Update of Reagent usage ui for addition of new reagents.
This commit is contained in:
lwark
@@ -183,7 +183,7 @@ class PydReagent(PydBaseClass):
|
||||
case _:
|
||||
return convert_nans_to_nones(str(value))
|
||||
if value is None:
|
||||
value = date.today()
|
||||
value = datetime.combine(date.today(), datetime.max.time())
|
||||
return value
|
||||
|
||||
@field_validator("expiry")
|
||||
@@ -201,6 +201,11 @@ class PydReagent(PydBaseClass):
|
||||
else:
|
||||
return values.data['reagentrole'].strip()
|
||||
|
||||
# @field_validator("reagentrole", mode="before")
|
||||
# @classmethod
|
||||
# def rescue_reagentrole(cls, value):
|
||||
# if
|
||||
|
||||
def improved_dict(self) -> dict:
|
||||
"""
|
||||
Constructs a dictionary consisting of model.fields and model.extras
|
||||
@@ -226,23 +231,26 @@ class PydReagent(PydBaseClass):
|
||||
report = Report()
|
||||
if self.model_extra is not None:
|
||||
self.__dict__.update(self.model_extra)
|
||||
reagent = Reagent.query(lot=self.lot, name=self.name)
|
||||
reagent, new = Reagent.query_or_create(lot=self.lot, name=self.name)
|
||||
# logger.debug(f"Reagent: {reagent}")
|
||||
if reagent is None:
|
||||
reagent = Reagent()
|
||||
for key, value in self.__dict__.items():
|
||||
if isinstance(value, dict):
|
||||
value = value['value']
|
||||
# NOTE: reagent method sets fields based on keys in dictionary
|
||||
reagent.set_attribute(key, value)
|
||||
if procedure is not None and reagent not in procedure.reagents:
|
||||
assoc = ProcedureReagentAssociation(reagent=reagent, procedure=procedure)
|
||||
assoc.comments = self.comment
|
||||
else:
|
||||
assoc = None
|
||||
else:
|
||||
if submission is not None and reagent not in submission.reagents:
|
||||
submission.update_reagentassoc(reagent=reagent, role=self.role)
|
||||
# if reagent is None:
|
||||
# reagent = Reagent()
|
||||
# for key, value in self.__dict__.items():
|
||||
# if isinstance(value, dict):
|
||||
# if key == "misc_info":
|
||||
# value = value
|
||||
# else:
|
||||
# value = value['value']
|
||||
# # NOTE: reagent method sets fields based on keys in dictionary
|
||||
# reagent.set_attribute(key, value)
|
||||
# if procedure is not None and reagent not in procedure.reagents:
|
||||
# assoc = ProcedureReagentAssociation(reagent=reagent, procedure=procedure)
|
||||
# assoc.comments = self.comment
|
||||
# else:
|
||||
# assoc = None
|
||||
# else:
|
||||
# if submission is not None and reagent not in submission.reagents:
|
||||
# submission.update_reagentassoc(reagent=reagent, role=self.role)
|
||||
return reagent, report
|
||||
|
||||
|
||||
@@ -1486,8 +1494,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
if isinstance(kittype, str):
|
||||
kittype_obj = KitType.query(name=kittype)
|
||||
try:
|
||||
self.reagentrole = {item.name: item.get_reagents(kittype=kittype_obj) + ["New"] for item in
|
||||
kittype_obj.get_reagents(proceduretype=self.proceduretype)}
|
||||
self.reagentrole = {
|
||||
item.name: item.get_reagents(kittype=kittype_obj) + [PydReagent(name="--New--", lot="", reagentrole="")]
|
||||
for item in
|
||||
kittype_obj.get_reagents(proceduretype=self.proceduretype)}
|
||||
except AttributeError:
|
||||
self.reagentrole = {}
|
||||
|
||||
@@ -1511,19 +1521,19 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
|
||||
for sample_dict in sample_list:
|
||||
if sample_dict['sample_id'].startswith("blank_"):
|
||||
continue
|
||||
sample_dict['sample_id'] = ""
|
||||
row, column = self.proceduretype.ranked_plate[sample_dict['index']]
|
||||
logger.debug(f"Row: {row}, Column: {column}")
|
||||
try:
|
||||
sample = next(
|
||||
(item for item in self.samples if item.sample_id.upper() == sample_dict['sample_id'].upper()))
|
||||
(item for item in self.sample if item.sample_id.upper() == sample_dict['sample_id'].upper()))
|
||||
except StopIteration:
