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Fix formatting with black

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This commit is contained in:
GotthardG
2024-12-16 10:41:56 +01:00
parent 57763970f9
commit a0be71bdfe
26 changed files with 1657 additions and 645 deletions
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204
backend/app/sample_models.py
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@ -6,16 +6,17 @@ from typing_extensions import Annotated
class SpreadsheetModel(BaseModel):
dewarname: str = Field(..., alias='dewarname')
puckname: str = Field(..., alias='puckname')
dewarname: str = Field(..., alias="dewarname")
puckname: str = Field(..., alias="puckname")
pucktype: Optional[str] = Field(None, alias="pucktype")
crystalname: Annotated[
str,
Field(...,
max_length=64,
title="Crystal Name",
description="max_length imposed by MTZ file header format https://www.ccp4.ac.uk/html/mtzformat.html",
alias='crystalname'
Field(
...,
max_length=64,
title="Crystal Name",
description="max_length imposed by MTZ file header format https://www.ccp4.ac.uk/html/mtzformat.html",
alias="crystalname",
),
]
positioninpuck: int # Only accept positive integers between 1 and 16
@ -26,17 +27,31 @@ class SpreadsheetModel(BaseModel):
oscillation: Optional[float] = None # Only accept positive float
exposure: Optional[float] = None # Only accept positive floats between 0 and 1
totalrange: Optional[int] = None # Only accept positive integers between 0 and 360
transmission: Optional[int] = None # Only accept positive integers between 0 and 100
transmission: Optional[int] = (
None # Only accept positive integers between 0 and 100
)
targetresolution: Optional[float] = None # Only accept positive float
aperture: Optional[str] = None # Optional string field
datacollectiontype: Optional[str] = None # Only accept "standard", other types might be added later
processingpipeline: Optional[str] = "" # Only accept "gopy", "autoproc", "xia2dials"
spacegroupnumber: Optional[int] = None # Only accept positive integers between 1 and 230
cellparameters: Optional[str] = None # Must be a set of six positive floats or integers
datacollectiontype: Optional[str] = (
None # Only accept "standard", other types might be added later
)
processingpipeline: Optional[str] = (
"" # Only accept "gopy", "autoproc", "xia2dials"
)
spacegroupnumber: Optional[int] = (
None # Only accept positive integers between 1 and 230
)
cellparameters: Optional[str] = (
None # Must be a set of six positive floats or integers
)
rescutkey: Optional[str] = None # Only accept "is" or "cchalf"
rescutvalue: Optional[float] = None # Must be a positive float if rescutkey is provided
rescutvalue: Optional[float] = (
None # Must be a positive float if rescutkey is provided
)
userresolution: Optional[float] = None
pdbid: Optional[str] = "" # Accepts either the format of the protein data bank code or {provided}
pdbid: Optional[str] = (
"" # Accepts either the format of the protein data bank code or {provided}
)
autoprocfull: Optional[bool] = None
procfull: Optional[bool] = None
adpenabled: Optional[bool] = None
@ -48,7 +63,7 @@ class SpreadsheetModel(BaseModel):
dose: Optional[float] = None # Optional float field
# Add pucktype validation
@field_validator('pucktype', mode="before")
@field_validator("pucktype", mode="before")
@classmethod
def validate_pucktype(cls, v):
if v != "unipuck":
@ -56,7 +71,7 @@ class SpreadsheetModel(BaseModel):
return v
# Validators
@field_validator('dewarname', 'puckname', mode="before")
@field_validator("dewarname", "puckname", mode="before")
@classmethod
def dewarname_puckname_characters(cls, v):
if v:
@ -67,17 +82,19 @@ class SpreadsheetModel(BaseModel):
return v
raise ValueError("Value must be provided for dewarname and puckname.")
