New Excel writer.
This commit is contained in:
lwark
@@ -7,13 +7,17 @@ from jinja2 import Template
|
||||
|
||||
logger = logging.getLogger(f"submissions.{__name__}")
|
||||
|
||||
|
||||
class RSLNamer(object):
|
||||
"""
|
||||
Object that will enforce proper formatting on RSL plate names.
|
||||
"""
|
||||
def __init__(self, filename:str, sub_type:str|None=None, data:dict|None=None):
|
||||
|
||||
def __init__(self, filename: str, sub_type: str | None = None, data: dict | None = None):
|
||||
# NOTE: Preferred method is path retrieval, but might also need validation for just string.
|
||||
filename = Path(filename) if Path(filename).exists() else filename
|
||||
self.submission_type = sub_type
|
||||
if self.submission_type == None:
|
||||
if self.submission_type is None:
|
||||
# logger.debug("Creating submission type because none exists")
|
||||
self.submission_type = self.retrieve_submission_type(filename=filename)
|
||||
logger.debug(f"got submission type: {self.submission_type}")
|
||||
@@ -21,14 +25,14 @@ class RSLNamer(object):
|
||||
# logger.debug("Retrieving BasicSubmission subclass")
|
||||
enforcer = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
|
||||
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=enforcer.get_regex())
|
||||
if data == None:
|
||||
if data is None:
|
||||
data = dict(submission_type=self.submission_type)
|
||||
if "submission_type" not in data.keys():
|
||||
data['submission_type'] = self.submission_type
|
||||
self.parsed_name = enforcer.enforce_name(instr=self.parsed_name, data=data)
|
||||
|
||||
@classmethod
|
||||
def retrieve_submission_type(cls, filename:str|Path) -> str:
|
||||
def retrieve_submission_type(cls, filename: str | Path) -> str:
|
||||
"""
|
||||
Gets submission type from excel file properties or sheet names or regex pattern match or user input
|
||||
|
||||
@@ -37,7 +41,7 @@ class RSLNamer(object):
|
||||
|
||||
Returns:
|
||||
str: parsed submission type
|
||||
"""
|
||||
"""
|
||||
match filename:
|
||||
case Path():
|
||||
logger.debug(f"Using path method for {filename}.")
|
||||
@@ -47,8 +51,8 @@ class RSLNamer(object):
|
||||
submission_type = [item.strip().title() for item in wb.properties.category.split(";")][0]
|
||||
except AttributeError:
|
||||
try:
|
||||
sts = {item.name:item.get_template_file_sheets() for item in SubmissionType.query()}
|
||||
for k,v in sts.items():
|
||||
sts = {item.name: item.get_template_file_sheets() for item in SubmissionType.query()}
|
||||
for k, v in sts.items():
|
||||
# This gets the *first* submission type that matches the sheet names in the workbook
|
||||
if wb.sheetnames == v:
|
||||
submission_type = k.title()
|
||||
@@ -69,28 +73,30 @@ class RSLNamer(object):
|
||||
case _:
|
||||
submission_type = None
|
||||
try:
|
||||
check = submission_type == None
|
||||
check = submission_type is None
|
||||
except UnboundLocalError:
|
||||
check = True
|
||||
if check:
|
||||
# logger.debug("Final option, ask the user for submission type")
|
||||
from frontend.widgets import ObjectSelector
|
||||
dlg = ObjectSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.", obj_type=SubmissionType)
|
||||
dlg = ObjectSelector(title="Couldn't parse submission type.",
|
||||
message="Please select submission type from list below.", obj_type=SubmissionType)
|
||||
if dlg.exec():
|
||||
submission_type = dlg.parse_form()
|
||||
submission_type = submission_type.replace("_", " ")
|
||||
return submission_type
|
||||
|
||||
@classmethod
|
||||
def retrieve_rsl_number(cls, filename:str|Path, regex:str|None=None):
|
||||
def retrieve_rsl_number(cls, filename: str | Path, regex: str | None = None):
|
||||
"""
|
||||
Uses regex to retrieve the plate number and submission type from an input string
|
||||
|
||||
Args:
|
||||
in_str (str): string to be parsed
|
||||
"""
|
||||
regex (str): string to construct pattern
|
||||
filename (str): string to be parsed
|
||||
"""
|
||||
logger.debug(f"Input string to be parsed: {filename}")
|
||||
if regex == None:
|
||||
if regex is None:
|
||||
regex = BasicSubmission.construct_regex()
|
||||
else:
|
||||
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
|
||||
@@ -102,19 +108,19 @@ class RSLNamer(object):
|
||||
logger.debug(f"Using string method.")
|
||||
m = regex.search(filename)
|
||||
case _:
|
||||
pass
|
||||
if m != None:
|
||||
m = None
|
||||
if m is not None:
|
||||
try:
|
||||
parsed_name = m.group().upper().strip(".")
|
||||
except:
|
||||
parsed_name = None
|
||||
else:
|
||||
else:
|
||||
parsed_name = None
|
||||
logger.debug(f"Got parsed submission name: {parsed_name}")
|
||||
return parsed_name
|
||||
|
||||
|
||||
@classmethod
|
||||
def construct_new_plate_name(cls, data:dict) -> str:
|
||||
def construct_new_plate_name(cls, data: dict) -> str:
|
||||
"""
|
||||
Make a brand new plate name from submission data.
