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Removed Kittype.

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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
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2
src/submissions/frontend/widgets/app.py
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@@ -13,7 +13,7 @@ from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
from pandas import ExcelWriter
from backend.db.models import Reagent, KitType
from backend.db.models import Reagent
from tools import (
check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
under_development

2
src/submissions/frontend/widgets/controls_chart.py
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@@ -6,7 +6,7 @@ from PyQt6.QtWidgets import (
QWidget, QComboBox, QPushButton
)
from PyQt6.QtCore import QSignalBlocker
from backend import ChartReportMaker
from backend.excel.reports import ChartReportMaker
from backend.db import ControlType
import logging
from tools import Report, report_result

2
src/submissions/frontend/widgets/date_type_picker.py
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@@ -2,7 +2,7 @@ from PyQt6.QtWidgets import (
QVBoxLayout, QDialog, QDialogButtonBox
)
from .misc import CheckableComboBox, StartEndDatePicker
from backend.db.models.kits import SubmissionType
from backend.db.models.procedures import SubmissionType
class DateTypePicker(QDialog):

2
src/submissions/frontend/widgets/equipment_usage.py
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@@ -21,7 +21,7 @@ class EquipmentUsage(QDialog):
self.procedure = procedure
self.setWindowTitle(f"Equipment Checklist - {procedure.name}")
self.used_equipment = self.procedure.equipment
self.kit = self.procedure.kittype
# self.kit = self.procedure.kittype
self.opt_equipment = procedure.proceduretype.get_equipment()
self.layout = QVBoxLayout()
self.setLayout(self.layout)

2
src/submissions/frontend/widgets/equipment_usage_2.py
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@@ -57,7 +57,7 @@ class EquipmentUsage(QDialog):
proceduretype = procedure.proceduretype
proceduretype_dict = proceduretype.details_dict()
run = procedure.run
proceduretype_dict['equipment_json'] = flatten_list([item['equipment_json'] for item in proceduretype_dict['equipment']])
# proceduretype_dict['equipment_json'] = flatten_list([item['equipment_json'] for item in proceduretype_dict['equipment']])
# proceduretype_dict['equipment_json'] = [
# {'name': 'Liquid Handler', 'equipment': [
# {'name': 'Other', 'asset_number': 'XXX', 'processes': [

33
src/submissions/frontend/widgets/procedure_creation.py
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@@ -20,7 +20,7 @@ from typing import TYPE_CHECKING, Any, List
if TYPE_CHECKING:
from backend.db.models import Run, Procedure
from backend.validators import PydProcedure
from tools import jinja_template_loading, get_application_from_parent, render_details_template
from tools import jinja_template_loading, get_application_from_parent, render_details_template, sanitize_object_for_json
logger = logging.getLogger(f"submissions.{__name__}")
@@ -32,10 +32,11 @@ class ProcedureCreation(QDialog):
self.edit = edit
self.run = procedure.run
self.procedure = procedure
logger.debug(f"procedure: {pformat(self.procedure.__dict__)}")
self.proceduretype = procedure.proceduretype
self.setWindowTitle(f"New {self.proceduretype.name} for {self.run.rsl_plate_number}")
# self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
self.procedure.update_kittype_reagentroles(kittype=self.procedure.possible_kits[0])
# self.procedure.update_kittype_reagentroles(kittype=self.procedure.possible_kits[0])
# self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
# logger.debug(f"Samples to map\n{pformat(self.created_procedure.samples)}")
@@ -70,8 +71,13 @@ class ProcedureCreation(QDialog):
def set_html(self):
from .equipment_usage_2 import EquipmentUsage
logger.debug(f"Edit: {self.edit}")
# logger.debug(f"Edit: {self.edit}")
proceduretype_dict = self.proceduretype.details_dict()
logger.debug(f"Reagent roles: {self.procedure.reagentrole}")
logger.debug(f"Equipment roles: {pformat(proceduretype_dict['equipment'])}")
# NOTE: Add --New-- as an option for reagents.
for key, value in self.procedure.reagentrole.items():
value.append(dict(name="--New--"))
if self.procedure.equipment:
for equipmentrole in proceduretype_dict['equipment']:
# NOTE: Check if procedure equipment is present and move to head of the list if so.
@@ -85,6 +91,8 @@ class ProcedureCreation(QDialog):
equipmentrole['equipment'].insert(0, equipmentrole['equipment'].pop(
equipmentrole['equipment'].index(item_in_er_list)))
proceduretype_dict['equipment_section'] = EquipmentUsage.construct_html(procedure=self.procedure, child=True)
proceduretype_dict['equipment'] = [sanitize_object_for_json(object) for object in proceduretype_dict['equipment']]
self.update_equipment = EquipmentUsage.update_equipment
regex = re.compile(r".*R\d$")
proceduretype_dict['previous'] = [""] + [item.name for item in self.run.procedure if item.proceduretype == self.proceduretype and not bool(regex.match(item.name))]
@@ -94,12 +102,13 @@ class ProcedureCreation(QDialog):
js_in=["procedure_form", "grid_drag", "context_menu"],
proceduretype=proceduretype_dict,
run=self.run.details_dict(),
procedure=self.procedure.__dict__,
# procedure=self.procedure.__dict__,
procedure=self.procedure,
plate_map=self.plate_map,
edit=self.edit
)
# with open("procedure_creation_rendered.html", "w") as f:
# f.write(html)
with open("procedure_creation_rendered.html", "w") as f:
f.write(html)
self.webview.setHtml(html)
@pyqtSlot(str, str, str, str)
@@ -119,11 +128,13 @@ class ProcedureCreation(QDialog):
eoi.name = equipment.name
eoi.asset_number = equipment.asset_number
eoi.nickname = equipment.nickname
process = next((prcss for prcss in equipment.process if prcss.name == process))
eoi.process = process.to_pydantic()
tips = next((tps for tps in equipment.tips if tps.name == tips))
eoi.tips = tips.to_pydantic()
self.procedure.equipment.append(eoi)
process = next((prcss for prcss in equipment.process if prcss.name == process), None)
if process:
eoi.process = process.to_pydantic()
tips = next((tps for tps in equipment.tips if tps.name == tips), None)
if tips:
eoi.tips = tips.to_pydantic()
self.procedure.equipment.append(eoi)
logger.debug(f"Updated equipment: {self.procedure.equipment}")
@pyqtSlot(str, str)

