def test_run_02(error, info):
"""It handles a timeout error."""
args = {'assembler': 'my_assembler', 'timeout': 10}
asm = BaseAssembler(args, 'cxn')
asm.assemble = MagicMock(side_effect=TimeoutError())
with pytest.raises(TimeoutError) as timeout_error:
asm.run()
error_msg = str(timeout_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
'Time ran out for the assembler after 0:00:10 (HH:MM:SS).')
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], asm.state['iteration'])
info.assert_called_once_with(expect)
# Python 3.6 formats exceptions differently so we need to do this
assert error.call_count == 1
regex = re.compile(
r'Time ran out for the assembler after 0:00:10 \(HH:MM:SS\)')
assert regex.match(error.call_args[0][0])
def test_initialize_iteration(self, blast_db, query_file, iteration):
output_files = [
'prefix/dir/' + f for f in [
'output.fasta', 'paired_1.fasta', 'paired_2.fasta',
'single_1.fasta', 'single_2.fasta', 'single_any.fasta'
]
]
assembler = BaseAssembler('args', 'db_conn')
assembler.iter_file = MagicMock(side_effect=output_files)
assembler.initialize_iteration(blast_db, query_file, iteration)
assert blast_db == assembler.state['blast_db']
assert query_file == assembler.state['query_file']
assert iteration == assembler.state['iteration']
assert assembler.file['long_reads'] == ''
assert output_files[0] == assembler.file['output']
assert output_files[1] == assembler.file['paired_1']
assert output_files[2] == assembler.file['paired_2']
assert output_files[3] == assembler.file['single_1']
assert output_files[4] == assembler.file['single_2']
assert output_files[5] == assembler.file['single_any']
assert assembler.file['paired_count'] == 0
assert assembler.file['single_1_count'] == 0
assert assembler.file['single_2_count'] == 0
assert assembler.file['single_any_count'] == 0
def test_run_02(error, info):
"""It handles a timeout error."""
args = {'assembler': 'my_assembler', 'timeout': 10}
asm = BaseAssembler(args, 'cxn')
asm.assemble = MagicMock(side_effect=TimeoutError())
with pytest.raises(TimeoutError) as timeout_error:
asm.run()
error_msg = str(timeout_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
'Time ran out for the assembler after 0:00:10 (HH:MM:SS).')
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], asm.state['iteration'])
info.assert_called_once_with(expect)
# Python 3.6 formats exceptions differently so we need to do this
assert error.call_count == 1
regex = re.compile(
r'Time ran out for the assembler after 0:00:10 \(HH:MM:SS\)')
assert regex.match(error.call_args[0][0])
def test_no_blast_hits_false(self, sra_blast_hits_count, info):
assembler = BaseAssembler('args', 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
sra_blast_hits_count.return_value = 1
assert not assembler.no_blast_hits()
info.assert_not_called()
def test_no_blast_hits_true(self, sra_blast_hits_count, info):
assembler = BaseAssembler('args', 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
sra_blast_hits_count.return_value = 0
assert assembler.no_blast_hits()
info.assert_called_once_with('No blast hits in iteration {}'.format(
assembler.state['iteration']))
def build_assembler(self):
args = {'bit_score': 44, 'contig_length': 55}
state = {
'blast_db': 'my_blast_db',
'query_file': 'my_query_file',
'query_target': 'my_query_name',
'iteration': 99
}
assembler = BaseAssembler(args, 'my_db_conn')
assembler.set_state(state['blast_db'], state['query_file'],
state['iteration'])
return assembler
def test_iter_dir(self, args, blast_db, query_file, iteration):
assume(re.search(r'\w', query_file))
assembler = BaseAssembler(args, 'db_conn')
assembler.set_state(blast_db, query_file, iteration)
base_blast_db = basename(blast_db)
base_query_file = basename(query_file) if iteration == 1 else ''
dir_name = '{}_{}_{:02d}'.format(base_blast_db, base_query_file,
iteration)
expect = join(args['temp_dir'], dir_name)
assert expect == assembler.iter_dir()
def build_assembler():
"""Build a generic assembler."""
