def create_model(self):
allkeys = set(self.allinfo_local) | set(self.allinfo_remote)
allkeys = sorted(allkeys)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(self._header_labels)
current_index = -1
for i, file_path in enumerate(allkeys):
datainfo = self._parse_info(file_path)
item1 = QStandardItem()
item1.setData(" " if datainfo.islocal else "", Qt.DisplayRole)
item1.setData(datainfo, Qt.UserRole)
item2 = QStandardItem(datainfo.title)
item3 = QStandardItem()
item3.setData(datainfo.size, Qt.DisplayRole)
item4 = QStandardItem()
item4.setData(datainfo.instances, Qt.DisplayRole)
item5 = QStandardItem()
item5.setData(datainfo.variables, Qt.DisplayRole)
item6 = QStandardItem()
item6.setData(datainfo.target, Qt.DisplayRole)
if datainfo.target:
item6.setIcon(variable_icon(datainfo.target))
item7 = QStandardItem()
item7.setData(", ".join(datainfo.tags) if datainfo.tags else "",
Qt.DisplayRole)
row = [item1, item2, item3, item4, item5, item6, item7]
model.appendRow(row)
if os.path.join(*file_path) == self.selected_id:
current_index = i
return model, current_index
def __init__(self, var, lc, widget_parent=None, widget=None):
QWidget.__init__(self)
self.list_view = QListView()
text = []
model = QStandardItemModel(self.list_view)
for (i, val) in enumerate(var.values):
item = QStandardItem(val)
item.setCheckable(True)
if i + 1 in lc:
item.setCheckState(Qt.Checked)
text.append(val)
model.appendRow(item)
model.itemChanged.connect(widget_parent.conditions_changed)
self.list_view.setModel(model)
layout = QGridLayout(self)
layout.addWidget(self.list_view)
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.adjustSize()
self.setWindowFlags(Qt.Popup)
self.widget = widget
self.widget.desc_text = ', '.join(text)
self.widget.set_text()
def test_tooltree(self):
tree = ToolTree()
role = tree.actionRole()
model = QStandardItemModel()
tree.setModel(model)
item = QStandardItem("One")
item.setData(QAction("One", tree), role)
model.appendRow([item])
cat = QStandardItem("A Category")
item = QStandardItem("Two")
item.setData(QAction("Two", tree), role)
cat.appendRow([item])
item = QStandardItem("Three")
item.setData(QAction("Three", tree), role)
cat.appendRow([item])
model.appendRow([cat])
def p(action):
print("triggered", action.text())
tree.triggered.connect(p)
tree.show()
self.qWait()
def create_model(self):
allkeys = set(self.allinfo_local) | set(self.allinfo_remote)
allkeys = sorted(allkeys)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(self._header_labels)
current_index = -1
for i, file_path in enumerate(allkeys):
datainfo = self._parse_info(file_path)
item1 = QStandardItem()
item1.setData(" " if datainfo.islocal else "", Qt.DisplayRole)
item1.setData(self.IndicatorBrushes[0], Qt.ForegroundRole)
item1.setData(datainfo, Qt.UserRole)
item2 = QStandardItem(datainfo.title)
item3 = QStandardItem()
item3.setData(datainfo.size, Qt.DisplayRole)
item4 = QStandardItem()
item4.setData(datainfo.instances, Qt.DisplayRole)
item5 = QStandardItem()
item5.setData(datainfo.variables, Qt.DisplayRole)
item6 = QStandardItem()
item6.setData(datainfo.target, Qt.DisplayRole)
if datainfo.target:
item6.setIcon(variable_icon(datainfo.target))
item7 = QStandardItem()
item7.setData(", ".join(datainfo.tags) if datainfo.tags else "",
Qt.DisplayRole)
row = [item1, item2, item3, item4, item5, item6, item7]
model.appendRow(row)
if os.path.join(*file_path) == self.selected_id:
current_index = i
return model, current_index
def test_tooltree(self):
tree = ToolTree()
role = tree.actionRole()
model = QStandardItemModel()
tree.setModel(model)
item = QStandardItem("One")
item.setData(QAction("One", tree), role)
model.appendRow([item])
cat = QStandardItem("A Category")
item = QStandardItem("Two")
item.setData(QAction("Two", tree), role)
cat.appendRow([item])
item = QStandardItem("Three")
item.setData(QAction("Three", tree), role)
cat.appendRow([item])
model.appendRow([cat])
def p(action):
print("triggered", action.text())
tree.triggered.connect(p)
tree.show()
self.app.exec_()
def __init__(self, var, lc, widget_parent=None, widget=None):
QWidget.__init__(self)
self.list_view = QListView()
text = []
model = QStandardItemModel(self.list_view)
for (i, val) in enumerate(var.values):
item = QStandardItem(val)
item.setCheckable(True)
if i + 1 in lc:
item.setCheckState(Qt.Checked)
text.append(val)
model.appendRow(item)
model.itemChanged.connect(widget_parent.conditions_changed)
self.list_view.setModel(model)
layout = QGridLayout(self)
layout.addWidget(self.list_view)
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.adjustSize()
self.setWindowFlags(Qt.Popup)
self.widget = widget
self.widget.desc_text = ', '.join(text)
self.widget.set_text()
def color_palette_model(palettes, iconsize=QSize(64, 16)):
model = QStandardItemModel()
for name, palette in palettes:
_, colors = max(palette.items())
colors = [QColor(*c) for c in colors]
item = QStandardItem(name)
item.setIcon(QIcon(palette_pixmap(colors, iconsize)))
item.setData(palette, Qt.UserRole)
model.appendRow([item])
return model
def color_palette_model(palettes, iconsize=QSize(64, 16)):
model = QStandardItemModel()
for name, palette in palettes:
_, colors = max(palette.items())
colors = [QColor(*c) for c in colors]
item = QStandardItem(name)
item.setIcon(QIcon(palette_pixmap(colors, iconsize)))
item.setData(palette, Qt.UserRole)
model.appendRow([item])
return model
def on_done(self, result: Results):
model = QStandardItemModel()
for item in result.items:
model.appendRow(item)
model.setSortRole(Qt.UserRole)
model.setHorizontalHeaderLabels(Header.labels())
self.filter_proxy_model.setSourceModel(model)
self.tree_view.selectionModel().selectionChanged.connect(self.commit)
self.filter_view()
self.update_info_box()
def create_list_model(
items: Iterable[Mapping[Qt.ItemDataRole, Any]],
parent: Optional[QObject] = None,
) -> QStandardItemModel:
"""Create list model from an item date iterable."""
model = QStandardItemModel(parent)
for item in items:
sitem = QStandardItem()
for role, value in item.items():
sitem.setData(value, role)
model.appendRow([sitem])
return model
def create_model(self):
allkeys = set(self.allinfo_local)
if self.allinfo_remote is not None:
allkeys = allkeys | set(self.allinfo_remote)
allkeys = sorted(allkeys)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(self._header_labels)
current_index = -1
for i, file_path in enumerate(allkeys):
data_info = self._parse_info(file_path)
row = []
for info_tag, header_setting in self.HEADER_SCHEMA:
item = QStandardItem()
try:
data = data_info.__getattribute__(info_tag)
except AttributeError:
# unknown tag in JSON
data = ''
# first column indicating cached data sets
if info_tag == 'islocal':
item.setData(' ' if data else '', Qt.DisplayRole)
item.setData(data_info, Qt.UserRole)
else:
# parse taxid to common name
if info_tag == 'taxid' and data in common_taxids():
data = shortname(data)[0].title()
if info_tag == 'tags':
data = ', '.join(data) if data else ''
item.setData(data, Qt.DisplayRole)
# set icon to Target column
if info_tag == 'target' and data:
item.setIcon(
Orange.widgets.data.owdatasets.variable_icon(data))
row.append(item)
model.appendRow(row)
if os.path.join(*file_path) == self.selected_id:
current_index = i
return model, current_index
def initialize(self, data):
"""Initialize widget state from the data."""