10
src/submissions/frontend/widgets/submission_details.py
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@@ -7,7 +7,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtCore import Qt, pyqtSlot
from jinja2 import TemplateNotFound
from backend.db.models import Run, Sample, Reagent, KitType, Equipment, Process, Tips
from backend.db.models import Run, Sample, Reagent, ProcedureType, Equipment, Process, Tips
from tools import is_power_user, jinja_template_loading, timezone, get_application_from_parent, list_str_comparator
from .functions import select_save_file, save_pdf
from pathlib import Path
@@ -161,7 +161,7 @@ class SubmissionDetails(QDialog):
self.setWindowTitle(f"Sample Details - {sample.sample_id}")
@pyqtSlot(str, str)
def reagent_details(self, reagent: str | Reagent, kit: str | KitType):
def reagent_details(self, reagent: str | Reagent, proceduretype: str | ProcedureType):
"""
Changes details view to summary of Reagent
@@ -172,9 +172,9 @@ class SubmissionDetails(QDialog):
logger.debug(f"Reagent details.")
if isinstance(reagent, str):
reagent = Reagent.query(lot=reagent)
if isinstance(kit, str):
self.kit = KitType.query(name=kit)
base_dict = reagent.to_sub_dict(kittype=self.kit, full_data=True)
if isinstance(proceduretype, str):
self.proceduretype = ProcedureType.query(name=proceduretype)
base_dict = reagent.to_sub_dict(proceduretype=self.proceduretype, full_data=True)
env = jinja_template_loading()
temp_name = "reagent_details.html"
try:

6
src/submissions/frontend/widgets/submission_widget.py
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@@ -15,7 +15,7 @@ from tools import Report, Result, check_not_nan, main_form_style, report_result,
from backend.validators import PydReagent, PydClientSubmission, PydSample
from backend.db import (
ClientLab, SubmissionType, Reagent,
ReagentRole, KitTypeReagentRoleAssociation, Run, ClientSubmission
ReagentRole, ProcedureTypeReagentRoleAssociation, Run, ClientSubmission
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -760,8 +760,8 @@ class SubmissionFormWidget(QWidget):
def __init__(self, scrollWidget, reagent, extraction_kit: str) -> None:
super().__init__(scrollWidget=scrollWidget)
self.setEditable(True)
looked_up_rt = KitTypeReagentRoleAssociation.query(reagentrole=reagent.equipmentrole,
kittype=extraction_kit)
looked_up_rt = ProcedureTypeReagentRoleAssociation.query(reagentrole=reagent.reagentrole,
proceduretype=extraction_kit)
relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()]
# NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
if str(reagent.lot) not in relevant_reagents:

2
src/submissions/frontend/widgets/summary.py
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@@ -4,7 +4,7 @@ Pane to hold information e.g. cost summary.
from .info_tab import InfoPane
from PyQt6.QtWidgets import QWidget, QLabel, QPushButton
from backend.db import ClientLab
from backend.excel import ReportMaker
from backend.excel.reports import ReportMaker
from .misc import CheckableComboBox
import logging