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Improvements to JSON updaters.

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This commit is contained in:
Landon Wark
2024-04-19 12:41:26 -05:00
parent c9bd8d1425
commit d91591e4ba
11 changed files with 266 additions and 226 deletions
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27
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -7,24 +7,26 @@ from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
)
import numpy as np
import pyqtgraph as pg
from PyQt6.QtGui import QIcon
from PyQt6.QtGui import QIcon, QFont
from PIL import Image
import numpy as np
import logging
from pprint import pformat
from typing import Tuple, List
from pathlib import Path
from backend.db.models import WastewaterArtic
logger = logging.getLogger(f"submissions.{__name__}")
# Main window class
class GelBox(QDialog):
def __init__(self, parent, img_path:str|Path):
def __init__(self, parent, img_path:str|Path, submission:WastewaterArtic):
super().__init__(parent)
# setting title
self.setWindowTitle("PyQtGraph")
self.img_path = img_path
self.submission = submission
# setting geometry
self.setGeometry(50, 50, 1200, 900)
# icon
@@ -57,7 +59,11 @@ class GelBox(QDialog):
# plot window goes on right side, spanning 3 rows
layout.addWidget(self.imv, 1, 1,20,20)
# setting this widget as central widget of the main window
self.form = ControlsForm(parent=self)
try:
control_info = sorted(self.submission.gel_controls, key=lambda d: d['location'])
except KeyError:
control_info = None
self.form = ControlsForm(parent=self, control_info=control_info)
layout.addWidget(self.form,22,1,1,4)
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
@@ -79,16 +85,24 @@ class GelBox(QDialog):
class ControlsForm(QWidget):
def __init__(self, parent) -> None:
def __init__(self, parent, control_info:List=None) -> None:
super().__init__(parent)
self.layout = QGridLayout()
columns = []
rows = []
try:
tt_text = "\n".join([f"{item['sample_id']} - CELL {item['location']}" for item in control_info])
except TypeError:
tt_text = None
for iii, item in enumerate(["Negative Control Key", "Description", "Results - 65 C", "Results - 63 C", "Results - Spike"]):
label = QLabel(item)
self.layout.addWidget(label, 0, iii,1,1)
if iii > 1:
columns.append(item)
elif iii == 0:
if tt_text:
label.setStyleSheet("font-weight: bold; color: blue; text-decoration: underline;")
label.setToolTip(tt_text)
for iii, item in enumerate(["RSL-NTC", "ENC-NTC", "NTC"], start=1):
label = QLabel(item)
self.layout.addWidget(label, iii, 0, 1, 1)
@@ -102,6 +116,11 @@ class ControlsForm(QWidget):
widge.setText("Neg")
widge.setObjectName(f"{rows[iii]} : {columns[jjj]}")
self.layout.addWidget(widge, iii+1, jjj+2, 1, 1)
# try:
# for iii, item in enumerate(control_info, start=1):
# self.layout.addWidget(QLabel(f"{item['sample_id']} - {item['location']}"), iii+4, 1)
# except TypeError:
# pass
self.layout.addWidget(QLabel("Comments:"), 0,5,1,1)
self.comment_field = QTextEdit(self)
self.comment_field.setFixedHeight(50)

6
src/submissions/frontend/widgets/submission_details.py
View File

@@ -95,8 +95,8 @@ class SubmissionDetails(QDialog):
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.webview.setHtml(self.html)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
with open("details.html", "w") as f:
f.write(self.html)
# with open("details.html", "w") as f:
# f.write(self.html)
@pyqtSlot(str)
def sign_off(self, submission:str|BasicSubmission):
@@ -171,7 +171,7 @@ class SubmissionComment(QDialog):
commenter = getuser()
comment = self.txt_editor.toPlainText()
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
full_comment = [{"name":commenter, "time": dt, "text": comment}]
full_comment = {"name":commenter, "time": dt, "text": comment}
logger.debug(f"Full comment: {full_comment}")
return full_comment

