Merge from main

.vscode/settings.json

@@ -1,6 +1,6 @@
 {
   "python.testing.pytestArgs": [
-    "test"
+    "tests"
   ],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true

README.md

@@ -6,17 +6,17 @@
 |-|-|-|
 | ![Python][python-badge] | [![Bunny Docker Images][docker-badge]][bunny-containers] | [![Bunny Docs][docs-badge]][bunny-docs] |
 
-An HDR UK Cohort Discovery Task Resolver.
+A Cohort Discovery Task Resolver.
 
-Fetches and resolves Availability and Distribution Queries against an OMOP-CDM database.
+Fetches and resolves Availability and Distribution Queries against an OMOP CDM database.
 
 [hutch-logo]: https://raw.githubusercontent.com/HDRUK/hutch/main/assets/Hutch%20splash%20bg.svg
 [hutch-repo]: https://github.com/health-informatics-uon/hutch
 
 [bunny-docs]: https://health-informatics-uon.github.io/hutch/bunny
-[bunny-containers]: https://github.com/Health-Informatics-UoN/hutch-cohort-discovery/pkgs/container/hutch%2Fbunny
+[bunny-containers]: https://github.com/Health-Informatics-UoN/hutch-bunny/pkgs/container/hutch%2Fbunny
 
-[license-badge]: https://img.shields.io/github/license/health-informatics-uon/hutch-cohort-discovery.svg
+[license-badge]: https://img.shields.io/github/license/health-informatics-uon/hutch-bunny.svg
 [python-badge]: https://img.shields.io/badge/Python-3776AB?style=for-the-badge&logo=python&logoColor=white
 [docker-badge]: https://img.shields.io/badge/docker-%230db7ed.svg?style=for-the-badge&logo=docker&logoColor=white
 [docs-badge]: https://img.shields.io/badge/docs-black?style=for-the-badge&labelColor=%23222

pyproject.toml

@@ -38,4 +38,10 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [dependency-groups]
-dev = ["ruff>=0.8.6", "pytest>=8.3.4"]
+dev = [
+    "ruff>=0.8.6",
+    "pytest>=8.3.4",
+    "pandas-stubs>=2.2.3.241126",
+    "mypy>=1.14.1",
+    "types-requests>=2.32.0.20241016",
+]

src/hutch_bunny/cli.py

@@ -1,5 +1,5 @@
 import json
-from hutch_bunny.core.obfuscation import get_results_modifiers_from_str
+from hutch_bunny.core.results_modifiers import get_results_modifiers_from_str
 from hutch_bunny.core.execute_query import execute_query
 from hutch_bunny.core.rquest_dto.result import RquestResult
 from hutch_bunny.core.parser import parser

src/hutch_bunny/core/execute_query.py

@@ -3,7 +3,7 @@
 from hutch_bunny.core import query_solvers
 from hutch_bunny.core.rquest_dto.query import AvailabilityQuery, DistributionQuery
 from hutch_bunny.core.obfuscation import (
-    apply_filters_v2,
+    apply_filters,
 )
 from hutch_bunny.core.rquest_dto.result import RquestResult
 
@@ -50,7 +50,7 @@ def execute_query(
             result = query_solvers.solve_availability(
                 db_manager=db_manager, query=query
             )
-            result.count = apply_filters_v2(result.count, results_modifiers)
+            result.count = apply_filters(result.count, results_modifiers)
             return result
         except TypeError as te:  # raised if the distribution query json format is wrong
             logger.error(str(te), exc_info=True)

src/hutch_bunny/core/obfuscation.py

@@ -1,58 +1,8 @@
-import json
-import os
-import requests
-from typing import Union
-
-
-def get_results_modifiers(activity_source_id: int) -> list:
-    """Get the results modifiers for a given activity source.
-
-    Args:
-        activity_source_id (int): The acivity source ID.
-
-    Returns:
-        list: The modifiers for the given activity source.
-
-    Raises:
-        HTTPError: raised when this function can't get the results modifiers.
-    """
-    res = requests.get(
-        f"{os.getenv('MANAGER_URL')}/api/activitysources/{activity_source_id}/resultsmodifiers",
-        verify=int(os.getenv("MANAGER_VERIFY_SSL", 1)),
-    )
-    res.raise_for_status()
-    modifiers = res.json()
-    return modifiers
-
-
-def get_results_modifiers_from_str(params: str) -> list:
-    """Deserialise a JSON list containing results modifiers
-
-    Args:
-        params (str):
-        The JSON string containing list of parameter objects for results modifiers
-
-    Raises:
-        ValueError: The parsed string does not produce a list
-
-    Returns:
-        list: The list of parameter dicts of results modifiers
-    """
-    deserialised_params = json.loads(params)
-    if not isinstance(deserialised_params, list):
-        raise ValueError(
-            f"{get_results_modifiers_from_str.__name__} requires a JSON list"
-        )
-    return deserialised_params
-
-
-def low_number_suppression(
-    value: Union[int, float], threshold: int = 10
-) -> Union[int, float]:
+def low_number_suppression(value: int | float, threshold: int = 10) -> int | float:
     """Suppress values that fall below a given threshold.
 
     Args:
-        value (Union[int, float]): The value to evaluate.
+        value (int | float): The value to evaluate.
         threshold (int): The threshold to beat.
 
