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Upgrade of WastewaterArtic parsers/writers for flexibility.

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This commit is contained in:
lwark
2024-07-09 13:09:27 -05:00
parent e589420815
commit 54e1e55804
11 changed files with 122 additions and 56 deletions
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2
src/submissions/__init__.py
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@@ -15,10 +15,12 @@ def get_week_of_month() -> int:
if day in week:
return ii + 1
# Automatically completes project info for help menu and compiling.
__project__ = "submissions"
__version__ = f"{year}{str(month).zfill(2)}.{get_week_of_month()}b"
__author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
__copyright__ = f"2022-{date.today().year}, Government of Canada"
__github__ = "https://github.com/landowark/submissions"
project_path = Path(__file__).parents[2].absolute()

5
src/submissions/backend/db/models/kits.py
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@@ -672,8 +672,8 @@ class SubmissionType(BaseClass):
Returns:
dict: Map of locations
"""
info = self.info_map
# logger.debug(f"Info map: {info}")
info = {k:v for k,v in self.info_map.items() if k != "custom"}
logger.debug(f"Info map: {info}")
output = {}
match mode:
case "read":
@@ -681,6 +681,7 @@ class SubmissionType(BaseClass):
case "write":
output = {k: v[mode] + v['read'] for k, v in info.items() if v[mode] or v['read']}
output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
output['custom'] = self.info_map['custom']
return output
def construct_sample_map(self) -> dict:

47
src/submissions/backend/db/models/submissions.py
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@@ -685,7 +685,7 @@ class BasicSubmission(BaseClass):
# Child class custom functions
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information
@@ -731,7 +731,7 @@ class BasicSubmission(BaseClass):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
"""
Adds custom autofill methods for submission
@@ -1307,6 +1307,7 @@ class BacterialCulture(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
@@ -1345,7 +1346,7 @@ class Wastewater(BasicSubmission):
return output
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information. Extends parent
@@ -1550,7 +1551,6 @@ class Wastewater(BasicSubmission):
return input_dict
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
@@ -1597,7 +1597,7 @@ class WastewaterArtic(BasicSubmission):
return output
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information
@@ -1608,16 +1608,20 @@ class WastewaterArtic(BasicSubmission):
Returns:
dict: Updated sample dictionary
"""
# TODO: Clean up and move range start/stops to db somehow.
input_dict = super().custom_info_parser(input_dict)
ws = xl['Egel results']
data = [ws.cell(row=ii, column=jj) for jj in range(15, 27) for ii in range(10, 18)]
egel_section = custom_fields['egel_results']
ws = xl[egel_section['sheet']]
data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for ii in range(egel_section['start_row'], egel_section['end_row'])]
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
input_dict['gel_controls'] = [
dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
data]
ws = xl['First Strand List']
data = [dict(plate=ws.cell(row=ii, column=3).value, starting_sample=ws.cell(row=ii, column=4).value) for ii in
range(8, 11)]
# NOTE: Get source plate information
source_plates_section = custom_fields['source_plates']
ws = xl[source_plates_section['sheet']]
data = [dict(plate=ws.cell(row=ii, column=source_plates_section['plate_column']).value, starting_sample=ws.cell(row=ii, column=source_plates_section['starting_sample_column']).value) for ii in
range(source_plates_section['start_row'], source_plates_section['end_row'])]
for datum in data:
if datum['plate'] in ["None", None, ""]:
continue
@@ -1808,7 +1812,7 @@ class WastewaterArtic(BasicSubmission):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
"""
Adds custom autofill methods for submission. Extends Parent
@@ -1822,30 +1826,33 @@ class WastewaterArtic(BasicSubmission):
"""
input_excel = super().custom_info_writer(input_excel, info, backup)
# logger.debug(f"Info:\n{pformat(info)}")
# logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
# NOTE: check for source plate information
source_plates_section = custom_fields['source_plates']
if check_key_or_attr(key='source_plates', interest=info, check_none=True):
worksheet = input_excel['First Strand List']
start_row = 8
worksheet = input_excel[source_plates_section['sheet']]
start_row = source_plates_section['start_row']
# NOTE: write source plates to First strand list
for iii, plate in enumerate(info['source_plates']['value']):
# logger.debug(f"Plate: {plate}")
row = start_row + iii
try:
worksheet.cell(row=row, column=3, value=plate['plate'])
worksheet.cell(row=row, column=source_plates_section['plate_column'], value=plate['plate'])
except TypeError:
pass
try:
worksheet.cell(row=row, column=4, value=plate['starting_sample'])
worksheet.cell(row=row, column=source_plates_section['starting_sample_column'], value=plate['starting_sample'])
except TypeError:
pass
# NOTE: check for gel information
egel_section = custom_fields['egel_results']
if check_key_or_attr(key='gel_info', interest=info, check_none=True):
# logger.debug(f"Gel info check passed.")
# NOTE: print json field gel results to Egel results
worksheet = input_excel['Egel results']
worksheet = input_excel[egel_section['sheet']]
# TODO: Move all this into a seperate function?
start_row = 21
start_column = 15
start_row = egel_section['start_row']
start_column = egel_section['start_column']
for row, ki in enumerate(info['gel_info']['value'], start=1):
# logger.debug(f"ki: {ki}")
# logger.debug(f"vi: {vi}")
@@ -1862,14 +1869,14 @@ class WastewaterArtic(BasicSubmission):
except AttributeError:
logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
worksheet = input_excel['Egel results']
worksheet = input_excel[egel_section['sheet']]
# logger.debug(f"We got an image: {info['gel_image']}")
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
z = zipped.extract(info['gel_image_path']['value'], Path(TemporaryDirectory().name))
img = OpenpyxlImage(z)
img.height = 400 # insert image height in pixels as float or int (e.g. 305.5)
img.width = 600
img.anchor = 'B9'
img.anchor = egel_section['img_anchor']
worksheet.add_image(img)
return input_excel

