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lwark
@@ -22,11 +22,12 @@ from sqlalchemy.orm.relationships import _RelationshipDeclared
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from sqlalchemy.orm.attributes import InstrumentedAttribute
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from PyQt6.QtWidgets import QWidget
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logger = logging.getLogger(f"procedure.{__name__}")
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logger = logging.getLogger(f"submission.{__name__}")
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class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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_sql_object: ClassVar = None
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# _misc_info: dict|None = None
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@model_validator(mode="before")
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@@ -113,7 +114,8 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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if hasattr(self, "misc_info") and "info_placement" in self.misc_info:
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for k, v in output.items():
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try:
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output[k]['location'] = [item['location'] for item in self.misc_info['info_placement'] if item['name'] == k]
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output[k]['location'] = [item['location'] for item in self.misc_info['info_placement'] if
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item['name'] == k]
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except (TypeError, KeyError):
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continue
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return output
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@@ -128,9 +130,6 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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return sql
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class PydReagent(PydBaseClass):
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lot: str | None
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reagentrole: str | None
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@@ -299,9 +298,19 @@ class PydSample(PydBaseClass):
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@field_validator("row", mode="before")
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@classmethod
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def str_to_int(cls, value):
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def row_str_to_int(cls, value):
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if isinstance(value, str):
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value = row_keys[value]
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try:
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value = row_keys[value]
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except KeyError:
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value = 0
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return value
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@field_validator("column", mode="before")
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@classmethod
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def column_str_to_int(cls, value):
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if isinstance(value, str):
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value = 0
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return value
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def improved_dict(self, dictionaries: bool = True) -> dict:
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@@ -316,7 +325,7 @@ class PydSample(PydBaseClass):
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return sql
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class PydTips(BaseModel):
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class PydTips(PydBaseClass):
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name: str
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lot: str | None = Field(default=None)
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tiprole: str
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@@ -354,7 +363,7 @@ class PydTips(BaseModel):
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return assoc, report
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class PydEquipment(BaseModel, extra='ignore'):
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class PydEquipment(PydBaseClass, extra='ignore'):
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asset_number: str
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name: str
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nickname: str | None
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@@ -473,66 +482,74 @@ class PydEquipment(BaseModel, extra='ignore'):
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return {k: getattr(self, k) for k in fields}
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class PydSubmission(BaseModel, extra='allow'):
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filepath: Path
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submissiontype: dict | None
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submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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class PydRun(PydBaseClass, extra='allow'):
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clientsubmission: PydClientSubmission | None = Field(default=None)
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rsl_plate_number: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
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clientlab: dict | None
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started_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
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completed_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
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sample_count: dict | None
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kittype: dict | None
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technician: dict | None
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submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
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reagent: List[dict] | List[PydReagent] = []
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sample: List[PydSample] | Generator
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equipment: List[PydEquipment] | None = []
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cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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tips: List[PydTips] | None = []
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sample: List[PydSample] | Generator = Field(default=[])
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run_cost: float | dict = Field(default=dict(value=0.0, missing=True))
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signed_by: str | dict = Field(default="", validate_default=True)
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procedure: List[PydProcedure] | Generator = Field(default=[])
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@field_validator("tips", mode="before")
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@field_validator("signed_by")
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@classmethod
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def expand_tips(cls, value):
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if isinstance(value, dict):
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value = value['value']
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if isinstance(value, Generator):
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return [PydTips(**tips) for tips in value]
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if not value:
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return []
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def rescue_signed_by(cls, value):
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if isinstance(value, str):
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value = dict(value=value, missing=True)
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return value
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@field_validator('equipment', mode='before')
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# @field_validator("tips", mode="before")
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# @classmethod
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# def expand_tips(cls, value):
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# if isinstance(value, dict):
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# value = value['value']
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# if isinstance(value, Generator):
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# return [PydTips(**tips) for tips in value]
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# if not value:
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# return []
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# return value
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#
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# @field_validator('equipment', mode='before')
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# @classmethod
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# def convert_equipment_dict(cls, value):
