# Copyright 2024 Google LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # pylint: disable=missing-module-docstring # pylint: disable=protected-access # pylint: disable=redefined-outer-name import pytest from speciesnet.taxonomy_utils import get_ancestor_at_level from speciesnet.taxonomy_utils import get_full_class_string # fmt: off # pylint: disable=line-too-long BLANK = "f1856211-cfb7-4a5b-9158-c0f72fd09ee6;;;;;;blank" BLANK_FC = ";;;;" HUMAN = "990ae9dd-7a59-4344-afcb-1b7b21368000;mammalia;primates;hominidae;homo;sapiens;human" HUMAN_FC = "mammalia;primates;hominidae;homo;sapiens" VEHICLE = "e2895ed5-780b-48f6-8a11-9e27cb594511;;;;;;vehicle" VEHICLE_FC = ";;;;" LION = "ddf59264-185a-4d35-b647-2785792bdf54;mammalia;carnivora;felidae;panthera;leo;lion" LION_FC = "mammalia;carnivora;felidae;panthera;leo" PANTHERA_GENUS = "fbb23d07-6677-43db-b650-f99ac452c50f;mammalia;carnivora;felidae;panthera;;panthera species" PANTHERA_GENUS_FC = "mammalia;carnivora;felidae;panthera;" FELIDAE_FAMILY = "df8514b0-10a5-411f-8ed6-0f415e8153a3;mammalia;carnivora;felidae;;;cat family" FELIDAE_FAMILY_FC = "mammalia;carnivora;felidae;;" CARNIVORA_ORDER = "eeeb5d26-2a47-4d01-a3de-10b33ec0aee4;mammalia;carnivora;;;;carnivorous mammal" CARNIVORA_ORDER_FC = "mammalia;carnivora;;;" MAMMALIA_CLASS = "f2d233e3-80e3-433d-9687-e29ecc7a467a;mammalia;;;;;mammal" MAMMALIA_CLASS_FC = "mammalia;;;;" ANIMAL_KINGDOM = "1f689929-883d-4dae-958c-3d57ab5b6c16;;;;;;animal" ANIMAL_KINGDOM_FC = ";;;;" BROWN_BEAR = "330bb1e9-84d6-4e41-afa9-938aee17ea29;mammalia;carnivora;ursidae;ursus;arctos;brown bear" BROWN_BEAR_FC = "mammalia;carnivora;ursidae;ursus;arctos" POLAR_BEAR = "e7f83bf6-df2c-4ce0-97fc-2f233df23ec4;mammalia;carnivora;ursidae;ursus;maritimus;polar bear" POLAR_BEAR_FC = "mammalia;carnivora;ursidae;ursus;maritimus" GIANT_PANDA = "85662682-67c1-4ecb-ba05-ba12e2df6b65;mammalia;carnivora;ursidae;ailuropoda;melanoleuca;giant panda" GIANT_PANDA_FC = "mammalia;carnivora;ursidae;ailuropoda;melanoleuca" URSUS_GENUS = "5a0f5e3f-c634-4b86-910a-b105cb526a24;mammalia;carnivora;ursidae;ursus;;ursus species" URSUS_GENUS_FC = "mammalia;carnivora;ursidae;ursus;" URSIDAE_FAMILY = "ec1a70f4-41c0-4aba-9150-292fb2b7a324;mammalia;carnivora;ursidae;;;bear family" URSIDAE_FAMILY_FC = "mammalia;carnivora;ursidae;;" PUMA = "9c564562-9429-405c-8529-04cff7752282;mammalia;carnivora;felidae;puma;concolor;puma" PUMA_FC = "mammalia;carnivora;felidae;puma;concolor" SAND_CAT = "e588253d-d61d-4149-a96c-8c245927a80f;mammalia;carnivora;felidae;felis;margarita;sand cat" SAND_CAT_FC = "mammalia;carnivora;felidae;felis;margarita" # pylint: enable=line-too-long # fmt: on @pytest.fixture def taxonomy_map(): return { BLANK_FC: BLANK, HUMAN_FC: HUMAN, VEHICLE_FC: VEHICLE, LION_FC: LION, PANTHERA_GENUS_FC: PANTHERA_GENUS, FELIDAE_FAMILY_FC: FELIDAE_FAMILY, CARNIVORA_ORDER_FC: CARNIVORA_ORDER, MAMMALIA_CLASS_FC: MAMMALIA_CLASS, ANIMAL_KINGDOM_FC: ANIMAL_KINGDOM, BROWN_BEAR_FC: BROWN_BEAR, POLAR_BEAR_FC: POLAR_BEAR, GIANT_PANDA_FC: GIANT_PANDA, URSUS_GENUS_FC: URSUS_GENUS, URSIDAE_FAMILY_FC: URSIDAE_FAMILY, } class TestTaxonomyUtils: """Tests for the taxonomy utility functions.""" def test_get_ancestor_at_level(self, taxonomy_map) -> None: # Test all ancestors of LION. assert get_ancestor_at_level(LION, "species", taxonomy_map) == LION assert get_ancestor_at_level(LION, "genus", taxonomy_map) == PANTHERA_GENUS assert get_ancestor_at_level(LION, "family", taxonomy_map) == FELIDAE_FAMILY assert get_ancestor_at_level(LION, "order", taxonomy_map) == CARNIVORA_ORDER assert get_ancestor_at_level(LION, "class", taxonomy_map) == MAMMALIA_CLASS assert get_ancestor_at_level(LION, "kingdom", taxonomy_map) == ANIMAL_KINGDOM # Test all ancestors of PANTHERA_GENUS. assert get_ancestor_at_level(PANTHERA_GENUS, "species", taxonomy_map) is None assert ( get_ancestor_at_level(PANTHERA_GENUS, "genus", taxonomy_map) == PANTHERA_GENUS ) assert ( get_ancestor_at_level(PANTHERA_GENUS, "family", taxonomy_map) == FELIDAE_FAMILY ) assert ( get_ancestor_at_level(PANTHERA_GENUS, "order", taxonomy_map) == CARNIVORA_ORDER ) assert ( get_ancestor_at_level(PANTHERA_GENUS, "class", taxonomy_map) == MAMMALIA_CLASS ) assert ( get_ancestor_at_level(PANTHERA_GENUS, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test all ancestors of FELIDAE_FAMILY. assert get_ancestor_at_level(FELIDAE_FAMILY, "species", taxonomy_map) is None assert get_ancestor_at_level(FELIDAE_FAMILY, "genus", taxonomy_map) is None assert ( get_ancestor_at_level(FELIDAE_FAMILY, "family", taxonomy_map) == FELIDAE_FAMILY ) assert ( get_ancestor_at_level(FELIDAE_FAMILY, "order", taxonomy_map) == CARNIVORA_ORDER ) assert ( get_ancestor_at_level(FELIDAE_FAMILY, "class", taxonomy_map) == MAMMALIA_CLASS ) assert ( get_ancestor_at_level(FELIDAE_FAMILY, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test all ancestors of CARNIVORA_ORDER. assert get_ancestor_at_level(CARNIVORA_ORDER, "species", taxonomy_map) is None assert get_ancestor_at_level(CARNIVORA_ORDER, "genus", taxonomy_map) is None assert get_ancestor_at_level(CARNIVORA_ORDER, "family", taxonomy_map) is None assert ( get_ancestor_at_level(CARNIVORA_ORDER, "order", taxonomy_map) == CARNIVORA_ORDER ) assert ( get_ancestor_at_level(CARNIVORA_ORDER, "class", taxonomy_map) == MAMMALIA_CLASS ) assert ( get_ancestor_at_level(CARNIVORA_ORDER, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test all ancestors of MAMMALIA_CLASS. assert get_ancestor_at_level(MAMMALIA_CLASS, "species", taxonomy_map) is None assert get_ancestor_at_level(MAMMALIA_CLASS, "genus", taxonomy_map) is None assert get_ancestor_at_level(MAMMALIA_CLASS, "family", taxonomy_map) is None assert get_ancestor_at_level(MAMMALIA_CLASS, "order", taxonomy_map) is None assert ( get_ancestor_at_level(MAMMALIA_CLASS, "class", taxonomy_map) == MAMMALIA_CLASS ) assert ( get_ancestor_at_level(MAMMALIA_CLASS, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test all ancestors of ANIMAL_KINGDOM. assert get_ancestor_at_level(ANIMAL_KINGDOM, "species", taxonomy_map) is None assert get_ancestor_at_level(ANIMAL_KINGDOM, "genus", taxonomy_map) is None assert get_ancestor_at_level(ANIMAL_KINGDOM, "family", taxonomy_map) is None assert get_ancestor_at_level(ANIMAL_KINGDOM, "order", taxonomy_map) is None assert get_ancestor_at_level(ANIMAL_KINGDOM, "class", taxonomy_map) is None assert ( get_ancestor_at_level(ANIMAL_KINGDOM, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test all ancestors of BLANK. assert