|
||||
|
||||
@@ -123,7 +129,7 @@ class RSLNamer(object):
|
||||
|
||||
Returns:
|
||||
str: Output filename
|
||||
"""
|
||||
"""
|
||||
if "submitted_date" in data.keys():
|
||||
if isinstance(data['submitted_date'], dict):
|
||||
if data['submitted_date']['value'] != None:
|
||||
@@ -144,9 +150,9 @@ class RSLNamer(object):
|
||||
previous = BasicSubmission.query(start_date=today, end_date=today, submission_type=data['submission_type'])
|
||||
plate_number = len(previous) + 1
|
||||
return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
|
||||
|
||||
|
||||
@classmethod
|
||||
def construct_export_name(cls, template:Template, **kwargs) -> str:
|
||||
def construct_export_name(cls, template: Template, **kwargs) -> str:
|
||||
"""
|
||||
Make export file name from jinja template. (currently unused)
|
||||
|
||||
@@ -155,11 +161,13 @@ class RSLNamer(object):
|
||||
|
||||
Returns:
|
||||
str: output file name.
|
||||
"""
|
||||
"""
|
||||
logger.debug(f"Kwargs: {kwargs}")
|
||||
logger.debug(f"Template: {template}")
|
||||
environment = jinja_template_loading()
|
||||
template = environment.from_string(template)
|
||||
return template.render(**kwargs)
|
||||
|
||||
from .pydant import *
|
||||
|
||||
|
||||
from .pydant import PydSubmission, PydKit, PydContact, PydOrganization, PydSample, PydReagent, PydReagentType, \
|
||||
PydEquipment, PydEquipmentRole
|
||||
|
||||
@@ -4,10 +4,11 @@ Contains pydantic models and accompanying validators
|
||||
from __future__ import annotations
|
||||
from operator import attrgetter
|
||||
import uuid, re, logging
|
||||
from pydantic import BaseModel, field_validator, Field
|
||||
from pydantic import BaseModel, field_validator, Field, model_validator
|
||||
from datetime import date, datetime, timedelta
|
||||
from dateutil.parser import parse
|
||||
from dateutil.parser._parser import ParserError
|
||||
# from dateutil.parser._parser import ParserError
|
||||
from dateutil.parser import ParserError
|
||||
from typing import List, Tuple, Literal
|
||||
from . import RSLNamer
|
||||
from pathlib import Path
|
||||
@@ -20,14 +21,17 @@ from io import BytesIO
|
||||
|
||||
logger = logging.getLogger(f"submissions.{__name__}")
|
||||
|
||||
|
||||
# class PydMixin(object):
|
||||
|
||||
|
||||
class PydReagent(BaseModel):
|
||||
|
||||
lot: str|None
|
||||
type: str|None
|
||||
expiry: date|Literal['NA']|None
|
||||
name: str|None
|
||||
lot: str | None
|
||||
type: str | None
|
||||
expiry: date | Literal['NA'] | None
|
||||
name: str | None
|
||||
missing: bool = Field(default=True)
|
||||
comment: str|None = Field(default="", validate_default=True)
|
||||
comment: str | None = Field(default="", validate_default=True)
|
||||
|
||||
@field_validator('comment', mode='before')
|
||||
@classmethod
|
||||
@@ -44,7 +48,7 @@ class PydReagent(BaseModel):
|
||||
return None
|
||||
case _:
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("type")
|
||||
@classmethod
|
||||
def rescue_type_with_lookup(cls, value, values):
|
||||
@@ -62,14 +66,14 @@ class PydReagent(BaseModel):
|
||||
if value != None:
|
||||
return convert_nans_to_nones(str(value))
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("lot")
|
||||
@classmethod
|
||||
def enforce_lot_string(cls, value):
|
||||
if value != None:
|
||||
return value.upper()
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("expiry", mode="before")
|
||||
@classmethod
|
||||
def enforce_date(cls, value):
|
||||
@@ -88,14 +92,14 @@ class PydReagent(BaseModel):
|
||||
if value == None:
|
||||
value = date.today()
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("expiry")
|
||||
@classmethod
|
||||
def date_na(cls, value):
|
||||
if isinstance(value, date) and value.year == 1970:
|
||||
value = "NA"
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("name", mode="before")
|
||||
@classmethod
|
||||
def enforce_name(cls, value, values):
|
||||
@@ -104,13 +108,30 @@ class PydReagent(BaseModel):
|
||||
else:
|
||||
return values.data['type']
|
||||
|
||||
def toSQL(self, submission:BasicSubmission|str=None) -> Tuple[Reagent, Report]:
|
||||
def improved_dict(self) -> dict:
|
||||
try:
|
||||
extras = list(self.model_extra.keys())
|
||||
except AttributeError:
|
||||
extras = []
|
||||
fields = list(self.model_fields.keys()) + extras
|
||||
# output = {}
|
||||
# for k in fields:
|
||||
# value = getattr(self, k)
|
||||
# match value:
|
||||
# case date():
|
||||
# value = value.strftime("%Y-%m-%d")
|
||||
# case _:
|
||||
# pass
|
||||
# output[k] = value
|
||||
return {k: getattr(self, k) for k in fields}
|
||||
|
||||
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, Report]:
|
||||
"""
|
||||
Converts this instance into a backend.db.models.kit.Reagent instance
|
||||
|
||||
Returns:
|
||||
Tuple[Reagent, Report]: Reagent instance and result of function
|
||||
"""
|
||||
"""
|
||||
report = Report()
