landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Removed Kittype.

Browse Source
This commit is contained in:
lwark
2025-08-12 11:14:33 -05:00
parent 087bf9bcb7
commit 6380f1e2a9
22 changed files with 1129 additions and 2231 deletions
Download Patch File Download Diff File Expand all files Collapse all files

129
src/submissions/backend/validators/pydant.py
View File

@@ -250,7 +250,7 @@ class PydReagent(PydBaseClass):
report = Report()
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
reagent, new = Reagent.query_or_create(lot=self.lot, name=self.name)
reagent, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
if new:
reagentrole = ReagentRole.query(name=self.reagentrole)
reagent.reagentrole = reagentrole
@@ -374,7 +374,7 @@ class PydEquipment(PydBaseClass):
name: str
nickname: str | None
# process: List[dict] | None
process: PydProcess | None
process: List[PydProcess] | PydProcess | None
equipmentrole: str | PydEquipmentRole | None
tips: List[PydTips] | PydTips | None = Field(default=[])
@@ -402,7 +402,7 @@ class PydEquipment(PydBaseClass):
value = convert_nans_to_nones(value)
if not value:
value = ['']
logger.debug(value)
# logger.debug(value)
try:
# value = [item.strip() for item in value]
value = next((PydProcess(**process.details_dict()) for process in value))
@@ -435,7 +435,7 @@ class PydEquipment(PydBaseClass):
return value
@report_result
def to_sql(self, procedure: Procedure | str = None, kittype: KitType | str = None) -> Tuple[
def to_sql(self, procedure: Procedure | str = None, proceduretype: ProcedureType | str = None) -> Tuple[
Equipment, ProcedureEquipmentAssociation]:
"""
Creates Equipment and SubmssionEquipmentAssociations for this PydEquipment
@@ -449,8 +449,8 @@ class PydEquipment(PydBaseClass):
report = Report()
if isinstance(procedure, str):
procedure = Procedure.query(name=procedure)
if isinstance(kittype, str):
kittype = KitType.query(name=kittype)
if isinstance(proceduretype, str):
proceduretype = ProcedureType.query(name=proceduretype)
logger.debug(f"Querying equipment: {self.asset_number}")
equipment = Equipment.query(asset_number=self.asset_number)
if equipment is None:
@@ -470,8 +470,7 @@ class PydEquipment(PydBaseClass):
# NOTE: It looks like the way fetching the process is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
# NOTE: I need to find a way to filter this by the kittype involved.
if len(self.processes) > 1:
process = Process.query(proceduretype=procedure.get_submission_type(), kittype=kittype,
equipmentrole=self.role)
process = Process.query(proceduretype=procedure.get_submission_type(), equipmentrole=self.role)
else:
process = Process.query(name=self.processes[0])
if process is None:
@@ -879,15 +878,15 @@ class PydRun(PydBaseClass): #, extra='allow'):
pass
return SubmissionFormWidget(parent=parent, pyd=self, disable=disable)
def to_writer(self) -> "SheetWriter":
"""
Sends data here to the sheet writer.
Returns:
SheetWriter: Sheetwriter object that will perform writing.
"""
from backend.excel.writer import SheetWriter
return SheetWriter(self)
# def to_writer(self) -> "SheetWriter":
# """
# Sends data here to the sheet writer.
#
# Returns:
# SheetWriter: Sheetwriter object that will perform writing.
# """
# from backend.excel.writer import SheetWriter
# return SheetWriter(self)
def construct_filename(self) -> str:
"""
@@ -1166,10 +1165,10 @@ class PydProcess(PydBaseClass, extra="allow"):
proceduretype: List[str]
equipment: List[str]
equipmentrole: List[str]
kittype: List[str]
# kittype: List[str]
tiprole: List[str]
@field_validator("proceduretype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
@field_validator("proceduretype", "equipment", "equipmentrole", "tiprole", mode="before")
@classmethod
def enforce_list(cls, value):
if not isinstance(value, list):
@@ -1249,8 +1248,8 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
technician: dict = Field(default=dict(value="NA", missing=True))
repeat: bool = Field(default=False)
repeat_of: str | None = Field(default=None)
kittype: dict = Field(default=dict(value="NA", missing=True))
possible_kits: list | None = Field(default=[], validate_default=True)
# kittype: dict = Field(default=dict(value="NA", missing=True))
# possible_kits: list | None = Field(default=[], validate_default=True)
plate_map: str | None = Field(default=None)
reagent: list | None = Field(default=[])
reagentrole: dict | None = Field(default={}, validate_default=True)
@@ -1258,7 +1257,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
equipment: List[PydEquipment] = Field(default=[])
result: List[PydResults] | List[dict] = Field(default=[])
@field_validator("name", "technician", "kittype", mode="before")
@field_validator("name", "technician", mode="before")#"kittype", mode="before")
@classmethod
def convert_to_dict(cls, value):
if not value:
@@ -1295,18 +1294,18 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
value['missing'] = True
return value
@field_validator("possible_kits")
@classmethod
def rescue_possible_kits(cls, value, values):
if not value:
try:
if values.data['proceduretype']:
value = [kittype.__dict__['name'] for kittype in values.data['proceduretype'].kittype]
except KeyError:
pass
return value