col_targets, row_targets = grouputils.group_candidates(data)
modelitems = [guiutils.standarditem_from(obj)
for obj in col_targets + row_targets]
model = QStandardItemModel()
for item in modelitems:
model.appendRow(item)
self.label_selection_widget.setModel(model)
self.targets = col_targets + row_targets
# Default selections for all group keys
# (the first value is selected)
self.stored_selections = [[0] for _ in self.targets]
def initialize(self, data):
"""Initialize widget state from the data."""
col_targets, row_targets = grouputils.group_candidates(data)
modelitems = [guiutils.standarditem_from(obj)
for obj in col_targets + row_targets]
model = QStandardItemModel()
for item in modelitems:
model.appendRow(item)
self.label_selection_widget.setModel(model)
self.targets = col_targets + row_targets
# Default selections for all group keys
# (the first value is selected)
self.stored_selections = [[0] for _ in self.targets]
def set_data(self, parent, data):
""" Initialize widget state after receiving new data.
"""
self.__parent = parent
# self.__currentIndex = parent.current_group_index
if data is not None:
column_groups, row_groups = group_candidates(data)
self.targets = column_groups + row_groups
model = QStandardItemModel()
for item in [standarditem_from(desc) for desc in self.targets]:
model.appendRow(item)
self.setModel(model)
else:
self.targets = []
self.setModel(None)
def init_from_data(self):
"""Initialize widget state after receiving new data.
"""
if self.data is not None:
column_groups, row_groups = grouputils.group_candidates(self.data)
self.targets = column_groups + row_groups
self.stored_selections = [[0] for _ in self.targets]
targetitems = [guiutils.standarditem_from(desc)
for desc in self.targets]
model = QStandardItemModel()
for item in targetitems:
model.appendRow(item)
with blocked_signals(self.target_widget):
self.target_widget.setModel(model)
else:
self.targets = []
self.stored_selections = []
with blocked_signals(self.target_widget):
self.target_widget.setModel(None)
def find_patterns(self):
print(self.sampling_type)
db = self.data
ps = PrefixSpan(db)
n_items = len(db)
result = None
opts = {
"closed": self.closed,
# Somehow does not work
#"generator": self.generator
}
from pprint import pprint
pprint(opts)
if self.sampling_type:
result = ps.topk(self.k, **opts)
else:
print("Support value:", self.min_support)
print("Size:", n_items)
print("Support:", n_items * self.min_support / 100)
result = ps.frequent((self.min_support * n_items / 100.0), **opts)
self.table.model().clear()
model = QStandardItemModel(self.table)
model.clear()
for col, label in enumerate(["Support", "Pattern"]):
item = QStandardItem(label)
model.setHorizontalHeaderItem(col, item)
sequences = []
for support, pattern in result:
if len(pattern) < self.min_len:
continue
support /= n_items
sequences.append((support, pattern))
sitem = self.NumericItem(support)
pitem = QStandardItem(str(pattern))
model.appendRow([sitem, pitem])
self.Outputs.object.send(sequences)
self.table.setModel(model)
def init_from_data(self):
"""Initialize widget state after receiving new data.
"""
if self.data is not None:
column_groups, row_groups = grouputils.group_candidates(self.data)
self.targets = column_groups + row_groups
self.stored_selections = [[0] for _ in self.targets]
targetitems = [
guiutils.standarditem_from(desc) for desc in self.targets
]
model = QStandardItemModel()
for item in targetitems:
model.appendRow(item)
with blocked_signals(self.target_widget):
self.target_widget.setModel(model)
else:
self.targets = []
self.stored_selections = []
with blocked_signals(self.target_widget):
self.target_widget.setModel(None)
class SelectionSetsWidget(QFrame):
"""
Widget for managing multiple stored item selections
"""
selectionModified = Signal(bool)
def __init__(self, parent):
QFrame.__init__(self, parent)
self.setContentsMargins(0, 0, 0, 0)
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(1)
self._setNameLineEdit = QLineEdit(self)
layout.addWidget(self._setNameLineEdit)
self._setListView = QListView(self)
self._listModel = QStandardItemModel(self)
self._proxyModel = QSortFilterProxyModel(self)
self._proxyModel.setSourceModel(self._listModel)
self._setListView.setModel(self._proxyModel)
self._setListView.setItemDelegate(ListItemDelegate(self))
self._setNameLineEdit.textChanged.connect(
self._proxyModel.setFilterFixedString)
self._completer = QCompleter(self._listModel, self)
self._setNameLineEdit.setCompleter(self._completer)
self._listModel.itemChanged.connect(self._onSetNameChange)
layout.addWidget(self._setListView)
buttonLayout = QHBoxLayout()
self._addAction = QAction(
"+", self, toolTip="Add a new sort key")
self._updateAction = QAction(
"Update", self, toolTip="Update/save current selection")
self._removeAction = QAction(
"\u2212", self, toolTip="Remove selected sort key.")
self._addToolButton = QToolButton(self)
self._updateToolButton = QToolButton(self)
self._removeToolButton = QToolButton(self)
self._updateToolButton.setSizePolicy(
QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self._addToolButton.setDefaultAction(self._addAction)
self._updateToolButton.setDefaultAction(self._updateAction)
self._removeToolButton.setDefaultAction(self._removeAction)
buttonLayout.addWidget(self._addToolButton)
buttonLayout.addWidget(self._updateToolButton)
buttonLayout.addWidget(self._removeToolButton)
layout.addLayout(buttonLayout)
self.setLayout(layout)
self._addAction.triggered.connect(self.addCurrentSelection)
self._updateAction.triggered.connect(self.updateSelectedSelection)
self._removeAction.triggered.connect(self.removeSelectedSelection)
self._setListView.selectionModel().selectionChanged.connect(
self._onListViewSelectionChanged)
self.selectionModel = None
self._selections = []
def sizeHint(self):
size = QFrame.sizeHint(self)
return QSize(size.width(), 150)
def _onSelectionChanged(self, selected, deselected):
self.setSelectionModified(True)
def _onListViewSelectionChanged(self, selected, deselected):
try:
index = self._setListView.selectedIndexes()[0]
except IndexError:
return
self.commitSelection(self._proxyModel.mapToSource(index).row())
def _onSetNameChange(self, item):
self.selections[item.row()].name = str(item.text())
def _setButtonStates(self, val):
self._updateToolButton.setEnabled(val)
def setSelectionModel(self, selectionModel):
if self.selectionModel:
self.selectionModel.selectionChanged.disconnect(
self._onSelectionChanged)
self.selectionModel = selectionModel
self.selectionModel.selectionChanged.connect(self._onSelectionChanged)
def addCurrentSelection(self):
item = self.addSelection(
SelectionByKey(self.selectionModel.selection(),
name="New selection",
key=(1, 2, 3, 10)))
index = self._proxyModel.mapFromSource(item.index())
self._setListView.setCurrentIndex(index)
self._setListView.edit(index)
self.setSelectionModified(False)
def removeSelectedSelection(self):
i = self._proxyModel.mapToSource(self._setListView.currentIndex()).row()
self._listModel.takeRow(i)
del self.selections[i]
def updateCurentSelection(self):
i = self._proxyModel.mapToSource(self._setListView.selectedIndex()).row()
self.selections[i].setSelection(self.selectionModel.selection())
self.setSelectionModified(False)
def addSelection(self, selection, name=""):
self._selections.append(selection)
item = QStandardItem(selection.name)
item.setFlags(item.flags() ^ Qt.ItemIsDropEnabled)
self._listModel.appendRow(item)
self.setSelectionModified(False)
return item
def updateSelectedSelection(self):
i = self._proxyModel.mapToSource(self._setListView.currentIndex()).row()
self.selections[i].setSelection(self.selectionModel.selection())
self.setSelectionModified(False)
def setSelectionModified(self, val):
self._selectionModified = val
self._setButtonStates(val)
self.selectionModified.emit(bool(val))
def commitSelection(self, index):
selection = self.selections[index]
selection.select(self.selectionModel)
def setSelections(self, selections):
self._listModel.clear()
for selection in selections:
self.addSelection(selection)
def selections(self):
return self._selections
selections = property(selections, setSelections)
def get_gds_model(progress=lambda val: None):
"""
Initialize and return a GDS datasets model.
