def setUp(self):
self.client = ENASequenceSearchClient()
def setUp(self):
self.client = ENASequenceSearchClient()
class ENASequenceSearchTest(unittest.TestCase):
"""
Tests for the Python ENA REST API client.
"""
def setUp(self):
self.client = ENASequenceSearchClient()
def __verify_results(self, test_case):
"""
Verify that a predefined accession is present in the response text.
"""
# check whether the ENA accession is returned
data = self.client.search(test_case['sequence'], map_ids=False)
self.assertTrue(test_case['accession'] in json.dumps(data))
# check whether the RNAcentral ids are mapped correctly
data = self.client.search(test_case['sequence'], map_ids=True)
self.assertTrue(test_case['upi'] in json.dumps(data))
def test_find_itself_refseq_sequence(self):
"""
To test that RefSeq product is searched correctly.
"""
test_case = {
'sequence':
'UUUAAAUCAUACCAAUUGAACCGAGCCUUGUAGAAACACUAUCACCUACGCAUACCUCUGCUUCUUUUCAUUAACCUGCUAUCCUCUUUACAAAUGGGAUUCUUCACCCACUCCCUUCUUCUAGAUUAGCAAUGCCCUGUUAAGUAAACGAACACGAAAUUCAAAGGGAAACAGGAGCAAUCAUCAUUACCAGCUGCCGUGUUAAGCAUUGCGAAAACGCUCACGAUUCACAGAAAAAUCCAUGCUGUUCUUUGAAGGCAUUCAAGCCUUAAUAGCUAGCUGGAUGAAUGUUUAACUUCUAGGCCAGGCACUACUCUGUCCCAACAAUAAGCCCUGUACAUUGGGAAAGGUGCCGAGACAUGAACUUUGGUCUUCUCUGCAAUCCAUCUGGAGCAUUCACUGACAACAUCGACUUUGAAGUUGCACUGACCUGGCCAGCCCUGCCACUUACCAGGUUGGCUCUGUAUGGCUAAGCGUUUUCUCCUAAAAUCCCUUGAAAACUGUGAGAAGACCAUAAGAAGAUCAUAUCUUUAAUUCUAUUUCACAAGUCACACAAUAUUCCAAUCAAAUACAGAUGGUUGAGAAAAGUCAUCCAUCUUCCCUCCCCACCCUCCCACAGCCCCUCAACCACUGCCCUGAAACUUAUAUGCUGUUAUCCGCAGCUCCAUCUGGAGCAUCACAGCUACUGUCAACCCUGACGCUCUUUCUGAAAAAACACCGGAUGGACAUCAGAACUAUUUCUUUAAGGAUGUUACUGAGCCACACAGGAAAACUUGCCUUAUGAUUUUGAAUGCACGGAUCUGAUUUGACUAAACAUGAUAACUAGAGAAUCACCCAAUCUACUCCCAUUUUCAACUCUAAAUCAUCAGAGUGUCUCAAAUCCAAAGCACACACAGACCAGCCUGGCCAACACGGUGAAACUCCACCCCUACUAAAAGUAUAAAAAUUAUCCAGGUGUGGUGGCGGGCGCCUGUAAUCCAAGCUACUUGGGAGUCUGGAGGCAGGAGAAUCCCUUGAACCUGGGAGAUGGAGGUUGCAGUGAGCAGAGAUCACACCACCGCACUCUAGCCUGGGCCACAAAUCAACAACAACAACAACAACAAAAAACAAAGCGCACACAGAGACUGAGGUCCUCUUUGGCAUUGAGAAGAUGGCUAUGCAAGUCCCAACUAGCAAGUGCAAACUUCCCAGCUUCACUUCUGCCAGUGUCCCUUCACCCCUUCUCAACCCCACUGGGAGGCAGGAGGGUGCUUGACAAUAACAGCCUUGGCAUCACUCUGCCAGGGUGUAAUAGGAACUGUUACAAUUCUGAGAUUCUGUGUAAGCACUGGCCUUUCUGCCUAGAAUGCCUUCUCCUCUCUUUUUUAACUGCAUGCUCCUAUUUAUCUUUCAAAGCCCGGAAAAAAUAACACUGCACACGGGAAAUGCUCCCUUCCUACUGCAGUCAUUUAGAUGACUCUAUGCCAUUCCAUUCAUUUCUCUUUCCUACCACAGAAGUGCUUUGAGAUUUUGGAGUCAGACUGCUUGAACUUGAAUCCUGGCCCUCUCAUCAGAGACUUGACUUAUUUUAGGCAAGUUAUAUAACCAAUUUUACCUCAGUUCCUUACCCAUAAAAUGGGUCUAAUGAGAGUACCUACCACACAGAAUUUUGAUGAAAACUGAAUGAGAUGAAGGCCUUUAAGGCAGUGGUCCCCAACCCUGGGGACACAGACAGGUACCAUUUUGUGGCCUGUUAGGAACUGGGCCACACAGCAGGAGGUGAGCAGUGGGUGAGUGAGAUCAGCGUUAUUUACAGCUGCUCCCCAUUGCUCACCUUACUGCCUGAGCUCCACCUCCUGUCAGAUCAGCAGUGGCAUUAAAUUCUCAUAGCAGCACAAACCCUGUCAUGAACUGCACAUGCGAGGGAUCUAGGUUGUGCGCUCCUUAUGAGAAUCUAAUGCCUAAUGACCUGUCACCGUCUCCCAUCACCCCUAGAUGGGAGUGUCUAGUUGCAGGAAACAAGCUCAGGGCUUCCACUGAUUCUACAUUAUGGUGAGUUGUAUAAUUAUUUCAUUAUAUAAUACAAUGUAAUAAUAAUAGAAACACAGUGCACAACAAAUGUAAUGUGCUUGAAUCAUCCCCAAACCAUCCCAGUCCACGGUCUUCCACAUUUUGUCUUUUCACAAAAUUGUCUUCCACAAAACUGGUCCCUGGUGCCAAAAAGGCUUGGGACCACUGCUUUAAAGCCUUUGCAUAGUGCUUAGAAUUGAGGGGGAAAAAAAAAACAAAAACAAUGUAGCUAGUUGCUACAAUCACUAUAUUGGUGAGUUUCAAAAGGAAAAGAAUUCUGUCCCAUUUAUGCUUGAGCCUUGAGUUGCUAACCAAGCCUGACACAAAAUUACUGUUGAAGGGAUGUGUGAGUCCUAAUUGAAAUGAGGCCUCUUAAGGGAAUUGUGGACCAAACCCCAAGCAGGCAGAAAGCCGUAUCUUAAUUAUUGCAAGUAUUUCAGGCAAGGUGUGGAUGGCCAUUUGAAUUCAAGCAGACUAGGACCUGGGAUGAGAAAGAAGGUGUGUACGUGACUUGAUCUUUGAACUUUAGCUCACCAUCUGGAAGAAGGCUGAGUAUUCUCUGCACUCACAUAGUAGCUAAUGCCUACUCCCCAGCCACCCACAAUUCUUUCUGUAGGAAGGCUCGCUAGAAUACUUUGUGAUAUUGGAUAUUAGUUCCAUAUUCUACUGUGUAUCUUAGUUCAACCAAAUUGUAAUCAUCUGAUAUUUAUUUCUUUUAAUAUAAAUAUAAGUAUAUUAAGUCUUGG', # pylint: disable=line-too-long
'accession': 'NR_108049.1:1..2795:ncRNA',
'upi': 'URS000075ADFF',
}
self.__verify_results(test_case)
def test_find_itself_rdp_sequence(self):
"""
To test that RDP product is searched correctly.
"""
test_case = {
'sequence':
'UAAUUUGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAACGAACUCUGGUAUUGAUUGGUGCUUGCAUCAUGAUUUACAUUUGAGUGAGUGGCGAACUGGUGAGUAACACGUGGGAAACCUGCCCAGAAGCGGGGGAUAACACCUGGAAACAGAUGCUAAUACCGCAUAACAACUUGGACCGCAUGGUCCGAGUUUGAAAGAUGGCUUCGGCUAUCACUUUUGGAUGGUCCCGCGGCGUAUUAGCUAGAUGGUGAGGUAACGGCUCACCAUGGCAAUGAUACGUAGCCGACCUGAGAGGGUAAUCGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGACGAAAGUCUGAUGGAGCAACGCCGCGUGAGUGAAGAAGGGUUUCGGCUCGUAAAACUCUGUUGUUAAAGAAGAACAUAUCUGAGAGUAACUGUUCAGGUAUUGACGGUAUUUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAUUUAUUGGGCGUAAAGCGAGCGCAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCUUCGGCUCAACCGAAGAAGUGCAUCGGAAACUGGGAAACUUGAGUGCAGAAGAGGACAGUGGAACUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGUGGCGAAGGCGGCUGUCUGGUCUGUAACUGACGCUGAGGCUCGAAAGUAUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCAUACCGUAAACGAUGAAUGCUAAGUGUUGGAGGGUUUCCGCCCUUCAGUGCUGCAGCUAACGCAUUAAGCAUUCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCUACGCGAAGAACCUUACCAGGUCUUGACAUACUAUGCAAAUCUAAGAGAUUAGACGUUCCCUUCGGGGACAUGGAUACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUAUCAGUUGCCAGCAUUAAGUUGGGCACUCUGGUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGAUGGUACAACGAGUUGCGAACUCGCGAGAGUAAGCUAAUCUCUUAAAGCCAUUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGUUUGUAACACCCAAAGUCGGUGGGGUAACCUUUUAGGAACCAGCCGCCUAAGGUGGGACAGAUGAUUAGGGUGAAGUCGUAACAAGGUAGCCGUAGGAGAACCUGCGGCUGGAUCACCUCCUUU', # pylint: disable=line-too-long
'accession': 'CP006033.1:2356030..2357596:RDP',
'upi': 'URS000078956F',
}
self.__verify_results(test_case)
def test_find_itself_rfam_sequence(self):
"""
To test that RFAM product is searched correctly.
"""
test_case = {
'sequence':
'AACTACATTATCGATGTATAGATTCACCCGCGAGATGATGTGGCTGTTTCACCTAGGACGAGGACATGGCATCCTATTACCAGCCATCGCACGAAATTAATATGATGCCACGTCCTCATACTAGATGAAACAACCACGTCGTCATATCACAAGTGAATCCATTCATCGATAGTGTGGTT', # pylint: disable=line-too-long
'accession': 'AAAA02000007.1:34766..34944:rfam',
'upi': 'URS000063CC7F',
}
self.__verify_results(test_case)
def test_find_itself_minimum_length(self):
"""
20 nucleotides, minimum length
"""
test_case = {
'sequence': 'ACCAGUGUUCAGACGGUGGA',
'accession': 'DQ930848.1:1..20:misc_RNA',
'upi': 'URS00003989D1',
}
self.__verify_results(test_case)
def test_find_itself_interface_example_1(self):
"""
This sequence is used as an example in the user interface.
