def test_multiple_spaces_between_size_and_suffix_is_valid(self):
s = "500 MB"
actual = Memory.from_str(s)
expected = Memory(500, Unit.MEGA)
assert actual == expected
def test_suffix_is_case_insensitive(self):
s = "500zb"
actual = Memory.from_str(s).bytes()
expected = Memory(500, Unit.ZETTA).bytes()
assert actual == expected
def test_same_value_and_unit(self):
value = 50
unit = Unit.PETA
mem1 = Memory(value, unit)
mem2 = Memory(value, unit)
assert mem1 == mem2
def test_no_suffix_returns_bytes(self):
s = "500"
actual = Memory.from_str(s)
expected = Memory(500)
assert actual == expected
def test_bytes_suffix_is_valid(self):
s = "7B"
actual = Memory.from_str(s)
expected = Memory(7)
assert actual == expected
def test_no_suffix_and_float_returns_bytes(self):
s = "500.8"
actual = Memory.from_str(s)
expected = Memory(500.8)
assert actual == expected
def test_b_suffix_is_valid(self):
s = "500MB"
actual = Memory.from_str(s)
expected = Memory(500, Unit.MEGA)
assert actual == expected
def test_terabytes_to_megabytes(self):
memory = Memory(30, Unit.TERA)
desired_units = Unit.MEGA
actual = memory.to(desired_units)
expected = Memory(30000000, desired_units)
assert actual == expected
def test_bytes_to_megabytes(self):
memory = Memory(2500)
desired_units = Unit.MEGA
actual = memory.to(desired_units)
expected = Memory(0.0025, desired_units)
assert actual == expected
def test_bytes_to_kilobytes(self):
memory = Memory(10)
desired_units = Unit.KILO
actual = memory.to(desired_units)
expected = Memory(0.01, desired_units)
assert actual == expected
def test_different_value_same_unit(self):
value1 = 50
unit = Unit.PETA
mem1 = Memory(value1, unit)
value2 = 60
mem2 = Memory(value2, unit)
assert mem1 != mem2
def test_same_value_different_unit(self):
value = 50
unit1 = Unit.PETA
mem1 = Memory(value, unit1)
unit2 = Unit.KILO
mem2 = Memory(value, unit2)
assert mem1 != mem2
def test_memory_is_bytes_no_conversion_needed(self):
value = 40
mem = Memory(value)
actual = mem.bytes()
expected = value
assert actual == expected
def test_terabytes_to_kilobytes_in_binary(self):
memory = Memory(30, Unit.TERA)
desired_units = Unit.KILO
actual = memory.to(desired_units, decimal_multiples=False)
expected = Memory(32212254720, desired_units)
assert actual == expected
def test_bytes_to_bytes(self):
memory = Memory(10)
desired_units = Unit.BYTES
actual = memory.to(desired_units)
expected = Memory(10, desired_units)
assert actual == expected
def test_kilobytes_to_gigabytes(self):
memory = Memory(2500, Unit.KILO)
desired_units = Unit.GIGA
actual = memory.to(desired_units)
expected = Memory(0.0025, desired_units)
assert actual == expected
def test_memory_is_megabytes_conversion_needed(self):
value = 40
unit = Unit.MEGA
mem = Memory(value, unit)
actual = mem.bytes()
expected = 40000000
assert actual == expected
def test_large_floats_comparison(self):
value = 500
unit = Unit.ZETTA
mem = Memory(value, unit)
actual = mem.bytes()
expected = float(500000000000000000000000)
assert actual == expected
def test_float_as_value(self):
value = 0.5
unit = Unit.GIGA
mem = Memory(value, unit)
actual = mem.bytes()
expected = 500000000
assert actual == expected
def test_memory_is_kilobytes_nondecimal_returns_power_of_two(self):
value = 40
unit = Unit.KILO
mem = Memory(value, unit)
