def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump2.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
self.blast = BLASTNcbi(blast_type="remote",
voucher_code="CP100-10",
gene_code="COI-begin")
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLASTNcbi(voucher_code, gene_code)
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump2.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
self.blast = BLASTNcbi(blast_type="remote", voucher_code="CP100-10",
gene_code="COI-begin")
class TestNcbiBlast(TestCase):
def setUp(self):
args = []
opts = {
'dumpfile': settings.MEDIA_ROOT + 'test_data.xml',
'verbosity': 0
}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
self.blast = BLASTNcbi(blast_type="remote",
voucher_code="CP100-10",
gene_code="COI-begin")
@patch("Bio.Blast.NCBIWWW.qblast", return_value=ncbi_return_handle1)
def test_blast_with_accession_number_in_header(self, mock_qblast):
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.blast.delete_query_output_files()
self.assertTrue(len(result) > 0)
@patch("Bio.Blast.NCBIWWW.qblast", return_value=ncbi_return_handle2)
def test_index(self, mock_blast):
response = self.client.get('/blast_ncbi/CP100-10/COI-begin/')
self.assertEqual(200, response.status_code)
class TestNcbiBlast(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLASTNcbi(voucher_code, gene_code)
@unittest.skipIf(settings.TRAVIS is True,
'Testing using BLASTNcbi fails due to network problems')
def test_blast_with_accession_number_in_header(self):
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.blast.delete_query_output_files()
self.assertTrue(len(result) > 0)
@unittest.skipIf(settings.TRAVIS is True,
'Testing using BLASTNcbi fails due to network problems')
def test_index(self):
response = self.client.get('/blast_ncbi/CP100-10/COI/')
self.assertEqual(200, response.status_code)
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLASTNcbi(voucher_code, gene_code)
class TestNcbiBlast(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLASTNcbi(voucher_code, gene_code)
def test_blast_with_accession_number_in_header(self):
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.blast.delete_query_output_files()
self.assertTrue(len(result) > 0)
def test_index(self):
response = self.client.get('/blast_ncbi/CP100-10/COI/')
self.assertEqual(200, response.status_code)
class TestNcbiBlast(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump2.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
self.blast = BLASTNcbi(blast_type="remote", voucher_code="CP100-10",
gene_code="COI-begin")
@patch("Bio.Blast.NCBIWWW.qblast", return_value=ncbi_return_handle1)
def test_blast_with_accession_number_in_header(self, mock_qblast):
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.blast.delete_query_output_files()
self.assertTrue(len(result) > 0)
@patch("Bio.Blast.NCBIWWW.qblast", return_value=ncbi_return_handle2)
def test_index(self, mock_blast):
response = self.client.get('/blast_ncbi/CP100-10/COI-begin/')
self.assertEqual(200, response.status_code)
