def __init__(self):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(HEADER)
proxy = QSortFilterProxyModel()
proxy.setSourceModel(model)
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.view.setItemDelegateForColumn(
Header.Size, SizeDelegate(self))
self.view.setItemDelegateForColumn(
Header.Local, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.view.setItemDelegateForColumn(
Header.Instances, NumericalDelegate(self))
self.view.setItemDelegateForColumn(
Header.Variables, NumericalDelegate(self))
self.view.resizeColumnToContents(Header.Local)
if self.header_state:
self.view.header().restoreState(self.header_state)
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def showPopup(self):
# type: () -> None
"""
Reimplemented from QComboBox.showPopup
Popup up a customized view and filter edit line.
Note
----
The .popup(), .lineEdit(), .completer() of the base class are not used.
"""
if self.__popup is not None:
# We have user entered state that cannot be disturbed
# (entered filter text, scroll offset, ...)
return # pragma: no cover
if self.count() == 0:
return
opt = QStyleOptionComboBox()
self.initStyleOption(opt)
popup = QListView(
uniformItemSizes=True,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
verticalScrollBarPolicy=Qt.ScrollBarAsNeeded,
iconSize=self.iconSize(),
)
popup.setFocusProxy(self.__searchline)
popup.setParent(self, Qt.Popup | Qt.FramelessWindowHint)
popup.setItemDelegate(_ComboBoxListDelegate(popup))
proxy = QSortFilterProxyModel(
popup, filterCaseSensitivity=Qt.CaseInsensitive
)
proxy.setFilterKeyColumn(self.modelColumn())
proxy.setSourceModel(self.model())
popup.setModel(proxy)
root = proxy.mapFromSource(self.rootModelIndex())
popup.setRootIndex(root)
self.__popup = popup
self.__proxy = proxy
self.__searchline.setText("")
self.__searchline.setPlaceholderText("Filter...")
self.__searchline.setVisible(True)
self.__searchline.textEdited.connect(proxy.setFilterFixedString)
style = self.style() # type: QStyle
popuprect_origin = style.subControlRect(
QStyle.CC_ComboBox, opt, QStyle.SC_ComboBoxListBoxPopup, self
) # type: QRect
popuprect_origin = QRect(
self.mapToGlobal(popuprect_origin.topLeft()),
popuprect_origin.size()
)
editrect = style.subControlRect(
QStyle.CC_ComboBox, opt, QStyle.SC_ComboBoxEditField, self
) # type: QRect
self.__searchline.setGeometry(editrect)
desktop = QApplication.desktop()
screenrect = desktop.availableGeometry(self) # type: QRect
# get the height for the view
listrect = QRect()
for i in range(min(proxy.rowCount(root), self.maxVisibleItems())):
index = proxy.index(i, self.modelColumn(), root)
if index.isValid():
listrect = listrect.united(popup.visualRect(index))
if listrect.height() >= screenrect.height():
break
window = popup.window() # type: QWidget
window.ensurePolished()
if window.layout() is not None:
window.layout().activate()
else:
QApplication.sendEvent(window, QEvent(QEvent.LayoutRequest))
margins = qwidget_margin_within(popup.viewport(), window)
height = (listrect.height() + 2 * popup.spacing() +
margins.top() + margins.bottom())
popup_size = (QSize(popuprect_origin.width(), height)
.expandedTo(window.minimumSize())
.boundedTo(window.maximumSize())
.boundedTo(screenrect.size()))
popuprect = QRect(popuprect_origin.bottomLeft(), popup_size)
popuprect = dropdown_popup_geometry(
popuprect, popuprect_origin, screenrect)
popup.setGeometry(popuprect)
current = proxy.mapFromSource(
self.model().index(self.currentIndex(), self.modelColumn(),
self.rootModelIndex()))
popup.setCurrentIndex(current)
popup.scrollTo(current, QAbstractItemView.EnsureVisible)
popup.show()
popup.setFocus(Qt.PopupFocusReason)
popup.installEventFilter(self)
popup.viewport().installEventFilter(self)
popup.viewport().setMouseTracking(True)
self.update()
self.__popupTimer.restart()
def __init__(self):
super().__init__()
self.allinfo_local = {}
self.allinfo_remote = {}
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
# current_output does not equal selected_id when, for instance, the
# data is still downloading
self.current_output = None
self._header_labels = [
header['label'] for _, header in self.HEADER_SCHEMA]
self._header_index = namedtuple(
'_header_index', [info_tag for info_tag, _ in self.HEADER_SCHEMA])
self.Header = self._header_index(
*[index for index, _ in enumerate(self._header_labels)])
self.__awaiting_state = None # type: Optional[_FetchState]
self.filterLineEdit = QLineEdit(
textChanged=self.filter, placeholderText="Search for data set ..."
