class CheckHLayout(QHBoxLayout):
"""Check boxes hlayout with QButtonGroup"""
def __init__(self, boxes, checks, parent=None):
QHBoxLayout.__init__(self)
self.setSpacing(0)
self.group = QButtonGroup()
self.group.setExclusive(False)
for i, (box, check) in enumerate(zip(boxes, checks)):
cbx = QCheckBox(box)
cbx.setChecked(eval(check))
self.addWidget(cbx)
self.group.addButton(cbx, i)
def values(self):
return [cbx.isChecked() for cbx in self.group.buttons()]
def setStyleSheet(self, style):
for cbx in self.group.buttons():
cbx.setStyleSheet(style)
class RadioLayout(QVBoxLayout):
"""Radio buttons layout with QButtonGroup"""
def __init__(self, buttons, index, parent=None):
QVBoxLayout.__init__(self)
self.setSpacing(0)
self.group = QButtonGroup()
for i, button in enumerate(buttons):
btn = QRadioButton(button)
if i == index:
btn.setChecked(True)
self.addWidget(btn)
self.group.addButton(btn, i)
def currentIndex(self):
return self.group.checkedId()
def setStyleSheet(self, style):
for btn in self.group.buttons():
btn.setStyleSheet(style)
class MultiCheckWidget(QGroupBox):
"""Qt Widget to show multiple checkboxes for a sequence of numbers.
Args:
count: The number of checkboxes to show.
title: Display title for group of checkboxes.
selected: List of checkbox numbers to initially check.
default: Whether to default boxes as checked.
"""
def __init__(self,
*args,
count: int,
title: Optional[str] = "",
selected: Optional[List] = None,
default: Optional[bool] = False,
**kwargs):
super(MultiCheckWidget, self).__init__(*args, **kwargs)
# QButtonGroup is the logical container
# it allows us to get list of checked boxes more easily
self.check_group = QButtonGroup()
self.check_group.setExclusive(False) # more than one can be checked
if title != "":
self.setTitle(title)
self.setFlat(False)
else:
self.setFlat(True)
if selected is None:
selected = list(range(count)) if default else []
check_layout = QGridLayout()
self.setLayout(check_layout)
for i in range(count):
check = QCheckBox("%d" % (i))
# call signal/slot on self when one of the checkboxes is changed
check.stateChanged.connect(lambda e: self.selectionChanged.emit())
self.check_group.addButton(check, i)
check_layout.addWidget(check, i // 8, i % 8)
self.setSelected(selected)
"""
selectionChanged signal sent when a checkbox gets a stateChanged signal
"""
selectionChanged = Signal()
def getSelected(self) -> list:
"""Method to get list of the checked checkboxes.
Returns:
list of checked checkboxes
"""
selected = []
for check_button in self.check_group.buttons():
if check_button.isChecked():
selected.append(self.check_group.id(check_button))
return selected
def setSelected(self, selected: list):
"""Method to set some checkboxes as checked.
Args:
selected: List of checkboxes to check.
Returns:
None
"""
for check_button in self.check_group.buttons():
if self.check_group.id(check_button) in selected:
check_button.setChecked(True)
else:
check_button.setChecked(False)
def boundingRect(self) -> QRectF:
"""Method required by Qt.
"""
return QRectF()
def paint(self, painter, option, widget=None):
"""Method required by Qt.
"""
pass
class ParameterTagToolBar(QToolBar):
"""A toolbar to add items using drag and drop actions."""
tag_button_toggled = Signal("QVariant", "bool")
manage_tags_action_triggered = Signal("bool")
tag_actions_added = Signal("QVariant", "QVariant")
def __init__(self, parent, db_mngr, *db_maps):
"""
Args:
parent (DataStoreForm): tree or graph view form
db_mngr (SpineDBManager): the DB manager for interacting with the db
db_maps (iter): DiffDatabaseMapping instances
"""
super().__init__("Parameter Tag Toolbar", parent=parent)
self.db_mngr = db_mngr
self.db_maps = db_maps
label = QLabel("Parameter tag")
self.addWidget(label)
self.tag_button_group = QButtonGroup(self)
self.tag_button_group.setExclusive(False)
self.actions = []
self.db_map_ids = []
empty = QWidget()
empty.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.empty_action = self.addWidget(empty)
button = QPushButton("Manage tags...")
self.addWidget(button)
# noinspection PyUnresolvedReferences
# pylint: disable=unnecessary-lambda
button.clicked.connect(lambda checked: self.manage_tags_action_triggered.emit(checked))
self.setStyleSheet(PARAMETER_TAG_TOOLBAR_SS)
self.setObjectName("ParameterTagToolbar")
self.tag_actions_added.connect(self._add_db_map_tag_actions)
def init_toolbar(self):
for button in self.tag_button_group.buttons():
self.tag_button_group.removeButton(button)
for action in self.actions:
self.removeAction(action)
action = QAction("untagged")
self.insertAction(self.empty_action, action)
action.setCheckable(True)
button = self.widgetForAction(action)
self.tag_button_group.addButton(button, id=0)
self.actions = [action]
self.db_map_ids = [[(db_map, 0) for db_map in self.db_maps]]
tag_data = {}
for db_map in self.db_maps:
for parameter_tag in self.db_mngr.get_items(db_map, "parameter tag"):
tag_data.setdefault(parameter_tag["tag"], {})[db_map] = parameter_tag["id"]
for tag, db_map_data in tag_data.items():
action = QAction(tag)
self.insertAction(self.empty_action, action)
action.setCheckable(True)
button = self.widgetForAction(action)
self.tag_button_group.addButton(button, id=len(self.db_map_ids))
self.actions.append(action)
self.db_map_ids.append(list(db_map_data.items()))
self.tag_button_group.buttonToggled["int", "bool"].connect(
lambda i, checked: self.tag_button_toggled.emit(self.db_map_ids[i], checked)
)
def receive_parameter_tags_added(self, db_map_data):
for db_map, parameter_tags in db_map_data.items():
self.tag_actions_added.emit(db_map, parameter_tags)
@Slot("QVariant", "QVariant")
def _add_db_map_tag_actions(self, db_map, parameter_tags):
action_texts = [a.text() for a in self.actions]
for parameter_tag in parameter_tags:
if parameter_tag["tag"] in action_texts:
# Already a tag named after that, add db_map id information
i = action_texts.index(parameter_tag["tag"])
self.db_map_ids[i].append((db_map, parameter_tag["id"]))
else:
action = QAction(parameter_tag["tag"])
self.insertAction(self.empty_action, action)
action.setCheckable(True)
button = self.widgetForAction(action)
self.tag_button_group.addButton(button, id=len(self.db_map_ids))
self.actions.append(action)
self.db_map_ids.append([(db_map, parameter_tag["id"])])
action_texts.append(action.text())
def receive_parameter_tags_removed(self, db_map_data):
for db_map, parameter_tags in db_map_data.items():
parameter_tag_ids = {x["id"] for x in parameter_tags}
self._remove_db_map_tag_actions(db_map, parameter_tag_ids)
def _remove_db_map_tag_actions(self, db_map, parameter_tag_ids):
for tag_id in parameter_tag_ids:
i = next(k for k, x in enumerate(self.db_map_ids) if (db_map, tag_id) in x)
self.db_map_ids[i].remove((db_map, tag_id))
if not self.db_map_ids[i]:
self.db_map_ids.pop(i)
self.removeAction(self.actions.pop(i))
def receive_parameter_tags_updated(self, db_map_data):
for db_map, parameter_tags in db_map_data.items():
self._update_db_map_tag_actions(db_map, parameter_tags)
def _update_db_map_tag_actions(self, db_map, parameter_tags):
for parameter_tag in parameter_tags:
i = next(k for k, x in enumerate(self.db_map_ids) if (db_map, parameter_tag["id"]) in x)
action = self.actions[i]
action.setText(parameter_tag["tag"])
class SCOUTS(QMainWindow):
"""Main Window Widget for SCOUTS."""
style = {
'title': 'QLabel {font-size: 18pt; font-weight: 600}',
'header': 'QLabel {font-size: 12pt; font-weight: 520}',
'label': 'QLabel {font-size: 10pt}',
'button': 'QPushButton {font-size: 10pt}',
'md button': 'QPushButton {font-size: 12pt}',
'run button': 'QPushButton {font-size: 18pt; font-weight: 600}',
'line edit': 'QLineEdit {font-size: 10pt}',
'checkbox': 'QCheckBox {font-size: 10pt}',
'radio button': 'QRadioButton {font-size: 10pt}'
}
def __init__(self) -> None:
"""SCOUTS Constructor. Defines all aspects of the GUI."""
# ###
# ### Main Window setup
# ###
# Inherits from QMainWindow
super().__init__()
self.rootdir = get_project_root()
self.threadpool = QThreadPool()
# Sets values for QMainWindow
self.setWindowTitle("SCOUTS")
self.setWindowIcon(
QIcon(
os.path.abspath(os.path.join(self.rootdir, 'src',
'scouts.ico'))))
# Creates StackedWidget as QMainWindow's central widget
self.stacked_pages = QStackedWidget(self)
self.setCentralWidget(self.stacked_pages)
# Creates Widgets for individual "pages" and adds them to the StackedWidget
self.main_page = QWidget()
self.samples_page = QWidget()
self.gating_page = QWidget()
self.pages = (self.main_page, self.samples_page, self.gating_page)
for page in self.pages:
self.stacked_pages.addWidget(page)
# ## Sets widget at program startup
self.stacked_pages.setCurrentWidget(self.main_page)
# ###
# ### MAIN PAGE
# ###
# Main page layout
self.main_layout = QVBoxLayout(self.main_page)
# Title section
# Title
self.title = QLabel(self.main_page)
self.title.setText('SCOUTS - Single Cell Outlier Selector')
self.title.setStyleSheet(self.style['title'])
self.title.adjustSize()
self.main_layout.addWidget(self.title)
# ## Input section
# Input header
self.input_header = QLabel(self.main_page)
self.input_header.setText('Input settings')
self.input_header.setStyleSheet(self.style['header'])
self.main_layout.addChildWidget(self.input_header)
self.input_header.adjustSize()
self.main_layout.addWidget(self.input_header)
# Input frame
self.input_frame = QFrame(self.main_page)
self.input_frame.setFrameShape(QFrame.StyledPanel)
self.input_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.input_frame)
# Input button
self.input_button = QPushButton(self.main_page)
self.input_button.setStyleSheet(self.style['button'])
self.set_icon(self.input_button, 'x-office-spreadsheet')
self.input_button.setObjectName('input')
self.input_button.setText(' Select input file (.xlsx or .csv)')
self.input_button.clicked.connect(self.get_path)
# Input path box
self.input_path = QLineEdit(self.main_page)
self.input_path.setObjectName('input_path')
self.input_path.setStyleSheet(self.style['line edit'])
# Go to sample naming page
self.samples_button = QPushButton(self.main_page)
self.samples_button.setStyleSheet(self.style['button'])
self.set_icon(self.samples_button, 'preferences-other')
self.samples_button.setText(' Name samples...')
self.samples_button.clicked.connect(self.goto_samples_page)
# Go to gating page
self.gates_button = QPushButton(self.main_page)
self.gates_button.setStyleSheet(self.style['button'])
self.set_icon(self.gates_button, 'preferences-other')
self.gates_button.setText(' Gating && outlier options...')
self.gates_button.clicked.connect(self.goto_gates_page)
# Add widgets above to input frame Layout
self.input_frame.layout().addRow(self.input_button, self.input_path)
self.input_frame.layout().addRow(self.samples_button)
self.input_frame.layout().addRow(self.gates_button)
# ## Analysis section
# Analysis header
self.analysis_header = QLabel(self.main_page)
self.analysis_header.setText('Analysis settings')
self.analysis_header.setStyleSheet(self.style['header'])
self.analysis_header.adjustSize()
self.main_layout.addWidget(self.analysis_header)
# Analysis frame
self.analysis_frame = QFrame(self.main_page)
self.analysis_frame.setFrameShape(QFrame.StyledPanel)
self.analysis_frame.setLayout(QVBoxLayout())
self.main_layout.addWidget(self.analysis_frame)
# Cutoff text
self.cutoff_text = QLabel(self.main_page)
self.cutoff_text.setText('Type of outlier to select:')
self.cutoff_text.setToolTip(
'Choose whether to select outliers using the cutoff value from a reference\n'
'sample (OutR) or by using the cutoff value calculated for each sample\n'
'individually (OutS)')
self.cutoff_text.setStyleSheet(self.style['label'])
# Cutoff button group
self.cutoff_group = QButtonGroup(self)
# Cutoff by sample
self.cutoff_sample = QRadioButton(self.main_page)
self.cutoff_sample.setText('OutS')
self.cutoff_sample.setObjectName('sample')
self.cutoff_sample.setStyleSheet(self.style['radio button'])
self.cutoff_sample.setChecked(True)
self.cutoff_group.addButton(self.cutoff_sample)
# Cutoff by reference
self.cutoff_reference = QRadioButton(self.main_page)
self.cutoff_reference.setText('OutR')
self.cutoff_reference.setObjectName('ref')
self.cutoff_reference.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_reference)
# Both cutoffs
self.cutoff_both = QRadioButton(self.main_page)
self.cutoff_both.setText('both')
self.cutoff_both.setObjectName('sample ref')
self.cutoff_both.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_both)
# Markers text
self.markers_text = QLabel(self.main_page)
self.markers_text.setStyleSheet(self.style['label'])
self.markers_text.setText('Show results for:')
self.markers_text.setToolTip(
'Individual markers: for each marker, select outliers\n'
'Any marker: select cells that are outliers for AT LEAST one marker'
)
# Markers button group
self.markers_group = QButtonGroup(self)
# Single marker
self.single_marker = QRadioButton(self.main_page)
self.single_marker.setText('individual markers')
self.single_marker.setObjectName('single')
self.single_marker.setStyleSheet(self.style['radio button'])
self.single_marker.setChecked(True)
self.markers_group.addButton(self.single_marker)
# Any marker
self.any_marker = QRadioButton(self.main_page)
self.any_marker.setText('any marker')
self.any_marker.setObjectName('any')
self.any_marker.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.any_marker)
# Both methods
self.both_methods = QRadioButton(self.main_page)
