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Mid change in details templates

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This commit is contained in:
lwark
2024-06-20 07:46:46 -05:00
parent 12e552800a
commit 337112a27d
20 changed files with 575 additions and 300 deletions
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2
src/submissions/backend/validators/__init__.py
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@@ -141,7 +141,7 @@ class RSLNamer(object):
"""
if "submitted_date" in data.keys():
if isinstance(data['submitted_date'], dict):
if data['submitted_date']['value'] != None:
if data['submitted_date']['value'] is not None:
today = data['submitted_date']['value']
else:
today = datetime.now()

48
src/submissions/backend/validators/pydant.py
View File

@@ -33,7 +33,7 @@ class PydReagent(BaseModel):
@field_validator('comment', mode='before')
@classmethod
def create_comment(cls, value):
if value == None:
if value is None:
return ""
return value
@@ -49,7 +49,7 @@ class PydReagent(BaseModel):
@field_validator("role")
@classmethod
def rescue_type_with_lookup(cls, value, values):
if value == None and values.data['lot'] != None:
if value is None and values.data['lot'] is not None:
try:
# return lookup_reagents(ctx=values.data['ctx'], lot_number=values.data['lot']).name
return Reagent.query(lot_number=values.data['lot'].name)
@@ -60,21 +60,21 @@ class PydReagent(BaseModel):
@field_validator("lot", mode='before')
@classmethod
def rescue_lot_string(cls, value):
if value != None:
if value is not None:
return convert_nans_to_nones(str(value))
return value
@field_validator("lot")
@classmethod
def enforce_lot_string(cls, value):
if value != None:
if value is not None:
return value.upper()
return value
@field_validator("expiry", mode="before")
@classmethod
def enforce_date(cls, value):
if value != None:
if value is not None:
match value:
case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date()
@@ -86,7 +86,7 @@ class PydReagent(BaseModel):
return value
case _:
return convert_nans_to_nones(str(value))
if value == None:
if value is None:
value = date.today()
return value
@@ -100,7 +100,7 @@ class PydReagent(BaseModel):
@field_validator("name", mode="before")
@classmethod
def enforce_name(cls, value, values):
if value != None:
if value is not None:
return convert_nans_to_nones(str(value))
else:
return values.data['role']
@@ -131,7 +131,7 @@ class PydReagent(BaseModel):
"""
report = Report()
# logger.debug("Adding extra fields.")
if self.model_extra != None:
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
# logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot_number=self.lot, name=self.name)
@@ -181,6 +181,7 @@ class PydReagent(BaseModel):
return reagent, assoc, report
class PydSample(BaseModel, extra='allow'):
submitter_id: str
sample_type: str
@@ -299,10 +300,11 @@ class PydEquipment(BaseModel, extra='ignore'):
def make_empty_list(cls, value):
# logger.debug(f"Pydantic value: {value}")
value = convert_nans_to_nones(value)
if value == None:
if value is None:
value = ['']
if len(value) == 0:
value = ['']
value = [item.strip() for item in value]
return value
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
@@ -318,13 +320,13 @@ class PydEquipment(BaseModel, extra='ignore'):
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
equipment = Equipment.query(asset_number=self.asset_number)
if equipment == None:
if equipment is None:
return
if submission != None:
if submission is not None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
process = Process.query(name=self.processes[0])
if process == None:
# logger.debug("Adding in unknown process.")
if process is None:
logger.error(f"Found unknown process: {process}.")
from frontend.widgets.pop_ups import QuestionAsker
dlg = QuestionAsker(title="Add Process?",
message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
@@ -383,7 +385,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator('comment', mode='before')
@classmethod
def create_comment(cls, value):
if value == None:
if value is None:
return ""
return value
@@ -391,7 +393,7 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod
def enforce_with_uuid(cls, value):
# logger.debug(f"submitter_plate_num coming into pydantic: {value}")
if value['value'] == None or value['value'] == "None":
if value['value'] in [None, "None"]:
return dict(value=uuid.uuid4().hex.upper(), missing=True)
else:
return value
@@ -401,7 +403,7 @@ class PydSubmission(BaseModel, extra='allow'):
def rescue_date(cls, value):
# logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
try:
check = value['value'] == None
check = value['value'] is None
except TypeError:
check = True
if check:
@@ -468,7 +470,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("rsl_plate_num", mode='before')
@classmethod
def rescue_rsl_number(cls, value):
if value == None:
if value is None:
return dict(value=None, missing=True)
return value
@@ -491,7 +493,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("technician", mode="before")
@classmethod
def rescue_tech(cls, value):
if value == None:
if value is None:
return dict(value=None, missing=True)
return value
@@ -507,7 +509,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("sample_count", mode='before')
@classmethod
def rescue_sample_count(cls, value):
if value == None:
if value is None:
return dict(value=None, missing=True)
return value
@@ -521,7 +523,7 @@ class PydSubmission(BaseModel, extra='allow'):
return value
else:
raise ValueError(f"No extraction kit found.")
if value == None:
if value is None:
return dict(value=None, missing=True)
return value
@@ -923,14 +925,14 @@ class PydReagentRole(BaseModel):
ReagentRole: ReagentType instance
"""
instance: ReagentRole = ReagentRole.query(name=self.name)
if instance == None:
if instance is None:
instance = ReagentRole(name=self.name, eol_ext=self.eol_ext)
# logger.debug(f"This is the reagent type instance: {instance.__dict__}")
try:
assoc = KitTypeReagentRoleAssociation.query(reagent_role=instance, kit_type=kit)
except StatementError:
assoc = None
if assoc == None:
if assoc is None:
assoc = KitTypeReagentRoleAssociation(kit_type=kit, reagent_role=instance, uses=self.uses,
required=self.required)
return instance
@@ -949,7 +951,7 @@ class PydKit(BaseModel):
"""
report = Report()
instance = KitType.query(name=self.name)
if instance == None:
if instance is None:
instance = KitType(name=self.name)
[item.toSQL(instance) for item in self.reagent_roles]
return instance, report