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = TreeViewWithReturn(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
uniformRowHeights=True,
toolTip="Press Return or double-click to send"
)
# the method doesn't exists yet, pylint: disable=unnecessary-lambda
self.view.doubleClicked.connect(self.commit)
self.view.returnPressed.connect(self.commit)
box = gui.widgetBox(self.splitter, "说明", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
proxy = QSortFilterProxyModel()
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.assign_delegates()
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
class OWCreateInstance(OWWidget):
name = "Create Instance"
description = "Interactively create a data instance from sample dataset."
icon = "icons/CreateInstance.svg"
category = "Data"
keywords = ["simulator"]
priority = 4000
class Inputs:
data = Input("Data", Table)
reference = Input("Reference", Table)
class Outputs:
data = Output("Data", Table)
class Information(OWWidget.Information):
nans_removed = Msg("Variables with only missing values were "
"removed from the list.")
want_main_area = False
ACTIONS = ["median", "mean", "random", "input"]
HEADER = [["name", "Variable"], ["variable", "Value"]]
Header = namedtuple("header",
[tag for tag, _ in HEADER])(*range(len(HEADER)))
values: Dict[str, Union[float, str]] = Setting({}, schema_only=True)
append_to_data = Setting(True)
auto_commit = Setting(True)
def __init__(self):
super().__init__()
self.data: Optional[Table] = None
self.reference: Optional[Table] = None
self.filter_edit = QLineEdit(textChanged=self.__filter_edit_changed,
placeholderText="Filter...")
self.view = QTableView(sortingEnabled=True,
contextMenuPolicy=Qt.CustomContextMenu,
selectionMode=QTableView.NoSelection)
self.view.customContextMenuRequested.connect(self.__menu_requested)
self.view.setItemDelegateForColumn(self.Header.variable,
VariableDelegate(self))
self.view.verticalHeader().hide()
self.view.horizontalHeader().setStretchLastSection(True)
self.view.horizontalHeader().setMaximumSectionSize(350)
self.model = VariableItemModel(self)
self.model.setHorizontalHeaderLabels([x for _, x in self.HEADER])
self.model.dataChanged.connect(self.__table_data_changed)
self.model.dataHasNanColumn.connect(self.Information.nans_removed)
self.proxy_model = QSortFilterProxyModel()
self.proxy_model.setFilterKeyColumn(-1)
self.proxy_model.setFilterCaseSensitivity(False)
self.proxy_model.setSourceModel(self.model)
self.view.setModel(self.proxy_model)
vbox = gui.vBox(self.controlArea, box=True)
vbox.layout().addWidget(self.filter_edit)
vbox.layout().addWidget(self.view)
box = gui.hBox(vbox)
gui.rubber(box)
for name in self.ACTIONS:
gui.button(box,
self,
name.capitalize(),
lambda *args, fun=name: self._initialize_values(fun),
autoDefault=False)
gui.rubber(box)
box = gui.auto_apply(self.controlArea, self, "auto_commit")
box.button.setFixedWidth(180)
box.layout().insertStretch(0)
# pylint: disable=unnecessary-lambda
append = gui.checkBox(None,
self,
"append_to_data",
"Append this instance to input data",
callback=lambda: self.commit())
box.layout().insertWidget(0, append)
self._set_input_summary()
self._set_output_summary()
self.settingsAboutToBePacked.connect(self.pack_settings)
def __filter_edit_changed(self):
self.proxy_model.setFilterFixedString(self.filter_edit.text().strip())
def __table_data_changed(self):
self.commit()
def __menu_requested(self, point: QPoint):
index = self.view.indexAt(point)
model: QSortFilterProxyModel = index.model()
source_index = model.mapToSource(index)
menu = QMenu(self)
for action in self._create_actions(source_index):
menu.addAction(action)
menu.popup(self.view.viewport().mapToGlobal(point))
def _create_actions(self, index: QModelIndex) -> List[QAction]:
actions = []
for name in self.ACTIONS:
action = QAction(name.capitalize(), self)
action.triggered.connect(
lambda *args, fun=name: self._initialize_values(fun, [index]))
actions.append(action)
return actions
def _initialize_values(self, fun: str, indices: List[QModelIndex] = None):
cont_fun = {
"median": np.nanmedian,
"mean": np.nanmean,
"random": cont_random,
"input": np.nanmean
}.get(fun, NotImplemented)
disc_fun = {
"median": majority,
"mean": majority,
"random": disc_random,
"input": majority
}.get(fun, NotImplemented)
if not self.data or fun == "input" and not self.reference:
return
self.model.dataChanged.disconnect(self.__table_data_changed)
rows = range(self.proxy_model.rowCount()) if indices is None else \
[index.row() for index in indices]
for row in rows:
index = self.model.index(row, self.Header.variable)
