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Update of Reagent usage ui for addition of new reagents.

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This commit is contained in:
lwark
2025-07-02 13:42:40 -05:00
parent fd63608744
commit c4c330b90c
8 changed files with 154 additions and 83 deletions
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2
src/submissions/backend/db/models/__init__.py
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@@ -603,7 +603,7 @@ class BaseClass(Base):
pyd = getattr(pydant, pyd_model_name)
except AttributeError:
raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
return pyd(**self.details_dict())
return pyd(**self.details_dict(**kwargs))
def show_details(self, obj):
logger.debug("Show Details")

60
src/submissions/backend/db/models/kits.py
View File

@@ -5,13 +5,11 @@ from __future__ import annotations
import zipfile, logging, re
from operator import itemgetter
from pprint import pformat
import numpy as np
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date, datetime, timedelta
from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, timezone, \
jinja_template_loading, flatten_list
from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
@@ -562,7 +560,8 @@ class ReagentRole(BaseClass):
def get_reagents(self, kittype: str | KitType | None = None):
if not kittype:
return [f"{reagent.name} - {reagent.lot}" for reagent in self.reagent]
# return [f"{reagent.name} - {reagent.lot} - {reagent.expiry}" for reagent in self.reagent]
return [reagent.to_pydantic() for reagent in self.reagent]
if isinstance(kittype, str):
kittype = KitType.query(name=kittype)
assoc = next((item for item in self.reagentrolekittypeassociation if item.kittype == kittype), None)
@@ -571,7 +570,8 @@ class ReagentRole(BaseClass):
last_used = Reagent.query(name=assoc.last_used)
if last_used:
reagents.insert(0, reagents.pop(reagents.index(last_used)))
return [f"{reagent.name} - {reagent.lot}" for reagent in reagents]
# return [f"{reagent.name} - {reagent.lot} - {reagent.expiry}" for reagent in reagents]
return [reagent.to_pydantic(reagentrole=self.name) for reagent in reagents]
class Reagent(BaseClass, LogMixin):
@@ -680,24 +680,24 @@ class Reagent(BaseClass, LogMixin):
report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
return report
@classmethod
def query_or_create(cls, **kwargs) -> Reagent:
from backend.validators.pydant import PydReagent
new = False
disallowed = ['expiry']
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list):
if "reagentrole" not in kwargs:
try:
kwargs['reagentrole'] = kwargs['name']
except KeyError:
pass
instance = PydReagent(**kwargs)
new = True
instance = instance.to_sql()
logger.info(f"Instance from query or create: {instance}")
return instance, new
# @classmethod
# def query_or_create(cls, **kwargs) -> Reagent:
# from backend.validators.pydant import PydReagent
# new = False
# disallowed = ['expiry']
# sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
# instance = cls.query(**sanitized_kwargs)
# if not instance or isinstance(instance, list):
# if "reagentrole" not in kwargs:
# try:
# kwargs['reagentrole'] = kwargs['name']
# except KeyError:
# pass
# instance = PydReagent(**kwargs)
# new = True
# instance = instance.to_sql()
# logger.info(f"Instance from query or create: {instance}")
# return instance, new
@classmethod
@setup_lookup
@@ -800,6 +800,12 @@ class Reagent(BaseClass, LogMixin):
expiry="Use exact date on reagent.\nEOL will be calculated from kittype automatically"
)
def details_dict(self, reagentrole:str|None=None, **kwargs):
output = super().details_dict()
if reagentrole:
output['reagentrole'] = reagentrole
return output
class Discount(BaseClass):
"""
@@ -1278,7 +1284,7 @@ class ProcedureType(BaseClass):
if self.plate_rows == 0 or self.plate_columns == 0:
return "<br/>"
sample_dicts = self.pad_sample_dicts(sample_dicts=sample_dicts)
logger.debug(f"Sample dicts: {pformat(sample_dicts)}")
# logger.debug(f"Sample dicts: {pformat(sample_dicts)}")
vw = round((-0.07 * len(sample_dicts)) + 12.2, 1)
# NOTE: An overly complicated list comprehension create a list of sample locations
# NOTE: next will return a blank cell if no value found for row/column
@@ -1291,14 +1297,14 @@ class ProcedureType(BaseClass):
def pad_sample_dicts(self, sample_dicts: List["PydSample"]):
from backend.validators.pydant import PydSample
output = []
logger.debug(f"Rows: {self.plate_rows}")
logger.debug(f"Columns: {self.plate_columns}")
# logger.debug(f"Rows: {self.plate_rows}")
# logger.debug(f"Columns: {self.plate_columns}")
for row, column in self.ranked_plate.values():
sample = next((sample for sample in sample_dicts if sample.row == row and sample.column == column),
PydSample(**dict(sample_id="", row=row, column=column, enabled=False)))
sample.background_color = "#6ffe1d" if sample.enabled else "#ffffff"
output.append(sample)
logger.debug(f"Appending {sample} at row {row}, column {column}")
# logger.debug(f"Appending {sample} at row {row}, column {column}")
return output
@@ -1453,6 +1459,8 @@ class Procedure(BaseClass):
dlg = ProcedureCreation(parent=obj, procedure=self.to_pydantic(), edit=True)
if dlg.exec():
logger.debug("Edited")
sql, _ = dlg.return_sql()
sql.save()
def add_comment(self, obj):
logger.debug("Add Comment!")