:param progress: A progress callback.
:rval tuple:
A tuple of (QStandardItemModel, geo.GDSInfo, [geo.GDS])
.. note::
The returned QStandardItemModel's thread affinity is set to
the GUI thread.
"""
progress(1)
info = geo.GDSInfo()
search_keys = ["dataset_id", "title", "platform_organism", "description"]
cache_dir = serverfiles.localpath(geo.DOMAIN)
gds_link = "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc={0}"
pm_link = "http://www.ncbi.nlm.nih.gov/pubmed/{0}"
gds_list = []
def is_cached(gds):
return os.path.exists(
os.path.join(cache_dir, gds["dataset_id"]) + ".soft.gz")
def item(displayvalue, item_values={}):
item = QStandardItem()
item.setData(displayvalue, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
def gds_to_row(gds):
#: Text for easier full search.
search_text = " | ".join(
[gds.get(key, "").lower() for key in search_keys])
row = [
item(" " if is_cached(gds) else "", {TextFilterRole: search_text}),
item(gds["dataset_id"],
{LinkRole: gds_link.format(gds["dataset_id"])}),
item(gds["title"]),
item(gds["platform_organism"]),
item(len(gds["samples"])),
item(gds["feature_count"]),
item(gds["gene_count"]),
item(len(gds["subsets"])),
item(
gds.get("pubmed_id", ""), {
LinkRole:
pm_link.format(gds["pubmed_id"])
if gds.get("pubmed_id") else None
})
]
return row
model = QStandardItemModel()
model.setHorizontalHeaderLabels([
"", "ID", "Title", "Organism", "Samples", "Features", "Genes",
"Subsets", "PubMedID"
])
progress(20)
for gds in info.values():
model.appendRow(gds_to_row(gds))
gds_list.append(gds)
progress(50)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model, info, gds_list
class OWPreprocess(widget.OWWidget):
name = "Preprocess"
description = "Construct a data preprocessing pipeline."
icon = "icons/Preprocess.svg"
priority = 2105
class Inputs:
data = Input("Data", Orange.data.Table)
class Outputs:
preprocessor = Output("Preprocessor", preprocess.preprocess.Preprocess, dynamic=False)
preprocessed_data = Output("Preprocessed Data", Orange.data.Table)
storedsettings = settings.Setting({})
autocommit = settings.Setting(True)
def __init__(self):
super().__init__()
self.data = None
self._invalidated = False
# List of available preprocessors (DescriptionRole : Description)
self.preprocessors = QStandardItemModel()
def mimeData(indexlist):
assert len(indexlist) == 1
index = indexlist[0]
qname = index.data(DescriptionRole).qualname
m = QMimeData()
m.setData("application/x-qwidget-ref", qname.encode("utf-8"))
return m
# TODO: Fix this (subclass even if just to pass a function
# for mimeData delegate)
self.preprocessors.mimeData = mimeData
box = gui.vBox(self.controlArea, "Preprocessors")
self.preprocessorsView = view = QListView(
selectionMode=QListView.SingleSelection,
dragEnabled=True,
dragDropMode=QListView.DragOnly
)
view.setModel(self.preprocessors)
view.activated.connect(self.__activated)
box.layout().addWidget(view)
####
self._qname2ppdef = {ppdef.qualname: ppdef for ppdef in PREPROCESSORS}
# List of 'selected' preprocessors and their parameters.
self.preprocessormodel = None
self.flow_view = SequenceFlow()
self.controler = Controller(self.flow_view, parent=self)
self.overlay = OverlayWidget(self)
self.overlay.setAttribute(Qt.WA_TransparentForMouseEvents)
self.overlay.setWidget(self.flow_view)
self.overlay.setLayout(QVBoxLayout())
self.overlay.layout().addWidget(
QLabel("Drag items from the list on the left", wordWrap=True))
self.scroll_area = QScrollArea(
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn
)
self.scroll_area.viewport().setAcceptDrops(True)
self.scroll_area.setWidget(self.flow_view)
self.scroll_area.setWidgetResizable(True)
self.mainArea.layout().addWidget(self.scroll_area)
self.flow_view.installEventFilter(self)
box = gui.vBox(self.controlArea, "Output")
gui.auto_commit(box, self, "autocommit", "Send", box=False)
self._initialize()
def _initialize(self):
for pp_def in PREPROCESSORS:
description = pp_def.description
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item = QStandardItem(icon, description.title)
item.setToolTip(description.summary or "")
item.setData(pp_def, DescriptionRole)
item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable |
Qt.ItemIsDragEnabled)
self.preprocessors.appendRow([item])
try:
model = self.load(self.storedsettings)
except Exception:
model = self.load({})
self.set_model(model)
if not model.rowCount():
# enforce default width constraint if no preprocessors
# are instantiated (if the model is not empty the constraints
# will be triggered by LayoutRequest event on the `flow_view`)
self.__update_size_constraint()
self.apply()
def load(self, saved):
"""Load a preprocessor list from a dict."""
name = saved.get("name", "")
preprocessors = saved.get("preprocessors", [])
model = StandardItemModel()
def dropMimeData(data, action, row, column, parent):
if data.hasFormat("application/x-qwidget-ref") and \
action == Qt.CopyAction:
qname = bytes(data.data("application/x-qwidget-ref")).decode()
ppdef = self._qname2ppdef[qname]
item = QStandardItem(ppdef.description.title)
item.setData({}, ParametersRole)
item.setData(ppdef.description.title, Qt.DisplayRole)
item.setData(ppdef, DescriptionRole)
self.preprocessormodel.insertRow(row, [item])
return True
else:
return False
model.dropMimeData = dropMimeData
for qualname, params in preprocessors:
pp_def = self._qname2ppdef[qualname]
description = pp_def.description
item = QStandardItem(description.title)
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item.setIcon(icon)
item.setToolTip(description.summary)
item.setData(pp_def, DescriptionRole)
item.setData(params, ParametersRole)
model.appendRow(item)
return model
def save(self, model):
"""Save the preprocessor list to a dict."""
d = {"name": ""}
preprocessors = []
for i in range(model.rowCount()):
item = model.item(i)
pp_def = item.data(DescriptionRole)
params = item.data(ParametersRole)
preprocessors.append((pp_def.qualname, params))
d["preprocessors"] = preprocessors
return d
def set_model(self, ppmodel):
if self.preprocessormodel:
self.preprocessormodel.dataChanged.disconnect(self.__on_modelchanged)
self.preprocessormodel.rowsInserted.disconnect(self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.disconnect(self.__on_modelchanged)
self.preprocessormodel.rowsMoved.disconnect(self.__on_modelchanged)
self.preprocessormodel.deleteLater()
self.preprocessormodel = ppmodel
self.controler.setModel(ppmodel)
if ppmodel is not None:
self.preprocessormodel.dataChanged.connect(self.__on_modelchanged)
self.preprocessormodel.rowsInserted.connect(self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.connect(self.__on_modelchanged)
self.preprocessormodel.rowsMoved.connect(self.__on_modelchanged)
self.__update_overlay()
def __update_overlay(self):
if self.preprocessormodel is None or \
self.preprocessormodel.rowCount() == 0:
self.overlay.setWidget(self.flow_view)
self.overlay.show()
else:
self.overlay.setWidget(None)
self.overlay.hide()
def __on_modelchanged(self):
self.__update_overlay()
self.commit()
@Inputs.data
@check_sql_input
def set_data(self, data=None):
"""Set the input data set."""
