now with the heidi v1 spreadsheet validator
This commit is contained in:
GotthardG
@ -1,13 +1,6 @@
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"""
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Data model and validation for mandatory and single sample rows from
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spreadsheet. Can be imported by sample_importer.py and database services.
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"""
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import re
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from typing import Any, Optional, Union
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from pydantic import BaseModel, Field, validator
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from pydantic import BaseModel, Field, field_validator, AliasChoices
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from typing_extensions import Annotated
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@ -19,15 +12,15 @@ class SpreadsheetModel(BaseModel):
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crystalname: Annotated[
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str,
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Field(...,
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max_length=64,
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title="Crystal Name",
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description="""max_length imposed by MTZ file header format
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max_length=64,
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title="Crystal Name",
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description="""max_length imposed by MTZ file header format
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https://www.ccp4.ac.uk/html/mtzformat.html""",
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alias='crystalname'
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),
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alias='crystalname'
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),
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]
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positioninpuck: int
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priority: Optional[str]
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priority: Optional[int]
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comments: Optional[str]
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pinbarcode: Optional[str]
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directory: Optional[str]
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@ -55,20 +48,22 @@ class SpreadsheetModel(BaseModel):
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autoprocextraparams: Any = ""
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chiphiangles: Any = ""
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@validator("dewarname", "puckname")
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def dewarname_puckname_characters(cls, v, **kwargs):
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assert (
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len(str(v)) > 0
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), f"""" {v} " is not valid.
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value must be provided for all samples in spreadsheet."""
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v = str(v).replace(" ", "_")
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if re.search("\n", v):
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assert v.isalnum(), "is not valid. newline character detected."
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v = re.sub(r"\.0$", "", v)
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return v.upper()
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@field_validator('dewarname', 'puckname', mode="before")
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@classmethod
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def dewarname_puckname_characters(cls, v):
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if v:
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assert (
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len(str(v)) > 0
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), f"""" {v} " is not valid. Value must be provided for all samples in the spreadsheet."""
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v = str(v).replace(" ", "_")
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if re.search("\n", v):
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assert v.isalnum(), "is not valid. newline character detected."
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v = re.sub(r"\.0$", "", v)
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return v.upper()
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@validator("crystalname")
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def parameter_characters(cls, v, **kwargs):
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@field_validator('crystalname', mode="before")
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@classmethod
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def parameter_characters(cls, v):
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v = str(v).replace(" ", "_")
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if re.search("\n", v):
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assert v.isalnum(), "is not valid. newline character detected."
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@ -78,8 +73,9 @@ class SpreadsheetModel(BaseModel):
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v = re.sub(r"\.0$", "", v)
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return v
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@validator("directory")
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def directory_characters(cls, v, **kwargs):
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@field_validator('directory', mode="before")
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@classmethod
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def directory_characters(cls, v):
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if v:
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v = str(v).strip("/").replace(" ", "_")
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if re.search("\n", v):
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@ -116,8 +112,9 @@ class SpreadsheetModel(BaseModel):
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)
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return v
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@validator("positioninpuck", pre=True)
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def positioninpuck_possible(cls, v, **kwargs):
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@field_validator('positioninpuck', mode="before")
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@classmethod
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def positioninpuck_possible(cls, v):
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if v:
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try:
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v = int(float(v))
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@ -134,31 +131,37 @@ class SpreadsheetModel(BaseModel):
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raise ValueError("Value must be provided. Value must be from 1 to 16.")
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return v
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@validator("pucklocationindewar")
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def pucklocationindewar_convert_to_int(cls, v, **kwargs):
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return int(float(v)) if v else v
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@field_validator('pucklocationindewar', mode="before")
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@classmethod
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def pucklocationindewar_convert_to_str(cls, v):
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if v == "Unipuck":
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return v
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try:
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return str(int(float(v)))
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except ValueError:
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raise ValueError(f"Value error, could not convert string to float: '{v}'")
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@validator("priority")
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def priority_positive(cls, v, **kwargs):
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if v:
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@field_validator('priority', mode="before")
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@classmethod
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def priority_positive(cls, v):
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if v is not None:
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v = str(v).strip()
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v = re.sub(r"\.0$", "", v)
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try:
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if not int(v) > 0:
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if int(v) <= 0:
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raise ValueError(
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f"""" {v} " is not valid.
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value must be a positive integer."""
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f" '{v}' is not valid. Value must be a positive integer."
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)
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elif int(v) > 0:
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v = int(v)
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v = int(v)
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except (ValueError, TypeError) as e:
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raise ValueError(
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f"""" {v} " is not valid.
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value must be a positive integer."""
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f" '{v}' is not valid. Value must be a positive integer."
