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Renaming ReagentType to ReagentRole

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This commit is contained in:
lwark
2024-06-03 13:32:04 -05:00
parent 1a716984a7
commit cdcce80898
10 changed files with 182 additions and 140 deletions
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2
src/submissions/backend/validators/__init__.py
View File

@@ -178,5 +178,5 @@ class RSLNamer(object):
return template.render(**kwargs)
from .pydant import PydSubmission, PydKit, PydContact, PydOrganization, PydSample, PydReagent, PydReagentType, \
from .pydant import PydSubmission, PydKit, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
PydEquipment, PydEquipmentRole

44
src/submissions/backend/validators/pydant.py
View File

@@ -25,7 +25,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
class PydReagent(BaseModel):
lot: str | None
type: str | None
role: str | None
expiry: date | Literal['NA'] | None
name: str | None
missing: bool = Field(default=True)
@@ -38,7 +38,7 @@ class PydReagent(BaseModel):
return ""
return value
@field_validator("type", mode='before')
@field_validator("role", mode='before')
@classmethod
def remove_undesired_types(cls, value):
match value:
@@ -47,7 +47,7 @@ class PydReagent(BaseModel):
case _:
return value
@field_validator("type")
@field_validator("role")
@classmethod
def rescue_type_with_lookup(cls, value, values):
if value == None and values.data['lot'] != None:
@@ -147,10 +147,10 @@ class PydReagent(BaseModel):
match key:
case "lot":
reagent.lot = value.upper()
case "type":
reagent_type = ReagentType.query(name=value)
if reagent_type != None:
reagent.type.append(reagent_type)
case "role":
reagent_role = ReagentRole.query(name=value)
if reagent_role is not None:
reagent.role.append(reagent_role)
case "comment":
continue
case "expiry":
@@ -792,11 +792,11 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Kit reagents: {ext_kit_rtypes}")
# logger.debug(f"Submission reagents: {self.reagents}")
# Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.type for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
expected_check = [item.role for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
# logger.debug(f"Already have these reagent types: {output_reagents}")
missing_check = [item.type for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
missing_check = [item.role for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
missing_reagents += [rt for rt in output_reagents if rt.missing]
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
# logger.debug(f"Missing reagents types: {missing_reagents}")
@@ -805,7 +805,7 @@ class PydSubmission(BaseModel, extra='allow'):
result = None
else:
result = Result(
msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.role.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
status="Warning")
report.add_result(result)
return output_reagents, report
@@ -850,7 +850,7 @@ class PydOrganization(BaseModel):
return instance
class PydReagentType(BaseModel):
class PydReagentRole(BaseModel):
name: str
eol_ext: timedelta | int | None
uses: dict | None
@@ -863,33 +863,33 @@ class PydReagentType(BaseModel):
return timedelta(days=value)
return value
def toSQL(self, kit: KitType) -> ReagentType:
def toSQL(self, kit: KitType) -> ReagentRole:
"""
Converts this instance into a backend.db.models.ReagentType instance
Args:
kit (KitType): KitType joined to the reagenttype
kit (KitType): KitType joined to the reagentrole
Returns:
ReagentType: ReagentType instance
ReagentRole: ReagentType instance
"""
instance: ReagentType = ReagentType.query(name=self.name)
instance: ReagentRole = ReagentRole.query(name=self.name)
if instance == None:
instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
instance = ReagentRole(name=self.name, eol_ext=self.eol_ext)
# logger.debug(f"This is the reagent type instance: {instance.__dict__}")
try:
assoc = KitTypeReagentTypeAssociation.query(reagent_type=instance, kit_type=kit)
assoc = KitTypeReagentRoleAssociation.query(reagent_role=instance, kit_type=kit)
except StatementError:
assoc = None
if assoc == None:
assoc = KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=instance, uses=self.uses,
assoc = KitTypeReagentRoleAssociation(kit_type=kit, reagent_role=instance, uses=self.uses,
required=self.required)
return instance
class PydKit(BaseModel):
name: str
reagent_types: List[PydReagentType] = []
reagent_roles: List[PydReagentRole] = []
def toSQL(self) -> Tuple[KitType, Report]:
"""
@@ -902,7 +902,7 @@ class PydKit(BaseModel):
instance = KitType.query(name=self.name)
if instance == None:
instance = KitType(name=self.name)
[item.toSQL(instance) for item in self.reagent_types]
[item.toSQL(instance) for item in self.reagent_roles]
return instance, report