180 lines
4.8 KiB
Python
180 lines
4.8 KiB
Python
import requests
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from dataclasses import dataclass, asdict, fields
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from typing import Optional, Iterator
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DEFAULT_URL = "http://localhost:8444"
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@dataclass(frozen=True)
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class TemplateSet:
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TemplateId: int
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BatchCount: int
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@dataclass(frozen=True)
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class OrderRecipe:
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Description: str
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User: str
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Template: TemplateSet
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@dataclass(frozen=True)
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class OrderSample:
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Id: int
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OrderId: int
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PlateProtocolId: int
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Barcode: str
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class DataclassFromDict:
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@classmethod
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def from_dict(cls, env):
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return cls(**{
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k: v for k, v in env.items()
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if k in [x.name for x in fields(cls)]
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})
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@dataclass(frozen=True)
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class Order(DataclassFromDict):
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Id: int
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State: str
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ProtocolId: str
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ProtocolName: str
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StartTime: str
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EndTime: str
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OrderSamples: [OrderSample]
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@dataclass(frozen=True)
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class OrderParameter(DataclassFromDict):
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ProtocolParameterId: int
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RunOrderId: int
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OrderSampleId: int
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ParameterValue: str
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ParameterName: str
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Id: Optional[int] = None
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ParameterLevel: Optional[str] = None
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ParameterType: Optional[str] = None
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@dataclass(frozen=True)
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class ProtocolParameter(DataclassFromDict):
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Id: int
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ProtocolId: int
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ParameterName: str
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Name: str
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DefaultValue: str
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ParameterLevel: str
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ParameterType: str
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def serialize(obj) -> str:
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return asdict(obj, dict_factory=lambda x:
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{k: v for (k, v) in x if v is not None})
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def deserialize(obj: DataclassFromDict, json):
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return obj.from_dict(json)
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def create_order(baseUrl: str,
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templateSet: TemplateSet,
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User: str = "EAllison",
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Description: str = "Order generated by script") -> Order:
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recipe = OrderRecipe(Description=Description,
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User=User,
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Template=templateSet)
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recipe_json = serialize(recipe)
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print(recipe_json)
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req = requests.post(f"{baseUrl}/orders",
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json=recipe_json)
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if req.status_code == 200:
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req_json = req.json()
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order = deserialize(Order, req_json)
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return order
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else:
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print(req)
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return None
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def get_order_parameters(baseUrl: str,
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order: Order) -> [OrderParameter]:
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url = f"{baseUrl}/orders/{order.Id}/parameters"
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print(url)
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req = requests.get(url)
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if req.status_code == 200:
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res_json = req.json()
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return res_json
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def get_protocol_parameters(baseUrl: str,
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protocolId: int) -> [ProtocolParameter]:
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url = f"{baseUrl}/protocols/{protocolId}/parameters"
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req = requests.get(url)
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if req.status_code == 200:
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res_json = req.json()
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if res_json != []:
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return [deserialize(ProtocolParameter, x)
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for x in res_json]
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return None
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def set_sample_parameter(baseUrl: str,
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order: Order,
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parameter: ProtocolParameter,
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orderSampleId: int,
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value):
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newParameter = OrderParameter(RunOrderId=order.Id,
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ProtocolParameterId=parameter.Id,
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ParameterName=parameter.ParameterName,
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ParameterValue=value,
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OrderSampleId=orderSampleId
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)
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url = f"{baseUrl}/orders/{order.Id}/parameters"
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req_json = [serialize(newParameter)]
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print(url)
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print(req_json)
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req = requests.post(url, json=req_json)
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if req.status_code == 200:
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return req.json()
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if req.status_code == 400:
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if len(res_json := req.json()) == 1 and 'Message' in res_json:
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if 'already been created' in res_json['Message']:
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return True
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def get_order_samples(order: Order) -> Iterator[int]:
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return (sample['Id'] for sample in order.OrderSamples)
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def create_order_with_parameters(baseUrl: str,
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templateId: int,
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parameterName: str,
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parameterValues: [str],
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User: str = "EAllison",
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Description: str = "") -> Order:
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templateSet = TemplateSet(templateId, len(parameterValues))
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order = create_order(baseUrl, templateSet,
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User, Description)
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print(order)
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parameter = [x for x in
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get_protocol_parameters(baseUrl, order.ProtocolId)
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if x.ParameterName == parameterName][0]
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order_samples = get_order_samples(order)
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for (i, sampleId) in enumerate(order_samples):
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set_sample_parameter(baseUrl,
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order,
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parameter,
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sampleId,
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parameterValues[i])
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