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add skip validations to models.py #64

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add skip validations to models.py #64

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29 changes: 18 additions & 11 deletions openai_cfps/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ def generate_reagent_field(**kwargs):
description = kwargs.get("description", "")
out_of_stock = kwargs.get("out_of_stock", False)
default = kwargs.get("default", 0.0)

# Create the field description for Pydantic
out_of_stock_text = " Out of stock" if out_of_stock else ""
field_description = f"{description}, Components: {components}, Cost: {cost} USD/mL, Concentration: {concentration}, Category: {category}. {out_of_stock_text}"
Expand All @@ -48,6 +48,9 @@ class ReagentList(BaseModel):
# Reagents
# All values are in nanoliters with increments of 25nL

# Control flags (excluded from serialization so they're not treated as reagents)
skip_validation: bool = Field(default=False, exclude=True)

# Core Salt & Buffer Components
potassium_glutamate: float = generate_reagent_field(
concentration="0.85M",
Expand All @@ -59,7 +62,7 @@ class ReagentList(BaseModel):
default=0.0,
out_of_stock=False,
)

magnesium_glutamate: float = generate_reagent_field(
concentration="0.5M",
category="salts",
Expand Down Expand Up @@ -589,12 +592,13 @@ class ReagentList(BaseModel):
def validate_unavailable_reagents(self) -> bool:
unavailable_reagents = [
reagent for reagent, info in self.model_fields.items()
if info.json_schema_extra["out_of_stock"]
if not info.exclude and info.json_schema_extra.get("out_of_stock", False)
]
for reagent in unavailable_reagents:
assert getattr(self, reagent) == 0, (
f"{reagent} is out of stock and must be set to 0"
)
if not self.skip_validation:
for reagent in unavailable_reagents:
assert getattr(self, reagent) == 0, (
f"{reagent} is out of stock and must be set to 0"
)
return self

@model_validator(mode="after")
Expand All @@ -614,6 +618,8 @@ def validate_non_zero_default_values(self) -> bool:
"""
Values for non-zero reagents should match exactly what is defined in the model.
"""
if self.skip_validation:
return self
for key, value in self.model_dump().items():
default_value = self.model_fields[key].default
if default_value > 0:
Expand Down Expand Up @@ -687,7 +693,7 @@ def sample_cost(self) -> float:
return 0.02795 # Calculated from the cost of the reagents in the positive control mix
else:
return 0.0

cost_per_sample = 0.0
for reagent_name, reagent_value in self.reagent_list.model_dump().items():
reagent_field = ReagentList.model_fields[reagent_name]
Expand Down Expand Up @@ -737,7 +743,7 @@ def from_pherastar_data(cls, file_path: str) -> "LuminescenceResults":
"""
well_luminosity = cls.parse_pherastar_well_luminosity(file_path)
return cls(luminescence=well_luminosity)

def titer(self) -> Dict[str, float]:
"""
Calculate the concentration of the sample.
Expand Down Expand Up @@ -837,7 +843,7 @@ def from_pherastar_data(cls, file_path: str) -> "FluorescenceResults":

def titer(self) -> Dict[str, float]:
raise NotImplementedError("Titer calculation for fluorescence is not implemented yet")


class ConcentrationResults(BaseModel):
concentration_g_L: Dict[str, float]
Expand Down Expand Up @@ -997,7 +1003,8 @@ def get_plate_dataframe(self, include_qc=False) -> pd.DataFrame:
"""
Get the plate as a dataframe.
"""
reagent_columns = [f"{k}" for k in ReagentList.model_fields.keys()]
# Exclude non-reagent fields (e.g., control flags) from reagent columns
reagent_columns = [k for k, f in ReagentList.model_fields.items() if not f.exclude]
rows = []
sample_layout = self.get_plate_layout()
if self.luminescence_results:
Expand Down