self.both_methods.setText('both')
self.both_methods.setObjectName('single any')
self.both_methods.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.both_methods)
# Tukey text
self.tukey_text = QLabel(self.main_page)
self.tukey_text.setStyleSheet(self.style['label'])
# Tukey button group
self.tukey_text.setText('Tukey factor:')
self.tukey_group = QButtonGroup(self)
# Low Tukey value
self.tukey_low = QRadioButton(self.main_page)
self.tukey_low.setText('1.5')
self.tukey_low.setStyleSheet(self.style['radio button'])
self.tukey_low.setChecked(True)
self.tukey_group.addButton(self.tukey_low)
# High Tukey value
self.tukey_high = QRadioButton(self.main_page)
self.tukey_high.setText('3.0')
self.tukey_high.setStyleSheet(self.style['radio button'])
self.tukey_group.addButton(self.tukey_high)
# Add widgets above to analysis frame layout
self.analysis_frame.layout().addWidget(self.cutoff_text)
self.cutoff_buttons = QHBoxLayout()
for button in self.cutoff_group.buttons():
self.cutoff_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.cutoff_buttons)
self.analysis_frame.layout().addWidget(self.markers_text)
self.markers_buttons = QHBoxLayout()
for button in self.markers_group.buttons():
self.markers_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.markers_buttons)
self.analysis_frame.layout().addWidget(self.tukey_text)
self.tukey_buttons = QHBoxLayout()
for button in self.tukey_group.buttons():
self.tukey_buttons.addWidget(button)
self.tukey_buttons.addWidget(QLabel()) # aligns row with 2 buttons
self.analysis_frame.layout().addLayout(self.tukey_buttons)
# ## Output section
# Output header
self.output_header = QLabel(self.main_page)
self.output_header.setText('Output settings')
self.output_header.setStyleSheet(self.style['header'])
self.output_header.adjustSize()
self.main_layout.addWidget(self.output_header)
# Output frame
self.output_frame = QFrame(self.main_page)
self.output_frame.setFrameShape(QFrame.StyledPanel)
self.output_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.output_frame)
# Output button
self.output_button = QPushButton(self.main_page)
self.output_button.setStyleSheet(self.style['button'])
self.set_icon(self.output_button, 'folder')
self.output_button.setObjectName('output')
self.output_button.setText(' Select output folder')
self.output_button.clicked.connect(self.get_path)
# Output path box
self.output_path = QLineEdit(self.main_page)
self.output_path.setStyleSheet(self.style['line edit'])
# Generate CSV checkbox
self.output_csv = QCheckBox(self.main_page)
self.output_csv.setText('Export multiple text files (.csv)')
self.output_csv.setStyleSheet(self.style['checkbox'])
self.output_csv.setChecked(True)
# Generate XLSX checkbox
self.output_excel = QCheckBox(self.main_page)
self.output_excel.setText('Export multiple Excel spreadsheets (.xlsx)')
self.output_excel.setStyleSheet(self.style['checkbox'])
self.output_excel.clicked.connect(self.enable_single_excel)
# Generate single, large XLSX checkbox
self.single_excel = QCheckBox(self.main_page)
self.single_excel.setText(
'Also save one multi-sheet Excel spreadsheet')
self.single_excel.setToolTip(
'After generating all Excel spreadsheets, SCOUTS combines them into '
'a single\nExcel spreadsheet where each sheet corresponds to an output'
'file from SCOUTS')
self.single_excel.setStyleSheet(self.style['checkbox'])
self.single_excel.setEnabled(False)
self.single_excel.clicked.connect(self.memory_warning)
# Add widgets above to output frame layout
self.output_frame.layout().addRow(self.output_button, self.output_path)
self.output_frame.layout().addRow(self.output_csv)
self.output_frame.layout().addRow(self.output_excel)
self.output_frame.layout().addRow(self.single_excel)
# ## Run & help-quit section
# Run button (stand-alone)
self.run_button = QPushButton(self.main_page)
self.set_icon(self.run_button, 'system-run')
self.run_button.setText(' Run!')
self.run_button.setStyleSheet(self.style['run button'])
self.main_layout.addWidget(self.run_button)
self.run_button.clicked.connect(self.run)
# Help-quit frame (invisible)
self.helpquit_frame = QFrame(self.main_page)
self.helpquit_frame.setLayout(QHBoxLayout())
self.helpquit_frame.layout().setMargin(0)
self.main_layout.addWidget(self.helpquit_frame)
# Help button
self.help_button = QPushButton(self.main_page)
self.set_icon(self.help_button, 'help-about')
self.help_button.setText(' Help')
self.help_button.setStyleSheet(self.style['md button'])
self.help_button.clicked.connect(self.get_help)
# Quit button
self.quit_button = QPushButton(self.main_page)
self.set_icon(self.quit_button, 'process-stop')
self.quit_button.setText(' Quit')
self.quit_button.setStyleSheet(self.style['md button'])
self.quit_button.clicked.connect(self.close)
# Add widgets above to help-quit layout
self.helpquit_frame.layout().addWidget(self.help_button)
self.helpquit_frame.layout().addWidget(self.quit_button)
# ###
# ### SAMPLES PAGE
# ###
# Samples page layout
self.samples_layout = QVBoxLayout(self.samples_page)
# ## Title section
# Title
self.samples_title = QLabel(self.samples_page)
self.samples_title.setText('Name your samples')
self.samples_title.setStyleSheet(self.style['title'])
self.samples_title.adjustSize()
self.samples_layout.addWidget(self.samples_title)
# Subtitle
self.samples_subtitle = QLabel(self.samples_page)
string = (
'Please name the samples to be analysed by SCOUTS.\n\nSCOUTS searches the first '
'column of your data\nand locates the exact string as part of the sample name.'
)
self.samples_subtitle.setText(string)
self.samples_subtitle.setStyleSheet(self.style['label'])
self.samples_subtitle.adjustSize()
self.samples_layout.addWidget(self.samples_subtitle)
# ## Sample addition section
# Sample addition frame
self.samples_frame = QFrame(self.samples_page)
self.samples_frame.setFrameShape(QFrame.StyledPanel)
self.samples_frame.setLayout(QGridLayout())
self.samples_layout.addWidget(self.samples_frame)
# Sample name box
self.sample_name = QLineEdit(self.samples_page)
self.sample_name.setStyleSheet(self.style['line edit'])
self.sample_name.setPlaceholderText('Sample name ...')
