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documentation and converted to username based exclusion of adding new kits

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This commit is contained in:
Landon Wark
2023-01-30 12:07:38 -06:00
parent bbb65d3fe6
commit 1f832dccf2
16 changed files with 876 additions and 296 deletions
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181
src/submissions/frontend/custom_widgets/__init__.py
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@@ -4,7 +4,8 @@ from PyQt6.QtWidgets import (
QDialogButtonBox, QDateEdit, QTableView,
QTextEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QScrollArea, QHBoxLayout
QScrollBar, QScrollArea, QHBoxLayout,
QMessageBox
)
from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
from PyQt6.QtGui import QFontMetrics
@@ -26,7 +27,10 @@ loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
class AddReagentQuestion(QDialog):
def __init__(self, reagent_type:str, reagent_lot:str):
"""
dialog to ask about adding a new reagne to db
"""
def __init__(self, reagent_type:str, reagent_lot:str) -> None:
super().__init__()
self.setWindowTitle(f"Add {reagent_lot}?")
@@ -45,7 +49,10 @@ class AddReagentQuestion(QDialog):
class OverwriteSubQuestion(QDialog):
def __init__(self, message:str, rsl_plate_num:str):
"""
dialog to ask about overwriting existing submission
"""
def __init__(self, message:str, rsl_plate_num:str) -> None:
super().__init__()
self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
@@ -64,7 +71,10 @@ class OverwriteSubQuestion(QDialog):
class AddReagentForm(QDialog):
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None):
"""
dialog to add gather info about new reagent
"""
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None) -> None:
super().__init__()
if reagent_lot == None:
@@ -77,20 +87,23 @@ class AddReagentForm(QDialog):
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# get lot info
lot_input = QLineEdit()
lot_input.setText(reagent_lot)
# get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setDate(QDate.currentDate())
# get reagent type info
type_input = QComboBox()
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
reagent_type = reagent_type.replace("_", " ").title()
except AttributeError:
reagent_type = None
# set parsed reagent type to top of list
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
@@ -106,18 +119,38 @@ class AddReagentForm(QDialog):
class pandasModel(QAbstractTableModel):
def __init__(self, data):
"""
pandas model for inserting summary sheet into gui
"""
def __init__(self, data) -> None:
QAbstractTableModel.__init__(self)
self._data = data
def rowCount(self, parent=None):
def rowCount(self, parent=None) -> int:
"""
does what it says
Args:
parent (_type_, optional): _description_. Defaults to None.
Returns:
int: number of rows in data
"""
return self._data.shape[0]
def columnCount(self, parnet=None):
def columnCount(self, parnet=None) -> int:
"""
does what it says
Args:
parnet (_type_, optional): _description_. Defaults to None.
Returns:
int: number of columns in data
"""
return self._data.shape[1]
def data(self, index, role=Qt.ItemDataRole.DisplayRole):
def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
if index.isValid():
if role == Qt.ItemDataRole.DisplayRole:
return str(self._data.iloc[index.row(), index.column()])
@@ -130,7 +163,16 @@ class pandasModel(QAbstractTableModel):
class SubmissionsSheet(QTableView):
def __init__(self, ctx:dict):
"""
presents submission summary to user in tab1
"""
def __init__(self, ctx:dict) -> None:
"""
initialize
Args:
ctx (dict): settings passed from gui
"""
super().__init__()
self.ctx = ctx
self.setData()
@@ -139,20 +181,19 @@ class SubmissionsSheet(QTableView):
# self.clicked.connect(self.test)
self.doubleClicked.connect(self.show_details)
def setData(self):
# horHeaders = []
# for n, key in enumerate(sorted(self.data.keys())):
# horHeaders.append(key)
# for m, item in enumerate(self.data[key]):
# newitem = QTableWidgetItem(item)
# self.setItem(m, n, newitem)
# self.setHorizontalHeaderLabels(horHeaders)
def setData(self) -> None:
"""
sets data in model
"""
self.data = submissions_to_df(ctx=self.ctx)
self.model = pandasModel(self.data)
self.setModel(self.model)
# self.resize(800,600)
def show_details(self, item):
def show_details(self) -> None:
"""
creates detailed data to show in seperate window
"""
index=(self.selectionModel().currentIndex())
# logger.debug(index)
value=index.sibling(index.row(),0).data()
@@ -165,60 +206,65 @@ class SubmissionsSheet(QTableView):
class SubmissionDetails(QDialog):
"""
a window showing text details of submission
"""
def __init__(self, ctx:dict, id:int) -> None:
super().__init__()
self.setWindowTitle("Submission Details")
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
base_dict = data.to_dict()
# don't want id
del base_dict['id']
