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Ui updates.

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This commit is contained in:
lwark
2024-07-29 14:45:43 -05:00
parent 7a5b9533cc
commit 1f992978f4
6 changed files with 74 additions and 26 deletions
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4
CHANGELOG.md
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@@ -1,3 +1,7 @@
## 202407.05
- Ui updates.
## 202407.04
- Added support for postgresql databases (auto backup not functional).

2
README.md
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@@ -133,7 +133,7 @@ This is meant to import .xslx files created from the Design & Analysis Software
## First Run:
1. On first run, the application copies src/config.yml to C:\Users\{USERNAME}\Local\submissions\config
1. On first run, the application copies src/config.yml to C:\Users\{USERNAME}\AppData\Local\submissions\config
2. If this folder cannot be found, C:\Users\{USERNAME}\Documents\submissions will be used.
1. If using Postgres, the 'database_path' and other variables will have to be updated manually.
3. Initially, the config variables are set parsing the 'sqlalchemy.url' variable in alembic.ini

2
src/submissions/backend/validators/pydant.py
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@@ -824,7 +824,7 @@ class PydSubmission(BaseModel, extra='allow'):
SubmissionFormWidget: Submission form widget
"""
from frontend.widgets.submission_widget import SubmissionFormWidget
logger.debug(f"Disbable: {disable}")
# logger.debug(f"Disable: {disable}")
return SubmissionFormWidget(parent=parent, submission=self, disable=disable)
def to_writer(self) -> "SheetWriter":

26
src/submissions/frontend/widgets/submission_type_creator.py
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@@ -2,7 +2,7 @@ from PyQt6.QtCore import Qt
from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QScrollArea,
QGridLayout, QPushButton, QLabel,
QLineEdit, QSpinBox
QLineEdit, QSpinBox, QCheckBox
)
from sqlalchemy.orm.attributes import InstrumentedAttribute
from backend.db import SubmissionType, BasicSubmission
@@ -62,7 +62,7 @@ class SubmissionTypeAdder(QWidget):
ST.template_file = f.read()
except FileNotFoundError:
logger.error(f"Could not find template file: {self.template_path}")
ST.save(ctx=self.app.ctx)
ST.save()
def parse_form(self) -> dict:
"""
@@ -88,7 +88,10 @@ class InfoWidget(QWidget):
super().__init__(parent)
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel(key.replace("_", " ").title()),0,0,1,4)
self.active = QCheckBox()
self.active.setChecked(True)
grid.addWidget(self.active, 0,0,1,1)
grid.addWidget(QLabel(key.replace("_", " ").title()),0,1,1,4)
self.setObjectName(key)
grid.addWidget(QLabel("Sheet Names (comma seperated):"),1,0)
self.sheet = QLineEdit()
@@ -103,16 +106,19 @@ class InfoWidget(QWidget):
self.column.setObjectName("column")
grid.addWidget(self.column,2,3)
def parse_form(self) -> dict:
def parse_form(self) -> dict|None:
"""
Pulls info from the Info form.
Returns:
dict: sheets, row, column
"""
return dict(
sheets = self.sheet.text().split(","),
row = self.row.value(),
column = self.column.value()
)
"""
if self.active.isChecked():
return dict(
sheets = self.sheet.text().split(","),
row = self.row.value(),
column = self.column.value()
)
else:
return None

