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Overhauling database.

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This commit is contained in:
lwark
2025-05-13 13:20:01 -05:00
parent 0dbb4ae77a
commit 75c665ea05
21 changed files with 729 additions and 1727 deletions
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42
src/submissions/frontend/widgets/submission_widget.py
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@@ -1,5 +1,5 @@
"""
Contains all submission related frontend functions
Contains all run related frontend functions
"""
from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout,
@@ -10,11 +10,11 @@ from .functions import select_open_file, select_save_file
import logging
from pathlib import Path
from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
from backend.excel.parsers import SheetParser, InfoParserV2
from backend.excel import SheetParser, InfoParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
Organization, SubmissionType, Reagent,
ReagentRole, KitTypeReagentRoleAssociation, BasicSubmission
ReagentRole, KitTypeReagentRoleAssociation, BasicRun
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -93,7 +93,7 @@ class SubmissionFormContainer(QWidget):
@report_result
def import_submission_function(self, fname: Path | None = None) -> Report:
"""
Import a new submission to the app window
Import a new run to the app window
Args:
obj (QMainWindow): original app window
@@ -122,12 +122,12 @@ class SubmissionFormContainer(QWidget):
# NOTE: create sheetparser using excel sheet and context from gui
try:
# self.prsr = SheetParser(filepath=fname)
self.parser = InfoParserV2(filepath=fname)
self.parser = InfoParser(filepath=fname)
except PermissionError:
logger.error(f"Couldn't get permission to access file: {fname}")
return
except AttributeError:
self.parser = InfoParserV2(filepath=fname)
self.parser = InfoParser(filepath=fname)
self.pyd = self.parser.to_pydantic()
# logger.debug(f"Samples: {pformat(self.pyd.samples)}")
checker = SampleChecker(self, "Sample Checker", self.pyd)
@@ -150,7 +150,7 @@ class SubmissionFormContainer(QWidget):
instance (Reagent | None): Blank reagent instance to be edited and then added.
Returns:
models.Reagent: the constructed reagent object to add to submission
models.Reagent: the constructed reagent object to add to run
"""
report = Report()
if not instance:
@@ -178,7 +178,7 @@ class SubmissionFormWidget(QWidget):
self.missing_info = []
self.submission_type = SubmissionType.query(name=self.pyd.submission_type['value'])
basic_submission_class = self.submission_type.submission_class
logger.debug(f"Basic submission class: {basic_submission_class}")
logger.debug(f"Basic run class: {basic_submission_class}")
defaults = basic_submission_class.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore']
@@ -202,7 +202,7 @@ class SubmissionFormWidget(QWidget):
value = dict(value=None, missing=True)
logger.debug(f"Pydantic value: {value}")
add_widget = self.create_widget(key=k, value=value, submission_type=self.submission_type,
sub_obj=basic_submission_class, disable=check)
run_object=basic_submission_class, disable=check)
if add_widget is not None:
self.layout.addWidget(add_widget)
if k in self.__class__.update_reagent_fields:
@@ -223,7 +223,7 @@ class SubmissionFormWidget(QWidget):
reagent.flip_check(self.disabler.checkbox.isChecked())
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType | None = None,
extraction_kit: str | None = None, sub_obj: BasicSubmission | None = None,
extraction_kit: str | None = None, run_object: BasicRun | None = None,
disable: bool = False) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
@@ -248,7 +248,7 @@ class SubmissionFormWidget(QWidget):
widget = None
case _:
widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type,
sub_obj=sub_obj)
run_object=run_object)
if disable:
widget.input.setEnabled(False)
widget.input.setToolTip("Widget disabled to protect database integrity.")
@@ -373,14 +373,14 @@ class SubmissionFormWidget(QWidget):
return report
case _:
pass
# NOTE: add reagents to submission object
# NOTE: add reagents to run object
if base_submission is None:
return
for reagent in base_submission.reagents:
reagent.update_last_used(kit=base_submission.extraction_kit)
save_output = base_submission.save()
# NOTE: update summary sheet
self.app.table_widget.sub_wid.setData()
self.app.table_widget.sub_wid.set_data()
# NOTE: reset form
try:
check = save_output.results == []
@@ -393,7 +393,7 @@ class SubmissionFormWidget(QWidget):
def export_csv_function(self, fname: Path | None = None):
"""
Save the submission's csv file.
Save the run's csv file.
Args:
fname (Path | None, optional): Input filename. Defaults to None.
@@ -405,7 +405,7 @@ class SubmissionFormWidget(QWidget):
except PermissionError:
logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
except AttributeError:
logger.error(f"No csv file found in the submission at this point.")
logger.error(f"No csv file found in the run at this point.")
def parse_form(self) -> Report:
"""
@@ -446,14 +446,14 @@ class SubmissionFormWidget(QWidget):
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | SubmissionType | None = None,
sub_obj: BasicSubmission | None = None) -> None:
run_object: BasicRun | None = None) -> None:
super().__init__(parent)
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=parent, key=key, value=value, submission_type=submission_type,
sub_obj=sub_obj)
sub_obj=run_object)
self.setObjectName(key)
try:
self.missing: bool = value['missing']
@@ -492,7 +492,7 @@ class SubmissionFormWidget(QWidget):
def set_widget(self, parent: QWidget, key: str, value: dict,
submission_type: str | SubmissionType | None = None,
sub_obj: BasicSubmission | None = None) -> QWidget:
sub_obj: BasicRun | None = None) -> QWidget:
"""
Creates form widget
@@ -568,7 +568,7 @@ class SubmissionFormWidget(QWidget):
except ValueError:
categories.insert(0, categories.pop(categories.index(submission_type)))
add_widget.addItems(categories)
add_widget.setToolTip("Enter submission category or select from list.")
add_widget.setToolTip("Enter run category or select from list.")
case _:
if key in sub_obj.timestamps:
add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent)
@@ -692,7 +692,7 @@ class SubmissionFormWidget(QWidget):
wanted_reagent = self.parent.parent().add_reagent(instance=wanted_reagent)
return wanted_reagent, report
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# NOTE: In this case we will have an empty reagent and the run will fail kit integrity check
return None, report
else:
# NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
@@ -801,7 +801,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
Report: Report on status of parse.
"""
report = Report()
logger.info(f"Hello from client submission form parser!")
logger.info(f"Hello from client run form parser!")
info = {}
reagents = []
for widget in self.findChildren(QWidget):