args = {
'bit_score': 44,
'contig_length': 55,
'temp_dir': 'my_temp_dir',
'assembler': 'my_assembler'}
asm = BaseAssembler(args, 'my_db_conn')
asm.state = {
'blast_db': 'my_blast_db',
'query_file': 'my_query_file.seq',
'query_target': 'my_query_name',
'iter_dir': 'my_iter_dir',
'iteration': 99,
'cxn': 'my_cxn'}
return asm
def build_assembler():
"""Build a generic assembler."""
args = {
'bit_score': 44,
'contig_length': 55,
'temp_dir': 'my_temp_dir',
'assembler': 'my_assembler'
}
asm = BaseAssembler(args, 'my_db_conn')
asm.state = {
'blast_db': 'my_blast_db',
'query_file': 'my_query_file.seq',
'query_target': 'my_query_name',
'iter_dir': 'my_iter_dir',
'iteration': 99,
'cxn': 'my_cxn'
}
return asm
def setUp(self):
self.db_conn = 'db_conn'
self.args = {
'query': ['query_file_1', 'query_file_2'],
'blast_db': ['blast_db_1', 'blast_db_2'],
'iterations': 1,
'log_file': 'log_file_1',
'temp_dir': 'temp_dir_1'}
self.assembler = BaseAssembler(self.args, self.db_conn)
def set_up():
"""Setup a generic assembler."""
cxn = 'cxn'
args = {
'query': ['query_file_1', 'query_file_2'],
'blast_db': ['blast_db_1', 'blast_db_2'],
'iterations': 1,
'log_file': 'log_file_1',
'temp_dir': 'temp_dir_1'
}
assembler = BaseAssembler(args, cxn)
return args, cxn, assembler
def test_nothing_assembled_false(self, info):
assembler = BaseAssembler('args', 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.file['output'] = 'tests/data/load_seq1.txt'
assert not assembler.nothing_assembled()
info.assert_not_called()
def test_nothing_assembled_empty(self, info):
assembler = BaseAssembler('args', 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.file['output'] = 'tests/data/empty_file.txt'
assert assembler.nothing_assembled()
expect = 'No new assemblies in iteration {}'.format(
assembler.state['iteration'])
info.assert_called_once_with(expect)
def test_init(self, args, db_conn):
assembler = BaseAssembler(args, db_conn)
assert args == assembler.args
assert assembler.blast_only is False
assert [] == assembler.steps
assert {} == assembler.file
expected = {
'iteration': 0,
'query_target': '',
'query_file': '',
'blast_db': '',
'db_conn': db_conn
}
assert expected == assembler.state
def test_run_ok(self, info):
args = {'assembler': 'my_assembler', 'timeout': 10}
assembler = BaseAssembler(args, 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.assemble = MagicMock()
assembler.run()
info.assert_called_once_with('Assembling shards with {}: '
'iteration {}'.format(
args['assembler'],
assembler.state['iteration']))
def test_init_01():
"""It initializes an assembler object."""
asm = BaseAssembler('args', 'cxn')
assert asm.args == 'args'
assert asm.blast_only is False
assert asm.steps == []
assert asm.file == {}
expected = {
'iteration': 0,
'query_target': '',
'query_file': '',
'blast_db': '',
'iter_dir': '',
'cxn': 'cxn'
}
assert asm.state == expected
def test_run_called_process_error(self, error, info):
args = {'assembler': 'my_assembler', 'timeout': 10}
error_code = 88
cmd = 'my command'
error = subprocess.CalledProcessError(error_code, cmd)
assembler = BaseAssembler(args, 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.assemble = MagicMock(side_effect=error)
with pytest.raises(RuntimeError) as runtime_error:
assembler.run()
error_msg = str(runtime_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
"The assembler failed with error: Command 'my command' "
"returned non-zero exit status 88.")
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], assembler.state['iteration'])
info.assert_called_once_with(expect)
def test_work_path(self):
iter_dir = 'whatever'
assembler = BaseAssembler('args', 'db_conn')
assembler.iter_dir = MagicMock(return_value=iter_dir)
assert iter_dir == assembler.work_path()