ENH: add helper function to load clinical tables

Author: fedorov

idc_index/index.py

@@ -362,6 +362,29 @@ def fetch_index(self, index_name) -> None:
                     self.clinical_data_dir,
                 )
 
+    def get_clinical_table(self, table_name):
+        """
+        Returns the requested clinical table as a pandas DataFrame.
+
+        Args:
+            table_name (str): Name of the clinical table to be loaded.
+
+        Returns:
+            pandas.DataFrame: The requested clinical table.
+        """
+        if self.clinical_data_dir is None:
+            logger.error(
+                "Clinical data directory is not available. Please fetch clinical_index first."
+            )
+            return None
+
+        table_path = os.path.join(self.clinical_data_dir, table_name)
+        if not os.path.exists(table_path):
+            logger.error(f"Table {table_name} is not found in {table_path}.")
+            return None
+
+        return pd.read_parquet(table_path)
+
     def get_collections(self):
         """
         Returns the collections present in IDC

tests/idcindex.py

@@ -563,6 +563,9 @@ def test_clinical_index_install(self):
         assert i.indices_overview["clinical_index"]["installed"] is True
         assert len(os.listdir(i.clinical_data_dir)) > 0
 
+        nlst_clinical = i.get_clinical_table("nlst_clinical")
+        assert nlst_clinical is not None
+
 
 if __name__ == "__main__":
     unittest.main()