variable = self.model.data(index, VariableRole)
if fun == "input":
if variable not in self.reference.domain:
continue
values = self.reference.get_column_view(variable)[0]
if variable.is_primitive():
values = values.astype(float)
if all(np.isnan(values)):
continue
else:
values = self.model.data(index, ValuesRole)
if variable.is_continuous:
value = cont_fun(values)
value = round(value, variable.number_of_decimals)
elif variable.is_discrete:
value = disc_fun(values)
elif variable.is_string:
value = ""
else:
raise NotImplementedError
self.model.setData(index, value, ValueRole)
self.model.dataChanged.connect(self.__table_data_changed)
self.commit()
@Inputs.data
def set_data(self, data: Table):
self.data = data
self._set_input_summary()
self._set_model_data()
self.unconditional_commit()
def _set_model_data(self):
self.Information.nans_removed.clear()
self.model.removeRows(0, self.model.rowCount())
if not self.data:
return
self.model.set_data(self.data, self.values)
self.values = {}
self.view.horizontalHeader().setStretchLastSection(False)
self.view.resizeColumnsToContents()
self.view.resizeRowsToContents()
self.view.horizontalHeader().setStretchLastSection(True)
@Inputs.reference
def set_reference(self, data: Table):
self.reference = data
self._set_input_summary()
def _set_input_summary(self):
n_data = len(self.data) if self.data else 0
n_refs = len(self.reference) if self.reference else 0
summary, details, kwargs = self.info.NoInput, "", {}
if self.data or self.reference:
summary = f"{self.info.format_number(n_data)}, " \
f"{self.info.format_number(n_refs)}"
data_list = [("Data", self.data), ("Reference", self.reference)]
details = format_multiple_summaries(data_list)
kwargs = {"format": Qt.RichText}
self.info.set_input_summary(summary, details, **kwargs)
def _set_output_summary(self, data: Optional[Table] = None):
if data:
summary, details = len(data), format_summary_details(data)
else:
summary, details = self.info.NoOutput, ""
self.info.set_output_summary(summary, details)
def commit(self):
output_data = None
if self.data:
output_data = self._create_data_from_values()
if self.append_to_data:
output_data = self._append_to_data(output_data)
self._set_output_summary(output_data)
self.Outputs.data.send(output_data)
def _create_data_from_values(self) -> Table:
data = Table.from_domain(self.data.domain, 1)
data.name = "created"
data.X[:] = np.nan
data.Y[:] = np.nan
for i, m in enumerate(self.data.domain.metas):
data.metas[:, i] = "" if m.is_string else np.nan
values = self._get_values()
for var_name, value in values.items():
data[:, var_name] = value
return data
def _append_to_data(self, data: Table) -> Table:
assert self.data
assert len(data) == 1
var = DiscreteVariable("Source ID", values=(self.data.name, data.name))
data = Table.concatenate([self.data, data], axis=0)
domain = Domain(data.domain.attributes, data.domain.class_vars,
data.domain.metas + (var, ))
data = data.transform(domain)
data.metas[:len(self.data), -1] = 0
data.metas[len(self.data):, -1] = 1
return data
def _get_values(self) -> Dict[str, Union[str, float]]:
values = {}
for row in range(self.model.rowCount()):
index = self.model.index(row, self.Header.variable)
values[self.model.data(index, VariableRole).name] = \
self.model.data(index, ValueRole)
return values
def send_report(self):
if not self.data:
return
self.report_domain("Input", self.data.domain)
self.report_domain("Output", self.data.domain)
items = []
values: Dict = self._get_values()
for var in self.data.domain.variables + self.data.domain.metas:
val = values.get(var.name, np.nan)
if var.is_primitive():
val = var.repr_val(val)
items.append([f"{var.name}:", val])
self.report_table("Values", items)
@staticmethod
def sizeHint():
return QSize(600, 500)
def pack_settings(self):
self.values: Dict[str, Union[str, float]] = self._get_values()
def __init__(self):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self._header_labels = [header['label'] for _, header in self.HEADER_SCHEMA]
self._header_index = namedtuple('_header_index', [info_tag for info_tag, _ in self.HEADER_SCHEMA])
self.Header = self._header_index(*[index for index, _ in enumerate(self._header_labels)])
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
uniformRowHeights=True,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
proxy = QSortFilterProxyModel()
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.assign_delegates()
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def showPopup(self):
# type: () -> None
"""
Reimplemented from QComboBox.showPopup
Popup up a customized view and filter edit line.