58
src/submissions/frontend/widgets/submission_widget.py
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@@ -6,12 +6,12 @@ from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout,
QComboBox, QDateEdit, QLineEdit, QLabel
)
from PyQt6.QtCore import pyqtSignal
from PyQt6.QtCore import pyqtSignal, Qt
from pathlib import Path
from . import select_open_file, select_save_file
import logging, difflib, inspect
from pathlib import Path
from tools import Report, Result, check_not_nan, workbook_2_csv, main_form_style, report_result
from tools import Report, Result, check_not_nan, main_form_style, report_result
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
@@ -26,6 +26,31 @@ from datetime import date
logger = logging.getLogger(f"submissions.{__name__}")
class MyQComboBox(QComboBox):
def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQComboBox, self).__init__(*args, **kwargs)
self.scrollWidget=scrollWidget
self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
logger.debug(f"Scrollwidget: {scrollWidget}")
def wheelEvent(self, *args, **kwargs):
if self.hasFocus():
return QComboBox.wheelEvent(self, *args, **kwargs)
else:
return self.scrollWidget.wheelEvent(*args, **kwargs)
class MyQDateEdit(QDateEdit):
def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQDateEdit, self).__init__(*args, **kwargs)
self.scrollWidget=scrollWidget
self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
def wheelEvent(self, *args, **kwargs):
if self.hasFocus():
return QDateEdit.wheelEvent(self, *args, **kwargs)
else:
return self.scrollWidget.wheelEvent(*args, **kwargs)
class SubmissionFormContainer(QWidget):
# A signal carrying a path
@@ -37,6 +62,7 @@ class SubmissionFormContainer(QWidget):
self.app = self.parent().parent()
# logger.debug(f"App: {self.app}")
self.report = Report()
self.setStyleSheet('background-color: light grey;')
self.setAcceptDrops(True)
# NOTE: if import_drag is emitted, importSubmission will fire
self.import_drag.connect(self.importSubmission)
@@ -208,12 +234,11 @@ class SubmissionFormWidget(QWidget):
match value:
case PydReagent():
if value.name.lower() != "not applicable":
widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
widget = self.ReagentFormWidget(parent=self, reagent=value, extraction_kit=extraction_kit)
else:
widget = None
case _:
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
# logger.debug(f"Setting widget enabled to: {not disable}")
if disable:
widget.input.setEnabled(False)
@@ -422,7 +447,7 @@ class SubmissionFormWidget(QWidget):
super().__init__(parent)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type,
self.input: QWidget = self.set_widget(parent=parent, key=key, value=value, submission_type=submission_type,
sub_obj=sub_obj)
self.setObjectName(key)
try:
@@ -481,10 +506,12 @@ class SubmissionFormWidget(QWidget):
except (TypeError, KeyError):
pass
obj = parent.parent().parent()
logger.debug(f"Object: {obj}")
logger.debug(f"Parent: {parent.parent()}")
# logger.debug(f"Creating widget for: {key}")
match key:
case 'submitting_lab':
add_widget = QComboBox()
add_widget = MyQComboBox(scrollWidget=parent)
# lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
labs = [item.name for item in Organization.query()]
# try to set closest match to top of list
@@ -502,7 +529,7 @@ class SubmissionFormWidget(QWidget):
status="warning")
msg.exec()
# NOTE: create combobox to hold looked up kits
add_widget = QComboBox()
add_widget = MyQComboBox(scrollWidget=parent)
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in KitType.query(used_for=submission_type)]
@@ -518,7 +545,7 @@ class SubmissionFormWidget(QWidget):
add_widget.addItems(uses)
add_widget.setToolTip("Select extraction kit.")
case 'submission_category':
add_widget = QComboBox()
add_widget = MyQComboBox(scrollWidget=parent)
cats = ['Diagnostic', "Surveillance", "Research"]
cats += [item.name for item in SubmissionType.query()]
try:
@@ -529,7 +556,7 @@ class SubmissionFormWidget(QWidget):
add_widget.setToolTip("Enter submission category or select from list.")
case _:
if key in sub_obj.timestamps():
add_widget = QDateEdit(calendarPopup=True)
add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent)
# NOTE: sets submitted date based on date found in excel sheet
try:
add_widget.setDate(value)
@@ -601,7 +628,7 @@ class SubmissionFormWidget(QWidget):
layout = QVBoxLayout()
self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label)
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
self.lot = self.ReagentLot(scrollWidget=parent, reagent=reagent, extraction_kit=extraction_kit)
# self.lot.setStyleSheet(main_form_style)
layout.addWidget(self.lot)
# NOTE: Remove spacing between reagents
@@ -677,10 +704,10 @@ class SubmissionFormWidget(QWidget):
"""
self.setText(f"UPDATED {reagent_role}")
class ReagentLot(QComboBox):
class ReagentLot(MyQComboBox):
def __init__(self, reagent, extraction_kit: str) -> None:
super().__init__()
def __init__(self, scrollWidget, reagent, extraction_kit: str) -> None:
super().__init__(scrollWidget=scrollWidget)
self.setEditable(True)
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
@@ -731,3 +758,6 @@ class SubmissionFormWidget(QWidget):
self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")
# self.setStyleSheet(main_form_style)

8
src/submissions/templates/experiment_template.json Normal file
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@@ -0,0 +1,8 @@
{
"submission_type" : {
},
"kit_type": {
}
}