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Merge pull request #6 from Copper3D-brids/dev
Updates for observations value formats
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,2 @@ | ||
| from .measurement import Measurement | ||
| from .elements import ObservationValue, Coding, CodeableConcept, Range, Ratio, Period, SampledData, Quantity |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| from typing import Optional, Literal, List | ||
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| class Quantity: | ||
| def __init__(self, value: Optional[float] = None, comparator: Optional[Literal["<", "<=", ">=", ">"]] = None, | ||
| unit: Optional[str] = None, system: Optional[str] = "http://unitsofmeasure.org", | ||
| code: Optional[str] = None): | ||
| """ | ||
| :param value: Numerical value (with implicit precision) for Observation | ||
| :param comparator: < | <= | >= | > - how to understand the value | ||
| :param unit: Unit representation | ||
| :param system: System that defines coded unit form | ||
| :param code: Coded form of the unit | ||
| """ | ||
| self.value = value | ||
| self.comparator = comparator | ||
| self.unit = unit | ||
| self.system = system | ||
| self.code = code | ||
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| def get(self): | ||
| quantity = { | ||
| "value": self.value if isinstance(self.value, float) or isinstance(self.value, int) else None, | ||
| "comparator": self.comparator if self.comparator in ["<", "<=", ">=", ">"] else None, | ||
| "unit": self.unit if isinstance(self.unit, str) else None, | ||
| "system": self.system if isinstance(self.system, str) else None, | ||
| "code": self.code if isinstance(self.code, str) else None | ||
| } | ||
| return {k: v for k, v in quantity.items() if v not in ("", None)} | ||
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| class Coding: | ||
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| def __init__(self, system: str = "", version: str = "", code: str = "", display: Optional[str] = None, | ||
| user_selected: Optional[bool] = None): | ||
| self.system = system | ||
| self.version = version | ||
| self.code = code | ||
| self.display = display | ||
| self.user_selected = user_selected | ||
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| def get(self): | ||
| coding = { | ||
| "system": self.system if isinstance(self.system, str) else None, | ||
| "version": self.version if isinstance(self.version, str) else None, | ||
| "code": self.code if isinstance(self.code, str) else None, | ||
| "display": self.display if isinstance(self.display, str) else None, | ||
| "userSelected": self.user_selected if isinstance(self.user_selected, bool) else None | ||
| } | ||
| return {k: v for k, v in coding.items() if v not in ("", None)} | ||
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| class CodeableConcept: | ||
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| def __init__(self, codings: List[Coding] = None, text: str = ""): | ||
| self.codings = codings | ||
| self.text = text | ||
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| def get(self): | ||
| codeableconcept = { | ||
| "coding": [coding.get() for coding in self.codings if isinstance(coding, Coding)] if isinstance( | ||
| self.codings, list) else None, | ||
| "text": self.text if isinstance(self.text, str) else None | ||
| } | ||
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| return {k: v for k, v in codeableconcept.items() if v not in ("", None, [])} | ||
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| class Range: | ||
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| def __init__(self, low: Optional[float] = None, high: Optional[float] = None): | ||
| self.low = low | ||
| self.high = high | ||
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| def get(self): | ||
| _range = { | ||
| "low": self.low if isinstance(self.low, float) else None, | ||
| "high": self.high if isinstance(self.high, float) else None | ||
| } | ||
| return {k: v for k, v in _range.items() if v not in ("", None)} | ||
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| class Ratio: | ||
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| def __init__(self, numerator: Optional[Quantity] = None, denominator: Optional[Quantity] = None): | ||
| self.numerator = numerator | ||
| self.denominator = denominator | ||
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| def get(self): | ||
| ratio = { | ||
| "numerator": self.numerator.get() if isinstance(self.numerator, Quantity) else None, | ||
| "denominator": self.denominator.get() if isinstance(self.denominator, Quantity) else None | ||
| } | ||
| return {k: v for k, v in ratio.items() if v not in ("", None)} | ||
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| class SampledData: | ||
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| def __init__(self, origin: str, period: float, dimensions: int, factor: Optional[float] = None, | ||
| lower_limit: Optional[float] = None, upper_limit: Optional[float] = None, data: Optional[str] = None): | ||
| self.origin = origin | ||
| self.period = period | ||
| self.dimensions = dimensions | ||
| self.factor = factor | ||
| self.lower_limit = lower_limit | ||
| self.upper_limit = upper_limit | ||
| self.data = data | ||
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| def get(self): | ||
| sampled_data = { | ||
| "origin": self.origin if isinstance(self.origin, str) else None, | ||
| "period": self.period if isinstance(self.period, float) else None, | ||
| "factor": self.factor if isinstance(self.factor, float) else None, | ||
| "lowerLimit": self.lower_limit if isinstance(self.lower_limit, float) else None, | ||
| "upperLimit": self.upper_limit if isinstance(self.upper_limit, float) else None, | ||
