def test_description_updated_sample_must_be_exported(requireMocking):
for x in range(0, 10):
# upload data
data = json.dumps({
"job": "1234567",
"sample": "abc_{}".format(x),
"state": "scheduled"
})
result = tracking.create({'body': data}, {})
result = tracking.description({
"pathParameters": {
"job": "1234567",
"psize": 25,
}
}, {})
assert result is not None
assert result['statusCode'] == 200
assert len(json.loads(result['body'])) == 10
for x in json.loads(result['body']):
print(x)
def test_description(requireMocking):
for x in range(0, 40):
# upload data
data = json.dumps({
"job": "1234567",
"sample": "abc_{}".format(x),
"state": "scheduled"
})
result = tracking.create({'body': data}, {})
result = tracking.description({
"pathParameters": {
"job": "1234567",
"psize": 25,
}
}, {})
assert result is not None
assert result['statusCode'] == 200
samples = json.loads(result['body'])
assert len(samples) == 25
result = tracking.description({
"pathParameters": {
"job": "1234567",
"psize": 25,
"last_key": samples[-1]['id']
}
}, {})
assert result is not None
assert result['statusCode'] == 200
assert len(json.loads(result['body'])) == 15
def test_status(requireMocking):
for x in range(0, 100):
# upload data
data = json.dumps({
"job": "123456",
"sample": "abc_{}".format(x),
"state": "scheduled"
})
# store in stasis or we doomed!!!
response = create.create({'body': json.dumps({'sample': 'abc_{}'.format(x), 'status': 'scheduled'})}, {})
# store in the job state table
result = tracking.create({'body': data}, {})
assert result['statusCode'] == 200
set_job_state(job="123456", method="test", profile="test",
state=SCHEDULED)
result = tracking.status({
"pathParameters": {
"job": "123456",
}
}, {})
assert result is not None
assert result['statusCode'] == 200
assert json.loads(result['body'])['job_state'] == 'scheduled'
for x in range(0, 10):
# pretend stasis has now exported the data
response = create.create({'body': json.dumps({'sample': 'abc_{}'.format(x), 'status': 'exported'})}, {})
calculate_job_state("123456")
result = tracking.status({
"pathParameters": {
"job": "123456",
}
}, {})
# since not yet aggregated, the job should be in state processing
assert json.loads(result['body'])['job_state'] == 'processing'
for x in range(0, 100):
# pretend all samples are finished
response = create.create({'body': json.dumps({'sample': 'abc_{}'.format(x), 'status': "finished"})}, {})
result = tracking.status({
"pathParameters": {
"job": "123456",
}
}, {})
monitor_jobs({}, {})
assert json.loads(result['body'])['job_state'] == PROCESSING
result = tracking.status({
"pathParameters": {
"job": "123456",
},
"body": json.dumps({
'job_state': FAILED
})
}, {})
assert json.loads(result['body'])['job_state'] == FAILED
def test_create_and_get(requireMocking):
# upload data
data = json.dumps({
"job": "12345",
"sample": "abc",
"state": "scheduled"
})
result = tracking.create({'body': data}, {})
# ensure status is correct
assert result is not None
assert result['statusCode'] == 200
result = tracking.get({
"pathParameters": {
"sample": "abc",
"job": "12345"
}
}, {})
assert result is not None
assert result['statusCode'] == 200
assert 'body' in result
result = json.loads(result['body'])
# upload new data
# ensure status is updated now
assert 'job' in result
assert 'sample' in result
assert 'state' in result
assert 'id' in result
assert result['id'] == '12345_abc'
assert result['state'] == 'scheduled'
# check if update works correctly
data = json.dumps({
"job": "12345",
"sample": "abc",
"state": "processing"
})
result = tracking.create({'body': data}, {})
calculate_job_state("12345")
result = tracking.get({
"pathParameters": {
"sample": "abc",
"job": "12345"
}
}, {})
assert result is not None