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# if isinstance(value, dict):
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# return value['value']
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# if isinstance(value, Generator):
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# return [PydEquipment(**equipment) for equipment in value]
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# if not value:
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# return []
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# return value
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# @field_validator('comment', mode='before')
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# @classmethod
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# def create_comment(cls, value):
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# if value is None:
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# return ""
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# return value
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#
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# @field_validator("submitter_plate_id")
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# @classmethod
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# def enforce_with_uuid(cls, value):
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# if value['value'] in [None, "None"]:
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# return dict(value=uuid.uuid4().hex.upper(), missing=True)
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# else:
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# value['value'] = value['value'].strip()
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# return value
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@field_validator("run_cost")
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@classmethod
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def convert_equipment_dict(cls, value):
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if isinstance(value, dict):
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return value['value']
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if isinstance(value, Generator):
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return [PydEquipment(**equipment) for equipment in value]
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if not value:
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return []
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def rescue_run_cost(cls, value):
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if isinstance(value, float):
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value = dict(value=value, missing=False)
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return value
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@field_validator('comment', mode='before')
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@field_validator("started_date", mode="before")
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@classmethod
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def create_comment(cls, value):
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if value is None:
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return ""
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return value
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@field_validator("submitter_plate_id")
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@classmethod
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def enforce_with_uuid(cls, value):
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if value['value'] in [None, "None"]:
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return dict(value=uuid.uuid4().hex.upper(), missing=True)
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else:
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value['value'] = value['value'].strip()
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return value
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@field_validator("submitted_date", mode="before")
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@classmethod
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def rescue_date(cls, value):
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def rescue_start_date(cls, value):
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try:
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check = value['value'] is None
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except TypeError:
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@@ -541,9 +558,20 @@ class PydSubmission(BaseModel, extra='allow'):
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return dict(value=date.today(), missing=True)
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return value
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@field_validator("submitted_date")
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@field_validator("completed_date", mode="before")
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@classmethod
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def strip_datetime_string(cls, value):
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def rescue_completed_date(cls, value):
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try:
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check = value['value'] is None
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except TypeError:
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check = True
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if check:
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return dict(value=date.today(), missing=True)
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return value
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@field_validator("started_date")
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@classmethod
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def strip_started_datetime_string(cls, value):
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match value['value']:
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case date():
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output = datetime.combine(value['value'], datetime.min.time())
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@@ -567,35 +595,61 @@ class PydSubmission(BaseModel, extra='allow'):
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value['value'] = output.replace(tzinfo=timezone)
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return value
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@field_validator("clientlab", mode="before")
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@field_validator("completed_date")
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@classmethod
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def rescue_submitting_lab(cls, value):
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if value is None:
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return dict(value=None, missing=True)
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def strip_completed_datetime_string(cls, value):
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match value['value']:
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case date():
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output = datetime.combine(value['value'], datetime.min.time())
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case datetime():
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pass
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case int():
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output = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2)
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case str():
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string = re.sub(r"(_|-)\d(R\d)?$", "", value['value'])
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try:
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output = dict(value=parse(string).date(), missing=True)
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except ParserError as e:
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logger.error(f"Problem parsing date: {e}")
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try:
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output = parse(string.replace("-", "")).date()
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except Exception as e:
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logger.error(f"Problem with parse fallback: {e}")
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return value
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case _:
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raise ValueError(f"Could not get datetime from {value['value']}")
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value['value'] = output.replace(tzinfo=timezone)
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return value
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@field_validator("clientlab")
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@classmethod
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def lookup_submitting_lab(cls, value):
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if isinstance(value['value'], str):
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try:
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value['value'] = ClientLab.query(name=value['value']).name
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except AttributeError:
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value['value'] = None