6
src/submissions/backend/excel/parser.py
View File

@@ -212,12 +212,14 @@ class InfoParser(object):
"""
dicto = {}
# NOTE: This loop parses generic info
# logger.debug(f"Map: {self.map}")
logger.debug(f"Map: {self.map}")
for sheet in self.xl.sheetnames:
ws = self.xl[sheet]
relevant = []
for k, v in self.map.items():
# NOTE: If the value is hardcoded put it in the dictionary directly.
if k == "custom":
continue
if isinstance(v, str):
dicto[k] = dict(value=v, missing=False)
continue
@@ -265,7 +267,7 @@ class InfoParser(object):
except (KeyError, IndexError):
continue
# Return after running the parser components held in submission object.
return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl)
return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl, custom_fields=self.map['custom'])
class ReagentParser(object):

10
src/submissions/backend/excel/writer.py
View File

@@ -8,8 +8,6 @@ from pathlib import Path
# from pathlib import Path
from pprint import pformat
from typing import List
from collections import OrderedDict
from jinja2 import TemplateNotFound
from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission
@@ -135,8 +133,8 @@ class InfoWriter(object):
self.submission_type = submission_type
self.sub_object = sub_object
self.xl = xl
info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, info_map)
self.info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, self.info_map)
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
@@ -154,6 +152,8 @@ class InfoWriter(object):
for k, v in info_dict.items():
if v is None:
continue
if k == "custom":
continue
dicto = {}
try:
dicto['locations'] = info_map[k]
@@ -187,7 +187,7 @@ class InfoWriter(object):
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']]
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
return self.sub_object.custom_info_writer(self.xl, info=self.info)
return self.sub_object.custom_info_writer(self.xl, info=self.info, custom_fields=self.info_map['custom'])
class ReagentWriter(object):