"""
test_case = {
'sequence': 'UGAGGUAGUAGAUUGUAUAGUU',
'accession': 'HAAO01000006.1:1..22:ncRNA',
'upi': 'URS00003B7674',
}
self.__verify_results(test_case)
def test_find_itself_interface_example_2(self):
"""
This sequence is used as an example in the user interface.
"""
test_case = {
'sequence':
'UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU',
'accession': 'CU928163.2:4660940..4661059:rRNA',
'upi': 'URS0000049E57',
}
self.__verify_results(test_case)
def test_find_itself_long_sequence(self):
"""
4000 nucleotides long.
"""
test_case = {
'sequence':
'GGGGUCUCGGGUCACGUGACAGGCGGCCCAAUCGCACUCGCGCGACGGAAAGCGCCACGGACGUCGGAGGCCCAGGGGGCGGGGCUCCCGAGCUCCGCUCUUUCGUGGUCGGGCGGCGGACCGCACUGUAUUUUUUCCUUCCGGGGGCGGCGGAGCCCAGGGCUAUCCCGGCCUCCGCUCAUACCCGGAGGGCCGGCAGGCGUUCAGUCCUCCAGCCGGUGAGGCUCGGGCCGGGGUGUCGGGACCGCCUGAACACGCGGGCUCUGGGAGCUUCAGGGACCAGGGAGCCACCUCGGCCGAGUUGCGUCGCAGACUACAGCUCCCAGCAUGCGCCGCCGCUCCCAGCAUGCACCUUCCUCCCGAAACGCGUCUCUGCUUCCGGCGCUCUGCUGCGGAGGCCGUGGCCGCGGGUAGUUGGGAGGAACCGAGAUUUACGCUUGGUAAGGCAAGUUGCGAGCUGUCCGGCGCCGGUCGAGUUCCUGCCGCCGUCGUCGUCAGGCAGGGGAGAAGGGGGCCUCAACCCCUCUAGUGACAGCUGUUUGCUACCUAAUAGGGCUUUUCAUCCCACCGGGCCCCAGGGCCUUCGUUAGGAGCCCAGCAGGCUCAACUUCUUGCUGUGGUUCUGGAAAAGGGAGUGACCACCUGGCUCAACACCUCUCUCUGUGAUGUGUUUGGGAGUUUUGGGAAAUGAGACGGCUCCGAGGGAAGAGCUUGAGGGAGCGGCGUCGCACUCGUUCGACCUUCCCGGGCCUGGGCUUUGUUUCUAGGCAUUUUAGGUUGAACGCUCUACAUCUUAACUGGGGGCAGGGGAGGUGGCCAGAGCAUCCCGCUGAGCGUUUUCCGAUUCCCCAGAUGGCCAGGCACCUGGUCCUGGUGGCUGGACAGUGACCCCGUGGACGCACAUUUACAGCUAUAGCCAUUCAGUGCCGCGGGGAGGUGAGGAUAGUGAUCCUGGGACCUGCUCGAGGAUUCACCCUUGCCCCAAGAACCUGUUCCAUUCCCAGGAAUGAAGGCGGUCAGGCAGGGGAGGAGAAGGGGGCCUCAACUCUUCUAGUGACAGCAGUUUGCCACCUAAUAGAGCUUUUCAGAUUUUGCCUCCUCAGGCCAUUUUACUCAGCCUCGGACUAUCAAGGAUGGUCACAUUGAAGCUGUUUUUCUGCAGUCAGGAGCGAAAAGUCCCGGCUGUUGAAGGAGAAACUGAAUCUGGUUCAGGAGUCCCAGGUUCCUCCCUCUGAGAGGCCAGGUGGGGCCUGCGUGAGUAGCAGUUGUUCAGGUGGCAGGACACUGCUGUUUUCAUCCCACCUGGCCCCAGGCCCCUGAUUAGGGGCCCAGAGUGCUUAUGUACUUGCCUCGGUCUGAGAAAGGGAGUGACUGCAUAGCCCAACACCUGUGGGAUGCCUCACUGCCCAGAUGUUUCAUCUCCGGGAUGCUUCAUUGCCCAUUCAGCACCCUCUAUGGUGCUGACUCUUCCGGAAGAUGUUUCUGAUUCCUUGCUAGGCUGGUGGUUGCACCAUAGCUGAGAGGACUCAAGAAGAGCCUGGUCUCAGCUUCACCUAGGAGUCCCGGAGGAGUAAGAAACACGUAUCUUUCCUGUUCUGGGCACAUAUGGGUGGGUAGCAGAGCUGAGGCUAGCUGAGGAUCCCGACUCUCCUUUGGGAGCCUUUGUUGUGCCGCUCUCCCAGGCUGAUCAGAUCUGGAGAGCUAACAGCUUCCUGUGGCCACAUCUGUGUCCAAGGCUGGGCCCAUGCCUGUAGCCAGAUUGCCAGGAUCUGGAAGGGGCCAAGAGACAGCUGGUGCUGGGUAGGCAGCAGCCCUGUGUCAACCUGCCCCCACUAUUACCCCAUGCUGUGAUUUGCAUGUGGUCUGCCCCUGCCCAAAAUGGUAUUGAAAUUUGAGCCUCAAUGAGGCAGUGUUAGGAGGUGGUGCCUAGUAGGAGGAGUUUGGGUAAUAGGGGUGGAUCCCUCAUGGAUAGGUUAGUGUCCUUUGUGGAGGGGUGAGUUCCCAUGAGAGCUGGUUAGAGAGUCAGCCUUCCUGCGGUUGUCUCUUGCUUCCUCUCUCGCCAUAUGGCCACGUAAUCUCUUUGUGCAUGCCUCUCCCCUUCUACUUGCUGCCUUGAGUUGAAGUAGCAUGAGGCCCUCACCAGGUGCAGCUGCCCAAUCUUGAAAUUUCCACCAGAAUUUUGAGCCAAAUAAACCUGUUUUGCUUUUUUAAAAAAAUAAAUUCCCCCACCUUGGCUGGGCGCAGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGCGGAUCACGAGGUCAGAUCGAGACCAUCUUGGCUAACACGGUGAAACCCCAUCUCUACUGAAAAAAAAAAAGAAACAAAAAAAUUAGCCAGGUGUGGUGGCGGGCACCUGUAGUCCCAGCCCCUCACUCGGGAGGCUGAUUGAGGCAGGAGAAUGGUGUGAACCCGGGAGGCGGAGCUUGCAGUGAGCCCAGAUCGCACCACUGCACUCCAGCCUGGGCGACAGAGCGAGACUCCGUCUCUAAAUAAAUAAAUAAAUAAAUAAAACAAACCCAACCUCAGGUAUAGCAGUGUGAAACAGACUAAGACAUUCCACAUGCCCUGUGGUCCCAUCUGCUACCCCAGGGUGCAAAGAUGUUCCCUCAGCCCUGAAGAAUGACAUUCCCCCCGGCUCCUGGGAUAUCUGGAGGGGUUGUAAGCAGCUUGGGUUGGUGAGAUAAGGAGUUUGGGGGGCAGCUGAUUCAUGACCCUGGCCUCCUCAACUGCAGGCUCUUGGUCUGAAGUACUGUAAUUAAAGUAUGAGAGCCUCGGGGCCCUCACUUCAAGGAGGGAAGAGCAUCCCCAUGCCUCAGCGUUUGGGGAUUGUAGGGAGAUGAGAGUCCUUCAGGUGGGACUAGUUCCCGCCAUGACCCCACUGCUGGCCAGUGGCCUGAAACGCAUCUGACCACUUCUCAGGUUCAUGGGUGUUGAGGAGGAGCCCUGUGGAAUCAACCCUGUCUGCCUCCUCUUAUCCUGCCACUCCUCUUGCUCUGUCUGGAUGACUGCCCUUGUUUUUCAAGGGAAUGUUCCCUGUCUUCCUCAGCCAGGAUUUUUUCUGAACUUGACAUCUCCGUUUGUUCAGGGGGCAAUCAUUGGGCACUUCACUGUGCUGGUCCUUGCAUUCUCAUGGAGAUGCAGAGAUUAAAAAUUAGUAUCUUGUCCACAUACUGCCCAGAGUUAGCAAGGAUUGCUUUUCUGUGGAUUUGUCUCAGGUCGGGCACAGUGGGGGUAGGGUCCUUCUCGAACCUUUUCCUAGCCUAAAGGUUCCAGCUGAAUCUUCCCAGGCAGGGCUGAAACAGGAACCAUUUUAGGCUUUGCUGCAACCCAUGGUCAGUUCUCCAAGAAAAGUGAAGAGGGUUCCACCUGGGGCAGCCCUCAAGGGCUCAGAGGGCCAAAACACACGUACAACAUGUUGAGACACUGAGUUUGUGCGAUCCCCACACAUCUCAGCAGUGAGUAUUUCUGCCUCAUUUUACCGAUGAGGAACCUGAGCUUCAAAGGGAAGAGGUGACAGCUCAGGACCACACAGCUGUAGGUAGGAGGCAGGAAAAUAGGGUCUGAGUGCAGGGAACAUAGGCUGAUUCACACUUCAGUUAUGAUAGGAAAUACCUUCUCCAUAGGACAUAGGCCAAGCAAAUGACUUUGUAACUUCAUCCUCUCCAUCUGCAUAACGUGUGCCCCAAGUAACCAAUGGAAUCACCUAGAGGGUGUUUAAACUCUCAGAAGUUCUGUAACAGGCUCUCCAUCUACAUAACGUGUGCCCCAAGUAACCAAUGGAAUCACCUAGAGGGUAUUUAAACUCUCUGAAGUUCUGUAACAGGGCUUUUGUGCUCCUAUGCUCAGGCUCACCCCCACACUGUGGAGUGUACUUUCAUUUUCAAUAAAUCCCUUCAUUCCUUCUUUGCUCUCUGUGUGUGUUUUGUCCAAUUCUUUAUUUAAGACGCCAAGAACCUGG', # pylint: disable=line-too-long
'accession': 'HG495355.1:1..4000:ncRNA',
'upi': 'URS000016DD3F',
}
self.__verify_results(test_case)
def test_too_short(self):
"""
Should raise an error.
"""
sequence = 'A' * 4
with self.assertRaises(InvalidSequenceError) as context_manager:
self.client.submit_query(sequence)
exc = context_manager.exception
self.assertEqual(exc.message, 'Invalid sequence')
def test_get_non_existing_session_id(self):
"""
Should raise an error.