# convert sub objects to dicts
base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
# retrieve jinja template
template = env.get_template("submission_details.txt")
# render using object dict
text = template.render(sub=base_dict)
# create text field
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_field.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.MinimumExpanding)
# QBtn = QDialogButtonBox.StandardButton.Ok
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
txt_editor.setText(text)
# txt_editor.verticalScrollBar()
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
# self.layout.addWidget(txt_editor)
# self.layout.addStretch()
self.layout.addWidget(interior)
class ReportDatePicker(QDialog):
"""
custom dialog to ask for report start/stop dates
"""
def __init__(self) -> None:
super().__init__()
self.setWindowTitle("Select Report Date Range")
# make confirm/reject buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widgets to ask for dates
start_date = QDateEdit(calendarPopup=True)
start_date.setDate(QDate.currentDate())
end_date = QDateEdit(calendarPopup=True)
@@ -233,46 +279,61 @@ class ReportDatePicker(QDialog):
class KitAdder(QWidget):
def __init__(self, parent_ctx:dict):
"""
dialog to get information to add kit
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
self.ctx = parent_ctx
self.grid = QGridLayout()
self.setLayout(self.grid)
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Password:"),1,0)
self.grid.addWidget(QLineEdit(),1,1)
# need to exclude ordinary users to mitigate garbage database entries
# self.grid.addWidget(QLabel("Password:"),1,0)
# self.grid.addWidget(QLineEdit(),1,1)
self.grid.addWidget(QLabel("Kit Name:"),2,0)
self.grid.addWidget(QLineEdit(),2,1)
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
used_for = QComboBox()
# Insert all existing sample types
used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
used_for.setEditable(True)
self.grid.addWidget(used_for,3,1)
# set cost per run
self.grid.addWidget(QLabel("Cost per run:"),4,0)
cost = QSpinBox()
cost.setMinimum(0)
cost.setMaximum(9999)
self.grid.addWidget(cost,4,1)
# button to add additional reagent types
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
self.add_RT_btn.clicked.connect(self.add_RT)
self.submit_btn.clicked.connect(self.submit)
def add_RT(self):
def add_RT(self) -> None:
"""
insert new reagent type row
"""
maxrow = self.grid.rowCount()
self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
def submit(self):
def submit(self) -> None:
"""
send kit to database
"""
# get form info
labels, values, reagents = self.extract_form_info(self)
info = {item[0]:item[1] for item in zip(labels, values)}
logger.debug(info)
# info['reagenttypes'] = reagents
# del info['name']
# del info['extension_of_life_(months)']
yml_type = {}
yml_type['password'] = info['password']
try:
yml_type['password'] = info['password']
except KeyError:
pass
used = info['used_for_sample_type'].replace(" ", "_").lower()
yml_type[used] = {}
yml_type[used]['kits'] = {}
@@ -280,9 +341,32 @@ class KitAdder(QWidget):
yml_type[used]['kits'][info['kit_name']]['cost'] = info['cost_per_run']
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
logger.debug(yml_type)
create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
# send to kit constructor
result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
# result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg.setText("Kit added")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Kit added")
case 1:
msg.setText("Permission Error")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Permission Error")
msg.exec()
def extract_form_info(self, object):
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): the object to extract info from
Returns:
_type_: _description_
"""
labels = []
values = []
reagents = {}
@@ -317,26 +401,35 @@ class KitAdder(QWidget):
class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Name:"),0,0)
reagent_getter = QComboBox()
# lookup all reagent type names from db
reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
reagent_getter.setEditable(True)
grid.addWidget(reagent_getter,0,1)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# get extension of life
eol = QSpinBox()
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
class ControlsDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
"""
def __init__(self) -> None:
super().__init__()
self.start_date = QDateEdit(calendarPopup=True)
# start date is three month prior to end date by default
threemonthsago = QDate.currentDate().addDays(-90)
self.start_date.setDate(threemonthsago)
self.end_date = QDateEdit(calendarPopup=True)
@@ -350,5 +443,5 @@ class ControlsDatePicker(QWidget):
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
def sizeHint(self):
def sizeHint(self) -> QSize:
return QSize(80,20)