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) from e
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return v
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@validator("aperture")
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def aperture_selection(cls, v, **kwargs):
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@field_validator('aperture', mode="before")
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@classmethod
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def aperture_selection(cls, v):
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if v:
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try:
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v = int(float(v))
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@ -174,15 +177,17 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator(
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@field_validator(
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"oscillation",
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"exposure",
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"totalrange",
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"targetresolution",
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"rescutvalue",
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"userresolution",
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mode="before"
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)
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def parameter_positive_float(cls, v, **kwargs):
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@classmethod
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def parameter_positive_float(cls, v):
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if v:
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try:
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v = float(v)
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@ -198,8 +203,9 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator("transmission")
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def tranmission_fraction(cls, v, **kwargs):
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@field_validator('transmission', mode="before")
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@classmethod
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def tranmission_fraction(cls, v):
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if v:
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try:
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v = float(v)
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@ -217,8 +223,9 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator("datacollectiontype")
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def datacollectiontype_allowed(cls, v, **kwargs):
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@field_validator('datacollectiontype', mode="before")
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@classmethod
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def datacollectiontype_allowed(cls, v):
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if v:
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v = v.lower()
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allowed = ["standard", "serial-xtal", "multi-orientation"]
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@ -229,8 +236,9 @@ class SpreadsheetModel(BaseModel):
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)
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return v
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@validator("processingpipeline")
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def processingpipeline_allowed(cls, v, **kwargs):
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@field_validator('processingpipeline', mode="before")
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@classmethod
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def processingpipeline_allowed(cls, v):
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if v:
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v = v.lower()
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allowed = ["gopy", "autoproc", "xia2dials"]
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@ -241,8 +249,9 @@ class SpreadsheetModel(BaseModel):
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)
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return v
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@validator("spacegroupnumber")
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def spacegroupnumber_integer(cls, v, **kwargs):
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@field_validator('spacegroupnumber', mode="before")
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@classmethod
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def spacegroupnumber_integer(cls, v):
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if v:
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try:
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v = int(float(v))
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@ -258,8 +267,9 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator("cellparameters")
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def cellparameters_positive_floats(cls, v, **kwargs):
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@field_validator('cellparameters', mode="before")
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@classmethod
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def cellparameters_positive_floats(cls, v):
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if v:
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splitted = str(v).split(" ")
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if len(splitted) != 6:
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@ -279,8 +289,9 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator("rescutkey")
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def rescutkey_allowed(cls, v, **kwargs):
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@field_validator('rescutkey', mode="before")
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@classmethod
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def rescutkey_allowed(cls, v):
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if v:
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v = v.lower()
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allowed = ["is", "cchalf"]
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@ -288,8 +299,9 @@ class SpreadsheetModel(BaseModel):
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raise ValueError(f"' {v} ' is not valid. value must be ' {allowed} '.")
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return v
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@validator("autoprocfull", "procfull", "adpenabled", "noano", "ffcscampaign")
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def boolean_allowed(cls, v, **kwargs):
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@field_validator('autoprocfull', 'procfull', 'adpenabled', 'noano', 'ffcscampaign', mode="before")
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@classmethod
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def boolean_allowed(cls, v):
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if v:
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v = v.title()
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allowed = ["False", "True"]
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@ -300,8 +312,9 @@ class SpreadsheetModel(BaseModel):
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)
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return v
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@validator("trustedhigh")
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def trusted_float(cls, v, **kwargs):
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@field_validator('trustedhigh', mode="before")
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@classmethod
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def trusted_float(cls, v):
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if v:
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try:
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v = float(v)
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@ -319,8 +332,9 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator("proteinname")
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def proteinname_characters(cls, v, **kwargs):
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@field_validator('proteinname', mode="before")
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@classmethod
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def proteinname_characters(cls, v):
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if v:
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v = str(v).replace(" ", "_")
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if re.search("\n", v):
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@ -331,12 +345,13 @@ class SpreadsheetModel(BaseModel):
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v = re.sub(r"\.0$", "", v)
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return v
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@validator("chiphiangles")
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def chiphiangles_value(cls, v, **kwargs):
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@field_validator('chiphiangles', mode="before")
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@classmethod
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def chiphiangles_value(cls, v):
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if v:
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try:
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v = str(v)
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re.sub(r"(^\s*\[\s*|\s*\]\s*$)", "", v.strip())
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v = re.sub(r"(^\s*\[\s*|\s*\]\s*$)", "", v.strip())
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list_of_strings = re.findall(r"\(.*?\)", v)
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list_of_tuples = []
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for el in list_of_strings:
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@ -352,7 +367,7 @@ class SpreadsheetModel(BaseModel):
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) from e
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return v
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@validator(
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@field_validator(
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"priority",
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"comments",
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"pinbarcode",
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@ -380,12 +395,19 @@ class SpreadsheetModel(BaseModel):
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"ffcscampaign",
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"autoprocextraparams",
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"chiphiangles",
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mode="before"
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)
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def set_default_emptystring(cls, v, **kwargs):
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@classmethod
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def set_default_emptystring(cls, v):
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return v or ""
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class Config:
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anystr_strip_whitespace = True
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str_strip_whitespace = True
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aliases = {
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'dewarname': 'dewarname',
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'puckname': 'puckname',
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'crystalname': 'crystalname',
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}
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class TELLModel(SpreadsheetModel):
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@ -397,29 +419,3 @@ class TELLModel(SpreadsheetModel):
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puck_number: int
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prefix: Optional[str]
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folder: Optional[str]
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"""
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Following params appended in teller.py for updating SDU sample model
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class SDUTELLModel(TELLModel):
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sdudaq: str
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sdudiffcenter: str
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sduopticalcenter: str
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sdumount: str
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sdusafetycheck: str
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Following params returned in the format expected by tell.set_samples_info()
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{
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"userName": user,
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"dewarName": sample["dewarname"],
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"puckName": "", # FIXME at the moment this field is useless
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"puckType": "Unipuck",
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"puckAddress": sample["puckaddress"],
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"puckBarcode": sample["puckname"],
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"sampleBarcode": sample.get("pinbarcode", ""),
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"sampleMountCount": sample["samplemountcount"],
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"sampleName": sample["crystalname"],
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"samplePosition": sample["positioninpuck"],
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"sampleStatus": sample["samplestatus"],
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}
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"""
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