def test_get_with_reference(requireMocking):
# store data
tm = TableManager()
table = tm.get_acquisition_table()
item = {
'sample': '180415dZKsa20_1',
'experiment': '12345',
'acquisition': {
'instrument': 'Leco GC-Tof',
'name': 'GCTOF',
'ionisation': 'positive',
'method': 'gcms'
},
'metadata': {
'class': '382172',
'species': 'rat',
'organ': 'tissue'
},
'userdata': {
'label': 'GP_S_6_006',
'comment': ''
},
'processing': {
'method': 'gcms | test | test | positive'
},
'time': 1525121375499,
'id': '180415dZKsa20_1',
'references': [{
'name': 'minix',
'value': '12345'
}]
}
try:
validate(item, __ACQUISITION_SCHEMA__)
table.put_item(Item=tm.sanitize_json_for_dynamo(item))
except ValidationException as vex:
result = None
fail(str(vex.body))
except ClientError as cer:
result = None
fail(str(cer.response))
# process data
result = get.get({"pathParameters": {"sample": "180415dZKsa20_1"}}, {})
assert result['statusCode'] == 200
assert json.loads(result['body'])["id"] == "180415dZKsa20_1"
assert json.loads(
result['body'])["acquisition"]["instrument"] == "Leco GC-Tof"
assert json.loads(result['body'])["references"][0]["name"] == "minix"
assert json.loads(result['body'])["references"][0]["value"] == "12345"
def test_get_experiment(requireMocking, sample_count):
tm = TableManager()
table = tm.get_acquisition_table()
try:
for x in range(0, sample_count):
table.put_item(Item=tm.sanitize_json_for_dynamo({
"sample": f"test-{x:06d}",
"experiment": "1",
"id": f"test-{x:06d}",
"acquisition": {
"instrument": "random",
"ionisation": "positive",
"method": "test-method"
},
"metadata": {
"class": f"{x%100}",
"species": "rat",
"organ": "tissue"
},
"userdata": {
"label": "GP_S_6_006",
"comment": ""
},
"processing": {
"method": "test-method | random | test | positive"
}
}))
except ValidationException as vex:
result = None
fail(str(vex.body))
except ClientError as cer:
result = None
fail(str(cer.response))
page_size = 3
result = experiment.get(
{'pathParameters': {
'experiment': '1',
'psize': page_size
}}, {})
data = json.loads(result['body'])
assert result['statusCode'] == 200
assert len(data['items']) == page_size
assert data['last_item']['id'] == 'test-000002'
class DynamoDBBasedConfigManager(ConfigManager):
"""
configuration manager based on key/value storage of data in dynamodb
"""
def email_sender(self) -> str:
result = str(
self._get_item("sender", "*****@*****.**", "notification"))
return result
def notification_enabled(self) -> bool:
return bool(
self._get_item("automatic_notifications", False, "notification"))
def notification_emails(self) -> List[str]:
result = list(
self._get_item("notify", ["*****@*****.**"],
"notification"))
return result
def __init__(self):
self.tm = TableManager()
self.table = self.tm.get_configuration_table()
def _default_singular_tasks(self) -> List[str]:
"""
default value for tasks, which can not run in parallel
"""
return [SECURE_CARROT_STEAC]
def _default_tasks(self) -> Dict:
"""
default values for tasks
"""
return {
SECURE_CARROT_RUNNER: 10,
SECURE_CARROT_AGGREGATOR: 1,
SECURE_CARROT_STEAC: 1
}
def tasks(self) -> Dict[str, int]:
result = self._get_item("tasks", self._default_tasks())
return result
def max_allowed_tasks(self) -> int:
result = int(self._get_item("max_concurrent_tasks", 20))
return result
def max_tasks_for_service(self, service: str) -> int:
result = int(self._get_item(service, self._default_tasks()[service]))
return result
def is_singular(self, name: str) -> bool:
return name in self.singular_tasks()
def singular_tasks(self) -> List[str]:
return self._default_singular_tasks()
def automatic_scheduling(self) -> bool:
return bool(self._get_item("automatic_scheduling", True))
def _get_item(self, name, default_value, group: str = "fargate"):
results = self.table.query(KeyConditionExpression=Key("key").eq(name))
if results['Count'] == 0:
self.table.put_item(
Item=self.tm.sanitize_json_for_dynamo({
"key": name,
"range": group,
"value": default_value
}))
results = self.table.query(
KeyConditionExpression=Key("key").eq(name))
top = results['Items'][0]
return top['value']