|
||||
# logger.debug("Adding extra fields.")
|
||||
if self.model_extra != None:
|
||||
@@ -150,28 +171,51 @@ class PydReagent(BaseModel):
|
||||
# add end-of-life extension from reagent type to expiry date
|
||||
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
|
||||
return reagent, report
|
||||
|
||||
class PydSample(BaseModel, extra='allow'):
|
||||
|
||||
# def improved_dict(self) -> dict:
|
||||
# fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
|
||||
# return {k:getattr(self,k) for k in fields}
|
||||
|
||||
|
||||
class PydSample(BaseModel, extra='allow'):
|
||||
submitter_id: str
|
||||
sample_type: str
|
||||
row: int|List[int]|None
|
||||
column: int|List[int]|None
|
||||
assoc_id: int|List[int]|None = Field(default=None)
|
||||
row: int | List[int] | None
|
||||
column: int | List[int] | None
|
||||
assoc_id: int | List[int] | None = Field(default=None)
|
||||
submission_rank: int | List[int] | None
|
||||
|
||||
@field_validator("row", "column", "assoc_id")
|
||||
@model_validator(mode='after')
|
||||
@classmethod
|
||||
def validate_model(cls, data):
|
||||
logger.debug(f"Data for pydsample: {data}")
|
||||
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
|
||||
for k, v in data.model_extra.items():
|
||||
# print(k, v)
|
||||
if k in model.timestamps():
|
||||
if isinstance(v, str):
|
||||
v = datetime.strptime(v, "%Y-%m-%d")
|
||||
data.__setattr__(k, v)
|
||||
# print(dir(data))
|
||||
return data
|
||||
|
||||
@field_validator("row", "column", "assoc_id", "submission_rank")
|
||||
@classmethod
|
||||
def row_int_to_list(cls, value):
|
||||
if isinstance(value, int):
|
||||
return [value]
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("submitter_id", mode="before")
|
||||
@classmethod
|
||||
def int_to_str(cls, value):
|
||||
return str(value)
|
||||
|
||||
def toSQL(self, submission:BasicSubmission|str=None) -> Tuple[BasicSample, Result]:
|
||||
|
||||
def improved_dict(self) -> dict:
|
||||
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
|
||||
return {k: getattr(self, k) for k in fields}
|
||||
|
||||
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[BasicSample, Result]:
|
||||
"""
|
||||
Converts this instance into a backend.db.models.submissions.Sample object
|
||||
|
||||
@@ -180,7 +224,7 @@ class PydSample(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Tuple[BasicSample, Result]: Sample object and result object.
|
||||
"""
|
||||
"""
|
||||
report = None
|
||||
self.__dict__.update(self.model_extra)
|
||||
logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
|
||||
@@ -199,10 +243,10 @@ class PydSample(BaseModel, extra='allow'):
|
||||
for row, column, id in zip(self.row, self.column, self.assoc_id):
|
||||
logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
|
||||
logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
|
||||
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
|
||||
submission=submission,
|
||||
sample=instance,
|
||||
row=row, column=column, id=id)
|
||||
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
|
||||
submission=submission,
|
||||
sample=instance,
|
||||
row=row, column=column, id=id)
|
||||
# logger.debug(f"Using submission_sample_association: {association}")
|
||||
try:
|
||||
# instance.sample_submission_associations.append(association)
|
||||
@@ -212,13 +256,21 @@ class PydSample(BaseModel, extra='allow'):
|
||||
instance.metadata.session.rollback()
|
||||
return instance, out_associations, report
|
||||
|
||||
class PydEquipment(BaseModel, extra='ignore'):
|
||||
def improved_dict(self) -> dict:
|
||||
try:
|
||||
extras = list(self.model_extra.keys())
|
||||
except AttributeError:
|
||||
extras = []
|
||||
fields = list(self.model_fields.keys()) + extras
|
||||
return {k: getattr(self, k) for k in fields}
|
||||
|
||||
|
||||
class PydEquipment(BaseModel, extra='ignore'):
|
||||
asset_number: str
|
||||
name: str
|
||||
nickname: str|None
|
||||
processes: List[str]|None
|
||||
role: str|None
|
||||
nickname: str | None
|
||||
processes: List[str] | None
|
||||
role: str | None
|
||||
|
||||
@field_validator('processes', mode='before')
|
||||
@classmethod
|
||||
@@ -227,11 +279,11 @@ class PydEquipment(BaseModel, extra='ignore'):
|
||||
value = convert_nans_to_nones(value)
|
||||
if value == None:
|
||||
value = ['']
|
||||
if len(value)==0:
|
||||
value=['']
|
||||
if len(value) == 0:
|
||||
value = ['']
|
||||
return value
|
||||
|
||||
def toSQL(self, submission:BasicSubmission|str=None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
|
||||
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
|
||||
"""
|
||||
Creates Equipment and SubmssionEquipmentAssociations for this PydEquipment
|
||||
|
||||
@@ -240,7 +292,7 @@ class PydEquipment(BaseModel, extra='ignore'):
|
||||
|
||||
Returns:
|
||||
Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
|
||||
"""
|
||||
"""
|
||||
if isinstance(submission, str):
|
||||
submission = BasicSubmission.query(rsl_number=submission)
|
||||
equipment = Equipment.query(asset_number=self.asset_number)
|
||||
@@ -252,7 +304,8 @@ class PydEquipment(BaseModel, extra='ignore'):
|
||||
if process == None:
