async def test_get_mutation_info_database():
item = js.Item(
run_type="mutations",
args={
"job_id": "4a21dd",
"job_type": "database",
"protein_id": "O00522",
"mutations": "E567Q",
},
)
loop = asyncio.get_running_loop()
mutation_info_list = await get_mutation_info(item)
mutation_info_list = await loop.run_in_executor(None,
resolve_mutation_info,
mutation_info_list)
assert len(mutation_info_list) >= 2
for idx, mutation_info in enumerate(mutation_info_list):
if idx == 0:
assert mutation_info.coi == COI.CORE
else:
assert mutation_info.coi == COI.INTERFACE
assert Path(config.DATA_DIR).joinpath(
mutation_info.structure_file).is_file()
protein_info = extract_protein_info(mutation_info)
_validate_protein_info(protein_info, mutation_info)
async def test_elaspic2_collect_loop(mock_update_mutation_scores):
el2_web_url = urljoin(config.ELASPIC2_URL, "jobs/229764931")
mutation_info_list = [
MutationInfo(
1,
structure_file="1MFG.pdb",
chain_id="A",
mutation="G1A",
protein_id="1mfg-local",
coi=COI.CORE,
el2_web_url=el2_web_url,
),
MutationInfo(
1,
structure_file="1MFG.pdb",
chain_id="A",
mutation="G1A",
protein_id="1mfg-local",
coi=COI.INTERFACE,
el2_web_url=el2_web_url,
),
]
mutation_info_wscores_list = [
mutation_info_list[0]._replace(
protbert_score=0.011648587882518768,
proteinsolver_score=0.7335909865796566,
el2_score=0.3672627929817027,
),
mutation_info_list[1]._replace(
protbert_score=0.019379954785108566,
proteinsolver_score=0.6837433353066444,
el2_score=-0.969817502829359,
),
]
item = js.Item(
run_type="mutations",
args={
"job_id": "unk",
"job_type": "database",
"protein_id": "XXX",
"mutations": "G1A,G1C",
},
)
item.el2_mutation_info_list.extend(mutation_info_list)
ds = js.DataStructures()
await ds.elaspic2_running_queue.put(item)
with return_on_call(
"elaspic_rest_api.jobsubmitter.elaspic2.asyncio.sleep"):
await js.elaspic2_collect_loop(ds)
mock_update_mutation_scores.assert_called_once_with(
item.args["job_type"], mutation_info_wscores_list)
def parse_input_data(
data_in: DataIn) -> List[Tuple[js.Item, js.Item, Set[js.Item]]]:
items_list = []
for data in data_in.mutations:
args: js.Args = data.dict() # type: ignore
args["job_id"] = data_in.job_id
args["job_email"] = data_in.job_email
args["job_type"] = data_in.job_type
validate_args(args)
s = js.Item(run_type="sequence", args=args)
m = js.Item(run_type="model", args=args)
muts = set()
for mutation in args["mutations"].split(","):
args1 = args.copy()
args1["mutations"] = mutation
mut = js.Item(run_type="mutations", args=args1)
muts.add(mut)
items_list.append((s, m, muts))
return items_list
def test_send_admin_email_it():
item = js.Item(
run_type="mutations",
args={
"job_id": "test-send-job-failed-email",
"job_type": "mutations",
"protein_id": "4dkl",
"mutations": "G1A",
},
)
return_code = js.email.send_admin_email(
item, system_command="echo 'hello world'", restarting=False
)
assert not return_code
def test_send_admin_email(sendmail: MagicMock, restarting: bool):
item = js.Item(
run_type="mutations",
args={
"job_id": "test-send-job-failed-email",
"job_type": "mutations",
"protein_id": "4dkl",
"mutations": "G1A",
},
)
return_code = js.email.send_admin_email(
item, system_command="echo 'hello world'", restarting=restarting
)
assert not return_code
assert sendmail.calledonce()
async def test_get_mutation_info_local():
item = js.Item(
run_type="mutations",
args={
"job_id": 1,
"job_type": "local",
"protein_id": "d822d7",
"mutations": "P37A"
},
)
loop = asyncio.get_running_loop()
mutation_info_list = await get_mutation_info(item)
mutation_info_list = await loop.run_in_executor(None,
resolve_mutation_info,
mutation_info_list)
assert len(mutation_info_list) >= 2
for idx, mutation_info in enumerate(mutation_info_list):
assert Path(mutation_info.structure_file).is_file()
if idx == 0:
assert mutation_info.coi == COI.CORE
else:
assert mutation_info.coi == COI.INTERFACE
protein_info = extract_protein_info(mutation_info)
_validate_protein_info(protein_info, mutation_info)