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Converted client manager to new Omni pydantic version.

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This commit is contained in:
lwark
2025-04-04 13:09:54 -05:00
parent 3a318fff38
commit ac85be6414
12 changed files with 255 additions and 954 deletions
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77
src/submissions/frontend/widgets/app.py
View File

@@ -9,17 +9,19 @@ from PyQt6.QtWidgets import (
QHBoxLayout, QScrollArea, QMainWindow,
QToolBar
)
# import pickle
from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
from pandas import ExcelWriter
from __init__ import project_path
from backend import SubmissionType, Reagent, BasicSample, Organization, KitType
from backend import SubmissionType, Reagent, BasicSample, Organization, KitType, BasicSubmission
from tools import (
check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user, under_development
check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
under_development
)
from .functions import select_save_file, select_open_file
from .pop_ups import HTMLPop, AlertPop
from .date_type_picker import DateTypePicker
from .functions import select_save_file
from .pop_ups import HTMLPop
from .misc import Pagifier
from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer
@@ -80,7 +82,7 @@ class App(QMainWindow):
helpMenu.addAction(self.docsAction)
helpMenu.addAction(self.githubAction)
fileMenu.addAction(self.importAction)
# fileMenu.addAction(self.yamlExportAction)
fileMenu.addAction(self.archiveSubmissionsAction)
# fileMenu.addAction(self.yamlImportAction)
methodsMenu.addAction(self.searchSample)
maintenanceMenu.addAction(self.joinExtractionAction)
@@ -112,8 +114,7 @@ class App(QMainWindow):
self.docsAction = QAction("&Docs", self)
self.searchSample = QAction("Search Sample", self)
self.githubAction = QAction("Github", self)
# self.yamlExportAction = QAction("Export Type Example", self)
# self.yamlImportAction = QAction("Import Type Template", self)
self.archiveSubmissionsAction = QAction("Submissions to Excel", self)
self.editReagentAction = QAction("Edit Reagent", self)
self.manageOrgsAction = QAction("Manage Clients", self)
self.manageKitsAction = QAction("Manage Kits", self)
@@ -130,8 +131,7 @@ class App(QMainWindow):
self.docsAction.triggered.connect(self.openDocs)
self.searchSample.triggered.connect(self.runSampleSearch)
self.githubAction.triggered.connect(self.openGithub)
# self.yamlExportAction.triggered.connect(self.export_ST_yaml)
# self.yamlImportAction.triggered.connect(self.import_ST_yaml)
self.archiveSubmissionsAction.triggered.connect(self.submissions_to_excel)
self.table_widget.pager.current_page.textChanged.connect(self.update_data)
self.editReagentAction.triggered.connect(self.edit_reagent)
self.manageOrgsAction.triggered.connect(self.manage_orgs)
@@ -186,60 +186,18 @@ class App(QMainWindow):
dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
dlg.exec()
# def export_ST_yaml(self):
# """
# Copies submission type yaml to file system for editing and remport
#
# Returns:
# None
# """
# if check_if_app():
# yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
# else:
# yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
# fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
# shutil.copyfile(yaml_path, fname)
# @check_authorization
# def import_ST_yaml(self, *args, **kwargs):
# """
# Imports a yml form into a submission type.
#
# Args:
# *args ():
# **kwargs ():
#
# Returns:
#
# """
# fname = select_open_file(obj=self, file_extension="yml")
# if not fname:
# logger.info(f"Import cancelled.")
# return
# ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
# ap.exec()
# st = SubmissionType.import_from_json(filepath=fname)
# if st:
# # NOTE: Do not delete the print statement below.
# choice = input("Save the above submission type? [y/N]: ")
# if choice.lower() == "y":
# pass
# else:
# logger.warning("Save of submission type cancelled.")
def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
# TODO: Change this to the Pydantic version.
def manage_orgs(self):
from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
# dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
dlg = ManagerWindowPyd(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
if dlg.exec():
new_org = dlg.parse_form()
new_org.save()
# logger.debug(new_org.__dict__)
@under_development
def manage_kits(self, *args, **kwargs):
from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
@@ -252,6 +210,17 @@ class App(QMainWindow):
assert isinstance(sql, KitType)
sql.save()
@under_development
def submissions_to_excel(self, *args, **kwargs):
dlg = DateTypePicker(self)
if dlg.exec():
output = dlg.parse_form()
df = BasicSubmission.archive_submissions(**output)
filepath = select_save_file(self, f"Submissions {output['start_date']}-{output['end_date']}", "xlsx")
writer = ExcelWriter(filepath, "openpyxl")
df.to_excel(writer)
writer.close()
class AddSubForm(QWidget):

36
src/submissions/frontend/widgets/date_type_picker.py Normal file
View File

@@ -0,0 +1,36 @@
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox
)
from .misc import CheckableComboBox, StartEndDatePicker
from backend.db import SubmissionType
class DateTypePicker(QDialog):
def __init__(self, parent):
super().__init__(parent)
self.layout = QVBoxLayout()
self.setFixedWidth(500)
self.typepicker = CheckableComboBox(parent=self)
self.typepicker.setEditable(False)
self.typepicker.addItem("Select", header=True)
for org in [org.name for org in SubmissionType.query()]:
self.typepicker.addItem(org)
self.datepicker = StartEndDatePicker(-180)
self.layout.addWidget(self.typepicker)
self.layout.addWidget(self.datepicker)
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
def parse_form(self):
sub_types = [self.typepicker.itemText(i) for i in range(self.typepicker.count()) if self.typepicker.itemChecked(i)]
start_date = self.datepicker.start_date.date().toPyDate()
end_date = self.datepicker.end_date.date().toPyDate()
return dict(submissiontype=sub_types, start_date=start_date, end_date=end_date)

3
src/submissions/frontend/widgets/omni_manager_pydant.py
View File

@@ -269,6 +269,7 @@ class EditRelationship(QWidget):
from backend.db import models
super().__init__(parent)
self.class_object = getattr(models, class_object)
logger.debug(f"Attempt value: {value}")
# logger.debug(f"Class object: {self.class_object}")
self.setParent(parent)
# logger.debug(f"Edit relationship class_object: {self.class_object}")
@@ -388,7 +389,7 @@ class EditRelationship(QWidget):
"""
sets data in model
"""
# logger.debug(f"Self.data: {self.data}")
logger.debug(f"Self.data: {self.data}")
try:
records = [item.to_dataframe_dict() for item in self.data]
except AttributeError: