Adding residue index validator

tests/test_residue_index.py

@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+
+"""
+Copyright 2018 EMBL - European Bioinformatics Institute
+
+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 http://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.
+"""
+
+import json
+from unittest import TestCase
+
+from validator.residue_index import CheckResidueIndices
+
+with open("data/test_data.json", "r") as mock_data_file:
+    mock_data = json.load(mock_data_file)
+
+mock_data_no_pdb_id = {"foo": "bar"}
+
+mock_data_bad_numbering = {"pdb_id": "2aqa",
+                           "chains": [{"chain_label": "A",
+                                       "residues": [{"pdb_res_label": "2",
+                                                     "aa_type": "ALA"}]}]}
+
+
+def mock_get_residue_numbering_false(self):
+    return False
+
+
+def mock_get_residue_numbering_true(self):
+    return True
+
+
+def mock_compare_residue_number(self, foo, bar):
+    return False
+
+
+class TestCheckResidueIndices(TestCase):
+
+    def setUp(self):
+        self.cri = CheckResidueIndices(mock_data)
+
+    def test_loop_chains(self):
+        self.cri.get_residue_numbering = mock_get_residue_numbering_false
+        result = self.cri.loop_chains()
+        self.assertFalse(result)
+        self.cri.get_residue_numbering = mock_get_residue_numbering_true
+        result = self.cri.loop_chains()
+        self.assertTrue(result)
+        self.cri.pdb_id = None
+        self.assertFalse(self.cri.loop_chains())
+
+    def test_set_pdb_id(self):
+        self.assertIsNotNone(self.cri.set_pdb_id())
+        bad_cri = CheckResidueIndices(mock_data_no_pdb_id)
+        self.assertIsNone(bad_cri.set_pdb_id())
+
+    def test_check_numbering(self):
+        result = self.cri.check_numbering({}, {})
+        self.assertFalse(result)
+        self.cri.compare_residue_number = mock_compare_residue_number
+        result = self.cri.check_numbering({}, {"residues": [{"pdb_res_label": 0, "aa_type": "ALA"}]})
+        self.assertFalse(result)
+
+    def test_get_residue_numbering(self):
+        mock_data = {"chain_label": "A"}
+        self.cri.pdb_id = "1CBS"
+        self.cri.check_numbering = lambda x, y : True
+        result = self.cri.get_residue_numbering(mock_data)
+        self.assertTrue(result)
+        self.cri.pdb_id = "2H58"
+        result = self.cri.get_residue_numbering(mock_data)
+        self.assertFalse(result)
+
+    def test_recursive_loop(self):
+        result = self.cri.recursive_loop([{"foo": "bar"}], "foo", None, None)
+        self.assertFalse(result)
+
+    def test_with_bad_numbering(self):
+        cri_with_bad_numbering = CheckResidueIndices(mock_data_bad_numbering)
+        result = cri_with_bad_numbering.loop_chains()
+        self.assertFalse(result)
+
+    def test_process_residues(self):
+        result = self.cri.process_residues(
+            [{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
+        self.assertTrue(result)
+        result = self.cri.process_residues(
+            [{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": "C"}], "1C", "ALA")
+        self.assertTrue(result)
+        result = self.cri.process_residues(
+            [{"author_residue_number": 2, "residue_name": "ALA", "author_insertion_code": ""}], "1", "ALA")
+        self.assertFalse(result)
+        result = self.cri.process_residues(
+            [{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
+        self.assertFalse(result)