Note
----
The .popup(), .lineEdit(), .completer() of the base class are not used.
"""
if self.__popup is not None:
# We have user entered state that cannot be disturbed
# (entered filter text, scroll offset, ...)
return # pragma: no cover
if self.count() == 0:
return
opt = QStyleOptionComboBox()
self.initStyleOption(opt)
popup = QListView(
uniformItemSizes=True,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
verticalScrollBarPolicy=Qt.ScrollBarAsNeeded,
iconSize=self.iconSize(),
)
popup.setFocusProxy(self.__searchline)
popup.setParent(self, Qt.Popup | Qt.FramelessWindowHint)
popup.setItemDelegate(_ComboBoxListDelegate(popup))
proxy = QSortFilterProxyModel(
popup, filterCaseSensitivity=Qt.CaseInsensitive
)
proxy.setFilterKeyColumn(self.modelColumn())
proxy.setSourceModel(self.model())
popup.setModel(proxy)
root = proxy.mapFromSource(self.rootModelIndex())
popup.setRootIndex(root)
self.__popup = popup
self.__proxy = proxy
self.__searchline.setText("")
self.__searchline.setPlaceholderText("Filter...")
self.__searchline.setVisible(True)
self.__searchline.textEdited.connect(proxy.setFilterFixedString)
style = self.style() # type: QStyle
popuprect_origin = style.subControlRect(
QStyle.CC_ComboBox, opt, QStyle.SC_ComboBoxListBoxPopup, self
) # type: QRect
popuprect_origin = QRect(
self.mapToGlobal(popuprect_origin.topLeft()),
popuprect_origin.size()
)
editrect = style.subControlRect(
QStyle.CC_ComboBox, opt, QStyle.SC_ComboBoxEditField, self
) # type: QRect
self.__searchline.setGeometry(editrect)
desktop = QApplication.desktop()
screenrect = desktop.availableGeometry(self) # type: QRect
# get the height for the view
listrect = QRect()
for i in range(min(proxy.rowCount(root), self.maxVisibleItems())):
index = proxy.index(i, self.modelColumn(), root)
if index.isValid():
listrect = listrect.united(popup.visualRect(index))
if listrect.height() >= screenrect.height():
break
window = popup.window() # type: QWidget
window.ensurePolished()
if window.layout() is not None:
window.layout().activate()
else:
QApplication.sendEvent(window, QEvent(QEvent.LayoutRequest))
margins = qwidget_margin_within(popup.viewport(), window)
height = (listrect.height() + 2 * popup.spacing() +
margins.top() + margins.bottom())
popup_size = (QSize(popuprect_origin.width(), height)
.expandedTo(window.minimumSize())
.boundedTo(window.maximumSize())
.boundedTo(screenrect.size()))
popuprect = QRect(popuprect_origin.bottomLeft(), popup_size)
popuprect = dropdown_popup_geometry(
popuprect, popuprect_origin, screenrect)
popup.setGeometry(popuprect)
current = proxy.mapFromSource(
self.model().index(self.currentIndex(), self.modelColumn(),
self.rootModelIndex()))
popup.setCurrentIndex(current)
popup.scrollTo(current, QAbstractItemView.EnsureVisible)
popup.show()
popup.setFocus(Qt.PopupFocusReason)
popup.installEventFilter(self)
popup.viewport().installEventFilter(self)
popup.viewport().setMouseTracking(True)
self.update()
self.__popupTimer.restart()
class OWGeneSets(OWWidget):
name = "Gene Sets"
description = ""
icon = "icons/OWGeneSets.svg"
priority = 9
want_main_area = True
settingsHandler = OrganismContextHandler()
# settings
auto_commit = Setting(True)
stored_selections = ContextSetting([])
organism = ContextSetting(None)
class Inputs:
genes = Input("Genes", Table)
class Outputs:
matched_genes = Output("Matched Genes", Table)
class Information(OWWidget.Information):
pass
class Error(OWWidget.Error):
missing_annotation = Msg(ERROR_ON_MISSING_ANNOTATION)
missing_gene_id = Msg(ERROR_ON_MISSING_GENE_ID)
missing_tax_id = Msg(ERROR_ON_MISSING_TAX_ID)
cant_reach_host = Msg("Host orange.biolab.si is unreachable.")