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if value['value'] is None:
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value['missing'] = True
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if "pytest" in sys.modules:
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value['value'] = "Nosocomial"
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return value
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from frontend.widgets.pop_ups import ObjectSelector
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dlg = ObjectSelector(title="Missing Submitting Lab",
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message="We need a submitting lab. Please select from the list.",
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obj_type=ClientLab)
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if dlg.exec():
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value['value'] = dlg.parse_form()
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else:
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value['value'] = None
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return value
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# @field_validator("clientlab", mode="before")
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# @classmethod
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# def rescue_submitting_lab(cls, value):
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# if value is None:
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("clientlab")
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# @classmethod
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# def lookup_submitting_lab(cls, value):
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# if isinstance(value['value'], str):
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# try:
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# value['value'] = ClientLab.query(name=value['value']).name
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# except AttributeError:
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# value['value'] = None
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# if value['value'] is None:
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# value['missing'] = True
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# if "pytest" in sys.modules:
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# value['value'] = "Nosocomial"
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# return value
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# from frontend.widgets.pop_ups import ObjectSelector
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# dlg = ObjectSelector(title="Missing Submitting Lab",
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# message="We need a submitting lab. Please select from the list.",
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# obj_type=ClientLab)
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# if dlg.exec():
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# value['value'] = dlg.parse_form()
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# else:
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# value['value'] = None
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# return value
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@field_validator("rsl_plate_number", mode='before')
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@classmethod
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@@ -607,7 +661,7 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("rsl_plate_number")
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@classmethod
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def rsl_from_file(cls, value, values):
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sub_type = values.data['proceduretype']['value']
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sub_type = values.data['clientsubmission']
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if check_not_nan(value['value']):
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value['value'] = value['value'].strip()
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return value
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@@ -615,25 +669,28 @@ class PydSubmission(BaseModel, extra='allow'):
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if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicRun":
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output = "RSL-BS-Test001"
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else:
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output = RSLNamer(filename=values.data['filepath'].__str__(), submission_type=sub_type,
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# try:
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output = RSLNamer(filename=sub_type.filepath.__str__(), submission_type=sub_type.submissiontype,
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data=values.data).parsed_name
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return dict(value=output, missing=True)
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@field_validator("technician", mode="before")
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@classmethod
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def rescue_tech(cls, value):
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if value is None:
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return dict(value=None, missing=True)
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return value
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@field_validator("technician")
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@classmethod
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def enforce_tech(cls, value):
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if check_not_nan(value['value']):
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value['value'] = re.sub(r"\: \d", "", value['value'])
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return value
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else:
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return dict(value=convert_nans_to_nones(value['value']), missing=True)
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# @field_validator("technician", mode="before")
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# @classmethod
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# def rescue_tech(cls, value):
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# if value is None:
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("technician")
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# @classmethod
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# def enforce_tech(cls, value):
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# if check_not_nan(value['value']):
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# value['value'] = re.sub(r"\: \d", "", value['value'])
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# return value
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# else:
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# return dict(value=convert_nans_to_nones(value['value']), missing=True)
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@field_validator("sample_count", mode='before')
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@classmethod
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@@ -642,54 +699,54 @@ class PydSubmission(BaseModel, extra='allow'):
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return dict(value=None, missing=True)
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return value
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@field_validator("kittype", mode='before')
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@classmethod
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def rescue_kit(cls, value):
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if check_not_nan(value):
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if isinstance(value, str):
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return dict(value=value, missing=False)
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elif isinstance(value, dict):
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return value
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else:
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raise ValueError(f"No extraction kittype found.")
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if value is None:
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# NOTE: Kit selection is done in the clientsubmissionparser, so should not be necessary here.
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return dict(value=None, missing=True)
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return value
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# @field_validator("kittype", mode='before')
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# @classmethod
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# def rescue_kit(cls, value):
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# if check_not_nan(value):
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# if isinstance(value, str):
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# return dict(value=value, missing=False)
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# elif isinstance(value, dict):
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# return value
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# else:
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# raise ValueError(f"No extraction kittype found.")
