def test_default_present_without_underscores_returns_empty(self):
stream = StringIO("default:\n - '-q foo'\n - '-P project'")
config = Config.from_stream(stream)
actual = config.default_params()
expected = ""
assert actual == expected
def test_default_present_returns_params(self):
stream = StringIO("__default__: '-q foo'")
config = Config.from_stream(stream)
actual = config.default_params()
expected = "-q foo"
assert actual == expected
def test_default_present_params_are_list_returns_params(self):
stream = StringIO("__default__:\n - '-q foo'\n - '-P project'")
config = Config.from_stream(stream)
actual = config.default_params()
expected = "-q foo -P project"
assert actual == expected
def test_no_default_returns_empty(self):
stream = StringIO("key: 'foo'")
config = Config.from_stream(stream)
actual = config.default_params()
expected = ""
assert actual == expected
def test_get_empty_returns_default(self):
stream = StringIO("")
config = Config.from_stream(stream)
key = "key"
actual = config.get(key)
assert actual is None
def test_rule_present_but_not_default_returns_rule_params(self):
stream = StringIO("rule:\n - '-P project'\n - '-q bar'")
config = Config.from_stream(stream)
rulename = "rule"
actual = config.params_for_rule(rulename)
expected = "-P project -q bar"
assert actual == expected
def test_no_default_or_rule_returns_empty(self):
stream = StringIO("key: 'foo'")
config = Config.from_stream(stream)
rulename = "a"
actual = config.params_for_rule(rulename)
expected = ""
assert actual == expected
def test_get_key_in_yaml(self):
stream = StringIO("key: 'foo'")
key = "key"
config = Config.from_stream(stream)
actual = config.get(key)
expected = "foo"
assert actual == expected
def test_rule_and_default_present_returns_default_and_rule_params(self):
stream = StringIO("__default__: '-q foo'\nrule:\n - '-P project'\n")
config = Config.from_stream(stream)
rulename = "rule"
actual = config.params_for_rule(rulename)
expected = "-q foo -P project"
assert actual == expected
def test_default_present_but_not_rule_returns_default_params(self):
stream = StringIO("__default__: '-q foo'")
config = Config.from_stream(stream)
rulename = "a"
actual = config.params_for_rule(rulename)
expected = "-q foo"
assert actual == expected
def test_get_key_not_in_yaml_returns_default(self):
stream = StringIO("key: 'foo'")
key = "bar"
default = "default"
config = Config.from_stream(stream)
actual = config.get(key, default)
expected = default
assert actual == expected
def test_rule_and_default_have_same_params_rule_params_take_precedent(
self):
stream = StringIO(
"__default__: '-q foo'\nrule:\n - '-P project'\n - '-q bar'")
config = Config.from_stream(stream)
rulename = "rule"
actual = config.params_for_rule(rulename)
expected = "-q bar -P project"
assert actual == expected
def test_resource_requirements_one_level_of_quoting(self):
config_string = """
__default__:
- "-R 'select[mem>2000] rusage[mem=2000]'"
"""
stream = StringIO(config_string)
config = Config.from_stream(stream)
actual = config.params_for_rule("rule")
expected = "-R 'select[mem>2000] rusage[mem=2000]'"
assert actual == expected
def test_resource_requirements_two_levels_of_quoting(self):
config_string = """
__default__:
- "-R \\"select[hname!='escaped-hostname']\\""
"""
stream = StringIO(config_string)
config = Config.from_stream(stream)
actual = config.params_for_rule("rule")
expected = "-R 'select[hname!='\"'\"'escaped-hostname'\"'\"']'"
assert actual == expected
def test_rule_specific_params_are_submitted(self, *mocks):
argv = [
"script_name",
"cluster_opt_1",
"cluster_opt_2",
"cluster_opt_3",
"real_jobscript.sh",
]
content = """
__default__:
- "-R 'select[mem>2000]'"
- '-gpu -'
search_fasta_on_index: '-P project'
"""
stream = StringIO(content)
lsf_config = Config.from_stream(stream)
memory_units = Unit.MEGA
jobscript = argv[-1]
cluster_cmds = argv[1:-1]
lsf_submit = Submitter(
jobscript=jobscript,
cluster_cmds=cluster_cmds,
memory_units=memory_units,
lsf_config=lsf_config,
)
actual = lsf_submit.submit_cmd
expected_mem = "2662"
expected_outlog = (
Path("logdir") / "search_fasta_on_index" / "i=0" / "jobid2_random.out"
)
expected_errlog = (
Path("logdir") / "search_fasta_on_index" / "i=0" / "jobid2_random.err"
)
expected_jobinfo_cmd = (
'-o "{outlog}" -e "{errlog}" -J "search_fasta_on_index.i=0"'
).format(outlog=expected_outlog, errlog=expected_errlog)
expected = (
"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 "
"-R 'select[mem>2000]' -gpu - -P project "
"real_jobscript.sh".format(mem=expected_mem, jobinfo=expected_jobinfo_cmd)
)
assert actual == expected
def test_lsf_mem_unit_is_tb_and_mem_mb_is_converted_and_rounded_up_to_int(
self, *mocks
):
argv = [
"script_name",
"cluster_opt_1",
"cluster_opt_2",
"cluster_opt_3",
"real_jobscript.sh",
]
content = (
"__default__:\n - '-q queue'\n - '-gpu -'\n"
"search_fasta_on_index: '-P project'"
)
stream = StringIO(content)
lsf_config = Config.from_stream(stream)
lsf_mem_unit = Unit.TERA
jobscript = argv[-1]
cluster_cmds = argv[1:-1]
lsf_submit = Submitter(
jobscript=jobscript,
cluster_cmds=cluster_cmds,
memory_units=lsf_mem_unit,
lsf_config=lsf_config,
)
actual = lsf_submit.submit_cmd
expected_mem = "1"
expected_outlog = (
Path("logdir") / "search_fasta_on_index" / "i=0" / "jobid2_random.out"
)
expected_errlog = (
Path("logdir") / "search_fasta_on_index" / "i=0" / "jobid2_random.err"
)
expected_jobinfo_cmd = (
'-o "{outlog}" -e "{errlog}" -J "search_fasta_on_index.i=0"'
).format(outlog=expected_outlog, errlog=expected_errlog)
expected = (
"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 "
"-q queue -gpu - -P project "
"real_jobscript.sh".format(mem=expected_mem, jobinfo=expected_jobinfo_cmd)
)
assert actual == expected
def test_only_keys_are_tested_for_membership(self):
stream = StringIO("key: 'foo'")
item = "foo"
config = Config.from_stream(stream)
assert item not in config
def test_item_in_config(self):
stream = StringIO("key: 'foo'")
item = "key"
config = Config.from_stream(stream)
assert item in config