# Reference check
self.is_reference = QCheckBox(self.samples_page)
self.is_reference.setText('Reference?')
self.is_reference.setStyleSheet(self.style['checkbox'])
# Add sample to table
self.add_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Return"), self.add_sample_button,
self.write_to_sample_table)
self.set_icon(self.add_sample_button, 'list-add')
self.add_sample_button.setText(' Add sample (Enter)')
self.add_sample_button.setStyleSheet(self.style['button'])
self.add_sample_button.clicked.connect(self.write_to_sample_table)
# Remove sample from table
self.remove_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Delete"), self.remove_sample_button,
self.remove_from_sample_table)
self.set_icon(self.remove_sample_button, 'list-remove')
self.remove_sample_button.setText(' Remove sample (Del)')
self.remove_sample_button.setStyleSheet(self.style['button'])
self.remove_sample_button.clicked.connect(
self.remove_from_sample_table)
# Add widgets above to sample addition layout
self.samples_frame.layout().addWidget(self.sample_name, 0, 0)
self.samples_frame.layout().addWidget(self.is_reference, 1, 0)
self.samples_frame.layout().addWidget(self.add_sample_button, 0, 1)
self.samples_frame.layout().addWidget(self.remove_sample_button, 1, 1)
# ## Sample table
self.sample_table = QTableWidget(self.samples_page)
self.sample_table.setColumnCount(2)
self.sample_table.setHorizontalHeaderItem(0,
QTableWidgetItem('Sample'))
self.sample_table.setHorizontalHeaderItem(
1, QTableWidgetItem('Reference?'))
self.sample_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Stretch)
self.sample_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.ResizeToContents)
self.samples_layout.addWidget(self.sample_table)
# ## Save & clear buttons
# Save & clear frame (invisible)
self.saveclear_frame = QFrame(self.samples_page)
self.saveclear_frame.setLayout(QHBoxLayout())
self.saveclear_frame.layout().setMargin(0)
self.samples_layout.addWidget(self.saveclear_frame)
# Clear samples button
self.clear_samples = QPushButton(self.samples_page)
self.set_icon(self.clear_samples, 'edit-delete')
self.clear_samples.setText(' Clear table')
self.clear_samples.setStyleSheet(self.style['md button'])
self.clear_samples.clicked.connect(self.prompt_clear_data)
# Save samples button
self.save_samples = QPushButton(self.samples_page)
self.set_icon(self.save_samples, 'document-save')
self.save_samples.setText(' Save samples')
self.save_samples.setStyleSheet(self.style['md button'])
self.save_samples.clicked.connect(self.goto_main_page)
# Add widgets above to save & clear layout
self.saveclear_frame.layout().addWidget(self.clear_samples)
self.saveclear_frame.layout().addWidget(self.save_samples)
# ###
# ### GATING PAGE
# ###
# Gating page layout
self.gating_layout = QVBoxLayout(self.gating_page)
# ## Title section
# Title
self.gates_title = QLabel(self.gating_page)
self.gates_title.setText('Gating & outlier options')
self.gates_title.setStyleSheet(self.style['title'])
self.gates_title.adjustSize()
self.gating_layout.addWidget(self.gates_title)
# ## Gating options section
# Gating header
self.gate_header = QLabel(self.gating_page)
self.gate_header.setText('Gating')
self.gate_header.setStyleSheet(self.style['header'])
self.gate_header.adjustSize()
self.gating_layout.addWidget(self.gate_header)
# Gating frame
self.gate_frame = QFrame(self.gating_page)
self.gate_frame.setFrameShape(QFrame.StyledPanel)
self.gate_frame.setLayout(QFormLayout())
self.gating_layout.addWidget(self.gate_frame)
# Gating button group
self.gating_group = QButtonGroup(self)
# Do not gate samples
self.no_gates = QRadioButton(self.gating_page)
self.no_gates.setObjectName('no_gate')
self.no_gates.setText("Don't gate samples")
self.no_gates.setStyleSheet(self.style['radio button'])
self.no_gates.setChecked(True)
self.gating_group.addButton(self.no_gates)
self.no_gates.clicked.connect(self.activate_gate)
# CyToF gating
self.cytof_gates = QRadioButton(self.gating_page)
self.cytof_gates.setObjectName('cytof')
self.cytof_gates.setText('Mass Cytometry gating')
self.cytof_gates.setStyleSheet(self.style['radio button'])
self.cytof_gates.setToolTip(
'Exclude cells for which the average expression of all\n'
'markers is below the selected value')
self.gating_group.addButton(self.cytof_gates)
self.cytof_gates.clicked.connect(self.activate_gate)
# CyToF gating spinbox
self.cytof_gates_value = QDoubleSpinBox(self.gating_page)
self.cytof_gates_value.setMinimum(0)
self.cytof_gates_value.setMaximum(1)
self.cytof_gates_value.setValue(0.1)
self.cytof_gates_value.setSingleStep(0.05)
self.cytof_gates_value.setEnabled(False)
# scRNA-Seq gating
self.rnaseq_gates = QRadioButton(self.gating_page)
self.rnaseq_gates.setText('scRNA-Seq gating')
self.rnaseq_gates.setStyleSheet(self.style['radio button'])
self.rnaseq_gates.setToolTip(
'When calculating cutoff, ignore reads below the selected value')
self.rnaseq_gates.setObjectName('rnaseq')
self.gating_group.addButton(self.rnaseq_gates)
self.rnaseq_gates.clicked.connect(self.activate_gate)
# scRNA-Seq gating spinbox
self.rnaseq_gates_value = QDoubleSpinBox(self.gating_page)
self.rnaseq_gates_value.setMinimum(0)
self.rnaseq_gates_value.setMaximum(10)
self.rnaseq_gates_value.setValue(0)
self.rnaseq_gates_value.setSingleStep(1)
self.rnaseq_gates_value.setEnabled(False)
# export gated population checkbox
self.export_gated = QCheckBox(self.gating_page)
self.export_gated.setText('Export gated cells as an output file')
self.export_gated.setStyleSheet(self.style['checkbox'])
self.export_gated.setEnabled(False)
# Add widgets above to Gate frame layout
self.gate_frame.layout().addRow(self.no_gates, QLabel())
self.gate_frame.layout().addRow(self.cytof_gates,
self.cytof_gates_value)
self.gate_frame.layout().addRow(self.rnaseq_gates,
self.rnaseq_gates_value)
self.gate_frame.layout().addRow(self.export_gated, QLabel())
# ## Outlier options section
# Outlier header
self.outlier_header = QLabel(self.gating_page)
self.outlier_header.setText('Outliers')
self.outlier_header.setStyleSheet(self.style['header'])
self.outlier_header.adjustSize()
self.gating_layout.addWidget(self.outlier_header)
# Outlier frame
self.outlier_frame = QFrame(self.gating_page)
self.outlier_frame.setFrameShape(QFrame.StyledPanel)
self.outlier_frame.setLayout(QVBoxLayout())
self.gating_layout.addWidget(self.outlier_frame)
# Top outliers information
self.top_outliers = QLabel(self.gating_page)
self.top_outliers.setStyleSheet(self.style['label'])
self.top_outliers.setText(
'By default, SCOUTS selects the top outliers from the population')
self.top_outliers.setStyleSheet(self.style['label'])
# Bottom outliers data
self.bottom_outliers = QCheckBox(self.gating_page)
self.bottom_outliers.setText('Include results for low outliers')
self.bottom_outliers.setStyleSheet(self.style['checkbox'])
# Non-outliers data
self.not_outliers = QCheckBox(self.gating_page)
self.not_outliers.setText('Include results for non-outliers')
self.not_outliers.setStyleSheet(self.style['checkbox'])
# Add widgets above to Gate frame layout
self.outlier_frame.layout().addWidget(self.top_outliers)
self.outlier_frame.layout().addWidget(self.bottom_outliers)
self.outlier_frame.layout().addWidget(self.not_outliers)
# ## Save/back button
self.save_gates = QPushButton(self.gating_page)
self.set_icon(self.save_gates, 'go-next')
self.save_gates.setText(' Back to main menu')
self.save_gates.setStyleSheet(self.style['md button'])
self.gating_layout.addWidget(self.save_gates)
self.save_gates.clicked.connect(self.goto_main_page)
# ## Add empty label to take vertical space
self.empty_label = QLabel(self.gating_page)
self.empty_label.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.gating_layout.addWidget(self.empty_label)
# ###
# ### ICON SETTING
# ###
def set_icon(self, widget: QWidget, icon: str) -> None:
"""Associates an icon to a widget."""