|
||||
# NOTE: Code to check for added controls.
|
||||
logger.debug(
|
||||
f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
|
||||
try:
|
||||
sample = next(
|
||||
(item for item in self.samples if item.row == row and item.column == column))
|
||||
(item for item in self.sample if item.row == row and item.column == column))
|
||||
except StopIteration:
|
||||
logger.error(f"Couldn't find sample: {pformat(sample_dict)}")
|
||||
continue
|
||||
@@ -1532,7 +1542,23 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
sample.well_id = sample_dict['sample_id']
|
||||
sample.row = row
|
||||
sample.column = column
|
||||
logger.debug(f"Updated samples:\n{pformat(self.samples)}")
|
||||
# logger.debug(f"Updated samples:\n{pformat(self.sample)}")
|
||||
|
||||
def update_reagents(self, reagentrole: str, name: str, lot: str, expiry: str):
|
||||
removable = next((item for item in self.reagent if item.reagentrole == reagentrole), None)
|
||||
if removable:
|
||||
idx = self.reagent.index(removable)
|
||||
self.reagent.remove(removable)
|
||||
else:
|
||||
idx = 0
|
||||
insertable = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
|
||||
self.reagent.insert(idx, insertable)
|
||||
logger.debug(self.reagent)
|
||||
|
||||
@classmethod
|
||||
def update_new_reagents(cls, reagent: PydReagent):
|
||||
reg = reagent.to_sql()
|
||||
reg.save()
|
||||
|
||||
def to_sql(self):
|
||||
from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
|
||||
@@ -1540,12 +1566,24 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
# for result in self.results:
|
||||
# result, _ = result.to_sql()
|
||||
sql = super().to_sql()
|
||||
logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
|
||||
# logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
|
||||
# sql.results = [result.to_sql() for result in self.results]
|
||||
if self.run:
|
||||
sql.run = self.run
|
||||
if self.proceduretype:
|
||||
sql.proceduretype = self.proceduretype
|
||||
# Note: convert any new reagents to sql and save
|
||||
for reagentrole, reagents in self.reagentrole.items():
|
||||
for reagent in reagents:
|
||||
if not reagent.lot or reagent.name == "--New--":
|
||||
continue
|
||||
self.update_new_reagents(reagent)
|
||||
# NOTE: reset reagent associations.
|
||||
sql.procedurereagentassociation = []
|
||||
for reagent in self.reagent:
|
||||
reagent = reagent.to_sql()
|
||||
if reagent not in sql.reagent:
|
||||
reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql)
|
||||
try:
|
||||
start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
|
||||
except ValueError:
|
||||
@@ -1571,13 +1609,15 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
||||
kittype = KitType.query(name=self.kittype['value'], limit=1)
|
||||
if kittype:
|
||||
sql.kittype = kittype
|
||||
logger.debug(self.reagent)
|
||||
for equipment in self.equipment:
|
||||
equip = Equipment.query(name=equipment.name)
|
||||
if equip not in sql.equipment:
|
||||
equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql, equipmentrole=equip.equipmentrole[0])
|
||||
equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql,
|
||||
equipmentrole=equip.equipmentrole[0])
|
||||
process = equipment.process.to_sql()
|
||||
equip_assoc.process = process
|
||||
logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
|
||||
# logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
|
||||
return sql, None
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user