"""
job_id = '1234' * 6
jsession_id = 'ABCD' * 6
with self.assertRaises(StatusNotFoundError) as context_manager:
self.client.get_status(job_id, jsession_id)
exc = context_manager.exception
class ENASequenceSearchTest(unittest.TestCase):
"""
Tests for the Python ENA REST API client.
"""
def setUp(self):
self.client = ENASequenceSearchClient()
def __verify_results(self, test_case):
"""
Verify that a predefined accession is present in the response text.
"""
# check whether the ENA accession is returned
data = self.client.search(test_case['sequence'], map_ids=False)
self.assertTrue(test_case['accession'] in json.dumps(data))
# check whether the RNAcentral ids are mapped correctly
data = self.client.search(test_case['sequence'], map_ids=True)
self.assertTrue(test_case['upi'] in json.dumps(data))
def test_find_itself_refseq_sequence(self):
"""
To test that RefSeq product is searched correctly.
"""
test_case = {
'sequence': 'UUUAAAUCAUACCAAUUGAACCGAGCCUUGUAGAAACACUAUCACCUACGCAUACCUCUGCUUCUUUUCAUUAACCUGCUAUCCUCUUUACAAAUGGGAUUCUUCACCCACUCCCUUCUUCUAGAUUAGCAAUGCCCUGUUAAGUAAACGAACACGAAAUUCAAAGGGAAACAGGAGCAAUCAUCAUUACCAGCUGCCGUGUUAAGCAUUGCGAAAACGCUCACGAUUCACAGAAAAAUCCAUGCUGUUCUUUGAAGGCAUUCAAGCCUUAAUAGCUAGCUGGAUGAAUGUUUAACUUCUAGGCCAGGCACUACUCUGUCCCAACAAUAAGCCCUGUACAUUGGGAAAGGUGCCGAGACAUGAACUUUGGUCUUCUCUGCAAUCCAUCUGGAGCAUUCACUGACAACAUCGACUUUGAAGUUGCACUGACCUGGCCAGCCCUGCCACUUACCAGGUUGGCUCUGUAUGGCUAAGCGUUUUCUCCUAAAAUCCCUUGAAAACUGUGAGAAGACCAUAAGAAGAUCAUAUCUUUAAUUCUAUUUCACAAGUCACACAAUAUUCCAAUCAAAUACAGAUGGUUGAGAAAAGUCAUCCAUCUUCCCUCCCCACCCUCCCACAGCCCCUCAACCACUGCCCUGAAACUUAUAUGCUGUUAUCCGCAGCUCCAUCUGGAGCAUCACAGCUACUGUCAACCCUGACGCUCUUUCUGAAAAAACACCGGAUGGACAUCAGAACUAUUUCUUUAAGGAUGUUACUGAGCCACACAGGAAAACUUGCCUUAUGAUUUUGAAUGCACGGAUCUGAUUUGACUAAACAUGAUAACUAGAGAAUCACCCAAUCUACUCCCAUUUUCAACUCUAAAUCAUCAGAGUGUCUCAAAUCCAAAGCACACACAGACCAGCCUGGCCAACACGGUGAAACUCCACCCCUACUAAAAGUAUAAAAAUUAUCCAGGUGUGGUGGCGGGCGCCUGUAAUCCAAGCUACUUGGGAGUCUGGAGGCAGGAGAAUCCCUUGAACCUGGGAGAUGGAGGUUGCAGUGAGCAGAGAUCACACCACCGCACUCUAGCCUGGGCCACAAAUCAACAACAACAACAACAACAAAAAACAAAGCGCACACAGAGACUGAGGUCCUCUUUGGCAUUGAGAAGAUGGCUAUGCAAGUCCCAACUAGCAAGUGCAAACUUCCCAGCUUCACUUCUGCCAGUGUCCCUUCACCCCUUCUCAACCCCACUGGGAGGCAGGAGGGUGCUUGACAAUAACAGCCUUGGCAUCACUCUGCCAGGGUGUAAUAGGAACUGUUACAAUUCUGAGAUUCUGUGUAAGCACUGGCCUUUCUGCCUAGAAUGCCUUCUCCUCUCUUUUUUAACUGCAUGCUCCUAUUUAUCUUUCAAAGCCCGGAAAAAAUAACACUGCACACGGGAAAUGCUCCCUUCCUACUGCAGUCAUUUAGAUGACUCUAUGCCAUUCCAUUCAUUUCUCUUUCCUACCACAGAAGUGCUUUGAGAUUUUGGAGUCAGACUGCUUGAACUUGAAUCCUGGCCCUCUCAUCAGAGACUUGACUUAUUUUAGGCAAGUUAUAUAACCAAUUUUACCUCAGUUCCUUACCCAUAAAAUGGGUCUAAUGAGAGUACCUACCACACAGAAUUUUGAUGAAAACUGAAUGAGAUGAAGGCCUUUAAGGCAGUGGUCCCCAACCCUGGGGACACAGACAGGUACCAUUUUGUGGCCUGUUAGGAACUGGGCCACACAGCAGGAGGUGAGCAGUGGGUGAGUGAGAUCAGCGUUAUUUACAGCUGCUCCCCAUUGCUCACCUUACUGCCUGAGCUCCACCUCCUGUCAGAUCAGCAGUGGCAUUAAAUUCUCAUAGCAGCACAAACCCUGUCAUGAACUGCACAUGCGAGGGAUCUAGGUUGUGCGCUCCUUAUGAGAAUCUAAUGCCUAAUGACCUGUCACCGUCUCCCAUCACCCCUAGAUGGGAGUGUCUAGUUGCAGGAAACAAGCUCAGGGCUUCCACUGAUUCUACAUUAUGGUGAGUUGUAUAAUUAUUUCAUUAUAUAAUACAAUGUAAUAAUAAUAGAAACACAGUGCACAACAAAUGUAAUGUGCUUGAAUCAUCCCCAAACCAUCCCAGUCCACGGUCUUCCACAUUUUGUCUUUUCACAAAAUUGUCUUCCACAAAACUGGUCCCUGGUGCCAAAAAGGCUUGGGACCACUGCUUUAAAGCCUUUGCAUAGUGCUUAGAAUUGAGGGGGAAAAAAAAAACAAAAACAAUGUAGCUAGUUGCUACAAUCACUAUAUUGGUGAGUUUCAAAAGGAAAAGAAUUCUGUCCCAUUUAUGCUUGAGCCUUGAGUUGCUAACCAAGCCUGACACAAAAUUACUGUUGAAGGGAUGUGUGAGUCCUAAUUGAAAUGAGGCCUCUUAAGGGAAUUGUGGACCAAACCCCAAGCAGGCAGAAAGCCGUAUCUUAAUUAUUGCAAGUAUUUCAGGCAAGGUGUGGAUGGCCAUUUGAAUUCAAGCAGACUAGGACCUGGGAUGAGAAAGAAGGUGUGUACGUGACUUGAUCUUUGAACUUUAGCUCACCAUCUGGAAGAAGGCUGAGUAUUCUCUGCACUCACAUAGUAGCUAAUGCCUACUCCCCAGCCACCCACAAUUCUUUCUGUAGGAAGGCUCGCUAGAAUACUUUGUGAUAUUGGAUAUUAGUUCCAUAUUCUACUGUGUAUCUUAGUUCAACCAAAUUGUAAUCAUCUGAUAUUUAUUUCUUUUAAUAUAAAUAUAAGUAUAUUAAGUCUUGG', # pylint: disable=line-too-long
'accession': 'NR_108049.1:1..2795:ncRNA',
'upi': 'URS000075ADFF',
}
self.__verify_results(test_case)
def test_find_itself_rdp_sequence(self):
"""
To test that RDP product is searched correctly.
"""
test_case = {
'sequence': 'UAAUUUGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAACGAACUCUGGUAUUGAUUGGUGCUUGCAUCAUGAUUUACAUUUGAGUGAGUGGCGAACUGGUGAGUAACACGUGGGAAACCUGCCCAGAAGCGGGGGAUAACACCUGGAAACAGAUGCUAAUACCGCAUAACAACUUGGACCGCAUGGUCCGAGUUUGAAAGAUGGCUUCGGCUAUCACUUUUGGAUGGUCCCGCGGCGUAUUAGCUAGAUGGUGAGGUAACGGCUCACCAUGGCAAUGAUACGUAGCCGACCUGAGAGGGUAAUCGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGACGAAAGUCUGAUGGAGCAACGCCGCGUGAGUGAAGAAGGGUUUCGGCUCGUAAAACUCUGUUGUUAAAGAAGAACAUAUCUGAGAGUAACUGUUCAGGUAUUGACGGUAUUUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAUUUAUUGGGCGUAAAGCGAGCGCAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCUUCGGCUCAACCGAAGAAGUGCAUCGGAAACUGGGAAACUUGAGUGCAGAAGAGGACAGUGGAACUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGUGGCGAAGGCGGCUGUCUGGUCUGUAACUGACGCUGAGGCUCGAAAGUAUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCAUACCGUAAACGAUGAAUGCUAAGUGUUGGAGGGUUUCCGCCCUUCAGUGCUGCAGCUAACGCAUUAAGCAUUCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCUACGCGAAGAACCUUACCAGGUCUUGACAUACUAUGCAAAUCUAAGAGAUUAGACGUUCCCUUCGGGGACAUGGAUACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUAUCAGUUGCCAGCAUUAAGUUGGGCACUCUGGUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGAUGGUACAACGAGUUGCGAACUCGCGAGAGUAAGCUAAUCUCUUAAAGCCAUUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGUUUGUAACACCCAAAGUCGGUGGGGUAACCUUUUAGGAACCAGCCGCCUAAGGUGGGACAGAUGAUUAGGGUGAAGUCGUAACAAGGUAGCCGUAGGAGAACCUGCGGCUGGAUCACCUCCUUU', # pylint: disable=line-too-long
'accession': 'CP006033.1:2356030..2357596:RDP',
'upi': 'URS000078956F',
}
self.__verify_results(test_case)
def test_find_itself_rfam_sequence(self):
"""
To test that RFAM product is searched correctly.
"""
test_case = {
'sequence': 'AACTACATTATCGATGTATAGATTCACCCGCGAGATGATGTGGCTGTTTCACCTAGGACGAGGACATGGCATCCTATTACCAGCCATCGCACGAAATTAATATGATGCCACGTCCTCATACTAGATGAAACAACCACGTCGTCATATCACAAGTGAATCCATTCATCGATAGTGTGGTT', # pylint: disable=line-too-long
'accession': 'AAAA02000007.1:34766..34944:rfam',
'upi': 'URS000063CC7F',
}
self.__verify_results(test_case)
def test_find_itself_minimum_length(self):
"""
20 nucleotides, minimum length
"""
test_case = {
'sequence': 'ACCAGUGUUCAGACGGUGGA',
'accession': 'DQ930848.1:1..20:misc_RNA',
'upi': 'URS00003989D1',
}
self.__verify_results(test_case)
def test_find_itself_interface_example_1(self):
"""
This sequence is used as an example in the user interface.
