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This commit is contained in:
lwark
2024-06-10 14:18:11 -05:00
parent c94ead5db2
commit 3b9dc69618
14 changed files with 31 additions and 97 deletions
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1
src/submissions/backend/db/models/kits.py
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@@ -2,7 +2,6 @@
All kit and reagent related models
"""
from __future__ import annotations
from copy import copy
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy

6
src/submissions/backend/excel/parser.py
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@@ -8,8 +8,6 @@ from pprint import pformat
from typing import List
import pandas as pd
from openpyxl import load_workbook, Workbook
from openpyxl.worksheet.protection import SheetProtection
import numpy as np
from pathlib import Path
from backend.db.models import *
from backend.validators import PydSubmission, PydReagent, RSLNamer, PydSample, PydEquipment
@@ -17,14 +15,12 @@ import logging, re
from collections import OrderedDict
from datetime import date
from dateutil.parser import parse, ParserError
from tools import check_not_nan, convert_nans_to_nones, row_map, row_keys, is_missing, remove_key_from_list_of_dicts
from tools import check_not_nan, convert_nans_to_nones, is_missing, remove_key_from_list_of_dicts
logger = logging.getLogger(f"submissions.{__name__}")
# row_keys = {v:k for k,v in row_map.items()}
class SheetParser(object):
"""
object to pull and contain data from excel file

6
src/submissions/backend/excel/writer.py
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@@ -1,12 +1,10 @@
import logging
from copy import copy
from pathlib import Path
# from pathlib import Path
from pprint import pformat
from typing import List
from openpyxl import load_workbook, Workbook
from tools import row_keys
from backend.db.models import SubmissionType, KitType, BasicSample, BasicSubmission
from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission
from io import BytesIO
from collections import OrderedDict

1
src/submissions/backend/validators/pydant.py
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@@ -2,7 +2,6 @@
Contains pydantic models and accompanying validators
'''
from __future__ import annotations
import sys
from operator import attrgetter
import uuid, re, logging

2
src/submissions/frontend/widgets/functions.py
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@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import QMainWindow, QFileDialog
logger = logging.getLogger(f"submissions.{__name__}")
def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
"""
File dialog to select a file to read from
@@ -29,6 +30,7 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
obj.last_dir = fname.parent
return fname
def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
"""
File dialog to select a file to write to

5
src/submissions/frontend/widgets/gel_checker.py
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@@ -5,9 +5,8 @@ from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
QLabel, QLineEdit, QDialogButtonBox,
QTextEdit
)
import numpy as np
import pyqtgraph as pg
from PyQt6.QtGui import QIcon, QFont
from PyQt6.QtGui import QIcon
from PIL import Image
import numpy as np
import logging
@@ -18,6 +17,7 @@ from backend.db.models import WastewaterArtic
logger = logging.getLogger(f"submissions.{__name__}")
# Main window class
class GelBox(QDialog):
@@ -87,6 +87,7 @@ class GelBox(QDialog):
values, comment = self.form.parse_form()
return dna_core_submission_number, gel_barcode, self.img_path, values, comment
class ControlsForm(QWidget):
def __init__(self, parent, control_info:List=None) -> None:

1
src/submissions/frontend/widgets/kit_creator.py
View File

@@ -139,6 +139,7 @@ class KitAdder(QWidget):
info[widget.objectName()] = widget.date().toPyDate()
return info, reagents
class ReagentRoleForm(QWidget):
"""
custom widget to add information about a new reagenttype

6
src/submissions/frontend/widgets/misc.py
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@@ -13,12 +13,12 @@ from backend.db.models import *
import logging
from .pop_ups import AlertPop
from .functions import select_open_file
from tools import Settings
logger = logging.getLogger(f"submissions.{__name__}")
env = jinja_template_loading()
class AddReagentForm(QDialog):
"""
dialog to add gather info about new reagent
@@ -102,6 +102,7 @@ class AddReagentForm(QDialog):
lookup = Reagent.query(reagent_role=self.type_input.currentText())
self.name_input.addItems(list(set([item.name for item in lookup])))
class ReportDatePicker(QDialog):
"""
custom dialog to ask for report start/stop dates
@@ -138,6 +139,7 @@ class ReportDatePicker(QDialog):
"""
return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
class FirstStrandSalvage(QDialog):
def __init__(self, ctx:Settings, submitter_id:str, rsl_plate_num:str|None=None) -> None:
@@ -178,6 +180,7 @@ class FirstStrandSalvage(QDialog):
"""
return dict(plate=self.rsl_plate_num.text(), submitter_id=self.submitter_id_input.text(), well=f"{self.row_letter.currentText()}{self.column_number.currentText()}")
class LogParser(QDialog):
def __init__(self, parent):
@@ -197,7 +200,6 @@ class LogParser(QDialog):
self.btn.clicked.connect(self.runsearch)
self.setMinimumWidth(400)
def filelookup(self):
"""
Select file to search

