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Prior to moving settings to pydantic-settings

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This commit is contained in:
Landon Wark
2023-07-24 09:17:09 -05:00
parent f6e270f52d
commit 63308674c6
7 changed files with 85 additions and 86 deletions
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2
src/submissions/__init__.py
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@@ -4,7 +4,7 @@ from pathlib import Path
# Version of the realpython-reader package
__project__ = "submissions"
__version__ = "202307.3b"
__version__ = "202307.4b"
__author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
__copyright__ = "2022-2023, Government of Canada"

95
src/submissions/frontend/custom_widgets/sub_details.py
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@@ -11,8 +11,9 @@ from PyQt6.QtWidgets import (
QMessageBox, QFileDialog, QMenu, QLabel,
QDialogButtonBox, QToolBar
)
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QFontMetrics, QAction, QCursor, QPixmap, QPainter
from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
from backend.excel import make_hitpicks
from configure import jinja_template_loading
@@ -266,40 +267,25 @@ class SubmissionDetails(QDialog):
# don't want id
del self.base_dict['id']
# retrieve jinja template
template = env.get_template("submission_details.txt")
# template = env.get_template("submission_details.txt")
# render using object dict
text = template.render(sub=self.base_dict)
# text = template.render(sub=self.base_dict)
# create text field
txt_editor = QTextEdit(self)
txt_editor.setReadOnly(True)
txt_editor.document().setPlainText(text)
# txt_editor = QTextEdit(self)
# txt_editor.setReadOnly(True)
# txt_editor.document().setPlainText(text)
# resize
font = txt_editor.document().defaultFont()
fontMetrics = QFontMetrics(font)
textSize = fontMetrics.size(0, txt_editor.toPlainText())
w = textSize.width() + 10
h = textSize.height() + 10
txt_editor.setMinimumSize(w, h)
txt_editor.setMaximumSize(w, h)
txt_editor.resize(w, h)
interior.resize(w,900)
txt_editor.setText(text)
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
# button to export a pdf version
btn = QPushButton("Export PDF")
btn.setParent(self)
btn.setFixedWidth(w)
btn.clicked.connect(self.export)
def export(self):
"""
Renders submission to html, then creates and saves .pdf file to user selected file.
"""
template = env.get_template("submission_details.html")
# make barcode because, reasons
# font = txt_editor.document().defaultFont()
# fontMetrics = QFontMetrics(font)
# textSize = fontMetrics.size(0, txt_editor.toPlainText())
# w = textSize.width() + 10
# h = textSize.height() + 10
# txt_editor.setMinimumSize(w, h)
# txt_editor.setMaximumSize(w, h)
# txt_editor.resize(w, h)
# interior.resize(w,900)
# txt_editor.setText(text)
# interior.setWidget(txt_editor)
self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
plate_dicto = hitpick_plate(sub)
@@ -312,10 +298,45 @@ class SubmissionDetails(QDialog):
logger.error(f"No plate map found for {sub.rsl_plate_num}")
# platemap.save("test.jpg", 'JPEG')
self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
logger.debug(self.base_dict)
html = template.render(sub=self.base_dict)
with open("test.html", "w") as f:
f.write(html)
template = env.get_template("submission_details.html")
self.html = template.render(sub=self.base_dict)
webview = QWebEngineView()
webview.setMinimumSize(900, 500)
webview.setMaximumSize(900, 500)
webview.setHtml(self.html)
self.layout = QVBoxLayout()
interior.resize(900, 500)
interior.setWidget(webview)
self.setFixedSize(900, 500)
# button to export a pdf version
btn = QPushButton("Export PDF")
btn.setParent(self)
btn.setFixedWidth(900)
btn.clicked.connect(self.export)
def export(self):
"""
Renders submission to html, then creates and saves .pdf file to user selected file.
"""
# template = env.get_template("submission_details.html")
# # make barcode because, reasons
# self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
# sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
# plate_dicto = hitpick_plate(sub)
# platemap = make_plate_map(plate_dicto)
# logger.debug(f"platemap: {platemap}")
# image_io = BytesIO()
# try:
# platemap.save(image_io, 'JPEG')
# except AttributeError:
# logger.error(f"No plate map found for {sub.rsl_plate_num}")
# # platemap.save("test.jpg", 'JPEG')
# self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
# logger.debug(self.base_dict)
# html = template.render(sub=self.base_dict)
# with open("test.html", "w") as f:
# f.write(html)
try:
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
except FileNotFoundError:
@@ -326,7 +347,7 @@ class SubmissionDetails(QDialog):
return
try:
with open(fname, "w+b") as f:
pisa.CreatePDF(html, dest=f)
pisa.CreatePDF(self.html, dest=f)
except PermissionError as e:
logger.error(f"Error saving pdf: {e}")
msg = QMessageBox()

