fet(Cache): add a generic cache

RELEASE

@@ -1,3 +1,6 @@
+1.13.0 - Jun 8, 2021
+  - feat(Cache): add a simple and non-persitent cache of generic objects
+
 1.12.0 - May 27, 2021
   - feat(print): add print_OK_adv() func
   - feat(print): add print_title_adv() func

brs_utils/Cache.py

@@ -0,0 +1,177 @@
+"""A class to represent a cache of objects."""
+# The MIT License (MIT)
+#
+# Copyright (c) 2018 Institute for Molecular Systems Biology, ETH Zurich.
+# Copyright (c) 2019 Novo Nordisk Foundation Center for Biosustainability,
+# Technical University of Denmark
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+from typing import (
+    Dict,
+    List,
+    TypeVar
+)
+from logging import (
+    Logger,
+    getLogger,
+    ERROR
+)
+from copy import deepcopy
+
+
+class Cache:
+
+    # static and private
+    __objects = {}
+    __logger = getLogger(__name__)
+    __logger.setLevel(ERROR)
+
+    @staticmethod
+    def set_log_level(level: int) -> None:
+        Cache.__logger.setLevel(level)
+
+    @staticmethod
+    def get_log_level() -> None:
+        return Cache.__logger.level
+
+    @staticmethod
+    def add(obj: TypeVar, id: str = None) -> None:
+        '''
+        Add an object to the cache.
+
+        Parameters
+        ----------
+        object: TypeVar
+            The object to add
+        id: str
+            ID of the object to add
+        '''
+        if id is None:
+            try:
+                id = obj.get_id()
+            except AttributeError:
+                Cache.__logger.error(f'id is not given and obj has no attribute get_id, nothing added')
+        Cache.__objects[id] = obj
+
+    @staticmethod
+    def remove(obj: TypeVar) -> None:
+        '''
+        Del an object from the cache.
+
+        Parameters
+        ----------
+        object: TypeVar
+            The object to remove
+        '''
+        if obj is not None:
+            try:
+                # Find object by ID
+                Cache.remove_object_by_id(
+                    list(Cache.get_objects().keys())[list(Cache.get_objects().values()).index(object)]
+                )
+            except ValueError:
+                Cache.__logger.warning(f'No such object {id} found in cache, nothing deleted.')
+        else:
+            Cache.__logger.warning(f'Object passed is None, nothing deleted.')
+
+    @staticmethod
+    def clean(
+    ) -> None:
+        '''
+        Remove all objects from the cache.
+        '''
+        for obj_id in Cache.get_list_of_objects():
+            Cache.remove_object_by_id(obj_id)
+
+    @staticmethod
+    def rename(id: str, new_id: str) -> None:
+        '''
+        Rename an object of the cache.
+
+        Parameters
+        ----------
+        id: str
+            ID of the object to add
+        '''
+        if id not in Cache.get_list_of_objects():
+            Cache.__logger.warning(f'Compound {id} already in cache, nothing added.')
+        else:
+            Cache.__objects[new_id] = deepcopy(Cache.get(id))
+            Cache.remove_object_by_id(id)
+
+    @staticmethod
+    def remove_object_by_id(id: str) -> None:
+        '''
+        Del an object from the cache by ID.
+
+        Parameters
+        ----------
+        id: str
+            ID of the object to remove
+        '''
+        if id in Cache.get_list_of_objects():
+            del Cache.__objects[id]
+        else:
+            Cache.__logger.warning(f'No such object {id} found in cache, nothing deleted.')
+
+    @staticmethod
+    def get(id: str) -> TypeVar:
+        '''
+        Return the object with ID from the cache
+
+        Parameters
+        ----------
+        id: str
+            ID of the object to return from the cache
+
+        Returns
+        -------
+        object: TypeVar
+            The object with the given ID
+        '''
+        try:
+            return Cache.get_objects()[id]
+        except KeyError:
+            return None
+
+    @staticmethod
+    def get_objects() -> Dict:
+        '''
+        Return a dictionary of all objects in the cache.
+
+        Returns
+        -------
+        objects: Dict
+            All objects in the cache
+        '''
+        return Cache.__objects
+
+    @staticmethod
+    def get_list_of_objects() -> List[str]:
+        '''
+        Return IDs of all objects in the cache.
+
+        Returns
+        -------
+        object_ids: List
+            All object IDs in the cache
+        '''
+        return list(Cache.__objects.keys())
+

brs_utils/__init__.py

@@ -41,6 +41,7 @@
     create_logger,
     add_arguments as add_logger_args,
 )
+from brs_utils.Cache import Cache
 from brs_utils._version import (
     __version__
 )

brs_utils/_version.py

@@ -1 +1 @@
-__version__ = "1.12.0"
+__version__ = "1.13.0"

recipe/meta.yaml

@@ -28,9 +28,10 @@ test:
     - {{ name|lower }}
   requires:
     - pytest
+    - pytest-cov
   commands:
-    - cd tests
-    - pytest -v
+    - python -m {{ name|lower }} --help
+    - cd tests ; pytest -v --cov --cov-report term-missing
 
 about:
   home: https://github.com/brsynth/{{ name|lower }}

tests/test_Cache.py

@@ -0,0 +1,123 @@
+"""
+Created on June 17 2020
+
+@author: Joan Hérisson
+"""
+
+from unittest import TestCase
+
+from brs_utils import Cache
+
+
+class Test_Cache(TestCase):
+
+    def setUp(self):
+        self.__d = {'a': 1, 'b': 2}
+
+    def test_add_with_id(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        self.assertDictEqual(
+            Cache.get('d'),
+            self.__d
+        )
+
+    def test_add_wo_id(self):
+        Cache.clean()
+        Cache.add(self.__d)
+        self.assertEqual(
+            Cache.get('d'),
+            None
+        )
+
+    def test_log_level(self):
+        Cache.clean()
+        level = 40
+        Cache.set_log_level(level)
+        self.assertEqual(
+            Cache.get_log_level(),
+            level
+        )
+
+    def test_remove(self):
+        Cache.clean()
+        self.assertEqual(
+            Cache.remove('d'),
+            None
+        )
+
+    def test_remove_none(self):
+        Cache.clean()
+        self.assertEqual(
+            Cache.remove(None),
+            None
+        )
+
+    def test_rename(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        Cache.rename('d', 'd1')
+        self.assertDictEqual(
+            Cache.get('d1'),
+            self.__d
+        )
+        self.assertEqual(
+            Cache.get('d'),
+            None
+        )
+
+    def test_rename_wrong_id(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        Cache.rename('d2', 'd1')
+        self.assertEqual(
+            Cache.get('d1'),
+            None
+        )
+        self.assertDictEqual(
+            Cache.get('d'),
+            self.__d
+        )
+
+    def test_remove_object_by_id(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        Cache.remove_object_by_id('d')
+        self.assertEqual(
+            Cache.get('d'),
+            None
+        )
+
+    def test_remove_object_by_wrong_id(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        Cache.remove_object_by_id('d1')
+        self.assertDictEqual(
+            Cache.get('d'),
+            self.__d
+        )
+
+    def test_get_wrong_id(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        self.assertEqual(
+            Cache.get('d1'),
+            None
+        )
+
+    def test_get_objects(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        self.assertDictEqual(
+            Cache.get_objects(),
+            {'d': self.__d}
+        )
+
+    def test_get_list_of_objects(self):
+        Cache.clean()
+        Cache.add(self.__d, 'd')
+        self.assertListEqual(
+            Cache.get_list_of_objects(),
+            ['d']
+        )
+