70
src/submissions/frontend/widgets/pop_ups.py
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@@ -14,6 +14,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
env = jinja_template_loading()
class QuestionAsker(QDialog):
"""
dialog to ask yes/no questions
@@ -33,6 +34,7 @@ class QuestionAsker(QDialog):
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class AlertPop(QMessageBox):
"""
Dialog to show an alert.
@@ -45,6 +47,7 @@ class AlertPop(QMessageBox):
self.setInformativeText(message)
self.setWindowTitle(f"{owner} - {status.title()}")
class ObjectSelector(QDialog):
"""
dialog to input BaseClass type manually
@@ -79,70 +82,3 @@ class ObjectSelector(QDialog):
str: KitType as str
"""
return self.widget.currentText()
# class KitSelector(QDialog):
# """
# dialog to input KitType manually
# """
# def __init__(self, title:str, message:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(title)
# self.widget = QComboBox()
# kits = [item.name for item in KitType.query()]
# self.widget.addItems(kits)
# self.widget.setEditable(False)
# # set yes/no buttons
# QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# # Text for the yes/no question
# message = QLabel(message)
# self.layout.addWidget(message)
# self.layout.addWidget(self.widget)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# def getValues(self) -> str:
# """
# Get KitType(str) from widget
# Returns:
# str: KitType as str
# """
# return self.widget.currentText()
# class SubmissionTypeSelector(QDialog):
# """
# dialog to input SubmissionType manually
# """
# def __init__(self, title:str, message:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(title)
# self.widget = QComboBox()
# # sub_type = [item.name for item in lookup_submission_type(ctx=ctx)]
# sub_type = [item.name for item in SubmissionType.query()]
# self.widget.addItems(sub_type)
# self.widget.setEditable(False)
# # set yes/no buttons
# QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# # Text for the yes/no question
# message = QLabel(message)
# self.layout.addWidget(message)
# self.layout.addWidget(self.widget)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# def parse_form(self) -> str:
# """
# Pulls SubmissionType(str) from widget
# Returns:
# str: SubmissionType as str
# """
# return self.widget.currentText()

5
src/submissions/frontend/widgets/sample_search.py
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@@ -1,14 +1,13 @@
from pprint import pformat
from typing import Tuple
from pandas import DataFrame
from PyQt6.QtCore import QAbstractTableModel, Qt, QEvent, QSortFilterProxyModel
from PyQt6.QtCore import QSortFilterProxyModel
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
)
from backend.db.models import BasicSample
from .submission_table import pandasModel
from .submission_details import SubmissionDetails
import logging
logger = logging.getLogger(f"submissions.{__name__}")

9
src/submissions/frontend/widgets/submission_details.py
View File

@@ -21,6 +21,7 @@ from typing import List
logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionDetails(QDialog):
"""
a window showing text details of submission
@@ -92,8 +93,8 @@ class SubmissionDetails(QDialog):
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.webview.setHtml(self.html)
with open("test.html", "w") as f:
f.write(self.html)
# with open("test.html", "w") as f:
# f.write(self.html)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
@pyqtSlot(str)
@@ -125,8 +126,6 @@ class SubmissionDetails(QDialog):
del self.base_dict['platemap']
self.html2 = self.template.render(sub=self.base_dict)
try:
# with open(fname, "w+b") as f:
# pisa.CreatePDF(self.html2, dest=f)
html_to_pdf(html=self.html2, output_file=fname)
except PermissionError as e:
logger.error(f"Error saving pdf: {e}")
@@ -136,6 +135,7 @@ class SubmissionDetails(QDialog):
msg.setWindowTitle("Permission Error")
msg.exec()
class SubmissionComment(QDialog):
"""
a window for adding comment text to a submission
@@ -174,4 +174,3 @@ class SubmissionComment(QDialog):
full_comment = {"name":commenter, "time": dt, "text": comment}
# logger.debug(f"Full comment: {full_comment}")
return full_comment

3
src/submissions/frontend/widgets/submission_table.py
View File

@@ -9,7 +9,6 @@ from PyQt6.QtGui import QAction, QCursor
from backend.db.models import BasicSubmission
from backend.excel import make_report_html, make_report_xlsx
from tools import Report, Result, row_map, get_first_blank_df_row, html_to_pdf
# from xhtml2pdf import pisa
from .functions import select_save_file, select_open_file
from .misc import ReportDatePicker
import pandas as pd
@@ -17,6 +16,7 @@ from openpyxl.worksheet.worksheet import Worksheet
logger = logging.getLogger(f"submissions.{__name__}")
class pandasModel(QAbstractTableModel):
"""
pandas model for inserting summary sheet into gui
@@ -61,6 +61,7 @@ class pandasModel(QAbstractTableModel):
return self._data.columns[col]
return None
class SubmissionsSheet(QTableView):
"""
presents submission summary to user in tab1

2
src/submissions/frontend/widgets/submission_type_creator.py
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@@ -12,6 +12,7 @@ from .functions import select_open_file
logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionTypeAdder(QWidget):
def __init__(self, parent) -> None:
@@ -80,6 +81,7 @@ class SubmissionTypeAdder(QWidget):
self.template_path = select_open_file(obj=self, file_extension="xlsx")
self.template_label.setText(self.template_path.__str__())
class InfoWidget(QWidget):
def __init__(self, parent: QWidget, key) -> None:

3
src/submissions/tools.py
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@@ -4,7 +4,6 @@ Contains miscellaenous functions used by both frontend and backend.
from __future__ import annotations
import json
from pathlib import Path
import numpy as np
import logging, re, yaml, sys, os, stat, platform, getpass, inspect, csv
import pandas as pd
@@ -16,7 +15,7 @@ from sqlalchemy import create_engine, text
from pydantic import field_validator, BaseModel, Field
from pydantic_settings import BaseSettings, SettingsConfigDict
from typing import Any, Tuple, Literal, List
from PyQt6.QtGui import QTextDocument, QPageSize
from PyQt6.QtGui import QPageSize
from PyQt6.QtWebEngineWidgets import QWebEngineView
from openpyxl.worksheet.worksheet import Worksheet