self.data = data
def handleNewSignals(self):
self.apply()
def __activated(self, index):
item = self.preprocessors.itemFromIndex(index)
action = item.data(DescriptionRole)
item = QStandardItem()
item.setData({}, ParametersRole)
item.setData(action.description.title, Qt.DisplayRole)
item.setData(action, DescriptionRole)
self.preprocessormodel.appendRow([item])
def buildpreproc(self):
plist = []
for i in range(self.preprocessormodel.rowCount()):
item = self.preprocessormodel.item(i)
desc = item.data(DescriptionRole)
params = item.data(ParametersRole)
if not isinstance(params, dict):
params = {}
create = desc.viewclass.createinstance
plist.append(create(params))
if len(plist) == 1:
return plist[0]
else:
return preprocess.preprocess.PreprocessorList(plist)
def apply(self):
# Sync the model into storedsettings on every apply.
self.storeSpecificSettings()
preprocessor = self.buildpreproc()
if self.data is not None:
self.error()
try:
data = preprocessor(self.data)
except (ValueError, ZeroDivisionError) as e:
self.error(str(e))
return
else:
data = None
self.Outputs.preprocessor.send(preprocessor)
self.Outputs.preprocessed_data.send(data)
def commit(self):
if not self._invalidated:
self._invalidated = True
QApplication.postEvent(self, QEvent(QEvent.User))
def customEvent(self, event):
if event.type() == QEvent.User and self._invalidated:
self._invalidated = False
self.apply()
def eventFilter(self, receiver, event):
if receiver is self.flow_view and event.type() == QEvent.LayoutRequest:
QTimer.singleShot(0, self.__update_size_constraint)
return super().eventFilter(receiver, event)
def storeSpecificSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().storeSpecificSettings()
def saveSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().saveSettings()
def onDeleteWidget(self):
self.data = None
self.set_model(None)
super().onDeleteWidget()
@Slot()
def __update_size_constraint(self):
# Update minimum width constraint on the scroll area containing
# the 'instantiated' preprocessor list (to avoid the horizontal
# scroll bar).
sh = self.flow_view.minimumSizeHint()
scroll_width = self.scroll_area.verticalScrollBar().width()
self.scroll_area.setMinimumWidth(
min(max(sh.width() + scroll_width + 2, self.controlArea.width()),
520))
def sizeHint(self):
sh = super().sizeHint()
return sh.expandedTo(QSize(sh.width() + 300, 500))
def send_report(self):
pp = [(self.controler.model().index(i, 0).data(Qt.DisplayRole), w)
for i, w in enumerate(self.controler.view.widgets())]
if len(pp):
self.report_items("Settings", pp)
class SelectionSetsWidget(QFrame):
"""
Widget for managing multiple stored item selections
"""
selectionModified = Signal(bool)
def __init__(self, parent):
QFrame.__init__(self, parent)
self.setContentsMargins(0, 0, 0, 0)
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(1)
self._setNameLineEdit = QLineEdit(self)
layout.addWidget(self._setNameLineEdit)
self._setListView = QListView(self)
self._listModel = QStandardItemModel(self)
self._proxyModel = QSortFilterProxyModel(self)
self._proxyModel.setSourceModel(self._listModel)
self._setListView.setModel(self._proxyModel)
self._setListView.setItemDelegate(ListItemDelegate(self))
self._setNameLineEdit.textChanged.connect(
self._proxyModel.setFilterFixedString)
self._completer = QCompleter(self._listModel, self)
self._setNameLineEdit.setCompleter(self._completer)
self._listModel.itemChanged.connect(self._onSetNameChange)
layout.addWidget(self._setListView)
buttonLayout = QHBoxLayout()
self._addAction = QAction("+", self, toolTip="Add a new sort key")
self._updateAction = QAction("Update",
self,
toolTip="Update/save current selection")
self._removeAction = QAction("\u2212",
self,
toolTip="Remove selected sort key.")
self._addToolButton = QToolButton(self)
self._updateToolButton = QToolButton(self)
self._removeToolButton = QToolButton(self)
self._updateToolButton.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Minimum)
self._addToolButton.setDefaultAction(self._addAction)
self._updateToolButton.setDefaultAction(self._updateAction)
self._removeToolButton.setDefaultAction(self._removeAction)
buttonLayout.addWidget(self._addToolButton)
buttonLayout.addWidget(self._updateToolButton)
buttonLayout.addWidget(self._removeToolButton)
layout.addLayout(buttonLayout)
self.setLayout(layout)
self._addAction.triggered.connect(self.addCurrentSelection)
self._updateAction.triggered.connect(self.updateSelectedSelection)
self._removeAction.triggered.connect(self.removeSelectedSelection)
self._setListView.selectionModel().selectionChanged.connect(
self._onListViewSelectionChanged)
self.selectionModel = None
self._selections = []
def sizeHint(self):
size = QFrame.sizeHint(self)
return QSize(size.width(), 150)
def _onSelectionChanged(self, selected, deselected):
self.setSelectionModified(True)
def _onListViewSelectionChanged(self, selected, deselected):
try:
index = self._setListView.selectedIndexes()[0]
except IndexError:
return
self.commitSelection(self._proxyModel.mapToSource(index).row())
def _onSetNameChange(self, item):
self.selections[item.row()].name = str(item.text())
def _setButtonStates(self, val):
self._updateToolButton.setEnabled(val)
def setSelectionModel(self, selectionModel):
if self.selectionModel:
self.selectionModel.selectionChanged.disconnect(
self._onSelectionChanged)
self.selectionModel = selectionModel
self.selectionModel.selectionChanged.connect(self._onSelectionChanged)
def addCurrentSelection(self):
item = self.addSelection(
SelectionByKey(self.selectionModel.selection(),
name="New selection",
key=(1, 2, 3, 10)))
index = self._proxyModel.mapFromSource(item.index())
self._setListView.setCurrentIndex(index)
self._setListView.edit(index)
self.setSelectionModified(False)
def removeSelectedSelection(self):
i = self._proxyModel.mapToSource(
self._setListView.currentIndex()).row()
self._listModel.takeRow(i)
del self.selections[i]
def updateCurentSelection(self):
i = self._proxyModel.mapToSource(
self._setListView.selectedIndex()).row()
self.selections[i].setSelection(self.selectionModel.selection())
self.setSelectionModified(False)
def addSelection(self, selection, name=""):
self._selections.append(selection)
item = QStandardItem(selection.name)
item.setFlags(item.flags() ^ Qt.ItemIsDropEnabled)
self._listModel.appendRow(item)
self.setSelectionModified(False)
return item
def updateSelectedSelection(self):
i = self._proxyModel.mapToSource(
self._setListView.currentIndex()).row()
self.selections[i].setSelection(self.selectionModel.selection())
self.setSelectionModified(False)
def setSelectionModified(self, val):
self._selectionModified = val
self._setButtonStates(val)
self.selectionModified.emit(bool(val))
def commitSelection(self, index):
selection = self.selections[index]
selection.select(self.selectionModel)
def setSelections(self, selections):
self._listModel.clear()
for selection in selections:
self.addSelection(selection)
def selections(self):
return self._selections
selections = property(selections, setSelections)
class OWCorpusViewer(OWWidget):
name = "Corpus Viewer"
description = "Display corpus contents."
icon = "icons/CorpusViewer.svg"
priority = 70
inputs = [(IO.DATA, Table, 'set_data')]
outputs = [(IO.MATCHED, Corpus, widget.Default), (IO.UNMATCHED, Corpus)]
search_indices = ContextSetting([0]) # features included in search
display_indices = ContextSetting([0]) # features for display
show_tokens = Setting(False)
autocommit = Setting(True)
class Warning(OWWidget.Warning):
no_feats_search = Msg('No features included in search.')
no_feats_display = Msg('No features selected for display.')