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# if value is None:
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# # NOTE: Kit selection is done in the clientsubmissionparser, so should not be necessary here.
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("submissiontype", mode='before')
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# @classmethod
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# def make_submission_type(cls, value, values):
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# if not isinstance(value, dict):
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# value = dict(value=value)
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# if check_not_nan(value['value']):
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# value = value['value'].title()
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# return dict(value=value, missing=False)
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# else:
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# return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
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#
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# @field_validator("submission_category", mode="before")
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# @classmethod
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# def create_category(cls, value):
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# if not isinstance(value, dict):
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# return dict(value=value, missing=True)
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# return value
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#
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# @field_validator("submission_category")
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# @classmethod
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# def rescue_category(cls, value, values):
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# if isinstance(value['value'], str):
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# value['value'] = value['value'].title()
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# if value['value'] not in ["Research", "Diagnostic", "Surveillance", "Validation"]:
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# value['value'] = values.data['proceduretype']['value']
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# return value
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@field_validator("submissiontype", mode='before')
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@classmethod
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def make_submission_type(cls, value, values):
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if not isinstance(value, dict):
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value = dict(value=value)
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if check_not_nan(value['value']):
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value = value['value'].title()
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return dict(value=value, missing=False)
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else:
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return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
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@field_validator("submission_category", mode="before")
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@classmethod
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def create_category(cls, value):
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if not isinstance(value, dict):
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return dict(value=value, missing=True)
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return value
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@field_validator("submission_category")
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@classmethod
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def rescue_category(cls, value, values):
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if isinstance(value['value'], str):
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value['value'] = value['value'].title()
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if value['value'] not in ["Research", "Diagnostic", "Surveillance", "Validation"]:
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value['value'] = values.data['proceduretype']['value']
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return value
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@field_validator("reagent", mode="before")
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@classmethod
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def expand_reagents(cls, value):
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if isinstance(value, Generator):
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return [PydReagent(**reagent) for reagent in value]
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return value
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# @field_validator("reagent", mode="before")
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# @classmethod
|
||||
# def expand_reagents(cls, value):
|
||||
# if isinstance(value, Generator):
|
||||
# return [PydReagent(**reagent) for reagent in value]
|
||||
# return value
|
||||
|
||||
@field_validator("sample", mode="before")
|
||||
@classmethod
|
||||
@@ -698,80 +755,82 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
return [PydSample(**sample) for sample in value]
|
||||
return value
|
||||
|
||||
@field_validator("sample")
|
||||
@classmethod
|
||||
def assign_ids(cls, value):
|
||||
starting_id = ClientSubmissionSampleAssociation.autoincrement_id()
|
||||
for iii, sample in enumerate(value, start=starting_id):
|
||||
# NOTE: Why is this a list? Answer: to zip with the lists of rows and columns in case of multiple of the same sample.
|
||||
sample.assoc_id = [iii]