     Returns:
@@ -67,11 +17,11 @@ def low_number_suppression(
     return value if value > threshold else 0
 
 
-def rounding(value: Union[int, float], nearest: int = 10) -> int:
+def rounding(value: int | float, nearest: int = 10) -> int:
     """Round the value to the nearest base number, e.g. 10.
 
     Args:
-        value (Union[int, float]): The value to be rounded
+        value (int | float): The value to be rounded
         nearest (int, optional): Round value to this base. Defaults to 10.
 
     Returns:
@@ -86,36 +36,15 @@ def rounding(value: Union[int, float], nearest: int = 10) -> int:
     return nearest * round(value / nearest)
 
 
-def apply_filters(value: Union[int, float], filters: list) -> Union[int, float]:
-    """Iterate over a list of filters from the Manager and apply them to the
-    supplied value.
-
-    Args:
-        value (Union[int, float]): The value to be filtered.
-        filters (list): The filters applied to the value.
-
-    Returns:
-        Union[int, float]: The filtered value.
-    """
-    actions = {"Low Number Suppression": low_number_suppression, "Rounding": rounding}
-    result = value
-    for f in filters:
-        if action := actions.get(f["type"]["id"]):
-            result = action(result, **f["parameters"])
-            if result == 0:
-                break  # don't apply any more filters
-    return result
-
-
-def apply_filters_v2(value: Union[int, float], filters: list) -> Union[int, float]:
+def apply_filters(value: int | float, filters: list) -> int | float:
     """Iterate over a list of filters and apply them to the supplied value.
 
     Args:
-        value (Union[int, float]): The value to be filtered.
+        value (int | float): The value to be filtered.
         filters (list): The filters applied to the value.
 
     Returns:
-        Union[int, float]: The filtered value.
+        int | float: The filtered value.
     """
     actions = {"Low Number Suppression": low_number_suppression, "Rounding": rounding}
     result = value

src/hutch_bunny/core/results_modifiers.py

@@ -1,3 +1,6 @@
+import json
+
+
 def results_modifiers(
     low_number_suppression_threshold: int,
     rounding_target: int,
@@ -18,3 +21,24 @@ def results_modifiers(
             }
         )
     return results_modifiers
+
+
+def get_results_modifiers_from_str(params: str) -> list:
+    """Deserialise a JSON list containing results modifiers
+
+    Args:
+        params (str):
+        The JSON string containing list of parameter objects for results modifiers
+
+    Raises:
+        ValueError: The parsed string does not produce a list
+
+    Returns:
+        list: The list of parameter dicts of results modifiers
+    """
+    deserialised_params = json.loads(params)
+    if not isinstance(deserialised_params, list):
+        raise ValueError(
+            f"{get_results_modifiers_from_str.__name__} requires a JSON list"
+        )
+    return deserialised_params

tests/test_demographics_distribution_query.py

@@ -6,6 +6,7 @@
 from dotenv import load_dotenv
 import os
 import hutch_bunny.core.settings as settings
+import hutch_bunny.core.setting_database as db_settings
 
 load_dotenv()
 

tests/test_obfuscation.py

@@ -0,0 +1,66 @@
+from hutch_bunny.core.obfuscation import (
+    apply_filters,
+    low_number_suppression,
+    rounding,
+)
+
+
+def test_low_number_suppression():
+    # Test that the threshold is applied
+    assert low_number_suppression(99, threshold=100) == 0
+    assert low_number_suppression(100, threshold=100) == 0
+    assert low_number_suppression(101, threshold=100) == 101
+
+    # Test that the threshold can be set to 0
+    assert low_number_suppression(1, threshold=0) == 1
+
+    # Test negative threshold is ignored
+    assert low_number_suppression(1, threshold=-5) == 1
+
+
+def test_rounding():
+    # Test default nearest
+    assert rounding(9) == 10
+
+    # Test rounding is applied
+    assert rounding(123, nearest=100) == 100
+    assert rounding(123, nearest=10) == 120
+    assert rounding(123, nearest=1) == 123
+
+    # Test rounding is applied the boundary
+    assert rounding(150, nearest=100) == 200
+
+
+def test_apply_filters_rounding():
+    # Test rounding only
+    filters = [{"id": "Rounding", "nearest": 100}]
+    assert apply_filters(123, filters=filters) == 100
+
+
+def test_apply_filters_low_number_suppression():
+    # Test low number suppression only
+    filters = [{"id": "Low Number Suppression", "threshold": 100}]
+    assert apply_filters(123, filters=filters) == 123
+
+
+def test_apply_filters_combined():
+    # Test both filters
+    filters = [
+        {"id": "Low Number Suppression", "threshold": 100},
+        {"id": "Rounding", "nearest": 100},
+    ]
+    assert apply_filters(123, filters=filters) == 100
+
+
+def test_apply_filters_combined_leak():
+    # Test that putting the rounding filter first can leak the low number suppression filter
+    filters = [
+        {"id": "Rounding", "nearest": 100},
+        {"id": "Low Number Suppression", "threshold": 70},
+    ]
+    assert apply_filters(60, filters=filters) == 100
+
+
+def test_apply_filters_combined_empty_filter():
+    # Test that an empty filter list returns the original value
+    assert apply_filters(9, []) == 9

tests/test_return.py

@@ -11,6 +11,7 @@
 from dotenv import load_dotenv
 import os
 import hutch_bunny.core.settings as settings
+import hutch_bunny.core.setting_database as db_settings
 
 load_dotenv()