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"""Tests for the UniProt module."""
import unittest
from itertools import islice
import requires_internet
from Bio import UniProt
requires_internet.check()
class SearchTests(unittest.TestCase):
def test_search_result_count(self):
query = "(organism_id:2697049) AND (reviewed:true)"
results = UniProt.search(query)
search_result_count = len(results)
self.assertIsInstance(search_result_count, int)
self.assertGreaterEqual(search_result_count, 1)
self.assertEqual(search_result_count, len(list(results)))
def test_search_all_fields(self):
query = "Insulin AND (reviewed:true)"
results = list(islice(UniProt.search(query, batch_size=50), 50))
self.assertEqual(len(results), 50)
for result in results:
self.assertIsInstance(result, dict)
self.assertGreater(len(result), 0)
def test_search_with_fields(self):
query = "Insulin AND (reviewed:true)"
fields = ["id", "accession"]
results = list(islice(UniProt.search(query, fields=fields, batch_size=50), 50))
self.assertEqual(len(results), 50)
expected_keys = {"entryType", "primaryAccession", "uniProtkbId"}
for result in results:
self.assertIsInstance(result, dict)
self.assertGreater(len(result), 0)
self.assertEqual(set(result.keys()), expected_keys)
def test_search_results_slicing(self):
query = "Insulin AND (reviewed:true)"
results = UniProt.search(query, batch_size=25)
results_sliced = results[:50]
self.assertEqual(50, len(results_sliced))
results_list = list(islice(results, 50))
self.assertEqual(50, len(results_list))
self.assertEqual(results_sliced, results_list)
# We need to fetch the results again to reset the iterator
results = UniProt.search(query, batch_size=25)
results_sliced = results[49:30:-1]
self.assertEqual(19, len(results_sliced))
results_list = list(islice(results, 50))[49:30:-1]
self.assertEqual(19, len(results_list))
self.assertEqual(results_sliced, results_list)
results_sliced = results[0:0]
self.assertEqual(0, len(results_sliced))
# This query should return less than 500 results.
query = "(organism_id:2697049) AND (reviewed:true)"
results = UniProt.search(query)
results_sliced = results[-10:-5]
self.assertEqual(5, len(results_sliced))
results_list = list(results)[-10:-5]
self.assertEqual(5, len(results_list))
self.assertEqual(results_sliced, results_list)
results = UniProt.search(query)
results_sliced = results[-1_000_001:1_000_000]
self.assertEqual(len(results), len(results_sliced))
results_list = list(results)[-1_000_001:1_000_000]
self.assertEqual(len(results_list), len(results))
self.assertEqual(results_sliced, results_list)
def test_search_results_indexing(self):
query = "(organism_id:2697049) AND (reviewed:true)"
results = UniProt.search(query)
self.assertIsInstance(results[0], dict)
self.assertIsInstance(results[-1], dict)
with self.assertRaises(IndexError):
_ = results[1_000_000]
with self.assertRaises(IndexError):
_ = results[-1_000_000]
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