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.output_mask = [] # Output corpus indices
self.doc_webview = None # WebView for showing content
self.search_features = [] # two copies are needed since Display allows drag & drop
self.display_features = []
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Documents: %(n_documents)s')
gui.label(info_box, self, 'Preprocessed: %(is_preprocessed)s')
gui.label(info_box, self, ' ◦ Tokens: %(n_tokens)s')
gui.label(info_box, self, ' ◦ Types: %(n_types)s')
gui.label(info_box, self, 'POS tagged: %(is_pos_tagged)s')
gui.label(info_box, self, 'N-grams range: %(ngram_range)s')
gui.label(info_box, self, 'Matching: %(n_matching)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea, self, 'search_indices', 'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features', callback=self.regenerate_docs,)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box, self, 'display_indices', 'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs, enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box, self, 'show_tokens',
'Show Tokens && Tags', callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data', 'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea, self, '',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:')
self.filter_input.textChanged.connect(self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(self.show_docs)
# Document contents
# For PyQt5 WebEngine's setHtml grabs the focus and makes typing hard
# More info: http://stackoverflow.com/questions/36609489
# To bypass the annoying behaviour disable the widget for WebEngine
self.doc_webview = gui.WebviewWidget(self.splitter, self,
debug=True, enabled=HAVE_WEBKIT)
self.mainArea.layout().addWidget(self.splitter)
def copy_to_clipboard(self):
text = self.doc_webview.selectedText()
QApplication.clipboard().setText(text)
def set_data(self, data=None):
self.reset_widget()
self.corpus = data
if data is not None:
if not isinstance(data, Corpus):
self.corpus = Corpus.from_table(data.domain, data)
self.load_features()
self.regenerate_docs()
self.commit()
def reset_widget(self):
# Corpus
self.corpus = None
self.corpus_docs = None
self.output_mask = []
# Widgets
self.search_listbox.clear()
self.display_listbox.clear()
self.filter_input.clear()
self.update_info()
# Models/vars
self.search_features.clear()
self.display_features.clear()
self.search_indices.clear()
self.display_indices.clear()
self.doc_list_model.clear()
# Warnings
self.Warning.clear()
# WebView
self.doc_webview.setHtml('')
def load_features(self):
self.search_indices = []
self.display_indices = []
if self.corpus is not None:
domain = self.corpus.domain
self.search_features = list(filter_visible(chain(domain.variables, domain.metas)))
self.display_features = list(filter_visible(chain(domain.variables, domain.metas)))
# FIXME: Select features based on ContextSetting
self.search_indices = list(range(len(self.search_features)))
self.display_indices = list(range(len(self.display_features)))
# Enable/disable tokens checkbox
if not self.corpus.has_tokens():
self.show_tokens_checkbox.setCheckState(False)
self.show_tokens_checkbox.setEnabled(self.corpus.has_tokens())
def list_docs(self):
""" List documents into the left scrolling area """
search_keyword = self.filter_input.text().strip('|')
try:
reg = re.compile(search_keyword, re.IGNORECASE)
except sre_constants.error:
return
def is_match(x):
return not bool(search_keyword) or reg.search(x)
self.output_mask.clear()
self.doc_list_model.clear()
for i, (doc, title, content) in enumerate(zip(self.corpus, self.corpus.titles,
self.corpus_docs)):
if is_match(content):
item = QStandardItem()
item.setData(title, Qt.DisplayRole)
item.setData(doc, Qt.UserRole)
self.doc_list_model.appendRow(item)
self.output_mask.append(i)
if self.doc_list_model.rowCount() > 0:
self.doc_list.selectRow(0) # Select the first document
else:
self.doc_webview.setHtml('')
self.commit()
def show_docs(self):
""" Show the selected documents in the right area """
HTML = '''
<!doctype html>
<html>
<head>
<meta charset='utf-8'>
<style>
table {{ border-collapse: collapse; }}
mark {{ background: #FFCD28; }}
tr > td {{
padding-bottom: 3px;
padding-top: 3px;
}}
body {{
font-family: Helvetica;
font-size: 10pt;
}}
.line {{ border-bottom: 1px solid #000; }}
.separator {{ height: 5px; }}
.variables {{
vertical-align: top;
padding-right: 10px;
}}
.token {{
padding: 3px;
border: 1px #B0B0B0 solid;
margin-right: 5px;
margin-bottom: 5px;
display: inline-block;
}}
</style>
</head>
<body>
{}
</body>
</html>
'''
if self.corpus is None:
return
self.Warning.no_feats_display.clear()
if len(self.display_indices) == 0:
self.Warning.no_feats_display()
if self.show_tokens:
tokens = list(self.corpus.ngrams_iterator(include_postags=True))
marked_search_features = [f for i, f in enumerate(self.search_features)
if i in self.search_indices]
html = '<table>'
for doc_count, index in enumerate(self.doc_list.selectionModel().selectedRows()):
if doc_count > 0: # add split
html += '<tr class="line separator"><td/><td/></tr>' \
'<tr class="separator"><td/><td/></tr>'
row_ind = index.data(Qt.UserRole).row_index
for ind in self.display_indices:
feature = self.display_features[ind]
mark = 'class="mark-area"' if feature in marked_search_features else ''
value = index.data(Qt.UserRole)[feature.name]
html += '<tr><td class="variables"><strong>{}:</strong></td>' \
'<td {}>{}</td></tr>'.format(
feature.name, mark, value)
if self.show_tokens:
html += '<tr><td class="variables"><strong>Tokens & Tags:</strong></td>' \
'<td>{}</td></tr>'.format(''.join('<span class="token">{}</span>'.format(
token) for token in tokens[row_ind]))
html += '</table>'
self.doc_webview.setHtml(HTML.format(html))
self.load_js()
self.highlight_docs()
def load_js(self):
resources = os.path.join(os.path.dirname(__file__), 'resources')
for script in ('jquery-3.1.1.min.js', 'jquery.mark.min.js', 'highlighter.js', ):
self.doc_webview.evalJS(open(os.path.join(resources, script), encoding='utf-8').read())
def regenerate_docs(self):
self.corpus_docs = None
self.Warning.no_feats_search.clear()
if self.corpus is not None:
feats = [self.search_features[i] for i in self.search_indices]
if len(feats) == 0:
self.Warning.no_feats_search()
self.corpus_docs = self.corpus.documents_from_features(feats)
self.refresh_search()
def refresh_search(self):
if self.corpus:
self.list_docs()
self.update_info()
def highlight_docs(self):
search_keyword = self.filter_input.text().\
strip('|').replace('\\', '\\\\') # escape one \ to two for mark.js
if search_keyword:
self.doc_webview.evalJS('mark("{}");'.format(search_keyword))
def update_info(self):
if self.corpus is not None:
self.n_documents = len(self.corpus)
self.n_matching = '{}/{}'.format(self.doc_list_model.rowCount(), self.n_documents)
self.n_tokens = sum(map(len, self.corpus.tokens)) if self.corpus.has_tokens() else 'n/a'
self.n_types = len(self.corpus.dictionary) if self.corpus.has_tokens() else 'n/a'
self.is_preprocessed = self.corpus.has_tokens()
self.is_pos_tagged = self.corpus.pos_tags is not None
self.ngram_range = '{}-{}'.format(*self.corpus.ngram_range)
else:
self.n_documents = ''
self.n_matching = ''
self.n_tokens = ''
self.n_types = ''
self.is_preprocessed = ''
self.is_pos_tagged = ''
self.ngram_range = ''
def commit(self):
if self.corpus is not None:
matched = self.corpus[self.output_mask]
output_mask = set(self.output_mask)
unmatched_mask = [i for i in range(len(self.corpus)) if i not in output_mask]
unmatched = self.corpus[unmatched_mask]
self.send(IO.MATCHED, matched)
self.send(IO.UNMATCHED, unmatched)
else:
self.send(IO.MATCHED, None)
self.send(IO.UNMATCHED, None)
class OWCorpusViewer(OWWidget):
name = "Corpus Viewer"
description = "Display corpus contents."