i = QIcon()
i.addPixmap(
QPixmap(
os.path.abspath(
os.path.join(self.rootdir, 'src', 'default_icons',
f'{icon}.svg'))))
widget.setIcon(QIcon.fromTheme(icon, i))
# ###
# ### STACKED WIDGET PAGE SWITCHING
# ###
def goto_main_page(self) -> None:
"""Switches stacked widget pages to the main page."""
self.stacked_pages.setCurrentWidget(self.main_page)
def goto_samples_page(self) -> None:
"""Switches stacked widget pages to the samples table page."""
self.stacked_pages.setCurrentWidget(self.samples_page)
def goto_gates_page(self) -> None:
"""Switches stacked widget pages to the gating & other options page."""
self.stacked_pages.setCurrentWidget(self.gating_page)
# ###
# ### MAIN PAGE GUI LOGIC
# ###
def get_path(self) -> None:
"""Opens a dialog box and sets the chosen file/folder path, depending on the caller widget."""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
sender_name = self.sender().objectName()
if sender_name == 'input':
query, _ = QFileDialog.getOpenFileName(self,
"Select file",
"",
"All Files (*)",
options=options)
elif sender_name == 'output':
query = QFileDialog.getExistingDirectory(self,
"Select Directory",
options=options)
else:
return
if query:
getattr(self, f'{sender_name}_path').setText(query)
def enable_single_excel(self) -> None:
"""Enables checkbox for generating a single Excel output."""
if self.output_excel.isChecked():
self.single_excel.setEnabled(True)
else:
self.single_excel.setEnabled(False)
self.single_excel.setChecked(False)
# ###
# ### SAMPLE NAME/SAMPLE TABLE GUI LOGIC
# ###
def write_to_sample_table(self) -> None:
"""Writes data to sample table."""
table = self.sample_table
ref = 'no'
sample = self.sample_name.text()
if sample:
for cell in range(table.rowCount()):
item = table.item(cell, 0)
if item.text() == sample:
self.same_sample()
return
if self.is_reference.isChecked():
for cell in range(table.rowCount()):
item = table.item(cell, 1)
if item.text() == 'yes':
self.more_than_one_reference()
return
ref = 'yes'
sample = QTableWidgetItem(sample)
is_reference = QTableWidgetItem(ref)
is_reference.setFlags(Qt.ItemIsEnabled)
row_position = table.rowCount()
table.insertRow(row_position)
table.setItem(row_position, 0, sample)
table.setItem(row_position, 1, is_reference)
self.is_reference.setChecked(False)
self.sample_name.setText('')
def remove_from_sample_table(self) -> None:
"""Removes data from sample table."""
table = self.sample_table
rows = set(index.row() for index in table.selectedIndexes())
for index in sorted(rows, reverse=True):
self.sample_table.removeRow(index)
def prompt_clear_data(self) -> None:
"""Prompts option to clear all data in the sample table."""
if self.confirm_clear_data():
table = self.sample_table
while table.rowCount():
self.sample_table.removeRow(0)
# ###
# ### GATING GUI LOGIC
# ###
def activate_gate(self) -> None:
"""Activates/deactivates buttons related to gating."""
if self.sender().objectName() == 'no_gate':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(False)
self.export_gated.setChecked(False)
elif self.sender().objectName() == 'cytof':
self.cytof_gates_value.setEnabled(True)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(True)
elif self.sender().objectName() == 'rnaseq':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(True)
self.export_gated.setEnabled(True)
# ###
# ### CONNECT SCOUTS TO ANALYTICAL MODULES
# ###
def run(self) -> None:
"""Runs SCOUTS as a Worker, based on user input in the GUI."""
try:
data = self.parse_input()
except Exception as error:
trace = traceback.format_exc()
self.propagate_error((error, trace))
else:
data['widget'] = self
worker = Worker(func=start_scouts, **data)
worker.signals.started.connect(self.analysis_has_started)
worker.signals.finished.connect(self.analysis_has_finished)
worker.signals.success.connect(self.success_message)
worker.signals.error.connect(self.propagate_error)
self.threadpool.start(worker)
def parse_input(self) -> Dict:
"""Returns user input on the GUI as a dictionary."""
# Input and output
input_dict = {
'input_file': str(self.input_path.text()),
'output_folder': str(self.output_path.text())
}
if not input_dict['input_file'] or not input_dict['output_folder']:
raise NoIOPathError
# Set cutoff by reference or by sample rule
input_dict['cutoff_rule'] = self.cutoff_group.checkedButton(
).objectName() # 'sample', 'ref', 'sample ref'
# Outliers for each individual marker or any marker in row
input_dict['marker_rule'] = self.markers_group.checkedButton(
).objectName() # 'single', 'any', 'single any'
# Tukey factor used for calculating cutoff
input_dict['tukey_factor'] = float(
self.tukey_group.checkedButton().text()) # '1.5', '3.0'
# Output settings
input_dict['export_csv'] = True if self.output_csv.isChecked(
) else False
input_dict['export_excel'] = True if self.output_excel.isChecked(
) else False
input_dict['single_excel'] = True if self.single_excel.isChecked(
) else False
# Retrieve samples from sample table
input_dict['sample_list'] = []
for tuples in self.yield_samples_from_table():
input_dict['sample_list'].append(tuples)
if not input_dict['sample_list']:
raise NoSampleError
# Set gate cutoff (if any)
input_dict['gating'] = self.gating_group.checkedButton().objectName(
) # 'no_gate', 'cytof', 'rnaseq'
input_dict['gate_cutoff_value'] = None
if input_dict['gating'] != 'no_gate':
input_dict['gate_cutoff_value'] = getattr(
self, f'{input_dict["gating"]}_gates_value').value()
input_dict['export_gated'] = True if self.export_gated.isChecked(
) else False
# Generate results for non-outliers
input_dict['non_outliers'] = False
if self.not_outliers.isChecked():
input_dict['non_outliers'] = True
# Generate results for bottom outliers
input_dict['bottom_outliers'] = False
if self.bottom_outliers.isChecked():
input_dict['bottom_outliers'] = True
# return dictionary with all gathered inputs
return input_dict
def yield_samples_from_table(
self) -> Generator[Tuple[str, str], None, None]:
"""Yields sample names from the sample table."""
table = self.sample_table
for cell in range(table.rowCount()):
sample_name = table.item(cell, 0).text()
sample_type = table.item(cell, 1).text()
yield sample_name, sample_type
# ###
# ### MESSAGE BOXES
# ###
def analysis_has_started(self) -> None:
"""Disables run button while SCOUTS analysis is underway."""
self.run_button.setText(' Working...')
self.run_button.setEnabled(False)
def analysis_has_finished(self) -> None:
"""Enables run button after SCOUTS analysis has finished."""
self.run_button.setEnabled(True)
self.run_button.setText(' Run!')
def success_message(self) -> None:
"""Info message box used when SCOUTS finished without errors."""
title = "Analysis finished!"
mes = "Your analysis has finished. No errors were reported."
if self.stacked_pages.isEnabled() is True:
QMessageBox.information(self, title, mes)
def memory_warning(self) -> None:
"""Warning message box used when user wants to generate a single excel file."""
if self.sender().isChecked():
title = 'Memory warning!'
mes = (
"Depending on your dataset, this option can consume a LOT of memory and take"
" a long time to process. Please make sure that your computer can handle it!"