124
src/submissions/frontend/widgets/submission_table.py
View File

@@ -1,7 +1,7 @@
'''
Contains widgets specific to the submission summary and submission details.
'''
import logging, json
import logging
from pprint import pformat
from PyQt6.QtWidgets import QTableView, QMenu
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
@@ -177,35 +177,36 @@ class SubmissionsSheet(QTableView):
count += 1
except AttributeError:
continue
if sub.extraction_info != None:
# existing = json.loads(sub.extraction_info)
existing = sub.extraction_info
else:
existing = None
# Check if the new info already exists in the imported submission
try:
# if json.dumps(new_run) in sub.extraction_info:
if new_run in sub.extraction_info:
logger.debug(f"Looks like we already have that info.")
continue
except TypeError:
pass
# Update or create the extraction info
if existing != None:
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
existing.append(new_run)
logger.debug(f"Setting: {existing}")
# sub.extraction_info = json.dumps(existing)
sub.extraction_info = existing
except TypeError:
logger.error(f"Error updating!")
# sub.extraction_info = json.dumps([new_run])
sub.extraction_info = [new_run]
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
else:
# sub.extraction_info = json.dumps([new_run])
sub.extraction_info = [new_run]
sub.set_attribute('extraction_info', new_run)
# if sub.extraction_info != None:
# # existing = json.loads(sub.extraction_info)
# existing = sub.extraction_info
# else:
# existing = None
# # Check if the new info already exists in the imported submission
# try:
# # if json.dumps(new_run) in sub.extraction_info:
# if new_run in sub.extraction_info:
# logger.debug(f"Looks like we already have that info.")
# continue
# except TypeError:
# pass
# # Update or create the extraction info
# if existing != None:
# try:
# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
# existing.append(new_run)
# logger.debug(f"Setting: {existing}")
# # sub.extraction_info = json.dumps(existing)
# sub.extraction_info = existing
# except TypeError:
# logger.error(f"Error updating!")
# # sub.extraction_info = json.dumps([new_run])
# sub.extraction_info = [new_run]
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
# else:
# # sub.extraction_info = json.dumps([new_run])
# sub.extraction_info = [new_run]
sub.save()
self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
@@ -253,37 +254,38 @@ class SubmissionsSheet(QTableView):
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
continue
# check if pcr_info already exists
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
# existing = json.loads(sub.pcr_info)
existing = sub.pcr_info
else:
existing = None
# check if this entry already exists in imported submission
try:
# if json.dumps(new_run) in sub.pcr_info:
if new_run in sub.pcr_info:
logger.debug(f"Looks like we already have that info.")
continue
else:
count += 1
except TypeError:
logger.error(f"No json to dump")
if existing is not None:
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
existing.append(new_run)
logger.debug(f"Setting: {existing}")
# sub.pcr_info = json.dumps(existing)
sub.pcr_info = existing
except TypeError:
logger.error(f"Error updating!")
# sub.pcr_info = json.dumps([new_run])
sub.pcr_info = [new_run]
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
# sub.pcr_info = json.dumps([new_run])
sub.pcr_info = [new_run]
sub.set_attribute('pcr_info', new_run)
# # check if pcr_info already exists
# if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
# # existing = json.loads(sub.pcr_info)
# existing = sub.pcr_info
# else:
# existing = None
# # check if this entry already exists in imported submission
# try:
# # if json.dumps(new_run) in sub.pcr_info:
# if new_run in sub.pcr_info:
# logger.debug(f"Looks like we already have that info.")
# continue
# else:
# count += 1
# except TypeError:
# logger.error(f"No json to dump")
# if existing is not None:
# try:
# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
# existing.append(new_run)
# logger.debug(f"Setting: {existing}")
# # sub.pcr_info = json.dumps(existing)
# sub.pcr_info = existing
# except TypeError:
# logger.error(f"Error updating!")
# # sub.pcr_info = json.dumps([new_run])
# sub.pcr_info = [new_run]
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
# else:
# # sub.pcr_info = json.dumps([new_run])
# sub.pcr_info = [new_run]
sub.save()
self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))

8
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -5,14 +5,14 @@ from PyQt6.QtWidgets import (
from PyQt6.QtCore import pyqtSignal
from pathlib import Path
from . import select_open_file, select_save_file
import logging, difflib, inspect, pickle
import logging, difflib, inspect
from pathlib import Path
from tools import Report, Result, check_not_nan
from backend.excel.parser import SheetParser, PCRParser
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation, BasicSubmission
ReagentType, KitTypeReagentTypeAssociation
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -154,7 +154,7 @@ class SubmissionFormWidget(QWidget):
# self.samples = []
self.missing_info = []
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment',
'equipment', 'source_plates', 'id', 'cost', 'extraction_info',
'equipment', 'gel_controls', 'id', 'cost', 'extraction_info',
'controls', 'pcr_info', 'gel_info', 'gel_image']
self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
self.layout = QVBoxLayout()