icon = "icons/CorpusViewer.svg"
priority = 500
class Inputs:
corpus = Input("Corpus", Corpus, replaces=["Data"])
class Outputs:
matching_docs = Output("Matching Docs", Corpus, default=True)
other_docs = Output("Other Docs", Corpus)
corpus = Output("Corpus", Corpus)
settingsHandler = PerfectDomainContextHandler(
match_values = PerfectDomainContextHandler.MATCH_VALUES_ALL
)
search_indices = ContextSetting([], exclude_metas=False) # features included in search
display_indices = ContextSetting([], exclude_metas=False) # features for display
display_features = ContextSetting([], exclude_metas=False)
selected_documents = ContextSetting([])
regexp_filter = ContextSetting("")
show_tokens = Setting(False)
autocommit = Setting(True)
class Warning(OWWidget.Warning):
no_feats_search = Msg('No features included in search.')
no_feats_display = Msg('No features selected for display.')
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.doc_webview = None # WebView for showing content
self.search_features = [] # two copies are needed since Display allows drag & drop
self.display_list_indices = [0]
self.matches = 0 # Matches of the query
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Tokens: %(n_tokens)s')
gui.label(info_box, self, 'Types: %(n_types)s')
gui.label(info_box, self, 'Matching documents: %(n_matching)s')
gui.label(info_box, self, 'Matches: %(n_matches)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea, self, 'search_indices', 'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features', callback=self.search_features_changed)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box, self, 'display_list_indices', 'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs, enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box, self, 'show_tokens',
'Show Tokens && Tags', callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data', 'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea, self, 'regexp_filter',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:',
callback=self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(
self.selection_changed
)
# Document contents
self.doc_webview = gui.WebviewWidget(self.splitter, debug=False)
self.mainArea.layout().addWidget(self.splitter)
def copy_to_clipboard(self):
text = self.doc_webview.selectedText()
QApplication.clipboard().setText(text)
@Inputs.corpus
def set_data(self, corpus=None):
self.closeContext()
self.reset_widget()
self.corpus = corpus
self.search_features = []
if corpus is not None:
domain = self.corpus.domain
# Enable/disable tokens checkbox
if not self.corpus.has_tokens():
self.show_tokens_checkbox.setCheckState(False)
self.show_tokens_checkbox.setEnabled(self.corpus.has_tokens())
self.search_features = list(filter_visible(chain(domain.variables, domain.metas)))
self.display_features = list(filter_visible(chain(domain.variables, domain.metas)))
self.search_indices = list(range(len(self.search_features)))
self.display_indices = list(range(len(self.display_features)))
self.selected_documents = [corpus.titles[0]] if \
corpus.titles is not None and len(corpus.titles) else []
self.openContext(self.corpus)
self.display_list_indices = self.display_indices
self.regenerate_docs()
self.list_docs()
self.update_info()
self.set_selection()
self.show_docs()
self.commit()
def reset_widget(self):
# Corpus
self.corpus = None
self.corpus_docs = None
self.display_features = []
# Widgets
self.search_listbox.clear()
self.display_listbox.clear()
self.filter_input.clear()
self.update_info()
# Models/vars
self.search_features.clear()
self.search_indices.clear()
self.display_indices.clear()
self.doc_list_model.clear()
# Warnings
self.Warning.clear()
# WebView
self.doc_webview.setHtml('')
def list_docs(self):
""" List documents into the left scrolling area """
if self.corpus_docs is None:
return
# TODO: remove search_keyword??
search_keyword = self.regexp_filter.strip('|')
matches = 0
try:
reg = re.compile(search_keyword, re.IGNORECASE)
except sre_constants.error:
return
self.doc_list_model.clear()
for i, (doc, title, content) in enumerate(zip(self.corpus, self.corpus.titles,
self.corpus_docs)):
res = len(list(reg.finditer(content))) if self.regexp_filter else 0
if not self.regexp_filter or res:
matches += res
item = QStandardItem()
item.setData(str(title), Qt.DisplayRole)
item.setData(doc, Qt.UserRole)
self.doc_list_model.appendRow(item)
self.matches = matches
def get_selected_documents_from_view(self) -> Set[str]:
"""
Returns
-------
Set with names of selected documents in the QTableView
"""
return {
i.data(Qt.DisplayRole)
for i in self.doc_list.selectionModel().selectedRows()
}
def set_selection(self) -> None:
"""
Select documents in selected_documents attribute in the view
"""
view = self.doc_list
model = view.model()
previously_selected = self.selected_documents.copy()
selection = QItemSelection()
for row in range(model.rowCount()):
document = model.data(model.index(row, 0), Qt.DisplayRole)
if document in self.selected_documents:
selection.append(QItemSelectionRange(
view.model().index(row, 0),
view.model().index(row, 0)
))
view.selectionModel().select(
selection, QItemSelectionModel.ClearAndSelect
)
if len(selection) == 0:
# in cases when selection is empty qt's selection_changed is not
# called and so we need to manually trigger show_docs
self.show_docs()
# select emmit selection change signal which causes calling
# selection_changed when filtering it means that documents which
# are currently filtered out get removed from self.selected_douments
# we still want to keep them to be still selected after user removes
# filter
self.selected_documents = previously_selected
def selection_changed(self) -> None:
"""
Function is called every time the selection changes - when user select
new range of documents
"""
self.selected_documents = self.get_selected_documents_from_view()
self.show_docs()
self.commit()
def show_docs(self):
""" Show the selected documents in the right area """
HTML = '''
<!doctype html>
<html>
<head>