)
QMessageBox.information(self, title, mes)
def same_sample(self) -> None:
"""Error message box used when the user tries to input the same sample twice in the sample table."""
title = 'Error: sample name already in table'
mes = (
"Sorry, you can't do this because this sample name is already in the table. "
"Please select a different name.")
QMessageBox.critical(self, title, mes)
def more_than_one_reference(self) -> None:
"""Error message box used when the user tries to input two reference samples in the sample table."""
title = "Error: more than one reference selected"
mes = (
"Sorry, you can't do this because there is already a reference column in the table. "
"Please remove it before adding a reference.")
QMessageBox.critical(self, title, mes)
def confirm_clear_data(self) -> bool:
"""Question message box used to confirm user action of clearing sample table."""
title = 'Confirm Action'
mes = "Table will be cleared. Are you sure?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
return True
return False
# ###
# ### EXCEPTIONS & ERRORS
# ###
def propagate_error(self, error: Tuple[Exception, str]) -> None:
"""Calls the appropriate error message box based on type of Exception raised."""
if isinstance(error[0], NoIOPathError):
self.no_io_path_error_message()
elif isinstance(error[0], NoReferenceError):
self.no_reference_error_message()
elif isinstance(error[0], NoSampleError):
self.no_sample_error_message()
elif isinstance(error[0], PandasInputError):
self.pandas_input_error_message()
elif isinstance(error[0], SampleNamingError):
self.sample_naming_error_message()
else:
self.generic_error_message(error)
def no_io_path_error_message(self) -> None:
"""Message displayed when the user did not include an input file path, or an output folder path."""
title = 'Error: no file/folder'
message = ("Sorry, no input file and/or output folder was provided. "
"Please add the path to the necessary file/folder.")
QMessageBox.critical(self, title, message)
def no_reference_error_message(self) -> None:
"""Message displayed when the user wants to analyse cutoff based on a reference, but did not specify what
sample corresponds to the reference."""
title = "Error: No reference selected"
message = (
"Sorry, no reference sample was found on the sample list, but analysis was set to "
"reference. Please add a reference sample, or change the rule for cutoff calculation."
)
QMessageBox.critical(self, title, message)
def no_sample_error_message(self) -> None:
"""Message displayed when the user did not add any samples to the sample table."""
title = "Error: No samples selected"
message = (
"Sorry, the analysis cannot be performed because no sample names were input. "
"Please add your sample names.")
QMessageBox.critical(self, title, message)
def pandas_input_error_message(self) -> None:
"""Message displayed when the input file cannot be read (likely because it is not a Excel or csv file)."""
title = 'Error: unexpected input file'
message = (
"Sorry, the input file could not be read. Please make sure that "
"the data is save in a valid format (supported formats are: "
".csv, .xlsx).")
QMessageBox.critical(self, title, message)
def sample_naming_error_message(self) -> None:
"""Message displayed when none of the sample names passed by the user are found in the input DataFrame."""
title = 'Error: sample names not in input file'
message = (
"Sorry, your sample names were not found in the input file. Please "
"make sure that the names were typed correctly (case-sensitive).")
QMessageBox.critical(self, title, message)
def generic_error_message(self, error: Tuple[Exception, str]) -> None:
"""Error message box used to display any error message (including traceback) for any uncaught errors."""
title = 'An error occurred!'
name, trace = error
QMessageBox.critical(self, title,
f"{str(name)}\n\nfull traceback:\n{trace}")
def not_implemented_error_message(self) -> None:
"""Error message box used when the user accesses a functionality that hasn't been implemented yet."""
title = "Not yet implemented"
mes = "Sorry, this functionality has not been implemented yet."
QMessageBox.critical(self, title, mes)
# ###
# ### HELP & QUIT
# ###
@staticmethod
def get_help() -> None:
"""Opens SCOUTS documentation on the browser. Called when the user clicks the "help" button"""
webbrowser.open('https://scouts.readthedocs.io/en/master/')
def closeEvent(self, event: QEvent) -> None:
"""Defines the message box for when the user wants to quit SCOUTS."""
title = 'Quit SCOUTS'
mes = "Are you sure you want to quit?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
self.stacked_pages.setEnabled(False)
message = self.quit_message()
waiter = Waiter(waiter_func=self.threadpool.activeThreadCount)
waiter.signals.started.connect(message.show)
waiter.signals.finished.connect(message.destroy)
waiter.signals.finished.connect(sys.exit)
self.threadpool.start(waiter)
event.ignore()
def quit_message(self) -> QDialog:
"""Displays a window while SCOUTS is exiting"""
message = QDialog(self)
message.setWindowTitle('Exiting SCOUTS')
message.resize(300, 50)
label = QLabel('SCOUTS is exiting, please wait...', message)
label.setStyleSheet(self.style['label'])
label.adjustSize()
label.setAlignment(Qt.AlignCenter)
label.move(int((message.width() - label.width()) / 2),
int((message.height() - label.height()) / 2))
return message
class BreakpointDialog(QDialog):
"""
Dialog to edit breakpoints.