cant_load_organisms = Msg(
"No available organisms, please check your connection.")
def __init__(self):
super().__init__()
# commit
self.commit_button = None
# progress bar
self.progress_bar = None
self.progress_bar_iterations = None
# data
self.input_data = None
self.input_genes = None
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gene_id_column = None
self.input_info = None
self.num_of_sel_genes = 0
# filter
self.lineEdit_filter = None
self.search_pattern = ''
self.organism_select_combobox = None
# data model view
self.data_view = None
self.data_model = None
# gene matcher NCBI
self.gene_matcher = None
# filter proxy model
self.filter_proxy_model = None
# hierarchy widget
self.hierarchy_widget = None
self.hierarchy_state = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
# gui
self.setup_gui()
def _progress_advance(self):
# GUI should be updated in main thread. That's why we are calling advance method here
if self.progress_bar:
self.progress_bar.advance()
def __get_genes(self):
self.input_genes = []
if self.use_attr_names:
for variable in self.input_data.domain.attributes:
self.input_genes.append(
str(variable.attributes.get(self.gene_id_attribute, '?')))
else:
genes, _ = self.input_data.get_column_view(self.gene_id_column)
self.input_genes = [str(g) for g in genes]
@Inputs.genes
def handle_input(self, data):
self.closeContext()
self.Error.clear()
if data:
self.input_data = data
self.tax_id = str(self.input_data.attributes.get(TAX_ID, None))
self.use_attr_names = self.input_data.attributes.get(
GENE_AS_ATTRIBUTE_NAME, None)
self.gene_id_attribute = self.input_data.attributes.get(
GENE_ID_ATTRIBUTE, None)
self.gene_id_column = self.input_data.attributes.get(
GENE_ID_COLUMN, None)
if not (self.use_attr_names is not None and
((self.gene_id_attribute is None) ^
(self.gene_id_column is None))):
if self.tax_id is None:
self.Error.missing_annotation()
return
self.Error.missing_gene_id()
return
elif self.tax_id is None:
self.Error.missing_tax_id()
return
self.openContext(self.tax_id)
self.__get_genes()
self.download_gene_sets()
def update_info_box(self):
info_string = ''
if self.input_genes:
info_string += '{} unique gene names on input.\n'.format(
len(self.input_genes))
info_string += '{} genes on output.\n'.format(
self.num_of_sel_genes)
else:
info_string += 'No genes on input.\n'
self.input_info.setText(info_string)
def on_gene_sets_download(self, result):
# make sure this happens in the main thread.
# Qt insists that widgets be created within the GUI(main) thread.
assert threading.current_thread() == threading.main_thread()
self.progress_bar.finish()
self.setStatusMessage('')
tax_id, sets = result
self.set_hierarchy_model(self.hierarchy_widget,
*hierarchy_tree(tax_id, sets))
self.set_selected_hierarchies()
self.update_info_box()
self.workers = defaultdict(list)
self.progress_bar_iterations = dict()
for selected_hierarchy in self.get_hierarchies():
gene_sets = geneset.load_gene_sets(selected_hierarchy)
worker = Worker(get_collections,
gene_sets,
set(self.input_genes),
progress_callback=True,
partial_result=True)
worker.signals.error.connect(self.handle_error)
worker.signals.finished.connect(self.handle_worker_finished)
worker.signals.progress.connect(self._progress_advance)
worker.signals.partial_result.connect(self.populate_data_model)
worker.setAutoDelete(False)
self.workers[selected_hierarchy] = worker
self.progress_bar_iterations[selected_hierarchy] = len(gene_sets)
self.display_gene_sets()
def handle_worker_finished(self):