|
||||
# logger.debug("Adding in unknown 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?")
|
||||
dlg = QuestionAsker(title="Add Process?",
|
||||
message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
|
||||
if dlg.exec():
|
||||
kit = submission.extraction_kit
|
||||
submission_type = submission.submission_type
|
||||
@@ -267,24 +320,33 @@ class PydEquipment(BaseModel, extra='ignore'):
|
||||
assoc = None
|
||||
return equipment, assoc
|
||||
|
||||
def improved_dict(self) -> dict:
|
||||
try:
|
||||
extras = list(self.model_extra.keys())
|
||||
except AttributeError:
|
||||
extras = []
|
||||
fields = list(self.model_fields.keys()) + extras
|
||||
return {k: getattr(self, k) for k in fields}
|
||||
|
||||
|
||||
class PydSubmission(BaseModel, extra='allow'):
|
||||
filepath: Path
|
||||
submission_type: dict|None
|
||||
submission_type: dict | None
|
||||
# For defaults
|
||||
submitter_plate_num: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
submitted_date: dict|None
|
||||
rsl_plate_num: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
submitted_date: dict|None
|
||||
submitting_lab: dict|None
|
||||
sample_count: dict|None
|
||||
extraction_kit: dict|None
|
||||
technician: dict|None
|
||||
submission_category: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
comment: dict|None = Field(default=dict(value="", missing=True), validate_default=True)
|
||||
reagents: List[dict]|List[PydReagent] = []
|
||||
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
submitted_date: dict | None
|
||||
rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
submitted_date: dict | None
|
||||
submitting_lab: dict | None
|
||||
sample_count: dict | None
|
||||
extraction_kit: dict | None
|
||||
technician: dict | None
|
||||
submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
|
||||
reagents: List[dict] | List[PydReagent] = []
|
||||
samples: List[PydSample]
|
||||
equipment: List[PydEquipment]|None =[]
|
||||
cost_centre: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
equipment: List[PydEquipment] | None = []
|
||||
cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
||||
|
||||
@field_validator('equipment', mode='before')
|
||||
@classmethod
|
||||
@@ -309,7 +371,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
return dict(value=uuid.uuid4().hex.upper(), missing=True)
|
||||
else:
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("submitted_date", mode="before")
|
||||
@classmethod
|
||||
def rescue_date(cls, value):
|
||||
@@ -325,31 +387,32 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
@field_validator("submitted_date")
|
||||
@classmethod
|
||||
def strip_datetime_string(cls, value):
|
||||
|
||||
|
||||
if isinstance(value['value'], datetime):
|
||||
return value
|
||||
if isinstance(value['value'], date):
|
||||
return value
|
||||
if isinstance(value['value'], int):
|
||||
return dict(value=datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2).date(), missing=True)
|
||||
return dict(value=datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2).date(),
|
||||
missing=True)
|
||||
string = re.sub(r"(_|-)\d$", "", value['value'])
|
||||
try:
|
||||
output = dict(value=parse(string).date(), missing=True)
|
||||
except ParserError as e:
|
||||
logger.error(f"Problem parsing date: {e}")
|
||||
try:
|
||||
output = dict(value=parse(string.replace("-","")).date(), missing=True)
|
||||
output = dict(value=parse(string.replace("-", "")).date(), missing=True)
|
||||
except Exception as e:
|
||||
logger.error(f"Problem with parse fallback: {e}")
|
||||
return output
|
||||
|
||||
|
||||
@field_validator("submitting_lab", mode="before")
|
||||
@classmethod
|
||||
def rescue_submitting_lab(cls, value):
|
||||
if value is None:
|
||||
return dict(value=None, missing=True)
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("submitting_lab")
|
||||
@classmethod
|
||||
def lookup_submitting_lab(cls, value):
|
||||
@@ -361,13 +424,15 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
if value['value'] is None:
|
||||
value['missing'] = True
|
||||
from frontend.widgets.pop_ups import ObjectSelector
|
||||
dlg = ObjectSelector(title="Missing Submitting Lab", message="We need a submitting lab. Please select from the list.", obj_type=Organization)
|
||||
dlg = ObjectSelector(title="Missing Submitting Lab",
|
||||
message="We need a submitting lab. Please select from the list.",
|
||||
obj_type=Organization)
|
||||
if dlg.exec():
|
||||
value['value'] = dlg.parse_form()
|
||||
else:
|
||||
value['value'] = None
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("rsl_plate_num", mode='before')
|
||||
@classmethod
|
||||
def rescue_rsl_number(cls, value):
|
||||
@@ -383,7 +448,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
if check_not_nan(value['value']):
|
||||
return value
|
||||
else:
|
||||
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type, data=values.data).parsed_name
|
||||
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
|
||||
data=values.data).parsed_name
|
||||
return dict(value=output, missing=True)
|
||||
|
||||
@field_validator("technician", mode="before")
|
||||
@@ -401,14 +467,14 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
return value
|
||||
else:
|
||||
return dict(value=convert_nans_to_nones(value['value']), missing=True)
|
||||
|
||||
|
||||
@field_validator("sample_count", mode='before')
|
||||
@classmethod
|
||||
def rescue_sample_count(cls, value):
|
||||
if value == None:
|
||||
return dict(value=None, missing=True)
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("extraction_kit", mode='before')
|
||||
@classmethod
|
||||
def rescue_kit(cls, value):
|
||||
@@ -422,7 +488,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
if value == None:
|
||||
return dict(value=None, missing=True)
|
||||
return value
|
||||
|
||||
|
||||
@field_validator("submission_type", mode='before')
|
||||
@classmethod
|
||||
def make_submission_type(cls, value, values):
|
||||
@@ -434,7 +500,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
else:
|
||||
# return dict(value=RSLNamer(instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
|
||||
return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
|
||||
|
||||
|
||||
@field_validator("submission_category", mode="before")
|
||||
@classmethod
|
||||
def create_category(cls, value):
|
||||
@@ -490,25 +556,28 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
"""
|
||||
Collapses multiple samples with same submitter id into one with lists for rows, columns.
