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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
89 lines
3.3 KiB
Python
89 lines
3.3 KiB
Python
"""Tests for the UniProt module."""
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import unittest
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from itertools import islice
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import requires_internet
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from Bio import UniProt
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requires_internet.check()
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class SearchTests(unittest.TestCase):
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def test_search_result_count(self):
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query = "(organism_id:2697049) AND (reviewed:true)"
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results = UniProt.search(query)
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search_result_count = len(results)
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self.assertIsInstance(search_result_count, int)
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self.assertGreaterEqual(search_result_count, 1)
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self.assertEqual(search_result_count, len(list(results)))
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def test_search_all_fields(self):
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query = "Insulin AND (reviewed:true)"
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results = list(islice(UniProt.search(query, batch_size=50), 50))
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self.assertEqual(len(results), 50)
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for result in results:
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self.assertIsInstance(result, dict)
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self.assertGreater(len(result), 0)
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def test_search_with_fields(self):
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query = "Insulin AND (reviewed:true)"
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fields = ["id", "accession"]
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results = list(islice(UniProt.search(query, fields=fields, batch_size=50), 50))
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self.assertEqual(len(results), 50)
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expected_keys = {"entryType", "primaryAccession", "uniProtkbId"}
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for result in results:
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self.assertIsInstance(result, dict)
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self.assertGreater(len(result), 0)
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self.assertEqual(set(result.keys()), expected_keys)
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def test_search_results_slicing(self):
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query = "Insulin AND (reviewed:true)"
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results = UniProt.search(query, batch_size=25)
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results_sliced = results[:50]
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self.assertEqual(50, len(results_sliced))
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results_list = list(islice(results, 50))
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self.assertEqual(50, len(results_list))
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self.assertEqual(results_sliced, results_list)
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# We need to fetch the results again to reset the iterator
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results = UniProt.search(query, batch_size=25)
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results_sliced = results[49:30:-1]
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self.assertEqual(19, len(results_sliced))
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results_list = list(islice(results, 50))[49:30:-1]
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self.assertEqual(19, len(results_list))
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self.assertEqual(results_sliced, results_list)
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results_sliced = results[0:0]
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self.assertEqual(0, len(results_sliced))
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# This query should return less than 500 results.
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query = "(organism_id:2697049) AND (reviewed:true)"
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results = UniProt.search(query)
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results_sliced = results[-10:-5]
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self.assertEqual(5, len(results_sliced))
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results_list = list(results)[-10:-5]
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self.assertEqual(5, len(results_list))
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self.assertEqual(results_sliced, results_list)
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results = UniProt.search(query)
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results_sliced = results[-1_000_001:1_000_000]
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self.assertEqual(len(results), len(results_sliced))
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results_list = list(results)[-1_000_001:1_000_000]
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self.assertEqual(len(results_list), len(results))
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self.assertEqual(results_sliced, results_list)
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def test_search_results_indexing(self):
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query = "(organism_id:2697049) AND (reviewed:true)"
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results = UniProt.search(query)
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self.assertIsInstance(results[0], dict)
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self.assertIsInstance(results[-1], dict)
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with self.assertRaises(IndexError):
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_ = results[1_000_000]
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with self.assertRaises(IndexError):
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_ = results[-1_000_000]
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