50
src/submissions/frontend/widgets/app.py
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@@ -8,9 +8,12 @@ from PyQt6.QtWidgets import (
)
from PyQt6.QtGui import QAction
from pathlib import Path
from tools import check_if_app, Settings, Report
from markdown import markdown
from tools import check_if_app, Settings, Report, jinja_template_loading
from datetime import date
from .pop_ups import AlertPop
from .pop_ups import AlertPop, HTMLPop
from .misc import LogParser
import logging, webbrowser, sys, shutil
from .submission_table import SubmissionsSheet
@@ -31,22 +34,22 @@ class App(QMainWindow):
self.ctx = ctx
self.last_dir = ctx.directory_path
self.report = Report()
# indicate version and connected database in title bar
# NOTE: indicate version and connected database in title bar
try:
self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}"
except (AttributeError, KeyError):
self.title = f"Submissions App"
# set initial app position and size
# NOTE: set initial app position and size
self.left = 0
self.top = 0
self.width = 1300
self.height = 1000
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
# insert tabs into main app
# NOTE: insert tabs into main app
self.table_widget = AddSubForm(self)
self.setCentralWidget(self.table_widget)
# run initial setups
# NOTE: run initial setups
self._createActions()
self._createMenuBar()
self._createToolBar()
@@ -126,8 +129,11 @@ class App(QMainWindow):
"""
Show the 'about' message
"""
output = f"Version: {self.ctx.package.__version__}\n\nAuthor: {self.ctx.package.__author__['name']} - {self.ctx.package.__author__['email']}\n\nCopyright: {self.ctx.package.__copyright__}"
about = AlertPop(message=output, status="Information")
j_env = jinja_template_loading()
template = j_env.get_template("project.html")
html = template.render(info=self.ctx.package.__dict__)
# logger.debug(html)
about = HTMLPop(html=html, title="About")
about.exec()
def openDocs(self):
@@ -143,11 +149,21 @@ class App(QMainWindow):
def openGithub(self):
"""
Opens the instructions html page
Opens the github page
"""
url = "https://github.com/landowark/submissions"
webbrowser.get('windows-default').open(url)
def openInstructions(self):
if check_if_app():
url = Path(sys._MEIPASS).joinpath("files", "README.md")
else:
url = Path("README.md")
with open(url, "r", encoding="utf-8") as f:
html = markdown(f.read())
instr = HTMLPop(html=html, title="Instructions")
instr.exec()
def result_reporter(self):
"""
@@ -199,35 +215,35 @@ class AddSubForm(QWidget):
# logger.debug(f"Initializating subform...")
super(QWidget, self).__init__(parent)
self.layout = QVBoxLayout(self)
# Initialize tab screen
# NOTE: Initialize tab screen
self.tabs = QTabWidget()
self.tab1 = QWidget()
self.tab2 = QWidget()
self.tab3 = QWidget()
self.tab4 = QWidget()
self.tabs.resize(300,200)
# Add tabs
# NOTE: Add tabs
self.tabs.addTab(self.tab1,"Submissions")
self.tabs.addTab(self.tab2,"Controls")
self.tabs.addTab(self.tab3, "Add SubmissionType")
self.tabs.addTab(self.tab4, "Add Kit")
# Create submission adder form
# NOTE: Create submission adder form
self.formwidget = SubmissionFormContainer(self)
self.formlayout = QVBoxLayout(self)
self.formwidget.setLayout(self.formlayout)
self.formwidget.setFixedWidth(300)
# Make scrollable interior for form
# NOTE: Make scrollable interior for form
self.interior = QScrollArea(self.tab1)
self.interior.setWidgetResizable(True)
self.interior.setFixedWidth(325)
self.interior.setWidget(self.formwidget)
# Create sheet to hold existing submissions
# NOTE: Create sheet to hold existing submissions
self.sheetwidget = QWidget(self)
self.sheetlayout = QVBoxLayout(self)
self.sheetwidget.setLayout(self.sheetlayout)
self.sub_wid = SubmissionsSheet(parent=parent)
self.sheetlayout.addWidget(self.sub_wid)
# Create layout of first tab to hold form and sheet
# NOTE: Create layout of first tab to hold form and sheet
self.tab1.layout = QHBoxLayout(self)
self.tab1.setLayout(self.tab1.layout)
self.tab1.layout.addWidget(self.interior)
@@ -236,7 +252,7 @@ class AddSubForm(QWidget):
self.controls_viewer = ControlsViewer(self)
self.tab2.layout.addWidget(self.controls_viewer)
self.tab2.setLayout(self.tab2.layout)
# create custom widget to add new tabs
# NOTE: create custom widget to add new tabs
ST_adder = SubmissionTypeAdder(self)
self.tab3.layout = QVBoxLayout(self)
self.tab3.layout.addWidget(ST_adder)
@@ -245,6 +261,6 @@ class AddSubForm(QWidget):
self.tab4.layout = QVBoxLayout(self)
self.tab4.layout.addWidget(kit_adder)
self.tab4.setLayout(self.tab4.layout)
# add tabs to main widget
# NOTE: add tabs to main widget
self.layout.addWidget(self.tabs)
self.setLayout(self.layout)

