104 lines
No EOL
3.8 KiB
Python
104 lines
No EOL
3.8 KiB
Python
#!/usr/bin/env python3
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"""
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Copyright 2018 EMBL - European Bioinformatics Institute
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing,
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software distributed under the License is distributed on an
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"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
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either express or implied. See the License for the specific
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language governing permissions and limitations under the
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License.
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"""
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import json
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from unittest import TestCase
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from validator.residue_index import ResidueIndexes
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with open("data/test_data.json", "r") as mock_data_file:
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mock_data = json.load(mock_data_file)
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mock_data_no_pdb_id = {"foo": "bar"}
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mock_data_bad_numbering = {"pdb_id": "2aqa",
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"chains": [{"chain_label": "A",
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"residues": [{"pdb_res_label": "2",
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"aa_type": "ALA"}]}]}
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def mock_get_residue_numbering_false(self):
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return False
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def mock_get_residue_numbering_true(self):
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return True
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def mock_compare_residue_number(self, foo, bar):
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return False
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class TestCheckResidueIndices(TestCase):
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def setUp(self):
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self.cri = ResidueIndexes(mock_data)
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def test_loop_chains(self):
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self.cri._get_residue_numbering = mock_get_residue_numbering_false
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result = self.cri.check_every_residue()
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self.assertFalse(result)
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self.cri._get_residue_numbering = mock_get_residue_numbering_true
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result = self.cri.check_every_residue()
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self.assertTrue(result)
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self.cri.pdb_id = None
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self.assertFalse(self.cri.check_every_residue())
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def test_set_pdb_id(self):
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self.assertIsNotNone(self.cri._set_pdb_id())
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bad_cri = ResidueIndexes(mock_data_no_pdb_id)
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self.assertIsNone(bad_cri._set_pdb_id())
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def test_check_numbering(self):
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result = self.cri._check_numbering({}, {})
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self.assertFalse(result)
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self.cri._compare_residue_number = mock_compare_residue_number
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result = self.cri._check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
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self.assertFalse(result)
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def test_get_residue_numbering(self):
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mock_data = {"chain_label": "A"}
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self.cri.pdb_id = "1CBS"
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self.cri._check_numbering = lambda x, y : True
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result = self.cri._get_residue_numbering(mock_data)
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self.assertTrue(result)
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self.cri.pdb_id = "2H58"
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result = self.cri._get_residue_numbering(mock_data)
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self.assertFalse(result)
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def test_recursive_loop(self):
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result = self.cri._recursive_loop([{"foo": "bar"}], "foo", None, None)
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self.assertFalse(result)
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def test_with_bad_numbering(self):
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cri_with_bad_numbering = ResidueIndexes(mock_data_bad_numbering)
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result = cri_with_bad_numbering.check_every_residue()
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self.assertFalse(result)
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def test_process_residues(self):
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result = self.cri._process_residues(
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[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
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self.assertTrue(result)
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result = self.cri._process_residues(
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[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA")
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self.assertTrue(result)
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result = self.cri._process_residues(
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[{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
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self.assertFalse(result)
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result = self.cri._process_residues(
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[{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
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self.assertFalse(result) |