|
||||
Necessary to prevent trying to create duplicate samples in SQL creation.
|
||||
"""
|
||||
"""
|
||||
submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
|
||||
output = []
|
||||
for id in submitter_ids:
|
||||
relevants = [item for item in self.samples if item.submitter_id==id]
|
||||
relevants = [item for item in self.samples if item.submitter_id == id]
|
||||
if len(relevants) <= 1:
|
||||
output += relevants
|
||||
else:
|
||||
rows = [item.row[0] for item in relevants]
|
||||
columns = [item.column[0] for item in relevants]
|
||||
ids = [item.assoc_id[0] for item in relevants]
|
||||
ranks = [item.submission_rank[0] for item in relevants]
|
||||
dummy = relevants[0]
|
||||
dummy.assoc_id = ids
|
||||
dummy.row = rows
|
||||
dummy.column = columns
|
||||
dummy.submission_rank = ranks
|
||||
output.append(dummy)
|
||||
self.samples = output
|
||||
|
||||
def improved_dict(self, dictionaries:bool=True) -> dict:
|
||||
# TODO: Return samples, reagents, etc to dictionaries as well.
|
||||
def improved_dict(self, dictionaries: bool = True) -> dict:
|
||||
"""
|
||||
Adds model_extra to fields.
|
||||
|
||||
@@ -517,13 +586,18 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
dict: This instance as a dictionary
|
||||
"""
|
||||
"""
|
||||
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
|
||||
if dictionaries:
|
||||
output = {k:getattr(self, k) for k in fields}
|
||||
output = {k: getattr(self, k) for k in fields}
|
||||
output['reagents'] = [item.improved_dict() for item in self.reagents]
|
||||
output['samples'] = [item.improved_dict() for item in self.samples]
|
||||
output['equipment'] = [item.improved_dict() for item in self.equipment]
|
||||
else:
|
||||
# logger.debug("Extracting 'value' from attributes")
|
||||
output = {k:(getattr(self, k) if not isinstance(getattr(self, k), dict) else getattr(self, k)['value']) for k in fields}
|
||||
output = {k: (getattr(self, k) if not isinstance(getattr(self, k), dict) else getattr(self, k)['value']) for
|
||||
k in fields}
|
||||
|
||||
return output
|
||||
|
||||
def find_missing(self) -> Tuple[dict, dict]:
|
||||
@@ -532,9 +606,9 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Tuple[dict, dict]: Dict for missing info, dict for missing reagents.
|
||||
"""
|
||||
info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)}
|
||||
missing_info = {k:v for k,v in info.items() if v['missing']}
|
||||
"""
|
||||
info = {k: v for k, v in self.improved_dict().items() if isinstance(v, dict)}
|
||||
missing_info = {k: v for k, v in info.items() if v['missing']}
|
||||
missing_reagents = [reagent for reagent in self.reagents if reagent.missing]
|
||||
return missing_info, missing_reagents
|
||||
|
||||
@@ -544,10 +618,11 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
|
||||
"""
|
||||
"""
|
||||
# self.__dict__.update(self.model_extra)
|
||||
dicto = self.improved_dict()
|
||||
instance, code, msg = BasicSubmission.query_or_create(submission_type=self.submission_type['value'], rsl_plate_num=self.rsl_plate_num['value'])
|
||||
instance, code, msg = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
|
||||
rsl_plate_num=self.rsl_plate_num['value'])
|
||||
result = Result(msg=msg, code=code)
|
||||
self.handle_duplicate_samples()
|
||||
logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
|
||||
@@ -574,9 +649,19 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
equip, association = equip.toSQL(submission=instance)
|
||||
if association != None:
|
||||
association.save()
|
||||
logger.debug(f"Equipment association SQL object to be added to submission: {association.__dict__}")
|
||||
logger.debug(
|
||||
f"Equipment association SQL object to be added to submission: {association.__dict__}")
|
||||
instance.submission_equipment_associations.append(association)
|
||||
# TODO: case item if item in instance.jsons()
|
||||
case item if item in instance.jsons():
|
||||
logger.debug(f"{item} is a json.")