|
||||
return value
|
||||
# @field_validator("sample")
|
||||
# @classmethod
|
||||
# def assign_ids(cls, value):
|
||||
# starting_id = ClientSubmissionSampleAssociation.autoincrement_id()
|
||||
# for iii, sample in enumerate(value, start=starting_id):
|
||||
# # NOTE: Why is this a list? Answer: to zip with the lists of rows and columns in case of multiple of the same sample.
|
||||
# sample.assoc_id = [iii]
|
||||
# return value
|
||||
|
||||
@field_validator("cost_centre", mode="before")
|
||||
@classmethod
|
||||
def rescue_cost_centre(cls, value):
|
||||
match value:
|
||||
case dict():
|
||||
return value
|
||||
case _:
|
||||
return dict(value=value, missing=True)
|
||||
|
||||
@field_validator("cost_centre")
|
||||
@classmethod
|
||||
def get_cost_centre(cls, value, values):
|
||||
match value['value']:
|
||||
case None:
|
||||
from backend.db.models import Organization
|
||||
org = Organization.query(name=values.data['clientlab']['value'])
|
||||
try:
|
||||
return dict(value=org.cost_centre, missing=True)
|
||||
except AttributeError:
|
||||
return dict(value="xxx", missing=True)
|
||||
case _:
|
||||
return value
|
||||
|
||||
@field_validator("contact")
|
||||
@classmethod
|
||||
def get_contact_from_org(cls, value, values):
|
||||
# logger.debug(f"Value coming in: {value}")
|
||||
match value:
|
||||
case dict():
|
||||
if isinstance(value['value'], tuple):
|
||||
value['value'] = value['value'][0]
|
||||
case tuple():
|
||||
value = dict(value=value[0], missing=False)
|
||||
case _:
|
||||
value = dict(value=value, missing=False)
|
||||
# logger.debug(f"Value after match: {value}")
|
||||
check = Contact.query(name=value['value'])
|
||||
# logger.debug(f"Check came back with {check}")
|
||||
if not isinstance(check, Contact):
|
||||
org = values.data['clientlab']['value']
|
||||
# logger.debug(f"Checking organization: {org}")
|
||||
if isinstance(org, str):
|
||||
org = ClientLab.query(name=values.data['clientlab']['value'], limit=1)
|
||||
if isinstance(org, ClientLab):
|
||||
contact = org.contact[0].name
|
||||
else:
|
||||
logger.warning(f"All attempts at defaulting Contact failed, returning: {value}")
|
||||
return value
|
||||
if isinstance(contact, tuple):
|
||||
contact = contact[0]
|
||||
value = dict(value=f"Defaulted to: {contact}", missing=False)
|
||||
# logger.debug(f"Value after query: {value}")
|
||||
return value
|
||||
else:
|
||||
# logger.debug(f"Value after bypass check: {value}")
|
||||
return value
|
||||
# @field_validator("cost_centre", mode="before")
|
||||
# @classmethod
|
||||
# def rescue_cost_centre(cls, value):
|
||||
# match value:
|
||||
# case dict():
|
||||
# return value
|
||||
# case _:
|
||||
# return dict(value=value, missing=True)
|
||||
#
|
||||
# @field_validator("cost_centre")
|
||||
# @classmethod
|
||||
# def get_cost_centre(cls, value, values):
|
||||
# match value['value']:
|
||||
# case None:
|
||||
# from backend.db.models import Organization
|
||||
# org = Organization.query(name=values.data['clientlab']['value'])
|
||||
# try:
|
||||
# return dict(value=org.cost_centre, missing=True)
|
||||
# except AttributeError:
|
||||
# return dict(value="xxx", missing=True)
|
||||
# case _:
|
||||
# return value
|
||||
#
|
||||
# @field_validator("contact")
|
||||
# @classmethod
|
||||
# def get_contact_from_org(cls, value, values):
|
||||
# # logger.debug(f"Value coming in: {value}")
|
||||
# match value:
|
||||
# case dict():
|
||||
# if isinstance(value['value'], tuple):
|
||||
# value['value'] = value['value'][0]
|
||||
# case tuple():
|
||||
# value = dict(value=value[0], missing=False)
|
||||
# case _:
|
||||
# value = dict(value=value, missing=False)
|
||||
# # logger.debug(f"Value after match: {value}")
|
||||
# check = Contact.query(name=value['value'])
|
||||
# # logger.debug(f"Check came back with {check}")
|
||||
# if not isinstance(check, Contact):
|