<script type="text/javascript" src="resources/jquery-3.1.1.min.js">
</script>
<script type="text/javascript" src="resources/jquery.mark.min.js">
</script>
<script type="text/javascript" src="resources/highlighter.js">
</script>
<meta charset='utf-8'>
<style>
table {{ border-collapse: collapse; }}
mark {{ background: #FFCD28; }}
tr > td {{
padding-bottom: 3px;
padding-top: 3px;
}}
body {{
font-family: Helvetica;
font-size: 10pt;
}}
.line {{ border-bottom: 1px solid #000; }}
.separator {{ height: 5px; }}
.variables {{
vertical-align: top;
padding-right: 10px;
}}
.content {{
/* Adopted from https://css-tricks.com/snippets/css/prevent-long-urls-from-breaking-out-of-container/ */
/* These are technically the same, but use both */
overflow-wrap: break-word;
word-wrap: break-word;
-ms-word-break: break-all;
/* This is the dangerous one in WebKit, as it breaks things wherever */
word-break: break-all;
/* Instead use this non-standard one: */
word-break: break-word;
/* Adds a hyphen where the word breaks, if supported (No Blink) */
-ms-hyphens: auto;
-moz-hyphens: auto;
-webkit-hyphens: auto;
hyphens: auto;
}}
.token {{
padding: 3px;
border: 1px #B0B0B0 solid;
margin-right: 5px;
margin-bottom: 5px;
display: inline-block;
}}
img {{
max-width: 100%;
}}
</style>
</head>
<body>
{}
</body>
</html>
'''
self.display_indices = self.display_list_indices
if self.corpus is None:
return
self.Warning.no_feats_display.clear()
if len(self.display_indices) == 0:
self.Warning.no_feats_display()
if self.show_tokens:
tokens = list(self.corpus.ngrams_iterator(include_postags=True))
marked_search_features = [f for i, f in enumerate(self.search_features)
if i in self.search_indices]
html = '<table>'
for doc_count, index in enumerate(self.doc_list.selectionModel().selectedRows()):
if doc_count > 0: # add split
html += '<tr class="line separator"><td/><td/></tr>' \
'<tr class="separator"><td/><td/></tr>'
row_ind = index.data(Qt.UserRole).row_index
for ind in self.display_indices:
feature = self.display_features[ind]
value = str(index.data(Qt.UserRole)[feature.name])
if feature in marked_search_features:
value = self.__mark_text(value)
value = value.replace('\n', '<br/>')
is_image = feature.attributes.get('type', '') == 'image'
if is_image and value != '?':
value = '<img src="{}"></img>'.format(value)
html += '<tr><td class="variables"><strong>{}:</strong></td>' \
'<td class="content">{}</td></tr>'.format(
feature.name, value)
if self.show_tokens:
html += '<tr><td class="variables"><strong>Tokens & Tags:</strong></td>' \
'<td>{}</td></tr>'.format(''.join('<span class="token">{}</span>'.format(
token) for token in tokens[row_ind]))
html += '</table>'
base = QUrl.fromLocalFile(__file__)
self.doc_webview.setHtml(HTML.format(html), base)
def __mark_text(self, text):
search_keyword = self.regexp_filter.strip('|')
if not search_keyword:
return text
try:
reg = re.compile(search_keyword, re.IGNORECASE | re.MULTILINE)
except sre_constants.error:
return text
matches = list(reg.finditer(text))
if not matches:
return text
text = list(text)
for m in matches[::-1]:
text[m.start():m.end()] = list('<mark data-markjs="true">{}</mark>'\
.format("".join(text[m.start():m.end()])))
return "".join(text)
def search_features_changed(self):
self.regenerate_docs()
self.refresh_search()
def regenerate_docs(self):
self.corpus_docs = None
self.Warning.no_feats_search.clear()
if self.corpus is not None:
feats = [self.search_features[i] for i in self.search_indices]
if len(feats) == 0:
self.Warning.no_feats_search()
self.corpus_docs = self.corpus.documents_from_features(feats)
def refresh_search(self):
if self.corpus is not None:
self.list_docs()
self.set_selection()
self.update_info()
self.commit()
def update_info(self):
if self.corpus is not None:
self.n_matching = '{}/{}'.format(self.doc_list_model.rowCount(), len(self.corpus))
self.n_matches = self.matches if self.matches else 'n/a'
self.n_tokens = sum(map(len, self.corpus.tokens)) if self.corpus.has_tokens() else 'n/a'
self.n_types = len(self.corpus.dictionary) if self.corpus.has_tokens() else 'n/a'
else:
self.n_matching = ''
self.n_matches = ''
self.n_tokens = ''
self.n_types = ''
def commit(self):
matched = unmatched = annotated_corpus = None
corpus = self.corpus
if corpus is not None:
# it returns a set of selected documents which are in view
selected_docs = self.get_selected_documents_from_view()
titles = corpus.titles
matched_mask = [
i for i, t in enumerate(titles) if t in selected_docs
]
unmatched_mask = [
i for i, t in enumerate(titles) if t not in selected_docs
]
matched = corpus[matched_mask] if len(matched_mask) else None
unmatched = corpus[unmatched_mask] if len(unmatched_mask) else None
annotated_corpus = create_annotated_table(corpus, matched_mask)
self.Outputs.matching_docs.send(matched)
self.Outputs.other_docs.send(unmatched)
self.Outputs.corpus.send(annotated_corpus)
def send_report(self):
self.report_items((
("Query", self.regexp_filter),
("Matching documents", self.n_matching),
("Matches", self.n_matches)
))
def showEvent(self, event):
super().showEvent(event)
self.update_splitter()
def update_splitter(self):
"""
Update splitter that document list on the left never take more
than 1/3 of the space. It is only set on showEvent. If user
later changes sizes it stays as it is.
"""
w1, w2 = self.splitter.sizes()
ws = w1 + w2
if w2 < 2/3 * ws:
self.splitter.setSizes([ws * 1/3, ws * 2/3])
class OWCorpusViewer(OWWidget):
name = "Corpus Viewer"
description = "Display corpus contents."
icon = "icons/CorpusViewer.svg"
priority = 70
inputs = [(IO.DATA, Table, 'set_data')]
outputs = [(IO.MATCHED, Corpus, widget.Default), (IO.UNMATCHED, Corpus)]
search_indices = ContextSetting([0]) # features included in search
display_indices = ContextSetting([0]) # features for display
show_tokens = Setting(False)
autocommit = Setting(True)
class Warning(OWWidget.Warning):
no_feats_search = Msg('No features included in search.')
no_feats_display = Msg('No features selected for display.')