|
||||
try:
|
||||
ii = value.items()
|
||||
except AttributeError:
|
||||
ii = {}
|
||||
for k, v in ii:
|
||||
if isinstance(v, datetime):
|
||||
value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
|
||||
instance.set_attribute(key=key, value=value)
|
||||
case _:
|
||||
try:
|
||||
instance.set_attribute(key=key, value=value)
|
||||
@@ -598,7 +683,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
# Apply any discounts that are applicable for client and kit.
|
||||
try:
|
||||
logger.debug("Checking and applying discounts...")
|
||||
discounts = [item.amount for item in Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
|
||||
discounts = [item.amount for item in
|
||||
Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
|
||||
logger.debug(f"We got discounts: {discounts}")
|
||||
if len(discounts) > 0:
|
||||
discounts = sum(discounts)
|
||||
@@ -613,8 +699,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
|
||||
logger.debug(f"Constructed submissions message: {msg}")
|
||||
return instance, result
|
||||
|
||||
def toForm(self, parent:QWidget):
|
||||
|
||||
def toForm(self, parent: QWidget):
|
||||
"""
|
||||
Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget
|
||||
|
||||
@@ -623,11 +709,11 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
SubmissionFormWidget: Submission form widget
|
||||
"""
|
||||
"""
|
||||
from frontend.widgets.submission_widget import SubmissionFormWidget
|
||||
return SubmissionFormWidget(parent=parent, submission=self)
|
||||
|
||||
def autofill_excel(self, missing_only:bool=True, backup:bool=False) -> Workbook:
|
||||
def autofill_excel(self, missing_only: bool = True, backup: bool = False) -> Workbook:
|
||||
"""
|
||||
Fills in relevant information/reagent cells in an excel workbook.
|
||||
|
||||
@@ -637,13 +723,13 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Workbook: Filled in workbook
|
||||
"""
|
||||
"""
|
||||
# open a new workbook using openpyxl
|
||||
if self.filepath.stem.startswith("tmp"):
|
||||
template = SubmissionType.query(name=self.submission_type['value']).template_file
|
||||
workbook = load_workbook(BytesIO(template))
|
||||
missing_only = False
|
||||
else:
|
||||
else:
|
||||
try:
|
||||
workbook = load_workbook(self.filepath)
|
||||
except Exception as e:
|
||||
@@ -654,12 +740,12 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
if missing_only:
|
||||
info, reagents = self.find_missing()
|
||||
else:
|
||||
info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)}
|
||||
info = {k: v for k, v in self.improved_dict().items() if isinstance(v, dict)}
|
||||
reagents = self.reagents
|
||||
|
||||
if len(reagents + list(info.keys())) == 0:
|
||||
# logger.warning("No info to fill in, returning")
|
||||
return None
|
||||
logger.debug(f"Info: {pformat(info)}")
|
||||
logger.debug(f"We have blank info and/or reagents in the excel sheet.\n\tLet's try to fill them in.")
|
||||
# extraction_kit = lookup_kit_types(ctx=self.ctx, name=self.extraction_kit['value'])
|
||||
extraction_kit = KitType.query(name=self.extraction_kit['value'])
|
||||
@@ -687,7 +773,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
new_reagents.append(new_reagent)
|
||||
new_info = []
|
||||
# logger.debug("Constructing info map and values")
|
||||
for k,v in info.items():
|
||||
for k, v in info.items():
|
||||
try:
|
||||
new_item = {}
|
||||
new_item['type'] = k
|
||||
@@ -708,33 +794,38 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
# get list of sheet names
|
||||
for sheet in workbook.sheetnames:
|
||||
# open sheet
|
||||
worksheet=workbook[sheet]
|
||||
worksheet = workbook[sheet]
|
||||
# Get relevant reagents for that sheet
|
||||
sheet_reagents = [item for item in new_reagents if sheet in item['sheet']]
|
||||
for reagent in sheet_reagents:
|
||||
# logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}")
|
||||
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
|
||||
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'],
|
||||
value=reagent['lot']['value'])
|
||||
# logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}")
|
||||
if isinstance(reagent['expiry']['value'], date) and reagent['expiry']['value'].year == 1970:
|
||||
reagent['expiry']['value'] = "NA"
|
||||
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
|
||||
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'],
|
||||
value=reagent['expiry']['value'])
|
||||
try:
|
||||
# logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}")
|
||||
worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'])
|
||||
worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'],
|
||||
value=reagent['name']['value'])
|
||||
except Exception as e:
|
||||
logger.error(f"Could not write name {reagent['name']['value']} due to {e}")
|
||||
# Get relevant info for that sheet
|
||||
new_info = [item for item in new_info if isinstance(item['location'], dict)]
|
||||
sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
|
||||
logger.debug(f"New info: {pformat(new_info)}")
|
||||
sheet_info = [item for item in new_info if item['location']['sheet'] == sheet]
|
||||
for item in sheet_info:
|
||||
logger.debug(f"Attempting: {item['type']} in row {item['location']['row']}, column {item['location']['column']}")
|
||||
logger.debug(
|
||||
f"Attempting: {item['type']} in row {item['location']['row']}, column {item['location']['column']}")
|
||||
worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
|
||||
# Hacky way to pop in 'signed by'
|
||||
custom_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type['value'])
|
||||
workbook = custom_parser.custom_autofill(workbook, info=self.improved_dict(), backup=backup)
|
||||
return workbook
|
||||
|
||||
def autofill_samples(self, workbook:Workbook) -> Workbook:
|
||||
|
||||
def autofill_samples(self, workbook: Workbook) -> Workbook:
|
||||
"""
|
||||
Fill in sample rows on the excel sheet
|
||||
|
||||
@@ -743,8 +834,9 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Workbook: Updated excel workbook
|
||||
"""
|
||||
sample_info = SubmissionType.query(name=self.submission_type['value']).info_map['samples']
|
||||
"""
|
||||
# sample_info = SubmissionType.query(name=self.submission_type['value']).info_map['samples']
|
||||
sample_info = SubmissionType.query(name=self.submission_type['value']).construct_sample_map()
|
||||
logger.debug(f"Sample info: {pformat(sample_info)}")
|
||||
logger.debug(f"Workbook sheets: {workbook.sheetnames}")
|
||||
worksheet = workbook[sample_info["lookup_table"]['sheet']]
|
||||
@@ -762,10 +854,11 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
logger.debug(f"Writing to {row}")
|
||||
if row == None:
|
||||
row = sample_info['lookup_table']['start_row'] + iii
|
||||
fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
|
||||
fields = [field for field in list(sample.model_fields.keys()) +
|
||||
list(sample.model_extra.keys()) if field in sample_info['lookup_table']['sample_columns'].keys()]
|
||||
logger.debug(f"Here are the fields we are going to fill:\n\t{fields}")
|
||||
for field in fields:
|
||||
column = sample_info['sample_columns'][field]
|
||||
column = sample_info['lookup_table']['sample_columns'][field]
|
||||
value = getattr(sample, field)
|
||||
match value:
|
||||
case list():
|
||||
@@ -776,8 +869,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
value = row_map[value]
|
||||
worksheet.cell(row=row, column=column, value=value)
|
||||
return workbook
|
||||
|
||||
def autofill_equipment(self, workbook:Workbook) -> Workbook:
|
||||
|
||||
def autofill_equipment(self, workbook: Workbook) -> Workbook:
|
||||
"""
|
||||
Fill in equipment on the excel sheet
|
||||
|
||||
@@ -786,7 +879,7 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Workbook: Updated excel workbook
|
||||
"""
|
||||
"""
|
||||
equipment_map = SubmissionType.query(name=self.submission_type['value']).construct_equipment_map()
|
||||
logger.debug(f"Equipment map: {equipment_map}")
|
||||
# See if all equipment has a location map
|
||||
@@ -820,23 +913,31 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
case _:
|
||||
pass
|
||||
worksheet.cell(row=rel['name']['row'], column=rel['name']['column'], value=rel['name']['value'])
|
||||
worksheet.cell(row=rel['process']['row'], column=rel['process']['column'], value=rel['process']['value'])
|
||||
worksheet.cell(row=rel['process']['row'], column=rel['process']['column'],
|
||||
value=rel['process']['value'])
|
||||
return workbook
|
||||
|
||||
def toWriter(self):
|
||||
from backend.excel.writer import SheetWriter
|
||||
return SheetWriter(self)
|
||||
|
||||
def construct_filename(self) -> str:
|
||||
"""
|
||||
Creates filename for this instance
|
||||
|
||||
Returns:
|
||||
str: Output filename
|
||||
"""
|
||||
template = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type).filename_template()
|
||||
"""
|
||||
template = BasicSubmission.find_polymorphic_subclass(
|
||||
polymorphic_identity=self.submission_type).filename_template()
|
||||
# logger.debug(f"Using template string: {template}")
|
||||
render = RSLNamer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace("/", "")
|
||||
render = RSLNamer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace(
|
||||
"/", "")
|
||||
# logger.debug(f"Template rendered as: {render}")
|
||||
return render
|
||||
|
||||
def check_kit_integrity(self, reagenttypes:list=[], extraction_kit:str|dict|None=None) -> Tuple[List[PydReagent], Report]:
|
||||
def check_kit_integrity(self, reagenttypes: list = [], extraction_kit: str | dict | None = None) -> Tuple[
|
||||
List[PydReagent], Report]:
|
||||
"""
|
||||
Ensures all reagents expected in kit are listed in Submission
|
||||
|
||||
@@ -845,13 +946,13 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
|
||||
Returns:
|
||||
Report: Result object containing a message and any missing components.