# We check if all workers have completed. If not, continue
# dirty hax, is this ok?
if self.progress_bar and self.progress_bar.widget.progressBarValue == 100:
self.progress_bar.finish()
self.setStatusMessage('')
self.hierarchy_widget.setDisabled(False)
# adjust column width
for i in range(len(DATA_HEADER_LABELS) - 1):
self.data_view.resizeColumnToContents(i)
self.filter_proxy_model.setSourceModel(self.data_model)
def populate_data_model(self, partial_result):
assert threading.current_thread() == threading.main_thread()
if partial_result:
self.data_model.appendRow(partial_result)
def set_hierarchy_model(self, model, tax_id, sets):
def beautify_displayed_text(text):
if '_' in text:
return text.replace('_', ' ').title()
else:
return text
# TODO: maybe optimize this code?
for key, value in sets.items():
item = QTreeWidgetItem(model, [beautify_displayed_text(key)])
item.setFlags(item.flags()
& (Qt.ItemIsUserCheckable | ~Qt.ItemIsSelectable
| Qt.ItemIsEnabled))
item.setExpanded(True)
item.tax_id = tax_id
item.hierarchy = key
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
self.set_hierarchy_model(item, tax_id, value)
else:
if item.parent():
item.hierarchy = ((item.parent().hierarchy, key), tax_id)
if not item.childCount() and not item.parent():
item.hierarchy = ((key, ), tax_id)
def download_gene_sets(self):
self.Error.clear()
# reset hierarchy widget state
self.hierarchy_widget.clear()
# clear data view
self.init_item_model()
# get all gene sets for selected organism
gene_sets = geneset.list_all(organism=self.tax_id)
# init progress bar
self.progress_bar = ProgressBar(self, iterations=len(gene_sets) * 100)
# status message
self.setStatusMessage('downloading sets')
worker = Worker(download_gene_sets, gene_sets, progress_callback=True)
worker.signals.progress.connect(self._progress_advance)
worker.signals.result.connect(self.on_gene_sets_download)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def display_gene_sets(self):
self.init_item_model()
self.hierarchy_widget.setDisabled(True)
only_selected_hier = self.get_hierarchies(only_selected=True)
# init progress bar
iterations = sum([
self.progress_bar_iterations[hier] for hier in only_selected_hier
])
self.progress_bar = ProgressBar(self, iterations=iterations)
self.setStatusMessage('displaying gene sets')
if not only_selected_hier:
self.progress_bar.finish()
self.setStatusMessage('')
self.hierarchy_widget.setDisabled(False)
return
# save setting on selected hierarchies
self.stored_selections = only_selected_hier
# save context
self.closeContext()
for selected_hierarchy in only_selected_hier:
self.threadpool.start(self.workers[selected_hierarchy])
self.openContext(self.tax_id)
def handle_error(self, ex):
self.progress_bar.finish()
self.setStatusMessage('')
if isinstance(ex, ConnectionError):
self.Error.cant_reach_host()
print(ex)
def set_selected_hierarchies(self):
iterator = QTreeWidgetItemIterator(self.hierarchy_widget,
QTreeWidgetItemIterator.All)
while iterator.value():
# note: if hierarchy value is not a tuple, then this is just top level qTreeWidgetItem that
# holds subcategories. We don't want to display all sets from category
if type(iterator.value().hierarchy) is not str:
if iterator.value().hierarchy in self.stored_selections:
iterator.value().setCheckState(0, Qt.Checked)
else:
iterator.value().setCheckState(0, Qt.Unchecked)
iterator += 1
# if no items are checked, we check first one at random
if len(self.get_hierarchies(only_selected=True)) == 0:
iterator = QTreeWidgetItemIterator(
self.hierarchy_widget, QTreeWidgetItemIterator.NotChecked)
while iterator.value():
if type(iterator.value().hierarchy) is not str:
iterator.value().setCheckState(0, Qt.Checked)
return
iterator += 1
def get_hierarchies(self, **kwargs):
