir.resolve_batch([
+    {"system": "http://snomed.info/sct", "code": "44054006"},   # dict
+    FhirCoding(system="http://loinc.org", code="2339-0"),        # fhir.resources
+])
+```
+
+`fhir.resources` is **never** a required dependency. See [`examples/fhir_interop.py`](./examples/fhir_interop.py) for the full set of supported input shapes.
+
+### FHIR Client Interop
+
+Point external FHIR client libraries at OMOPHub's FHIR Terminology Service directly - useful when you need raw FHIR `Parameters` / `Bundle` responses instead of the Concept Resolver envelope.
+
+```python
+from omophub import OMOPHub, get_fhir_server_url
+
+client = OMOPHub(api_key="oh_xxx")
+
+# Property on the client returns the R4 base URL
+print(client.fhir_server_url)
+# "https://fhir.omophub.com/fhir/r4"
+
+# Helper for other FHIR versions
+print(get_fhir_server_url("r5"))
+# "https://fhir.omophub.com/fhir/r5"
+```
+
+For `fhirpy`, install the optional extra and use the pre-wired client:
+
+```bash
+pip install omophub[fhirpy]
+```
+
+```python
+from omophub import get_fhirpy_client
+
+fhir = get_fhirpy_client("oh_xxx")
+
+# Call CodeSystem/$lookup directly via fhirpy
+params = fhir.execute(
+    "CodeSystem/$lookup",
+    method="GET",
+    params={"system": "http://snomed.info/sct", "code": "44054006"},
+)
+```
+
+**When to use which**: the Concept Resolver (`client.fhir.resolve`) gives you OMOP-enriched answers - standard concept ID, CDM target table, mapping quality. Use `fhirpy` via `get_fhirpy_client()` when you need raw FHIR responses for FHIR-native tooling.
+
 ## Semantic Search
 
 Use natural language queries to find concepts using neural embeddings:

examples/async_usage.py

@@ -11,24 +11,23 @@ async def basic_async_usage() -> None:
     print("=== Basic Async Usage ===")
 
     # Use async context manager
-    async with omophub.AsyncOMOPHub(api_key="oh_your_api_key") as client:
+    async with omophub.AsyncOMOPHub() as client:
         # Get a concept
         concept = await client.concepts.get(201826)
         print(f"Concept: {concept['concept_name']}")
 
-        # Search
-        results = await client.search.basic("diabetes", page_size=5)
-        concepts = results.get("concepts", [])
+        # Search - returns a flat list of concept dicts
+        concepts = await client.search.basic("diabetes", page_size=5)
         print(f"Found {len(concepts)} concepts")
 
 
 async def concurrent_requests() -> None:
     """Demonstrate concurrent API requests."""
     print("\n=== Concurrent Requests ===")
 
-    async with omophub.AsyncOMOPHub(api_key="oh_your_api_key") as client:
+    async with omophub.AsyncOMOPHub() as client:
         # Fetch multiple concepts concurrently
-        concept_ids = [201826, 4329847, 1112807, 40483312, 37311061]
+        concept_ids = [201826, 4329847, 1112807, 316866, 37311061]
 
         tasks = [client.concepts.get(cid) for cid in concept_ids]
         concepts = await asyncio.gather(*tasks)
@@ -42,26 +41,20 @@ async def parallel_searches() -> None:
     """Demonstrate parallel search operations."""
     print("\n=== Parallel Searches ===")
 
-    async with omophub.AsyncOMOPHub(api_key="oh_your_api_key") as client:
-        # Run multiple searches in parallel
+    async with omophub.AsyncOMOPHub() as client:
+        # Run multiple searches in parallel. ``search.basic`` returns a
+        # flat list of concept dicts for the current page; for the full
+        # total count we iterate across pages via ``basic_iter``.
         search_terms = ["diabetes", "hypertension", "asthma", "depression"]
 
-        async def search_and_count(term: str) -> tuple[str, int]:
-            results = await client.search.basic(term, page_size=1)
-            # Get total from pagination metadata if available
-            meta = results.get("meta", {}).get("pagination", {})
-            total_items = meta.get("total_items")
-            if total_items is not None:
-                total = total_items
-            else:
-                concepts = results.get("concepts", [])
-                total = len(concepts) if isinstance(concepts, list) else 0
-            return term, total
-
-        tasks = [search_and_count(term) for term in search_terms]
+        async def page_count(term: str) -> tuple[str, int]:
+            concepts = await client.search.basic(term, page_size=50)
+            return term, len(concepts)
+
+        tasks = [page_count(term) for term in search_terms]
         results = await asyncio.gather(*tasks)
 
-        print("Search results:")
+        print("First-page hit counts:")
         for term, count in results:
             print(f"  '{term}': {count} concepts")
 

examples/basic_usage.py

@@ -6,9 +6,9 @@
 
 def main() -> None:
     """Demonstrate basic SDK usage."""
-    # Initialize the client with your API key
-    # You can also set OMOPHUB_API_KEY environment variable
-    client = omophub.OMOPHub(api_key="oh_your_api_key")
+    # Reads OMOPHUB_API_KEY from the environment. To pass it explicitly:
+    #   client = omophub.OMOPHub(api_key="oh_your_api_key")
+    client = omophub.OMOPHub()
 
     # Get a concept by ID
     concept = client.concepts.get(201826)
@@ -18,18 +18,18 @@ def main() -> None:
     print(f"  Domain: {concept['domain_id']}")
     print()
 
-    # Search for concepts
+    # Search for concepts - returns a list of concept dicts
     results = client.search.basic(
         "diabetes",
         vocabulary_ids=["SNOMED"],
         page_size=5,
     )
     print("Search results for 'diabetes':")
-    for c in results.get("concepts", []):
+    for c in results:
         print(f"  {c['concept_id']}: {c['concept_name']}")
     print()
 
-    # List vocabularies
+    # List vocabularies - returns a dict with a 'vocabularies' key
     vocabs = client.vocabularies.list(page_size=5)
     print("Available vocabularies:")
     for v in vocabs.get("vocabularies", []):

examples/error_handling.py

@@ -10,7 +10,7 @@ def handle_not_found() -> None:
     """Handle concept not found errors."""
     print("=== Handling Not Found ===")
 
-    client = omophub.OMOPHub(api_key="oh_your_api_key")
+    client = omophub.OMOPHub()
 
     try:
         # Try to get a non-existent concept
@@ -40,7 +40,7 @@ def handle_rate_limit() -> None:
     """Handle rate limit errors with retry."""
     print("\n=== Handling Rate Limits ===")
 
-    client = omophub.OMOPHub(api_key="oh_your_api_key")
+    client = omophub.OMOPHub()
 
     for i in range(5):
         try:
@@ -58,7 +58,7 @@ def handle_validation() -> None:
     """Handle validation errors."""
     print("\n=== Handling Validation Errors ===")
 
-    client = omophub.OMOPHub(api_key="oh_your_api_key")
+    client = omophub.OMOPHub()
 
     try:
         # Try an invalid request
@@ -73,7 +73,7 @@ def comprehensive_error_handling() -> None:
     """Demonstrate comprehensive error handling."""
     print("\n=== Comprehensive Error Handling ===")
 
-    client = omophub.OMOPHub(api_key="oh_your_api_key")
+    client = omophub.OMOPHub()
 
     try:
         concept = client.concepts.get(201826)