@field_validator('crystalname', mode="before")
@field_validator("crystalname", mode="before")
@classmethod
def parameter_characters(cls, v):
v = str(v).replace(" ", "_")
if re.search("\n", v):
assert v.isalnum(), "is not valid. newline character detected."
characters = re.sub("[._+-]", "", v)
assert characters.isalnum(), f" '{v}' is not valid. Only alphanumeric and . _ + - characters allowed."
assert (
characters.isalnum()
), f" '{v}' is not valid. Only alphanumeric and . _ + - characters allowed."
return v
@field_validator('directory', mode="before")
@field_validator("directory", mode="before")
@classmethod
def directory_characters(cls, v):
if v:
@ -85,37 +102,57 @@ class SpreadsheetModel(BaseModel):
if re.search("\n", v):
raise ValueError(f" '{v}' is not valid. newline character detected.")
valid_macros = ["{date}", "{prefix}", "{sgpuck}", "{puck}", "{beamline}", "{sgprefix}",
"{sgpriority}", "{sgposition}", "{protein}", "{method}"]
valid_macros = [
"{date}",
"{prefix}",
"{sgpuck}",
"{puck}",
"{beamline}",
"{sgprefix}",
"{sgpriority}",
"{sgposition}",
"{protein}",
"{method}",
]
pattern = re.compile("|".join(re.escape(macro) for macro in valid_macros))
v = pattern.sub('macro', v)
v = pattern.sub("macro", v)
allowed_chars = "[a-z0-9_.+-]"
directory_re = re.compile(f"^(({allowed_chars}*|{allowed_chars}+)*/*)*$", re.IGNORECASE)
directory_re = re.compile(
f"^(({allowed_chars}*|{allowed_chars}+)*/*)*$", re.IGNORECASE
)
if not directory_re.match(v):
raise ValueError(f" '{v}' is not valid. Value must be a valid path or macro.")
raise ValueError(
f" '{v}' is not valid. Value must be a valid path or macro."
)
return v
@field_validator('positioninpuck', mode="before")
@field_validator("positioninpuck", mode="before")
@classmethod
def positioninpuck_possible(cls, v):
if not isinstance(v, int) or v < 1 or v > 16:
raise ValueError(f" '{v}' is not valid. Value must be an integer between 1 and 16.")
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 1 and 16."
)
return v
@field_validator('priority', mode="before")
@field_validator("priority", mode="before")
@classmethod
def priority_positive(cls, v):
if v is not None:
try:
v = int(v)
if v <= 0:
raise ValueError(f" '{v}' is not valid. Value must be a positive integer.")
raise ValueError(
f" '{v}' is not valid. Value must be a positive integer."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a positive integer.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a positive integer."
) from e
return v
@field_validator('aperture', mode="before")
@field_validator("aperture", mode="before")
@classmethod
def aperture_selection(cls, v):
if v is not None:
@ -124,58 +161,76 @@ class SpreadsheetModel(BaseModel):
if v not in {1, 2, 3}:
raise ValueError(f" '{v}' is not valid. Value must be 1, 2, or 3.")
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be 1, 2, or 3.") from e
raise ValueError(
f" '{v}' is not valid. Value must be 1, 2, or 3."
) from e
return v
@field_validator('oscillation', 'targetresolution', mode="before")
@field_validator("oscillation", "targetresolution", mode="before")
@classmethod
def positive_float_validator(cls, v):
if v is not None:
try:
v = float(v)
if v <= 0:
raise ValueError(f" '{v}' is not valid. Value must be a positive float.")
raise ValueError(
f" '{v}' is not valid. Value must be a positive float."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a positive float.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a positive float."
) from e
return v
@field_validator('exposure', mode="before")
@field_validator("exposure", mode="before")
@classmethod
def exposure_in_range(cls, v):
if v is not None:
try:
v = float(v)
if not (0 <= v <= 1):
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 1.")
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 1."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 1.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 1."
) from e
return v
@field_validator('totalrange', mode="before")
@field_validator("totalrange", mode="before")
@classmethod
def totalrange_in_range(cls, v):
if v is not None:
try:
v = int(v)
if not (0 <= v <= 360):
raise ValueError(f" '{v}' is not valid. Value must be an integer between 0 and 360.")
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 0 and 360."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be an integer between 0 and 360.") from e
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 0 and 360."
) from e
return v
@field_validator('transmission', mode="before")
@field_validator("transmission", mode="before")
@classmethod
def transmission_fraction(cls, v):
if v is not None:
try:
v = int(v)
if not (0 <= v <= 100):
raise ValueError(f" '{v}' is not valid. Value must be an integer between 0 and 100.")
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 0 and 100."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be an integer between 0 and 100.") from e
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 0 and 100."