actual = mem.bytes(decimal_multiples=False)
expected = 40960
assert actual == expected
def test_memory_suffix():
mem = Memory(3, Unit.EXA)
actual = mem.suffix
expected = "EB"
assert actual == expected
def test_float_number_returns_float(self):
memory = Memory(50.2, Unit.ZETTA)
actual = str(memory)
expected = "50.2ZB"
assert actual == expected
def test_round_float_number_returns_int(self):
memory = Memory(50.0, Unit.KILO)
actual = str(memory)
expected = "50KB"
assert actual == expected
def test_memory_power():
mem = Memory(3, Unit.MEGA)
actual = mem.power
expected = 2
assert actual == expected
def test___several_trivial_getter_methods(self, *mocks):
argv = [
"script_name",
"cluster_opt_1",
"cluster_opt_2",
"cluster_opt_3",
"real_jobscript.sh",
]
memory_units = Unit.KILO
memory_mb_value = 2662
jobscript = argv[-1]
cluster_cmds = argv[1:-1]
lsf_submit = Submitter(jobscript=jobscript,
cluster_cmds=cluster_cmds,
memory_units=memory_units)
self.assertEqual(lsf_submit.jobscript, "real_jobscript.sh")
self.assertEqual(lsf_submit.cluster_cmd,
"cluster_opt_1 cluster_opt_2 cluster_opt_3")
self.assertEqual(lsf_submit.threads, 1)
self.assertEqual(lsf_submit.mem_mb, Memory(memory_mb_value, Unit.MEGA))
self.assertEqual(lsf_submit.jobid, "2")
expected_wildcards_str = "i=0"
self.assertEqual(lsf_submit.wildcards_str, expected_wildcards_str)
expected_rule_name = "search_fasta_on_index"
self.assertEqual(lsf_submit.rule_name, expected_rule_name)
self.assertEqual(lsf_submit.is_group_jobtype, False)
expected_mem = "{}000".format(memory_mb_value)
expected_resource_cmd = (
"-M {mem} -n 1 -R 'select[mem>{mem}] rusage[mem={mem}] span[hosts=1]'"
).format(mem=expected_mem)
self.assertEqual(
lsf_submit.resources_cmd,
expected_resource_cmd,
)
self.assertEqual(lsf_submit.jobname, "search_fasta_on_index.i=0")
expected_logdir = Path(
"logdir") / expected_rule_name / expected_wildcards_str
self.assertEqual(lsf_submit.logdir, expected_logdir)
expected_outlog = expected_logdir / "jobid2_random.out"
self.assertEqual(lsf_submit.outlog, expected_outlog)
expected_errlog = expected_logdir / "jobid2_random.err"
self.assertEqual(lsf_submit.errlog, expected_errlog)
expected_jobinfo_cmd = (
'-o "{outlog}" -e "{errlog}" -J "search_fasta_on_index.i=0"'
).format(outlog=expected_outlog, errlog=expected_errlog)
self.assertEqual(
lsf_submit.jobinfo_cmd,
expected_jobinfo_cmd,
)
self.assertEqual(lsf_submit.queue_cmd, "-q q1")
self.assertEqual(
lsf_submit.submit_cmd,
"bsub -M {mem} -n 1 -R 'select[mem>{mem}] rusage[mem={mem}] span[hosts=1]' "
"{jobinfo} -q q1 cluster_opt_1 cluster_opt_2 cluster_opt_3 "
"real_jobscript.sh".format(mem=expected_mem,
jobinfo=expected_jobinfo_cmd),
)
def test_empty_string_raises_error(self):
s = ""
with pytest.raises(InvalidMemoryString):
Memory.from_str(s)
def test_different_value_different_unit_different_bytes(self):
mem1 = Memory(500, Unit.KILO)
mem2 = Memory(0.5, Unit.GIGA)
assert mem1 != mem2
def test_invalid_suffix_raises_error(self):
s = "7LB"
with pytest.raises(InvalidMemoryString):
Memory.from_str(s)
def test_suffix_only_raises_error(self):
s = "TB"
with pytest.raises(InvalidMemoryString):
Memory.from_str(s)
def test_string_with_other_characters_raises_error(self):
s = "7KBY"
with pytest.raises(InvalidMemoryString):
Memory.from_str(s)