|
||||
"""
|
||||
"""
|
||||
report = Report()
|
||||
logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
|
||||
if isinstance(extraction_kit, str):
|
||||
extraction_kit = dict(value=extraction_kit)
|
||||
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
|
||||
self.extraction_kit['value'] = extraction_kit['value']
|
||||
self.extraction_kit['value'] = extraction_kit['value']
|
||||
# reagenttypes = []
|
||||
# else:
|
||||
# reagenttypes = [item.type for item in self.reagents]
|
||||
@@ -859,7 +960,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
# reagenttypes = [item.type for item in self.reagents]
|
||||
logger.debug(f"Looking up {self.extraction_kit['value']}")
|
||||
ext_kit = KitType.query(name=self.extraction_kit['value'])
|
||||
ext_kit_rtypes = [item.to_pydantic() for item in ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
|
||||
ext_kit_rtypes = [item.to_pydantic() for item in
|
||||
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
|
||||
logger.debug(f"Kit reagents: {ext_kit_rtypes}")
|
||||
logger.debug(f"Submission reagents: {self.reagents}")
|
||||
# check if lists are equal
|
||||
@@ -883,18 +985,20 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
|
||||
logger.debug(f"Missing reagents types: {missing_reagents}")
|
||||
# if lists are equal return no problem
|
||||
if len(missing_reagents)==0:
|
||||
if len(missing_reagents) == 0:
|
||||
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!", status="Warning")
|
||||
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!",
|
||||
status="Warning")
|
||||
report.add_result(result)
|
||||
return output_reagents, report
|
||||
|
||||
|
||||
class PydContact(BaseModel):
|
||||
|
||||
name: str
|
||||
phone: str|None
|
||||
email: str|None
|
||||
phone: str | None
|
||||
email: str | None
|
||||
|
||||
def toSQL(self) -> Contact:
|
||||
"""
|
||||
@@ -902,14 +1006,14 @@ class PydContact(BaseModel):
|
||||
|
||||
Returns:
|
||||
Contact: Contact instance
|
||||
"""
|
||||
"""
|
||||
return Contact(name=self.name, phone=self.phone, email=self.email)
|
||||
|
||||
class PydOrganization(BaseModel):
|
||||
|
||||
class PydOrganization(BaseModel):
|
||||
name: str
|
||||
cost_centre: str
|
||||
contacts: List[PydContact]|None
|
||||
contacts: List[PydContact] | None
|
||||
|
||||
def toSQL(self) -> Organization:
|
||||
"""
|
||||
@@ -917,7 +1021,7 @@ class PydOrganization(BaseModel):
|
||||
|
||||
Returns:
|
||||
Organization: Organization instance
|
||||
"""
|
||||
"""
|
||||
instance = Organization()
|
||||
for field in self.model_fields:
|
||||
match field:
|
||||
@@ -929,12 +1033,12 @@ class PydOrganization(BaseModel):
|
||||
instance.__setattr__(name=field, value=value)
|
||||
return instance
|
||||
|
||||
class PydReagentType(BaseModel):
|
||||
|
||||
class PydReagentType(BaseModel):
|
||||
name: str
|
||||
eol_ext: timedelta|int|None
|
||||
uses: dict|None
|
||||
required: int|None = Field(default=1)
|
||||
eol_ext: timedelta | int | None
|
||||
uses: dict | None
|
||||
required: int | None = Field(default=1)
|
||||
|
||||
@field_validator("eol_ext")
|
||||
@classmethod
|
||||
@@ -942,8 +1046,8 @@ class PydReagentType(BaseModel):
|
||||
if isinstance(value, int):
|
||||
return timedelta(days=value)
|
||||
return value
|
||||
|
||||
def toSQL(self, kit:KitType) -> ReagentType:
|
||||
|
||||
def toSQL(self, kit: KitType) -> ReagentType:
|
||||
"""
|
||||
Converts this instance into a backend.db.models.ReagentType instance
|
||||
|
||||
@@ -952,7 +1056,7 @@ class PydReagentType(BaseModel):
|
||||
|
||||
Returns:
|
||||
ReagentType: ReagentType instance
|
||||
"""
|
||||
"""
|
||||
instance: ReagentType = ReagentType.query(name=self.name)
|
||||
if instance == None:
|
||||
instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
|
||||
@@ -962,11 +1066,12 @@ class PydReagentType(BaseModel):
|
||||
except StatementError:
|
||||
assoc = None
|
||||
if assoc == None:
|
||||
assoc = KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=instance, uses=self.uses, required=self.required)
|
||||
assoc = KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=instance, uses=self.uses,
|
||||
required=self.required)
|
||||
return instance
|
||||
|
||||
class PydKit(BaseModel):
|
||||
|
||||
|
||||
class PydKit(BaseModel):
|
||||
name: str
|
||||
reagent_types: List[PydReagentType] = []
|
||||
|
||||
@@ -976,7 +1081,7 @@ class PydKit(BaseModel):
|
||||
|
||||
Returns:
|
||||
Tuple[KitType, Report]: KitType instance and report of results.
|
||||
"""
|
||||
"""
|
||||
report = Report()
|
||||
instance = KitType.query(name=self.name)
|
||||
if instance == None:
|
||||
@@ -984,13 +1089,13 @@ class PydKit(BaseModel):
|
||||
[item.toSQL(instance) for item in self.reagent_types]
|
||||
return instance, report
|
||||
|
||||
class PydEquipmentRole(BaseModel):
|
||||
|
||||
class PydEquipmentRole(BaseModel):
|
||||
name: str
|
||||
equipment: List[PydEquipment]
|
||||
processes: List[str]|None
|
||||
|
||||
def toForm(self, parent, used:list) -> "RoleComboBox":
|
||||
processes: List[str] | None
|
||||
|
||||
def toForm(self, parent, used: list) -> "RoleComboBox":
|
||||
"""
|
||||
Creates a widget for user input into this class.
|
||||
|
||||
@@ -1000,7 +1105,6 @@ class PydEquipmentRole(BaseModel):
|
||||
|
||||
Returns:
|
||||
RoleComboBox: widget
|
||||
"""
|
||||
"""
|
||||
from frontend.widgets.equipment_usage import RoleComboBox
|
||||
return RoleComboBox(parent=parent, role=self, used=used)
|
||||
|
||||
Reference in New Issue
Block a user