"""
def __init__(self,
breakpoint_: Breakpoint,
workspace: 'Workspace',
parent=None):
super().__init__(parent)
self.breakpoint = breakpoint_
self.workspace = workspace
self.setWindowTitle('Edit Breakpoint')
self.main_layout: QVBoxLayout = QVBoxLayout()
self._type_radio_group: Optional[QButtonGroup] = None
self._address_box: Optional[QAddressInput] = None
self._size_box: Optional[QLineEdit] = None
self._comment_box: Optional[QLineEdit] = None
self._status_label: Optional[QLabel] = None
self._ok_button: Optional[QPushButton] = None
self._init_widgets()
self.setLayout(self.main_layout)
self._validate()
#
# Private methods
#
def _init_widgets(self):
layout = QGridLayout()
self.main_layout.addLayout(layout)
self._status_label = QLabel(self)
row = 0
layout.addWidget(QLabel('Break on:', self), row, 0, Qt.AlignRight)
self._type_radio_group = QButtonGroup(self)
self._type_radio_group.addButton(QRadioButton('Execute', self),
BreakpointType.Execute.value)
self._type_radio_group.addButton(QRadioButton('Write', self),
BreakpointType.Write.value)
self._type_radio_group.addButton(QRadioButton('Read', self),
BreakpointType.Read.value)
for b in self._type_radio_group.buttons():
layout.addWidget(b, row, 1)
row += 1
self._type_radio_group.button(
self.breakpoint.type.value).setChecked(True)
layout.addWidget(QLabel('Address:', self), row, 0, Qt.AlignRight)
self._address_box = QAddressInput(self._on_address_changed,
self.workspace,
parent=self,
default=f'{self.breakpoint.addr:#x}')
layout.addWidget(self._address_box, row, 1)
row += 1
layout.addWidget(QLabel('Size:', self), row, 0, Qt.AlignRight)
self._size_box = QLineEdit(self)
self._size_box.setText(f'{self.breakpoint.size:#x}')
self._size_box.textChanged.connect(self._on_size_changed)
layout.addWidget(self._size_box, row, 1)
row += 1
layout.addWidget(QLabel('Comment:', self), row, 0, Qt.AlignRight)
self._comment_box = QLineEdit(self)
self._comment_box.setText(self.breakpoint.comment)
layout.addWidget(self._comment_box, row, 1)
row += 1
self.main_layout.addWidget(self._status_label)
buttons = QDialogButtonBox(parent=self)
buttons.setStandardButtons(QDialogButtonBox.StandardButton.Cancel
| QDialogButtonBox.StandardButton.Ok)
buttons.accepted.connect(self._on_ok_clicked)
buttons.rejected.connect(self.close)
self._ok_button = buttons.button(QDialogButtonBox.Ok)
self._ok_button.setEnabled(False)
self.main_layout.addWidget(buttons)
def _set_valid(self, valid: bool):
if not valid:
self._status_label.setText('Invalid')
self._status_label.setProperty('class', 'status_invalid')
else:
self._status_label.setText('Valid')
self._status_label.setProperty('class', 'status_valid')
self._ok_button.setEnabled(valid)
self._status_label.style().unpolish(self._status_label)
self._status_label.style().polish(self._status_label)
def _get_size(self):
try:
return int(self._size_box.text(), 0)
except ValueError:
pass
return None
#
# Event handlers
#
def _validate(self):
self._set_valid(
bool(self._address_box.target is not None and self._get_size()))
def _on_address_changed(self, new_text): # pylint: disable=unused-argument
self._validate()
def _on_size_changed(self, new_text): # pylint: disable=unused-argument
self._validate()
def _on_ok_clicked(self):
self.breakpoint.type = BreakpointType(
self._type_radio_group.checkedId())
self.breakpoint.addr = self._address_box.target
self.breakpoint.size = self._get_size()
self.breakpoint.comment = self._comment_box.text()
self.workspace.instance.breakpoint_mgr.breakpoints.am_event()
self.accept()
class MyWidget(QWidget):
def __init__(self, parent):
super().__init__(parent)
self.buttons_id_value = {
1: ('comma', ','),
2: ('space', '\b'),
3: ('tab', '\t'),
4: ('semicolon', ';')
}
self.separator = QButtonGroup()
lab = QLabel()
lab.setText('Choose a separator:')
for bid, value in self.buttons_id_value.items():
self.separator.addButton(QRadioButton(value[0]), id=bid)
self.separator.setExclusive(True)
self.default_button = self.separator.button(1)
button_layout = QHBoxLayout()
for button in self.separator.buttons():
button_layout.addWidget(button)
self.default_button.click()
openFileChooser = QPushButton('Choose')
fileChooser = QFileDialog(self, 'Open csv', str(os.getcwd()),
'Csv (*.csv *.tsv *.dat)')
fileChooser.setFileMode(QFileDialog.ExistingFile)
self.filePath = QLineEdit()
openFileChooser.released.connect(fileChooser.show)
fileChooser.fileSelected.connect(self.filePath.setText)
self.filePath.textChanged.connect(self.checkFileExists)
nameLabel = QLabel('Select a name:', self)
self.nameField = QLineEdit(self)
self.nameErrorLabel = QLabel(self)
self.file_layout = QVBoxLayout()
fileChooserLayout = QHBoxLayout()
nameRowLayout = QHBoxLayout()
fileChooserLayout.addWidget(openFileChooser)
fileChooserLayout.addWidget(self.filePath)
nameRowLayout.addWidget(nameLabel)
nameRowLayout.addWidget(self.nameField)
self.fileErrorLabel = QLabel(self)
self.file_layout.addLayout(fileChooserLayout)
self.file_layout.addWidget(self.fileErrorLabel)
self.file_layout.addLayout(nameRowLayout)
self.file_layout.addWidget(self.nameErrorLabel)
self.fileErrorLabel.hide()
self.nameErrorLabel.hide()
self.tablePreview = SearchableAttributeTableWidget(self, True)
self.tableSpinner = QtWaitingSpinner(
self.tablePreview,
centerOnParent=True,
disableParentWhenSpinning=True)
self.nameField.textEdited.connect(self.nameErrorLabel.hide)
# Split file by row
splitRowLayout = QHBoxLayout()
self.checkSplit = QCheckBox('Split file by rows', self)
self.numberRowsChunk = QLineEdit(self)
self.numberRowsChunk.setPlaceholderText(
'Number of rows per chunk')
self.numberRowsChunk.setValidator(QIntValidator(self))
splitRowLayout.addWidget(self.checkSplit)
splitRowLayout.addWidget(self.numberRowsChunk)
self.checkSplit.stateChanged.connect(self.toggleSplitRows)
layout = QVBoxLayout()
layout.addLayout(self.file_layout)
layout.addWidget(lab)
layout.addLayout(button_layout)
layout.addLayout(splitRowLayout)
layout.addWidget(QLabel('Preview'))
layout.addWidget(self.tablePreview)
self.setLayout(layout)
self.filePath.textChanged.connect(self.loadPreview)
self.separator.buttonClicked.connect(self.loadPreview)
@Slot(object)
def loadPreview(self) -> None:
if not os.path.isfile(self.filePath.text()):
return
class WorkerThread(QThread):
resultReady = Signal(Frame)
def __init__(self, path: str, separ: str, parent=None):
super().__init__(parent)
self.__path = path
self.__sep = separ
def run(self):
header = pd.read_csv(self.__path,
sep=self.__sep,
index_col=False,
nrows=0)
self.resultReady.emit(Frame(header))
sep: int = self.separator.checkedId()
sep_s: str = self.buttons_id_value[sep][
1] if sep != -1 else None
assert sep_s is not None
# Async call to load header
worker = WorkerThread(path=self.filePath.text(),
separ=sep_s,
parent=self)
worker.resultReady.connect(self.onPreviewComputed)
worker.finished.connect(worker.deleteLater)
self.tableSpinner.start()
worker.start()
@Slot(Frame)
def onPreviewComputed(self, header: Frame):
self.tablePreview.setSourceFrameModel(FrameModel(self, header))
self.tablePreview.model().setAllChecked(True)
self.tableSpinner.stop()
@Slot(str)
def checkFileExists(self, path: str) -> None:
file_exists = os.path.isfile(path)
if not file_exists:
self.fileErrorLabel.setText('File does not exists!')
self.fileErrorLabel.setStyleSheet('color: red')
self.filePath.setToolTip('File does not exists!')
