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Addition of procedure parser in import.

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This commit is contained in:
lwark
2025-06-17 15:09:51 -05:00
parent 0233bc3ac2
commit d8c3f3bbb2
31 changed files with 688 additions and 304 deletions
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36
src/submissions/backend/validators/pydant.py
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@@ -262,6 +262,12 @@ class PydSample(PydBaseClass):
pass
return value
@field_validator("row", mode="before")
@classmethod
def str_to_int(cls, value):
if isinstance(value, str):
value = row_keys[value]
return value
class PydTips(BaseModel):
name: str
@@ -298,7 +304,7 @@ class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str | None
processes: List[str] | None
process: List[str] | None
equipmentrole: str | None
tips: List[PydTips] | None = Field(default=None)
@@ -309,7 +315,7 @@ class PydEquipment(BaseModel, extra='ignore'):
value = value.name
return value
@field_validator('processes', mode='before')
@field_validator('process', mode='before')
@classmethod
def make_empty_list(cls, value):
# if isinstance(value, dict):
@@ -397,7 +403,7 @@ class PydSubmission(BaseModel, extra='allow'):
filepath: Path
submissiontype: dict | None
submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
rsl_plate_number: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
clientlab: dict | None
sample_count: dict | None
@@ -517,14 +523,14 @@ class PydSubmission(BaseModel, extra='allow'):
value['value'] = None
return value
@field_validator("rsl_plate_num", mode='before')
@field_validator("rsl_plate_number", mode='before')
@classmethod
def rescue_rsl_number(cls, value):
if value is None:
return dict(value=None, missing=True)
return value
@field_validator("rsl_plate_num")
@field_validator("rsl_plate_number")
@classmethod
def rsl_from_file(cls, value, values):
sub_type = values.data['proceduretype']['value']
@@ -689,7 +695,7 @@ class PydSubmission(BaseModel, extra='allow'):
# 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_num['value'], submission_type=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)
@@ -796,7 +802,7 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Pydantic procedure type: {self.proceduretype['value']}")
# logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
instance, result = Run.query_or_create(submissiontype=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
rsl_plate_number=self.rsl_plate_number['value'])
# logger.debug(f"Created or queried instance: {instance}")
if instance is None:
report.add_result(Result(msg="Overwrite Cancelled."))
@@ -1266,13 +1272,13 @@ class PydEquipmentRole(BaseModel):
class PydProcess(BaseModel, extra="allow"):
name: str
version: str = Field(default="1")
submissiontype: List[str]
proceduretype: List[str]
equipment: List[str]
equipmentrole: List[str]
kittype: List[str]
tiprole: List[str]
@field_validator("submissiontype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
@field_validator("proceduretype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
@classmethod
def enforce_list(cls, value):
if not isinstance(value, list):
@@ -1361,10 +1367,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
else:
procedure_type = None
if values.data['run']:
run = values.data['run'].rsl_plate_num
run = values.data['run'].rsl_plate_number
else:
run = None
value['value'] = f"{procedure_type}-{run}"
value['value'] = f"{run}-{procedure_type}"
value['missing'] = True
return value
@@ -1391,7 +1397,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
if not value:
if values.data['kittype']['value'] != cls.model_fields['kittype'].default['value']:
kittype = KitType.query(name=values.data['kittype']['value'])
value = {item.name: item.reagents for item in kittype.reagentrole}
value = {item.name: item.reagent for item in kittype.reagentrole}
return value
def update_kittype_reagentroles(self, kittype: str | KitType):
@@ -1545,11 +1551,13 @@ class PydClientSubmission(PydBaseClass):
class PydResults(PydBaseClass, arbitrary_types_allowed=True):
results: dict = Field(default={})
img: None = Field(default=None)
results_type: str = Field(default="NA")
img: None | bytes = Field(default=None)
parent: Procedure|ProcedureSampleAssociation|None = Field(default=None)
def to_sql(self):
sql = Results(result=self.results)
sql = Results(results_type=self.results_type, result=self.results)
sql.image = self.img
match self.parent:
case ProcedureSampleAssociation():
sql.sampleprocedureassociation = self.parent