13
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -3,7 +3,7 @@ Gel box for artic quality control
"""
from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
QLabel, QLineEdit, QDialogButtonBox,
QTextEdit
QTextEdit, QComboBox
)
import pyqtgraph as pg
from PyQt6.QtGui import QIcon
@@ -119,8 +119,11 @@ class ControlsForm(QWidget):
self.layout.addWidget(label, iii, 1, 1, 1)
for iii in range(3):
for jjj in range(3):
widge = QLineEdit()
widge.setText("Neg")
# widge = QLineEdit()
widge = QComboBox()
widge.addItems(['Neg', 'Pos'])
widge.setCurrentIndex(0)
widge.setEditable(True)
widge.setObjectName(f"{rows[iii]} : {columns[jjj]}")
self.layout.addWidget(widge, iii+1, jjj+2, 1, 1)
self.layout.addWidget(QLabel("Comments:"), 0,5,1,1)
@@ -137,13 +140,13 @@ class ControlsForm(QWidget):
List[dict]: output of values
"""
output = []
for le in self.findChildren(QLineEdit):
for le in self.findChildren(QComboBox):
label = [item.strip() for item in le.objectName().split(" : ")]
try:
dicto = [item for item in output if item['name']==label[0]][0]
except IndexError:
dicto = dict(name=label[0], values=[])
dicto['values'].append(dict(name=label[1], value=le.text()))
dicto['values'].append(dict(name=label[1], value=le.currentText()))
if label[0] not in [item['name'] for item in output]:
output.append(dicto)
# logger.debug(pformat(output))

21
src/submissions/frontend/widgets/pop_ups.py
View File

@@ -5,6 +5,8 @@ from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox
)
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtCore import Qt
from tools import jinja_template_loading
import logging
from backend.db import models
@@ -19,7 +21,7 @@ class QuestionAsker(QDialog):
"""
dialog to ask yes/no questions
"""
def __init__(self, title:str, message:str) -> QDialog:
def __init__(self, title:str, message:str):
super().__init__()
self.setWindowTitle(title)
# NOTE: set yes/no buttons
@@ -39,7 +41,7 @@ class AlertPop(QMessageBox):
"""
Dialog to show an alert.
"""
def __init__(self, message:str, status:Literal['Information', 'Question', 'Warning', 'Critical'], owner:str|None=None) -> QMessageBox:
def __init__(self, message:str, status:Literal['Information', 'Question', 'Warning', 'Critical'], owner:str|None=None):
super().__init__()
# NOTE: select icon by string
icon = getattr(QMessageBox.Icon, status)
@@ -47,12 +49,25 @@ class AlertPop(QMessageBox):
self.setInformativeText(message)
self.setWindowTitle(f"{owner} - {status.title()}")
class HTMLPop(QDialog):
def __init__(self, html:str, owner:str|None=None, title:str="python"):
super().__init__()
self.webview = QWebEngineView(parent=self)
self.layout = QVBoxLayout()
self.setWindowTitle(title)
self.webview.setHtml(html)
self.webview.setMinimumSize(600, 500)
self.webview.setMaximumSize(600, 500)
self.layout.addWidget(self.webview)
class ObjectSelector(QDialog):
"""
dialog to input BaseClass type manually
"""
def __init__(self, title:str, message:str, obj_type:str|models.BaseClass) -> QDialog:
def __init__(self, title:str, message:str, obj_type:str|models.BaseClass):
super().__init__()
self.setWindowTitle(title)
self.widget = QComboBox()

14
src/submissions/templates/project.html Normal file
View File

@@ -0,0 +1,14 @@
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<script src="qrc:///qtwebchannel/qwebchannel.js"></script>
<title>{{ title }}</title>
</head>
<body>
<p>Version: {{ info['__version__'] }}</p>
<p>Author: {{ info['__author__']['name'] }} - <a href="mailto:{{ info['__author__']['email' ] }}">{{ info['__author__']['email'] }}</a></p>
<p>Copyright: {{ info['__copyright__'] }}</p>
<p>Github: <a id="link" href="{{ info['__github__'] }}">{{ info['__github__'] }}</a></p>
</body>
</html>