18
src/submissions/frontend/main_window_functions.py
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@@ -816,7 +816,7 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_reagents:List[str], info:dict):
"""
Automatically fills in excel cells with reagent info.
Automatically fills in excel cells with submission info.
Args:
obj (QMainWindow): Original main app window
@@ -829,13 +829,15 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
logger.debug(f"Here is the info dict coming in:\n{pprint.pformat(info)}")
logger.debug(f"Here are the missing reagents:\n{missing_reagents}")
# pare down the xl map to only the missing data.
relevant_map = {k:v for k,v in xl_map.items() if k in missing_reagents}
# logger.debug(relevant_map)
# pare down reagents to only what's missing
relevant_reagents = [item for item in reagents if item['type'] in missing_reagents]
# hacky manipulation of submission type so it looks better.
info['submission_type'] = info['submission_type'].replace("_", " ").title()
# pare down info to just what's missing
relevant_info = {k:v for k,v in info.items() if k in missing_reagents}
logger.debug(f"Here is the relevant info: {pprint.pformat(relevant_info)}")
# logger.debug(f"Relevant reagents:\n{relevant_reagents}")
# construct new objects to put into excel sheets:
new_reagents = []
for reagent in relevant_reagents:
@@ -846,12 +848,14 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
new_reagent['expiry'] = relevant_map[new_reagent['type']]['expiry']
new_reagent['expiry']['value'] = reagent['expiry']
new_reagent['sheet'] = relevant_map[new_reagent['type']]['sheet']
# name is only present for Bacterial Culture
try:
new_reagent['name'] = relevant_map[new_reagent['type']]['name']
new_reagent['name']['value'] = reagent['type']
except:
pass
new_reagents.append(new_reagent)
# construct new info objects to put into excel sheets
new_info = []
for item in relevant_info:
new_item = {}
@@ -860,11 +864,15 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
new_item['value'] = relevant_info[item]
new_info.append(new_item)
logger.debug(f"New reagents: {new_reagents}")
# open the workbook using openpyxl
workbook = load_workbook(obj.xl)
# get list of sheet names
sheets = workbook.sheetnames
logger.debug(workbook.sheetnames)
# logger.debug(workbook.sheetnames)
for sheet in sheets:
# open sheet
worksheet=workbook[sheet]
# Get relevant reagents for that sheet
sheet_reagents = [item for item in new_reagents if sheet in item['sheet']]
for reagent in sheet_reagents:
logger.debug(f"Attempting: {reagent['type']}:")
@@ -874,10 +882,12 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'].replace("_", " ").upper())
except:
pass
# Get relevant info for that sheet
sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
for item in sheet_info:
logger.debug(f"Attempting: {item['type']}")
worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
# Hacky way to
if info['submission_type'] == "Bacterial Culture":
workbook["Sample List"].cell(row=14, column=2, value=getuser())
fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")

40
src/submissions/templates/submission_details.txt
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@@ -1,40 +0,0 @@
{# template for constructing submission details #}
{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments'] %}
{# for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' and key != 'ext_info' #}
{% for key, value in sub.items() if key not in excluded %}
{% if key=='Cost' %} {{ key }}: {{ "${:,.2f}".format(value) }} {% else %} {{ key }}: {{ value }} {% endif %}
{% endfor %}
Reagents:
{% for item in sub['reagents'] %}
{{ item['type'] }}: {{ item['lot'] }} (EXP: {{ item['expiry'] }}){% endfor %}
{% if sub['samples']%}
Samples:
{% for item in sub['samples'] %}
{{ item['well'] }}: {{ item['name'] }}{% endfor %}{% endif %}
{% if sub['controls'] %}
Attached Controls:
{% for item in sub['controls'] %}
{{ item['name'] }}: {{ item['type'] }} (Targets: {{ item['targets'] }})
{% if item['kraken'] %}
{{ item['name'] }} Top 5 Kraken Results
{% for genera in item['kraken'] %}
{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }}){% endfor %}{% endif %}
{% endfor %}{% endif %}
{% if sub['ext_info'] %}{% for entry in sub['ext_info'] %}
Extraction Status:
{% for key, value in entry.items() %}
{{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}{% endfor %}{% endif %}
{% if sub['pcr_info'] %}{% for entry in sub['pcr_info'] %}
{% if 'comment' not in entry.keys() %}qPCR Momentum Status:{% else %}
qPCR Status{% endif %}
{% for key, value in entry.items() if key != 'imported_by' %}
{{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}{% endfor %}
{% endif %}
{% if sub['comments'] %}
Comments:
{% for item in sub['comments'] %}
{{ item['name'] }}:
{{ item['text'] }}
- {{ item['time'] }}
{% endfor %}
{% endif %}