# @field_validator("possible_kits")
# @classmethod
# def rescue_possible_kits(cls, value, values):
# if not value:
# try:
# if values.data['proceduretype']:
# value = [kittype.__dict__['name'] for kittype in values.data['proceduretype'].kittype]
# except KeyError:
# pass
# return value
@field_validator("name", "technician", "kittype")
@field_validator("name", "technician")#, "kittype")
@classmethod
def set_colour(cls, value):
try:
@@ -1321,20 +1320,26 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
@field_validator("reagentrole")
@classmethod
def rescue_reagentrole(cls, value, values):
# if not value:
# match values.data['kittype']:
# case dict():
# if "value" in values.data['kittype'].keys():
# roi = values.data['kittype']['value']
# elif "name" in values.data['kittype'].keys():
# roi = values.data['kittype']['name']
# else:
# raise KeyError(f"Couldn't find kittype name in the dictionary: {values.data['kittype']}")
# case str():
# roi = values.data['kittype']
# if roi != cls.model_fields['kittype'].default['value']:
# kittype = KitType.query(name=roi)
# value = {item.name: item.reagent for item in kittype.reagentrole}
if not value:
match values.data['kittype']:
case dict():
if "value" in values.data['kittype'].keys():
roi = values.data['kittype']['value']
elif "name" in values.data['kittype'].keys():
roi = values.data['kittype']['name']
else:
raise KeyError(f"Couldn't find kittype name in the dictionary: {values.data['kittype']}")
case str():
roi = values.data['kittype']
if roi != cls.model_fields['kittype'].default['value']:
kittype = KitType.query(name=roi)
value = {item.name: item.reagent for item in kittype.reagentrole}
value = {}
for reagentrole in values.data['proceduretype'].reagentrole:
reagents = [reagent.lot_dicts for reagent in reagentrole.reagent]
value[reagentrole.name] = flatten_list(reagents)
# value = {item.name: item.reagent for item in values.data['proceduretype'].reagentrole}
return value
@field_validator("run")
@@ -1416,12 +1421,12 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
def update_samples(self, sample_list: List[dict]):
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
# logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
for iii, sample_dict in enumerate(sample_list, start=1):
if sample_dict['sample_id'].startswith("blank_"):
sample_dict['sample_id'] = ""
row, column = self.proceduretype.ranked_plate[sample_dict['index']]
logger.debug(f"Row: {row}, Column: {column}")
# logger.debug(f"Row: {row}, Column: {column}")
try:
sample = next(
(item for item in self.sample if item.sample_id.upper() == sample_dict['sample_id'].upper()))
@@ -1440,7 +1445,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
sample.row = row
sample.column = column
sample.procedure_rank = sample_dict['index']
logger.debug(f"Sample of interest: {sample.improved_dict()}")
# logger.debug(f"Sample of interest: {sample.improved_dict()}")
# logger.debug(f"Updated samples:\n{pformat(self.sample)}")
def update_reagents(self, reagentrole: str, name: str, lot: str, expiry: str):
@@ -1456,7 +1461,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
idx = 0
insertable = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
self.reagent.insert(idx, insertable)
logger.debug(self.reagent)
# logger.debug(self.reagent)
@classmethod
def update_new_reagents(cls, reagent: PydReagent):
@@ -1492,24 +1497,24 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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)
# for reagentrole, reagents in self.reagentrole.items():
for reagent in self.reagent:
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:
if isinstance(reagent, dict):
reagent = PydReagent(**reagent)
# logger.debug(reagent)
logger.debug(reagent)
reagentrole = reagent.reagentrole
reagent = reagent.to_sql()
# logger.debug(reagentrole)
if reagent not in sql.reagent:
if reagent not in sql.reagentlot:
# NOTE: Remove any previous association for this role.
if sql.id:
removable = ProcedureReagentAssociation.query(procedure=sql, reagentrole=reagentrole)
removable = ProcedureReagentLotAssociation.query(procedure=sql, reagentrole=reagentrole)
else:
removable = []
logger.debug(f"Removable: {removable}")
@@ -1520,7 +1525,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
else:
removable.delete()
# logger.debug(f"Adding {reagent} to {sql}")
reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql, reagentrole=reagentrole)
reagent_assoc = ProcedureReagentLotAssociation(reagentlot=reagent, procedure=sql, reagentrole=reagentrole)
try:
start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
except ValueError:
@@ -1543,10 +1548,6 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
row=sample.row, column=sample.column,
procedure_rank=sample.procedure_rank)
if self.kittype['value'] not in ["NA", None, ""]:
kittype = KitType.query(name=self.kittype['value'], limit=1)
if kittype:
sql.kittype = kittype
for equipment in self.equipment:
equip = Equipment.query(name=equipment.name)
if equip not in sql.equipment:
@@ -1729,7 +1730,7 @@ class PydClientSubmission(PydBaseClass):
case SubmissionType():
pass
case _:
sql.submissiontype = SubmissionType.query(name="Test")
sql.submissiontype = SubmissionType.query(name="Default")
for k in list(self.model_fields.keys()) + list(self.model_extra.keys()):
logger.debug(f"Running {k}")
attribute = getattr(self, k)