Merge pull request #169 from LanaNYC/pagination

Add pagination functionality to FHIRClient and related unit tests

Author: dogversioning

fhirclient/client.py

@@ -1,4 +1,9 @@
 import logging
+import urllib
+from typing import Optional, Iterable
+
+import requests
+from .models.bundle import Bundle
 
 from .server import FHIRServer, FHIRUnauthorizedException, FHIRNotFoundException
 
@@ -240,3 +245,118 @@ def from_state(self, state):
     def save_state (self):
         self._save_func(self.state)
 
+    # MARK: Pagination
+    def _fetch_next_page(self, bundle: Bundle) -> Optional[Bundle]:
+        """
+        Fetch the next page of results using the `next` link provided in the bundle.
+
+        Args:
+            bundle (Bundle): The FHIR Bundle containing the `next` link.
+
+        Returns:
+            Optional[Bundle]: The next page of results as a FHIR Bundle, or None if no "next" link is found.
+        """
+        next_link = self._get_next_link(bundle)
+        if next_link:
+            sanitized_next_link = self._sanitize_next_link(next_link)
+            return self._execute_pagination_request(sanitized_next_link)
+        return None
+
+    def _get_next_link(self, bundle: Bundle) -> Optional[str]:
+        """
+        Extract the `next` link from the Bundle's links.
+
+        Args:
+            bundle (Bundle): The FHIR Bundle containing pagination links.
+
+        Returns:
+            Optional[str]: The URL of the next page if available, None otherwise.
+        """
+        if not bundle.link:
+            return None
+
+        for link in bundle.link:
+            if link.relation == "next":
+                return link.url
+        return None
+
+    def _sanitize_next_link(self, next_link: str) -> str:
+        """
+        Sanitize the `next` link to ensure it is safe to use.
+
+        Args:
+            next_link (str): The raw `next` link URL.
+
+        Returns:
+            str: The sanitized URL.
+
+        Raises:
+            ValueError: If the URL scheme or domain is invalid.
+        """
+        parsed_url = urllib.parse.urlparse(next_link)
+
+        # Validate scheme and netloc (domain)
+        if parsed_url.scheme not in ["http", "https"]:
+            raise ValueError("Invalid URL scheme in `next` link.")
+        if not parsed_url.netloc:
+            raise ValueError("Invalid URL domain in `next` link.")
+
+        # Additional sanitization if necessary, e.g., removing dangerous query parameters
+        query_params = urllib.parse.parse_qs(parsed_url.query)
+        sanitized_query = {k: v for k, v in query_params.items()}
+
+        # Rebuild the sanitized URL
+        sanitized_url = urllib.parse.urlunparse(
+            (
+                parsed_url.scheme,
+                parsed_url.netloc,
+                parsed_url.path,
+                parsed_url.params,
+                urllib.parse.urlencode(sanitized_query, doseq=True),
+                parsed_url.fragment,
+            )
+        )
+
+        return sanitized_url
+
+    def _execute_pagination_request(self, sanitized_url: str) -> Optional[Bundle]:
+        """
+        Execute the request to retrieve the next page using the sanitized URL.
+
+        Args:
+            sanitized_url (str): The sanitized URL to fetch the next page.
+
+        Returns:
+            Optional[Bundle]: The next page of results as a FHIR Bundle, or None.
+
+        Raises:
+            HTTPError: If the request fails due to network issues or server errors.
+        """
+        try:
+            # Use requests.get directly to make the HTTP request
+            response = requests.get(sanitized_url)
+            response.raise_for_status()
+            next_bundle_data = response.json()
+            next_bundle = Bundle(next_bundle_data)
+
+            return next_bundle
+
+        except requests.exceptions.HTTPError as e:
+            # Handle specific HTTP errors as needed, possibly including retry logic
+            raise e
+
+    def iter_pages(self, first_bundle: Bundle) -> Iterable[Bundle]:
+        """
+        Iterator that yields each page of results as a FHIR Bundle.
+
+        Args:
+            first_bundle (Bundle): The first Bundle to start pagination.
+
+        Yields:
+            Bundle: Each page of results as a FHIR Bundle.
+        """
+        bundle = first_bundle
+        while bundle:
+            yield bundle
+            bundle = self._fetch_next_page(bundle)
+