| "dimensions": self.dimensions if isinstance(self.dimensions, int) and self.dimensions > 0 else None, | ||
| "data": self.data if isinstance(self.data, str) else None | ||
| } | ||
| return {k: v for k, v in sampled_data.items() if v not in ("", None)} | ||
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| class Period: | ||
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| def __init__(self, start: str = '', end: str = ''): | ||
| self.start = start | ||
| self.end = end | ||
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| def get(self): | ||
| period = { | ||
| "start": self.start if isinstance(self.start, str) else None, | ||
| "end": self.end if isinstance(self.end, str) else None | ||
| } | ||
| return {k: v for k, v in period.items() if v not in ("", None)} | ||
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| class ObservationValue: | ||
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| def __init__(self, value_quantity: Optional[Quantity] = None, | ||
| value_codeable_concept: Optional[CodeableConcept] = None, value_string: Optional[str] = None, | ||
| value_boolean: Optional[bool] = None, value_integer: Optional[int] = None, | ||
| value_range: Optional[Range] = None, value_ratio: Optional[Ratio] = None, | ||
| value_sampled_data: Optional[SampledData] = None, value_time: Optional[str] = None, | ||
| value_date_time: Optional[str] = None, value_period: Optional[Period] = None): | ||
| self.value_quantity = value_quantity | ||
| self.value_codeable_concept = value_codeable_concept | ||
| self.value_string = value_string | ||
| self.value_boolean = value_boolean | ||
| self.value_integer = value_integer | ||
| self.value_range = value_range | ||
| self.value_ratio = value_ratio | ||
| self.value_sampled_data = value_sampled_data | ||
| self.value_time = value_time | ||
| self.value_date_time = value_date_time | ||
| self.value_period = value_period | ||
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| def get(self): | ||
| value = { | ||
| "valueQuantity": self.value_quantity.get() if isinstance(self.value_quantity, Quantity) else None, | ||
| "valueCodeableConcept": self.value_codeable_concept.get() if isinstance(self.value_codeable_concept, | ||
| CodeableConcept) else None, | ||
| "valueString": self.value_string if isinstance(self.value_string, str) else None, | ||
| "valueBoolean": self.value_boolean if isinstance(self.value_boolean, bool) else None, | ||
| "valueInteger": self.value_integer if isinstance(self.value_integer, int) else None, | ||
| "valueRange": self.value_range.get() if isinstance(self.value_range, Range) else None, | ||
| "valueRatio": self.value_ratio.get() if isinstance(self.value_ratio, Ratio) else None, | ||
| "valueSampledData": self.value_sampled_data.get() if isinstance(self.value_sampled_data, | ||
| SampledData) else None, | ||
| "valueTime": self.value_time if isinstance(self.value_time, str) else None, | ||
| "valueDateTime": self.value_date_time if isinstance(self.value_date_time, str) else None, | ||
| "valuePeriod": self.value_period.get() if isinstance(self.value_period, Period) else None | ||
| } | ||
| return {k: v for k, v in value.items() if v not in ("", None)} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,36 +1,31 @@ | ||
| from typing import Union | ||
| from typing import Optional | ||
| from .elements import ObservationValue | ||
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| class Measurement: | ||
| def __init__(self, value: Union[str, int, float], code: str, units: str, code_system="http://loinc.org", | ||
| units_system="http://unitsofmeasure.org"): | ||
| def __init__(self, value: ObservationValue, code: str, code_system="http://loinc.org", | ||
| display: Optional[str] = None): | ||
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| if not isinstance(value, (str, int, float)) or isinstance(value, bool): | ||
| raise ValueError(f"value={value} is not an instance of any of the types in the tuple (str, int, float)") | ||
| if not isinstance(value, ObservationValue): | ||
| raise ValueError(f"value={value} is not an ObservationValue type") | ||
| elif not isinstance(code, str): | ||
| raise ValueError(f"code={code} is not an instance of type str") | ||
| elif not isinstance(units, str): | ||
| raise ValueError(f"units={units} is not an instance of type str") | ||
| elif not isinstance(code_system, str): | ||
| raise ValueError(f"value_system={code_system} is not an instance of type str") | ||
| elif not isinstance(units_system, str): | ||
| raise ValueError(f"units_system={units_system} is not an instance of type str") | ||
| elif display is not None and not isinstance(display, str): | ||
| raise ValueError(f"display={display} is not an instance of type str") | ||
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| self.value = value | ||
| self.code = code | ||
| self.units = units | ||
| self.code_system = code_system | ||
| self.units_system = units_system | ||
| self.display = display | ||
|
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| def __repr__(self): | ||
| return (f"Measurement(value={self.value}, code='{self.code}', units='{self.units}', " | ||
| f"value_system='{self.code_system}', units_system='{self.units_system}')") | ||
| return (f"Measurement(value={self.value}, code='{self.code}', value_system='{self.code_system}')") | ||
|
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| def get(self): | ||
| return { | ||
| "value": self.value, | ||
| measurement = { | ||
| "value": self.value.get(), | ||
| "code": self.code, | ||
| "units": self.units, | ||
| "codeSystem": self.code_system, | ||
| "unitsSystem": self.units_system | ||
| "display": self.display if isinstance(self.display, str) else "" | ||
| } | ||
| return {k: v for k, v in measurement.items() if v not in ("", None)} |
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