) from e
return v
@field_validator('datacollectiontype', mode="before")
@field_validator("datacollectiontype", mode="before")
@classmethod
def datacollectiontype_allowed(cls, v):
allowed = {"standard"} # Other types of data collection might be added later
@ -183,7 +238,7 @@ class SpreadsheetModel(BaseModel):
raise ValueError(f" '{v}' is not valid. Value must be one of {allowed}.")
return v
@field_validator('processingpipeline', mode="before")
@field_validator("processingpipeline", mode="before")
@classmethod
def processingpipeline_allowed(cls, v):
allowed = {"gopy", "autoproc", "xia2dials"}
@ -191,73 +246,93 @@ class SpreadsheetModel(BaseModel):
raise ValueError(f" '{v}' is not valid. Value must be one of {allowed}.")
return v
@field_validator('spacegroupnumber', mode="before")
@field_validator("spacegroupnumber", mode="before")
@classmethod
def spacegroupnumber_allowed(cls, v):
if v is not None:
try:
v = int(v)
if not (1 <= v <= 230):
raise ValueError(f" '{v}' is not valid. Value must be an integer between 1 and 230.")
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 1 and 230."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be an integer between 1 and 230.") from e
raise ValueError(
f" '{v}' is not valid. Value must be an integer between 1 and 230."
) from e
return v
@field_validator('cellparameters', mode="before")
@field_validator("cellparameters", mode="before")
@classmethod
def cellparameters_format(cls, v):
if v:
values = [float(i) for i in v.split(",")]
if len(values) != 6 or any(val <= 0 for val in values):
raise ValueError(f" '{v}' is not valid. Value must be a set of six positive floats or integers.")
raise ValueError(
f" '{v}' is not valid. Value must be a set of six positive floats or integers."
)
return v
@field_validator('rescutkey', 'rescutvalue', mode="before")
@field_validator("rescutkey", "rescutvalue", mode="before")
@classmethod
def rescutkey_value_pair(cls, values):
rescutkey = values.get('rescutkey')
rescutvalue = values.get('rescutvalue')
rescutkey = values.get("rescutkey")
rescutvalue = values.get("rescutvalue")
if rescutkey and rescutvalue:
if rescutkey not in {"is", "cchalf"}:
raise ValueError("Rescutkey must be either 'is' or 'cchalf'")
if not isinstance(rescutvalue, float) or rescutvalue <= 0:
raise ValueError("Rescutvalue must be a positive float if rescutkey is provided")
raise ValueError(
"Rescutvalue must be a positive float if rescutkey is provided"
)
return values
@field_validator('trustedhigh', mode="before")
@field_validator("trustedhigh", mode="before")
@classmethod
def trustedhigh_allowed(cls, v):
if v is not None:
try:
v = float(v)
if not (0 <= v <= 2.0):
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 2.0.")
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 2.0."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 2.0.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 2.0."
) from e
return v
@field_validator('chiphiangles', mode="before")
@field_validator("chiphiangles", mode="before")
@classmethod
def chiphiangles_allowed(cls, v):
if v is not None:
try:
v = float(v)
if not (0 <= v <= 30):
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 30.")
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 30."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a float between 0 and 30.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a float between 0 and 30."
) from e
return v
@field_validator('dose', mode="before")
@field_validator("dose", mode="before")
@classmethod
def dose_positive(cls, v):
if v is not None:
try:
v = float(v)
if v <= 0:
raise ValueError(f" '{v}' is not valid. Value must be a positive float.")
raise ValueError(
f" '{v}' is not valid. Value must be a positive float."
)
except (ValueError, TypeError) as e:
raise ValueError(f" '{v}' is not valid. Value must be a positive float.") from e
raise ValueError(
f" '{v}' is not valid. Value must be a positive float."
) from e
return v
class TELLModel(SpreadsheetModel):
@ -270,6 +345,7 @@ class SpreadsheetModel(BaseModel):
prefix: Optional[str]
folder: Optional[str]
class SpreadsheetResponse(BaseModel):
data: List[SpreadsheetModel] # Validated data rows as SpreadsheetModel instances
errors: List[Dict[str, Any]] # Errors encountered during validation
@ -283,4 +359,4 @@ class SpreadsheetResponse(BaseModel):
headers: Optional[List[str]] = None # Add headers if needed
__all__ = ['SpreadsheetModel', 'SpreadsheetResponse']
__all__ = ["SpreadsheetModel", "SpreadsheetResponse"]