Merge pull request #217 from lifeomic/fhir-sql

feat: adds new feature Fhir.es_sql()

CHANGELOG.md

@@ -7,6 +7,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 _(NOTE: All examples use fictitious data or freely available data sets.)_
 
+## [0.34.0] - 2024-03-13
+
+### Added
+
+- A New function `es_sql()` to `phc.services.Fhir` class to execute OpenSearch SQL.
+
+Example:
+
+```python
+df = Fhir(session).es_sql(
+    project_id='xxx',
+    statement='SELECT id, subject.reference FROM diagnostic_report WHERE identifier.system = ? LIMIT 10',
+    params=[{
+      "type": "string",
+      "value": "example-identifier-system"
+    }]
+).get_as_dataframe('datarows')
+```
+
 ## [0.33.4] - 2023-11-02
 
 ### Fixed

phc/api_response.py

@@ -120,6 +120,11 @@ def get_as_dataframe(
             mapped = list(map(mapFunc, self.data.get(key)))
             return _pd.DataFrame(mapped)
 
+        # support OpenSearch sql response
+        if key == "datarows" and self.data.get("schema") is not None:
+            column_names = [col["name"] for col in self.data.get("schema")]
+            return _pd.DataFrame(self.data.get(key), columns=column_names)
+
         return _pd.DataFrame(self.data.get(key))
 
     def validate(self):

phc/services/fhir.py

@@ -4,6 +4,7 @@
 
 from phc.base_client import BaseClient
 from phc import ApiResponse
+from typing import List, Dict
 
 
 class Fhir(BaseClient):
@@ -64,7 +65,7 @@ def sql(self, project: str, statement: str, scroll="") -> ApiResponse:
     def execute_sql(
         self, project_id: str, statement: str, scroll=""
     ) -> ApiResponse:
-        """Executes an SQL query against fhir-searh-service
+        """Executes an SQL query against fhir-search-service
 
         Parameters
         ----------
@@ -106,7 +107,7 @@ def execute_sql(
     def execute_es(
         self, project_id: str, query: dict, scroll=""
     ) -> ApiResponse:
-        """Executes an elasticsearch query against fhir-searh-service
+        """Executes an elasticsearch query against fhir-search-service
 
         Parameters
         ----------
@@ -127,3 +128,35 @@ def execute_es(
             json=query,
             params={"scroll": scroll},
         )
+
+    def es_sql(
+        self,
+        project_id: str,
+        statement: str,
+        params: List[Dict],
+        subject_id="",
+    ) -> ApiResponse:
+        """Executes an OpenSearch SQL against fhir-search-service
+
+        Parameters
+        ----------
+        project_id : str
+            The project ID
+        statement : str
+            The prepared OpenSearch SQL statement
+        params: List[Dict]
+
+        Returns
+        -------
+        phc.ApiResponse
+            The query response
+        """
+        api_path = f"fhir-search/sql/projects/{project_id}"
+        if subject_id is not None and subject_id != "":
+            api_path = f"{api_path}/patients/{subject_id}"
+
+        return self._api_call(
+            api_path=api_path,
+            http_verb="POST",
+            json={"query": statement, "parameters": params},
+        )

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phc"
-version = "0.33.4"
+version = "0.34.0"
 description = "Python SDK for the LifeOmic platform"
 authors = ["LifeOmic <[email protected]>"]
 license = "MIT"

tests/test_fhir_opensearch_sql.py

@@ -0,0 +1,32 @@
+from phc import Session
+import os
+from phc.services import Fhir
+from unittest.mock import patch
+from test_session import jwt, sample
+
+
+@patch("phc.base_client.BaseClient._api_call")
+def test_es_sql(mock_api_call):
+    session = Session(token=jwt.encode(sample, "secret"), account="bar")
+    fhir = Fhir(session)
+    project_id = "bar"
+    query = "SELECT id, subject FROM diagnostic_report WHERE identifier.system = ? LIMIT 10"
+    params = [
+        {
+            "type": "string",
+            "value": "lrn:lo:dev:fountainlife:ehr:fountainlife:d22c690b-fb45-4ff2-8cb3-eed9f665cb30/DiagnosticReport",
+        }
+    ]
+
+    res = fhir.es_sql(
+        project_id=project_id,
+        statement=query,
+        params=params,
+    )
+
+    mock_api_call.assert_called_once()
+    args, kwargs = mock_api_call.call_args
+
+    assert kwargs["api_path"] == f"fhir-search/sql/projects/{project_id}"
+    assert kwargs["json"]["query"] == query
+    assert kwargs["json"]["parameters"] == params