"""
test_case = {
'sequence': 'UGAGGUAGUAGAUUGUAUAGUU',
'accession': 'HAAO01000006.1:1..22:ncRNA',
'upi': 'URS00003B7674',
}
self.__verify_results(test_case)
def test_find_itself_interface_example_2(self):
"""
This sequence is used as an example in the user interface.
"""
test_case = {
'sequence': 'UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU',
'accession': 'CU928163.2:4660940..4661059:rRNA',
'upi': 'URS0000049E57',
}
self.__verify_results(test_case)
def test_find_itself_long_sequence(self):
"""
4000 nucleotides long.
"""
test_case = {
'sequence': 'GGGGUCUCGGGUCACGUGACAGGCGGCCCAAUCGCACUCGCGCGACGGAAAGCGCCACGGACGUCGGAGGCCCAGGGGGCGGGGCUCCCGAGCUCCGCUCUUUCGUGGUCGGGCGGCGGACCGCACUGUAUUUUUUCCUUCCGGGGGCGGCGGAGCCCAGGGCUAUCCCGGCCUCCGCUCAUACCCGGAGGGCCGGCAGGCGUUCAGUCCUCCAGCCGGUGAGGCUCGGGCCGGGGUGUCGGGACCGCCUGAACACGCGGGCUCUGGGAGCUUCAGGGACCAGGGAGCCACCUCGGCCGAGUUGCGUCGCAGACUACAGCUCCCAGCAUGCGCCGCCGCUCCCAGCAUGCACCUUCCUCCCGAAACGCGUCUCUGCUUCCGGCGCUCUGCUGCGGAGGCCGUGGCCGCGGGUAGUUGGGAGGAACCGAGAUUUACGCUUGGUAAGGCAAGUUGCGAGCUGUCCGGCGCCGGUCGAGUUCCUGCCGCCGUCGUCGUCAGGCAGGGGAGAAGGGGGCCUCAACCCCUCUAGUGACAGCUGUUUGCUACCUAAUAGGGCUUUUCAUCCCACCGGGCCCCAGGGCCUUCGUUAGGAGCCCAGCAGGCUCAACUUCUUGCUGUGGUUCUGGAAAAGGGAGUGACCACCUGGCUCAACACCUCUCUCUGUGAUGUGUUUGGGAGUUUUGGGAAAUGAGACGGCUCCGAGGGAAGAGCUUGAGGGAGCGGCGUCGCACUCGUUCGACCUUCCCGGGCCUGGGCUUUGUUUCUAGGCAUUUUAGGUUGAACGCUCUACAUCUUAACUGGGGGCAGGGGAGGUGGCCAGAGCAUCCCGCUGAGCGUUUUCCGAUUCCCCAGAUGGCCAGGCACCUGGUCCUGGUGGCUGGACAGUGACCCCGUGGACGCACAUUUACAGCUAUAGCCAUUCAGUGCCGCGGGGAGGUGAGGAUAGUGAUCCUGGGACCUGCUCGAGGAUUCACCCUUGCCCCAAGAACCUGUUCCAUUCCCAGGAAUGAAGGCGGUCAGGCAGGGGAGGAGAAGGGGGCCUCAACUCUUCUAGUGACAGCAGUUUGCCACCUAAUAGAGCUUUUCAGAUUUUGCCUCCUCAGGCCAUUUUACUCAGCCUCGGACUAUCAAGGAUGGUCACAUUGAAGCUGUUUUUCUGCAGUCAGGAGCGAAAAGUCCCGGCUGUUGAAGGAGAAACUGAAUCUGGUUCAGGAGUCCCAGGUUCCUCCCUCUGAGAGGCCAGGUGGGGCCUGCGUGAGUAGCAGUUGUUCAGGUGGCAGGACACUGCUGUUUUCAUCCCACCUGGCCCCAGGCCCCUGAUUAGGGGCCCAGAGUGCUUAUGUACUUGCCUCGGUCUGAGAAAGGGAGUGACUGCAUAGCCCAACACCUGUGGGAUGCCUCACUGCCCAGAUGUUUCAUCUCCGGGAUGCUUCAUUGCCCAUUCAGCACCCUCUAUGGUGCUGACUCUUCCGGAAGAUGUUUCUGAUUCCUUGCUAGGCUGGUGGUUGCACCAUAGCUGAGAGGACUCAAGAAGAGCCUGGUCUCAGCUUCACCUAGGAGUCCCGGAGGAGUAAGAAACACGUAUCUUUCCUGUUCUGGGCACAUAUGGGUGGGUAGCAGAGCUGAGGCUAGCUGAGGAUCCCGACUCUCCUUUGGGAGCCUUUGUUGUGCCGCUCUCCCAGGCUGAUCAGAUCUGGAGAGCUAACAGCUUCCUGUGGCCACAUCUGUGUCCAAGGCUGGGCCCAUGCCUGUAGCCAGAUUGCCAGGAUCUGGAAGGGGCCAAGAGACAGCUGGUGCUGGGUAGGCAGCAGCCCUGUGUCAACCUGCCCCCACUAUUACCCCAUGCUGUGAUUUGCAUGUGGUCUGCCCCUGCCCAAAAUGGUAUUGAAAUUUGAGCCUCAAUGAGGCAGUGUUAGGAGGUGGUGCCUAGUAGGAGGAGUUUGGGUAAUAGGGGUGGAUCCCUCAUGGAUAGGUUAGUGUCCUUUGUGGAGGGGUGAGUUCCCAUGAGAGCUGGUUAGAGAGUCAGCCUUCCUGCGGUUGUCUCUUGCUUCCUCUCUCGCCAUAUGGCCACGUAAUCUCUUUGUGCAUGCCUCUCCCCUUCUACUUGCUGCCUUGAGUUGAAGUAGCAUGAGGCCCUCACCAGGUGCAGCUGCCCAAUCUUGAAAUUUCCACCAGAAUUUUGAGCCAAAUAAACCUGUUUUGCUUUUUUAAAAAAAUAAAUUCCCCCACCUUGGCUGGGCGCAGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGCGGAUCACGAGGUCAGAUCGAGACCAUCUUGGCUAACACGGUGAAACCCCAUCUCUACUGAAAAAAAAAAAGAAACAAAAAAAUUAGCCAGGUGUGGUGGCGGGCACCUGUAGUCCCAGCCCCUCACUCGGGAGGCUGAUUGAGGCAGGAGAAUGGUGUGAACCCGGGAGGCGGAGCUUGCAGUGAGCCCAGAUCGCACCACUGCACUCCAGCCUGGGCGACAGAGCGAGACUCCGUCUCUAAAUAAAUAAAUAAAUAAAUAAAACAAACCCAACCUCAGGUAUAGCAGUGUGAAACAGACUAAGACAUUCCACAUGCCCUGUGGUCCCAUCUGCUACCCCAGGGUGCAAAGAUGUUCCCUCAGCCCUGAAGAAUGACAUUCCCCCCGGCUCCUGGGAUAUCUGGAGGGGUUGUAAGCAGCUUGGGUUGGUGAGAUAAGGAGUUUGGGGGGCAGCUGAUUCAUGACCCUGGCCUCCUCAACUGCAGGCUCUUGGUCUGAAGUACUGUAAUUAAAGUAUGAGAGCCUCGGGGCCCUCACUUCAAGGAGGGAAGAGCAUCCCCAUGCCUCAGCGUUUGGGGAUUGUAGGGAGAUGAGAGUCCUUCAGGUGGGACUAGUUCCCGCCAUGACCCCACUGCUGGCCAGUGGCCUGAAACGCAUCUGACCACUUCUCAGGUUCAUGGGUGUUGAGGAGGAGCCCUGUGGAAUCAACCCUGUCUGCCUCCUCUUAUCCUGCCACUCCUCUUGCUCUGUCUGGAUGACUGCCCUUGUUUUUCAAGGGAAUGUUCCCUGUCUUCCUCAGCCAGGAUUUUUUCUGAACUUGACAUCUCCGUUUGUUCAGGGGGCAAUCAUUGGGCACUUCACUGUGCUGGUCCUUGCAUUCUCAUGGAGAUGCAGAGAUUAAAAAUUAGUAUCUUGUCCACAUACUGCCCAGAGUUAGCAAGGAUUGCUUUUCUGUGGAUUUGUCUCAGGUCGGGCACAGUGGGGGUAGGGUCCUUCUCGAACCUUUUCCUAGCCUAAAGGUUCCAGCUGAAUCUUCCCAGGCAGGGCUGAAACAGGAACCAUUUUAGGCUUUGCUGCAACCCAUGGUCAGUUCUCCAAGAAAAGUGAAGAGGGUUCCACCUGGGGCAGCCCUCAAGGGCUCAGAGGGCCAAAACACACGUACAACAUGUUGAGACACUGAGUUUGUGCGAUCCCCACACAUCUCAGCAGUGAGUAUUUCUGCCUCAUUUUACCGAUGAGGAACCUGAGCUUCAAAGGGAAGAGGUGACAGCUCAGGACCACACAGCUGUAGGUAGGAGGCAGGAAAAUAGGGUCUGAGUGCAGGGAACAUAGGCUGAUUCACACUUCAGUUAUGAUAGGAAAUACCUUCUCCAUAGGACAUAGGCCAAGCAAAUGACUUUGUAACUUCAUCCUCUCCAUCUGCAUAACGUGUGCCCCAAGUAACCAAUGGAAUCACCUAGAGGGUGUUUAAACUCUCAGAAGUUCUGUAACAGGCUCUCCAUCUACAUAACGUGUGCCCCAAGUAACCAAUGGAAUCACCUAGAGGGUAUUUAAACUCUCUGAAGUUCUGUAACAGGGCUUUUGUGCUCCUAUGCUCAGGCUCACCCCCACACUGUGGAGUGUACUUUCAUUUUCAAUAAAUCCCUUCAUUCCUUCUUUGCUCUCUGUGUGUGUUUUGUCCAAUUCUUUAUUUAAGACGCCAAGAACCUGG', # pylint: disable=line-too-long
'accession': 'HG495355.1:1..4000:ncRNA',
'upi': 'URS000016DD3F',
}
self.__verify_results(test_case)
def test_too_short(self):
"""
Should raise an error.
"""
sequence = 'A'*4
with self.assertRaises(InvalidSequenceError) as context_manager:
self.client.submit_query(sequence)
exc = context_manager.exception
self.assertEqual(exc.message, 'Invalid sequence')
def test_get_non_existing_session_id(self):
"""
Should raise an error.
"""
job_id = '1234'*6
jsession_id = 'ABCD'*6
with self.assertRaises(StatusNotFoundError) as context_manager:
self.client.get_status(job_id, jsession_id)
exc = context_manager.exception