tests/client_pagination_test.py

@@ -0,0 +1,176 @@
+import unittest
+from unittest.mock import patch, MagicMock
+
+import requests
+from fhirclient.models.bundle import Bundle
+
+from fhirclient.client import FHIRClient
+
+
+class TestFHIRClientPagination(unittest.TestCase):
+    def setUp(self) -> None:
+        state = {
+            "app_id": "AppID",
+            "app_secret": "AppSecret",
+            "scope": "user/*.read",
+            "redirect": "http://test.invalid/redirect",
+            "patient_id": "PatientID",
+            "server": {
+                "base_uri": "http://test.invalid/",
+                "auth_type": "none",
+                "auth": {
+                    "app_id": "AppId",
+                },
+            },
+            "launch_token": "LaunchToken",
+            "launch_context": {
+                "encounter": "EncounterID",
+                "patient": "PatientID",
+            },
+            "jwt_token": "JwtToken",
+        }
+
+        # Confirm round trip
+        self.client = FHIRClient(state=state)
+
+        self.bundle = {
+            "resourceType": "Bundle",
+            "type": "searchset",
+            "link": [
+                {"relation": "self", "url": "http://example.com/fhir/Bundle/1"},
+                {"relation": "next", "url": "http://example.com/fhir/Bundle/2"},
+            ],
+            "entry": [
+                {
+                    "fullUrl": "http://example.com/fhir/Patient/1",
+                    "resource": {
+                        "resourceType": "Patient",
+                        "id": "1",
+                        "name": [{"family": "Doe", "given": ["John"]}],
+                        "gender": "male",
+                        "birthDate": "1980-01-01",
+                    },
+                },
+                {
+                    "fullUrl": "http://example.com/fhir/Patient/2",
+                    "resource": {
+                        "resourceType": "Patient",
+                        "id": "2",
+                        "name": [{"family": "Smith", "given": ["Jane"]}],
+                        "gender": "female",
+                        "birthDate": "1990-05-15",
+                    },
+                },
+            ],
+        }
+
+    def test_get_next_link(self):
+        next_link = self.client._get_next_link(Bundle(self.bundle))
+        self.assertEqual(next_link, "http://example.com/fhir/Bundle/2")
+
+    def test_get_next_link_no_next(self):
+        bundle_without_next = {
+            "resourceType": "Bundle",
+            "type": "searchset",
+            "link": [{"relation": "self", "url": "http://example.com/fhir/Bundle/1"}],
+        }
+        bundle = Bundle(bundle_without_next)
+        next_link = self.client._get_next_link(bundle)
+        self.assertIsNone(next_link)
+
+    def test_sanitize_next_link_valid(self):
+        next_link = "http://example.com/fhir/Bundle/2?page=2&size=10"
+        sanitized_link = self.client._sanitize_next_link(next_link)
+        self.assertEqual(sanitized_link, next_link)
+
+    def test_sanitize_next_link_invalid_scheme(self):
+        next_link = "ftp://example.com/fhir/Bundle/2?page=2&size=10"
+        with self.assertRaises(ValueError):
+            self.client._sanitize_next_link(next_link)
+
+    def test_sanitize_next_link_invalid_domain(self):
+        next_link = "http:///fhir/Bundle/2?page=2&size=10"
+        with self.assertRaises(ValueError):
+            self.client._sanitize_next_link(next_link)
+
+    @patch("requests.get")
+    def test_execute_pagination_request_success(self, mock_get):
+        mock_response = MagicMock()
+        # Set up the mock to return a specific JSON payload when its json() method is called
+        mock_response.json.return_value = self.bundle
+        mock_response.raise_for_status = MagicMock()
+        mock_get.return_value = mock_response
+
+        next_link = "http://example.com/fhir/Bundle/2"
+        sanitized_link = self.client._sanitize_next_link(next_link)
+        result = self.client._execute_pagination_request(sanitized_link)
+        self.assertIsInstance(result, Bundle)
+        self.assertIn("entry", result.as_json())
+        mock_get.assert_called_once_with(sanitized_link)
+
+    @patch("requests.get")
+    def test_execute_pagination_request_http_error(self, mock_get):
+        mock_get.side_effect = requests.exceptions.HTTPError("HTTP Error")
+
+        next_link = "http://example.com/fhir/Bundle/2"
+        sanitized_link = self.client._sanitize_next_link(next_link)
+
+        with self.assertRaises(requests.exceptions.HTTPError):
+            self.client._execute_pagination_request(sanitized_link)
+
+    @patch("requests.get")
+    def test_execute_pagination_request_returns_last_bundle_if_no_next_link(self, mock_get):
+        # Mock the response to simulate a Bundle with no next link
+        mock_response = MagicMock()
+        mock_response.json.return_value = {
+            "resourceType": "Bundle",
+            "type": "searchset",
+            "link": [{"relation": "self", "url": "http://example.com/fhir/Bundle/1"}],
+            "entry": [{"resource": {"resourceType": "Patient", "id": "1"}}],
+        }
+        mock_response.raise_for_status = MagicMock()
+        mock_get.return_value = mock_response
+
+        sanitized_link = "http://example.com/fhir/Bundle/1"
+        result = self.client._execute_pagination_request(sanitized_link)
+
+        # Check that the result is the Bundle itself, not None
+        self.assertIsInstance(result, Bundle)
+        self.assertTrue(hasattr(result, 'entry'))
+        mock_get.assert_called_once_with(sanitized_link)
+
+    @patch("fhirclient.client.FHIRClient._execute_pagination_request")
+    def test_fetch_next_page(self, mock_execute_request):
+        mock_execute_request.return_value = Bundle(self.bundle)
+        result = self.client._fetch_next_page(Bundle(self.bundle))
+        self.assertIsInstance(result, Bundle)
+        self.assertTrue(hasattr(result, "entry"))
+        mock_execute_request.assert_called_once()
+
+    def test_fetch_next_page_no_next_link(self):
+        bundle_without_next = {
+            "resourceType": "Bundle",
+            "type": "searchset",
+            "link": [{"relation": "self", "url": "http://example.com/fhir/Bundle/1"}],
+        }
+        bundle = Bundle(bundle_without_next)
+        result = self.client._fetch_next_page(bundle)
+        self.assertIsNone(result)
+
+    @patch("fhirclient.client.FHIRClient._fetch_next_page")
+    def test_iter_pages(self, mock_fetch_next_page):
+        # Set up the mock to return a new bundle, then None to stop iteration
+        mock_fetch_next_page.side_effect = [Bundle(self.bundle), None]
+        pages = list(self.client.iter_pages(Bundle(self.bundle)))
+
+        # Check that two bundles were returned (the first bundle and the one from mock)
+        self.assertEqual(len(pages), 2)
+        self.assertIsInstance(pages[0], Bundle)
+        self.assertIsInstance(pages[1], Bundle)
+
+        # Compare JSON representations instead of object instances
+        self.assertEqual(pages[0].as_json(), self.bundle)
+        self.assertEqual(pages[1].as_json(), self.bundle)
+
+        # Ensure that _fetch_next_page was called twice
+        self.assertEqual(mock_fetch_next_page.call_count, 2)