self.filePath.setStyleSheet('border: 1px solid red')
# self.file_layout.addWidget(self.fileErrorLabel)
self.parentWidget().disableOkButton()
self.fileErrorLabel.show()
else:
# self.file_layout.removeWidget(self.fileErrorLabel)
self.fileErrorLabel.hide()
self.filePath.setStyleSheet('')
self.parentWidget().enableOkButton()
if not self.nameField.text():
name: str = os.path.splitext(os.path.basename(path))[0]
self.nameField.setText(name)
@Slot(Qt.CheckState)
def toggleSplitRows(self, state: Qt.CheckState) -> None:
if state == Qt.Checked:
self.numberRowsChunk.setEnabled(True)
else:
self.numberRowsChunk.setDisabled(True)
def showNameError(self, msg: str) -> None:
self.nameErrorLabel.setText(msg)
self.nameErrorLabel.setStyleSheet('color: red')
self.nameErrorLabel.show()
class PreferencesDocumentPresetsPage(QWidget):
preferencesChanged = Signal()
def __init__(self, parent=None):
super().__init__(parent)
# Title
title = QLabel(
self.tr("<strong style=\"font-size:large;\">{0}</strong>").format(
self.title()))
#
# Content: Header Labels
rdbDefaultHeaderLabelHorizontalLetters = QRadioButton(
self.tr("Letters"))
rdbDefaultHeaderLabelHorizontalLetters.setToolTip(
self.
tr("Capital letters as default horizontal header labels of new documents"
))
rdbDefaultHeaderLabelHorizontalNumbers = QRadioButton(
self.tr("Numbers"))
rdbDefaultHeaderLabelHorizontalNumbers.setToolTip(
self.
tr("Decimal numbers as default horizontal header labels of new documents"
))
self._grpDefaultHeaderLabelHorizontal = QButtonGroup(self)
self._grpDefaultHeaderLabelHorizontal.addButton(
rdbDefaultHeaderLabelHorizontalLetters,
Preferences.HeaderLabel.Letter.value)
self._grpDefaultHeaderLabelHorizontal.addButton(
rdbDefaultHeaderLabelHorizontalNumbers,
Preferences.HeaderLabel.Decimal.value)
self._grpDefaultHeaderLabelHorizontal.buttonClicked.connect(
self._onPreferencesChanged)
defaultHeaderLabelHorizontalBox = QHBoxLayout()
defaultHeaderLabelHorizontalBox.addWidget(
rdbDefaultHeaderLabelHorizontalLetters)
defaultHeaderLabelHorizontalBox.addWidget(
rdbDefaultHeaderLabelHorizontalNumbers)
rdbDefaultHeaderLabelVerticalLetters = QRadioButton(self.tr("Letters"))
rdbDefaultHeaderLabelVerticalLetters.setToolTip(
self.
tr("Capital letters as default vertical header labels of new documents"
))
rdbDefaultHeaderLabelVerticalNumbers = QRadioButton(self.tr("Numbers"))
rdbDefaultHeaderLabelVerticalNumbers.setToolTip(
self.
tr("Decimal numbers as default vertical header labels of new documents"
))
self._grpDefaultHeaderLabelVertical = QButtonGroup()
self._grpDefaultHeaderLabelVertical.addButton(
rdbDefaultHeaderLabelVerticalLetters,
Preferences.HeaderLabel.Letter.value)
self._grpDefaultHeaderLabelVertical.addButton(
rdbDefaultHeaderLabelVerticalNumbers,
Preferences.HeaderLabel.Decimal.value)
self._grpDefaultHeaderLabelVertical.buttonClicked.connect(
self._onPreferencesChanged)
defaultHeaderLabelVerticalBox = QHBoxLayout()
defaultHeaderLabelVerticalBox.addWidget(
rdbDefaultHeaderLabelVerticalLetters)
defaultHeaderLabelVerticalBox.addWidget(
rdbDefaultHeaderLabelVerticalNumbers)
defaultHeaderLabelLayout = QFormLayout()
defaultHeaderLabelLayout.addRow(
self.tr("Labels of the horizontal header"),
defaultHeaderLabelHorizontalBox)
defaultHeaderLabelLayout.addRow(
self.tr("Labels of the vertical header"),
defaultHeaderLabelVerticalBox)
defaultHeaderLabelGroup = QGroupBox(self.tr("Header Labels"))
defaultHeaderLabelGroup.setLayout(defaultHeaderLabelLayout)
#
# Content: Cell Counts
self._spbDefaultCellCountColumn = QSpinBox()
self._spbDefaultCellCountColumn.setRange(1, 1000)
self._spbDefaultCellCountColumn.setToolTip(
self.tr("Default number of columns of new documents"))
self._spbDefaultCellCountColumn.valueChanged.connect(
self._onPreferencesChanged)
self._spbDefaultCellCountRow = QSpinBox()
self._spbDefaultCellCountRow.setRange(1, 1000)
self._spbDefaultCellCountRow.setToolTip(
self.tr("Default number of rows of new documents"))
self._spbDefaultCellCountRow.valueChanged.connect(
self._onPreferencesChanged)
defaultCellCountLayout = QFormLayout()
defaultCellCountLayout.addRow(self.tr("Number of columns"),
self._spbDefaultCellCountColumn)
defaultCellCountLayout.addRow(self.tr("Number of rows"),
self._spbDefaultCellCountRow)
defaultCellCountGroup = QGroupBox(self.tr("Cell Counts"))
defaultCellCountGroup.setLayout(defaultCellCountLayout)
# Main layout
self._layout = QVBoxLayout(self)
self._layout.addWidget(title)
self._layout.addWidget(defaultHeaderLabelGroup)
self._layout.addWidget(defaultCellCountGroup)
self._layout.addStretch(1)
def setZeroMargins(self):
self._layout.setContentsMargins(0, 0, 0, 0)
def title(self):
return self.tr("Document Presets")
def _onPreferencesChanged(self):
self.preferencesChanged.emit()
def setDefaultHeaderLabelHorizontal(self, type):
if type.value != self._grpDefaultHeaderLabelHorizontal.checkedId():
self._onPreferencesChanged()
for button in self._grpDefaultHeaderLabelHorizontal.buttons():
if self._grpDefaultHeaderLabelHorizontal.id(button) == type.value:
button.setChecked(True)
def defaultHeaderLabelHorizontal(self):
return Preferences.HeaderLabel(
self._grpDefaultHeaderLabelHorizontal.checkedId())
def setDefaultHeaderLabelVertical(self, type):
if type.value != self._grpDefaultHeaderLabelVertical.checkedId():
self._onPreferencesChanged()
for button in self._grpDefaultHeaderLabelVertical.buttons():
if self._grpDefaultHeaderLabelVertical.id(button) == type.value:
button.setChecked(True)
def defaultHeaderLabelVertical(self):
return Preferences.HeaderLabel(
self._grpDefaultHeaderLabelVertical.checkedId())
def setDefaultCellCountColumn(self, val):
self._spbDefaultCellCountColumn.setValue(val)
def defaultCellCountColumn(self):
return self._spbDefaultCellCountColumn.value()
def setDefaultCellCountRow(self, val):
self._spbDefaultCellCountRow.setValue(val)
def defaultCellCountRow(self):
return self._spbDefaultCellCountRow.value()