assert result['statusCode'] == 200
assert 'body' in result
result = json.loads(result['body'])
assert result['state'] == 'processing'
print(result)
assert 'past_states' in result
assert 'scheduled' in result['past_states']
def test_job_is_in_state_exported_even_with_a_failed_sample(requireMocking, mocked_10_sample_job):
for i in range(0, 10):
tracking.create({'body': json.dumps(
{
"job": "12345",
"sample": "abc_{}".format(i),
"state": "scheduled"
}
)}, {})
assert load_job_samples_with_states("12345")['abc_{}'.format(i)] == "scheduled"
# dummy stasis data which need to be in the system for this test to pass
new_states = [
{
"sample": "abc_{}".format(0),
"fileHandle": "abc_{}.d".format(0),
"priority": 1,
"time": 1563307359163,
"value": EXPORTED
},
{
"sample": "abc_{}".format(1),
"fileHandle": "abc_{}.d".format(1),
"priority": 100,
"time": 1563307360393,
"value": EXPORTED
},
{
"sample": "abc_{}".format(2),
"fileHandle": "abc_{}.mzml".format(2),
"priority": 200,
"time": 1563307361543,
"value": EXPORTED
},
{
"sample": "abc_{}".format(3),
"fileHandle": "abc_{}.mzml".format(3),
"priority": 300,
"time": 1563330092360,
"value": EXPORTED
},
{
"sample": "abc_{}".format(4),
"fileHandle": "abc_{}.mzml".format(4),
"priority": 410,
"time": 1563330183632,
"value": "exported"
},
{
"sample": "abc_{}".format(5),
"fileHandle": "abc_{}.mzml".format(5),
"priority": 420,
"time": 1563330184868,
"value": EXPORTED
},
{
"sample": "abc_{}".format(6),
"fileHandle": "abc_{}.mzml".format(6),
"priority": 430,
"time": 1563330189108,
"value": FAILED
},
{
"sample": "abc_{}".format(7),
"fileHandle": "abc_{}.mzml".format(7),
"priority": 440,
"time": 1563330190650,
"value": EXPORTED
},
{
"sample": "abc_{}".format(8),
"fileHandle": "abc_{}.mzml".format(8),
"priority": 900,
"time": 1563330244348,
"value": EXPORTED
},
{
"sample": "abc_{}".format(9),
"fileHandle": "abc_{}.mzml".format(8),
"priority": 900,
"time": 1563330244348,
"value": EXPORTED
}
]
for x in new_states:
set_sample_job_state(
sample=x['sample'],
job="12345",
state=x['value'],
reason="it's a test"
)
state = calculate_job_state(job="12345")
assert state == EXPORTED
def test_sync_currently_processing(requireMocking, mocked_10_sample_job):
tm = TableManager()
for i in range(0, 10):
tracking.create({'body': json.dumps(
{
"job": "12345",
"sample": "abc_{}".format(i),
"state": SCHEDULED
}
)}, {})
assert load_job_samples_with_states("12345")['abc_{}'.format(i)] == "scheduled"
# dummy stasis data which need to be in the system for this test to pass
tm.get_tracking_table().put_item(Item=
{
"experiment": "12345",
"id": "abc_{}".format(i),
"sample": "abc_{}".format(i),
"status": [
{
"fileHandle": "abc_{}.d".format(i),
"priority": 1,
"time": 1563307359163,
"value": "entered"
},
{
"fileHandle": "abc_{}.d".format(i),
"priority": 100,
"time": 1563307360393,
"value": "acquired"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 200,
"time": 1563307361543,
"value": "converted"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 300,
"time": 1563330092360,
"value": "scheduled"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 410,
"time": 1563330183632,
"value": "deconvoluted"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 420,
"time": 1563330184868,
"value": "corrected"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 430,
"time": 1563330189108,
"value": "annotated"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 440,
"time": 1563330190650,
"value": "quantified"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 450,
"time": 1563330244348,
"value": "replaced"
}
]
}
)
calculate_job_state(job="12345")
assert all(value == str(REPLACED) for value in load_job_samples_with_states("12345").values())