||||
# org = values.data['clientlab']['value']
|
||||
# # logger.debug(f"Checking organization: {org}")
|
||||
# if isinstance(org, str):
|
||||
# org = ClientLab.query(name=values.data['clientlab']['value'], limit=1)
|
||||
# if isinstance(org, ClientLab):
|
||||
# contact = org.contact[0].name
|
||||
# else:
|
||||
# logger.warning(f"All attempts at defaulting Contact failed, returning: {value}")
|
||||
# return value
|
||||
# if isinstance(contact, tuple):
|
||||
# contact = contact[0]
|
||||
# value = dict(value=f"Defaulted to: {contact}", missing=False)
|
||||
# # logger.debug(f"Value after query: {value}")
|
||||
# return value
|
||||
# else:
|
||||
# # logger.debug(f"Value after bypass check: {value}")
|
||||
# return value
|
||||
|
||||
def __init__(self, run_custom: bool = False, **data):
|
||||
super().__init__(**data)
|
||||
# NOTE: this could also be done with default_factory
|
||||
self.submission_object = Run.find_polymorphic_subclass(
|
||||
polymorphic_identity=self.submission_type['value'])
|
||||
self.namer = RSLNamer(self.rsl_plate_number['value'], submission_type=self.submission_type['value'])
|
||||
if run_custom:
|
||||
self.submission_object.custom_validation(pyd=self)
|
||||
# self.submission_object = Run.find_polymorphic_subclass(
|
||||
# polymorphic_identity=self.submission_type['value'])
|
||||
submission_type = self.clientsubmission.submissiontype
|
||||
# logger.debug(submission_type)
|
||||
self.namer = RSLNamer(self.rsl_plate_number['value'], submission_type=submission_type)
|
||||
# if run_custom:
|
||||
# self.submission_object.custom_validation(pyd=self)
|
||||
|
||||
def set_attribute(self, key: str, value):
|
||||
"""
|
||||
@@ -1020,7 +1079,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
Returns:
|
||||
str: Output filename
|
||||
"""
|
||||
template = self.submission_object.filename_template()
|
||||
template = self.clientsubmission.filename_template
|
||||
render = self.namer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace(
|
||||
"/", "")
|
||||
return render
|
||||
@@ -1537,7 +1596,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
self.kittype['value'] = kittype
|
||||
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
|
||||
|
||||
def reorder_reagents(self, reagentrole: str, options:list):
|
||||
def reorder_reagents(self, reagentrole: str, options: list):
|
||||
reagent_used = next((reagent for reagent in self.reagent if reagent.reagentrole == reagentrole), None)
|
||||
if not reagent_used:
|
||||
return options
|
||||
@@ -1547,8 +1606,6 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
options.insert(0, options.pop(options.index(roi)))
|
||||
return options
|
||||
|
||||
|
||||
|
||||
def update_kittype_equipmentroles(self, kittype: str | KitType):
|
||||
if kittype == self.__class__.model_fields['kittype'].default['value']:
|
||||
return
|
||||
@@ -1808,6 +1865,23 @@ class PydClientSubmission(PydBaseClass):
|
||||
sql._misc_info['info_placement'] = info_placement
|
||||
return sql
|
||||
|
||||
def pad_samples_to_length(self, row_count, column_names):
|
||||
output_samples = []
|
||||
for iii in range(1, row_count + 1):
|
||||
try:
|
||||
sample = next((item for item in self.model_extra['samples'] if item.submission_rank == iii))
|
||||
except StopIteration:
|
||||
sample = PydSample(sample_id="")
|
||||
for column in column_names:
|
||||
setattr(sample, column[0], "")
|
||||
sample.submission_rank = iii
|
||||
output_samples.append(sample)
|
||||
return sorted(output_samples, key=lambda x: x.submission_rank)
|
||||
|
||||
@property
|
||||
def filename_template(self):
|
||||
submissiontype = SubmissionType.query(name=self.submissiontype['value'])
|
||||
return submissiontype.defaults['filename_template']
|
||||
|
||||
|
||||
class PydResults(PydBaseClass, arbitrary_types_allowed=True):
|
||||
|
||||
Reference in New Issue
Block a user