""" return selected hierarchy
"""
only_selected = kwargs.get('only_selected', None)
sets_to_display = list()
if only_selected:
iterator = QTreeWidgetItemIterator(self.hierarchy_widget,
QTreeWidgetItemIterator.Checked)
else:
iterator = QTreeWidgetItemIterator(self.hierarchy_widget)
while iterator.value():
# note: if hierarchy value is not a tuple, then this is just top level qTreeWidgetItem that
# holds subcategories. We don't want to display all sets from category
if type(iterator.value().hierarchy) is not str:
if not only_selected:
sets_to_display.append(iterator.value().hierarchy)
else:
if not iterator.value().isDisabled():
sets_to_display.append(iterator.value().hierarchy)
iterator += 1
return sets_to_display
def commit(self):
selection_model = self.data_view.selectionModel()
if selection_model:
# genes_from_set = selection_model.selectedRows(GENES)
matched_genes = selection_model.selectedRows(MATCHED)
if matched_genes and self.input_genes:
genes = [
model_index.data(Qt.UserRole)
for model_index in matched_genes
]
output_genes = [
gene_name for gene_name in list(set.union(*genes))
]
self.num_of_sel_genes = len(output_genes)
self.update_info_box()
if self.use_attr_names:
selected = [
column for column in self.input_data.domain.attributes
if self.gene_id_attribute in column.attributes
and str(column.attributes[
self.gene_id_attribute]) in output_genes
]
domain = Domain(selected,
self.input_data.domain.class_vars,
self.input_data.domain.metas)
new_data = self.input_data.from_table(
domain, self.input_data)
self.Outputs.matched_genes.send(new_data)
else:
selected_rows = []
for row_index, row in enumerate(self.input_data):
gene_in_row = str(row[self.gene_id_column])
if gene_in_row in self.input_genes and gene_in_row in output_genes:
selected_rows.append(row_index)
if selected_rows:
selected = self.input_data[selected_rows]
else:
selected = None
self.Outputs.matched_genes.send(selected)
def setup_gui(self):
# control area
info_box = vBox(self.controlArea, 'Input info')
self.input_info = widgetLabel(info_box)
hierarchy_box = widgetBox(self.controlArea, "Entity Sets")
self.hierarchy_widget = QTreeWidget(self)
self.hierarchy_widget.setEditTriggers(QTreeView.NoEditTriggers)
self.hierarchy_widget.setHeaderLabels(HIERARCHY_HEADER_LABELS)
self.hierarchy_widget.itemClicked.connect(self.display_gene_sets)
hierarchy_box.layout().addWidget(self.hierarchy_widget)
self.commit_button = auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# rubber(self.controlArea)
# main area
self.filter_proxy_model = QSortFilterProxyModel(self.data_view)
self.filter_proxy_model.setFilterKeyColumn(3)
self.data_view = QTreeView()
self.data_view.setModel(self.filter_proxy_model)
self.data_view.setAlternatingRowColors(True)
self.data_view.sortByColumn(2, Qt.DescendingOrder)
self.data_view.setSortingEnabled(True)
self.data_view.setSelectionMode(QTreeView.ExtendedSelection)
self.data_view.setEditTriggers(QTreeView.NoEditTriggers)
self.data_view.viewport().setMouseTracking(True)
self.data_view.setItemDelegateForColumn(
TERM, LinkStyledItemDelegate(self.data_view))
self.data_view.selectionModel().selectionChanged.connect(self.commit)
self.lineEdit_filter = lineEdit(self.mainArea, self, 'search_pattern',
'Filter gene sets:')
self.lineEdit_filter.setPlaceholderText('search pattern ...')
self.lineEdit_filter.textChanged.connect(
self.filter_proxy_model.setFilterRegExp)
self.mainArea.layout().addWidget(self.data_view)
def init_item_model(self):
if self.data_model:
self.data_model.clear()
self.filter_proxy_model.setSourceModel(None)
else:
self.data_model = QStandardItemModel()
self.data_model.setSortRole(Qt.UserRole)
self.data_model.setHorizontalHeaderLabels(DATA_HEADER_LABELS)
def sizeHint(self):
return QSize(1280, 960)