get_ancestor_at_level(BLANK, "species", taxonomy_map) is None assert get_ancestor_at_level(BLANK, "genus", taxonomy_map) is None assert get_ancestor_at_level(BLANK, "family", taxonomy_map) is None assert get_ancestor_at_level(BLANK, "order", taxonomy_map) is None assert get_ancestor_at_level(BLANK, "class", taxonomy_map) is None assert get_ancestor_at_level(BLANK, "kingdom", taxonomy_map) is None # Test all ancestors of HUMAN, when its genus, family and order are missing from # the mock taxonomy mapping. assert get_ancestor_at_level(HUMAN, "species", taxonomy_map) == HUMAN assert get_ancestor_at_level(HUMAN, "genus", taxonomy_map) is None assert get_ancestor_at_level(HUMAN, "family", taxonomy_map) is None assert get_ancestor_at_level(HUMAN, "order", taxonomy_map) is None assert get_ancestor_at_level(HUMAN, "class", taxonomy_map) == MAMMALIA_CLASS assert get_ancestor_at_level(HUMAN, "kingdom", taxonomy_map) == ANIMAL_KINGDOM # Test all ancestors of VEHICLE. assert get_ancestor_at_level(VEHICLE, "species", taxonomy_map) is None assert get_ancestor_at_level(VEHICLE, "genus", taxonomy_map) is None assert get_ancestor_at_level(VEHICLE, "family", taxonomy_map) is None assert get_ancestor_at_level(VEHICLE, "order", taxonomy_map) is None assert get_ancestor_at_level(VEHICLE, "class", taxonomy_map) is None assert get_ancestor_at_level(VEHICLE, "kingdom", taxonomy_map) is None # Test all ancestors of an unseen species. unseen_species = "uuid;class;order;family;genus;species;common_name" assert get_ancestor_at_level(unseen_species, "species", taxonomy_map) is None assert get_ancestor_at_level(unseen_species, "genus", taxonomy_map) is None assert get_ancestor_at_level(unseen_species, "family", taxonomy_map) is None assert get_ancestor_at_level(unseen_species, "order", taxonomy_map) is None assert get_ancestor_at_level(unseen_species, "class", taxonomy_map) is None assert ( get_ancestor_at_level(unseen_species, "kingdom", taxonomy_map) == ANIMAL_KINGDOM ) # Test errors due to invalid labels. with pytest.raises(ValueError): invalid_label = "uuid;class;order;family;genus;species" get_ancestor_at_level(invalid_label, "kingdom", taxonomy_map) with pytest.raises(ValueError): invalid_label = "uuid;class;order;family;genus;species;common_name;extra" get_ancestor_at_level(invalid_label, "kingdom", taxonomy_map) def test_get_full_class_string(self) -> None: # Test BLANK/HUMAN/VEHICLE. assert get_full_class_string(BLANK) == BLANK_FC assert get_full_class_string(HUMAN) == HUMAN_FC assert get_full_class_string(VEHICLE) == VEHICLE_FC # Test valid labels at different taxonomy levels. assert get_full_class_string(LION) == LION_FC assert get_full_class_string(PANTHERA_GENUS) == PANTHERA_GENUS_FC assert get_full_class_string(FELIDAE_FAMILY) == FELIDAE_FAMILY_FC assert get_full_class_string(CARNIVORA_ORDER) == CARNIVORA_ORDER_FC assert get_full_class_string(MAMMALIA_CLASS) == MAMMALIA_CLASS_FC assert get_full_class_string(ANIMAL_KINGDOM) == ANIMAL_KINGDOM_FC # Test errors due to invalid labels. with pytest.raises(ValueError): invalid_label = "uuid;class;order;family;genus;species" get_full_class_string(invalid_label) with pytest.raises(ValueError): invalid_label = "uuid;class;order;family;genus;species;common_name;extra" get_full_class_string(invalid_label)