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.output_mask = [] # Output corpus indices
self.doc_webview = None # WebView for showing content
self.search_features = [
] # two copies are needed since Display allows drag & drop
self.display_features = []
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Documents: %(n_documents)s')
gui.label(info_box, self, 'Preprocessed: %(is_preprocessed)s')
gui.label(info_box, self, ' ◦ Tokens: %(n_tokens)s')
gui.label(info_box, self, ' ◦ Types: %(n_types)s')
gui.label(info_box, self, 'POS tagged: %(is_pos_tagged)s')
gui.label(info_box, self, 'N-grams range: %(ngram_range)s')
gui.label(info_box, self, 'Matching: %(n_matching)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea,
self,
'search_indices',
'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features',
callback=self.regenerate_docs,
)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box,
self,
'display_indices',
'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs,
enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box,
self,
'show_tokens',
'Show Tokens && Tags',
callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data',
'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea,
self,
'',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(
QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:')
self.filter_input.textChanged.connect(self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(self.show_docs)
# Document contents
self.doc_webview = gui.WebviewWidget(self.splitter, debug=False)
self.mainArea.layout().addWidget(self.splitter)
def copy_to_clipboard(self):
text = self.doc_webview.selectedText()
QApplication.clipboard().setText(text)
def set_data(self, data=None):
self.reset_widget()
self.corpus = data
if data is not None:
if not isinstance(data, Corpus):
self.corpus = Corpus.from_table(data.domain, data)
self.load_features()
self.regenerate_docs()
self.commit()
def reset_widget(self):
# Corpus
self.corpus = None
self.corpus_docs = None
self.output_mask = []
# Widgets
self.search_listbox.clear()
self.display_listbox.clear()
self.filter_input.clear()
self.update_info()
# Models/vars
self.search_features.clear()
self.display_features.clear()
self.search_indices.clear()
self.display_indices.clear()
self.doc_list_model.clear()
# Warnings
self.Warning.clear()
# WebView
self.doc_webview.setHtml('')
def load_features(self):
self.search_indices = []
self.display_indices = []
if self.corpus is not None:
domain = self.corpus.domain
self.search_features = list(
filter_visible(chain(domain.variables, domain.metas)))
self.display_features = list(
filter_visible(chain(domain.variables, domain.metas)))
# FIXME: Select features based on ContextSetting
self.search_indices = list(range(len(self.search_features)))
self.display_indices = list(range(len(self.display_features)))
# Enable/disable tokens checkbox
if not self.corpus.has_tokens():
self.show_tokens_checkbox.setCheckState(False)
self.show_tokens_checkbox.setEnabled(self.corpus.has_tokens())
def list_docs(self):
""" List documents into the left scrolling area """
search_keyword = self.filter_input.text().strip('|')
try:
reg = re.compile(search_keyword, re.IGNORECASE)
except sre_constants.error:
return
def is_match(x):
return not bool(search_keyword) or reg.search(x)
self.output_mask.clear()
self.doc_list_model.clear()
for i, (doc, title, content) in enumerate(
zip(self.corpus, self.corpus.titles, self.corpus_docs)):
if is_match(content):
item = QStandardItem()
item.setData(title, Qt.DisplayRole)
item.setData(doc, Qt.UserRole)
self.doc_list_model.appendRow(item)
self.output_mask.append(i)
if self.doc_list_model.rowCount() > 0:
self.doc_list.selectRow(0) # Select the first document
else:
self.doc_webview.setHtml('')
self.commit()
def show_docs(self):
""" Show the selected documents in the right area """
HTML = '''
<!doctype html>
<html>
<head>
<meta charset='utf-8'>
<style>
table {{ border-collapse: collapse; }}
mark {{ background: #FFCD28; }}
tr > td {{
padding-bottom: 3px;
padding-top: 3px;
}}
body {{
font-family: Helvetica;
font-size: 10pt;
}}
.line {{ border-bottom: 1px solid #000; }}
.separator {{ height: 5px; }}
.variables {{
vertical-align: top;
padding-right: 10px;
}}
.token {{
padding: 3px;
border: 1px #B0B0B0 solid;
margin-right: 5px;
margin-bottom: 5px;
display: inline-block;
}}
img {{
max-width: 100%;
}}
</style>
</head>
<body>
{}
</body>
</html>
'''
if self.corpus is None:
return
self.Warning.no_feats_display.clear()
if len(self.display_indices) == 0:
self.Warning.no_feats_display()
if self.show_tokens:
tokens = list(self.corpus.ngrams_iterator(include_postags=True))
marked_search_features = [
f for i, f in enumerate(self.search_features)
if i in self.search_indices
]
html = '<table>'
for doc_count, index in enumerate(
self.doc_list.selectionModel().selectedRows()):
if doc_count > 0: # add split
html += '<tr class="line separator"><td/><td/></tr>' \
'<tr class="separator"><td/><td/></tr>'
row_ind = index.data(Qt.UserRole).row_index
for ind in self.display_indices:
feature = self.display_features[ind]
mark = 'class="mark-area"' if feature in marked_search_features else ''
value = str(index.data(Qt.UserRole)[feature.name])
is_image = feature.attributes.get('type', '') == 'image'
if is_image and value != '?':
value = '<img src="{}"></img>'.format(value)
html += '<tr><td class="variables"><strong>{}:</strong></td>' \
'<td {}>{}</td></tr>'.format(
feature.name, mark, value)
if self.show_tokens:
html += '<tr><td class="variables"><strong>Tokens & Tags:</strong></td>' \
'<td>{}</td></tr>'.format(''.join('<span class="token">{}</span>'.format(
token) for token in tokens[row_ind]))
html += '</table>'
# QUrl is a workaround to allow local resources
# https://bugreports.qt.io/browse/QTBUG-55902?focusedCommentId=335945
self.doc_webview.setHtml(HTML.format(html), QUrl("file://"))
self.load_js()
self.highlight_docs()
def load_js(self):
resources = os.path.join(os.path.dirname(__file__), 'resources')
for script in (
'jquery-3.1.1.min.js',
'jquery.mark.min.js',
'highlighter.js',
):
self.doc_webview.evalJS(
open(os.path.join(resources, script), encoding='utf-8').read())
def regenerate_docs(self):
self.corpus_docs = None
self.Warning.no_feats_search.clear()
if self.corpus is not None:
feats = [self.search_features[i] for i in self.search_indices]
if len(feats) == 0:
self.Warning.no_feats_search()
self.corpus_docs = self.corpus.documents_from_features(feats)
self.refresh_search()
def refresh_search(self):
if self.corpus is not None:
self.list_docs()
self.update_info()
def highlight_docs(self):
search_keyword = self.filter_input.text().\
strip('|').replace('\\', '\\\\') # escape one \ to two for mark.js
if search_keyword:
self.doc_webview.evalJS('mark("{}");'.format(search_keyword))
def update_info(self):
if self.corpus is not None:
self.n_documents = len(self.corpus)
self.n_matching = '{}/{}'.format(self.doc_list_model.rowCount(),
self.n_documents)
self.n_tokens = sum(
map(len,
self.corpus.tokens)) if self.corpus.has_tokens() else 'n/a'
self.n_types = len(
self.corpus.dictionary) if self.corpus.has_tokens() else 'n/a'
self.is_preprocessed = self.corpus.has_tokens()
self.is_pos_tagged = self.corpus.pos_tags is not None
self.ngram_range = '{}-{}'.format(*self.corpus.ngram_range)
else:
self.n_documents = ''
self.n_matching = ''
self.n_tokens = ''
self.n_types = ''
self.is_preprocessed = ''
self.is_pos_tagged = ''
self.ngram_range = ''
def commit(self):
if self.corpus is not None:
matched = self.corpus[self.output_mask]
output_mask = set(self.output_mask)
unmatched_mask = [
i for i in range(len(self.corpus)) if i not in output_mask
]
unmatched = self.corpus[unmatched_mask]
self.send(IO.MATCHED, matched)
self.send(IO.UNMATCHED, unmatched)
else:
self.send(IO.MATCHED, None)
self.send(IO.UNMATCHED, None)
def get_gds_model(progress=lambda val: None):
"""
Initialize and return a GDS datasets model.
:param progress: A progress callback.
:rval tuple:
A tuple of (QStandardItemModel, geo.GDSInfo, [geo.GDS])
.. note::
The returned QStandardItemModel's thread affinity is set to
the GUI thread.
"""
progress(1)
info = geo.GDSInfo()
search_keys = ["dataset_id", "title", "platform_organism", "description"]
cache_dir = serverfiles.localpath(geo.DOMAIN)
gds_link = "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc={0}"
pm_link = "http://www.ncbi.nlm.nih.gov/pubmed/{0}"
gds_list = []
def is_cached(gds):
return os.path.exists(os.path.join(cache_dir, gds["dataset_id"]) +
".soft.gz")
def item(displayvalue, item_values={}):
item = QStandardItem()
item.setData(displayvalue, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
def gds_to_row(gds):
#: Text for easier full search.
search_text = " | ".join([gds.get(key, "").lower()
for key in search_keys])
row = [
item(" " if is_cached(gds) else "",
{TextFilterRole: search_text}),
item(gds["dataset_id"],
{LinkRole: gds_link.format(gds["dataset_id"])}),
item(gds["title"]),
item(gds["platform_organism"]),
item(len(gds["samples"])),
item(gds["feature_count"]),
item(gds["gene_count"]),
item(len(gds["subsets"])),
item(gds.get("pubmed_id", ""),
{LinkRole: pm_link.format(gds["pubmed_id"])
if gds.get("pubmed_id")
else None})
]
return row
model = QStandardItemModel()
model.setHorizontalHeaderLabels(
["", "ID", "Title", "Organism", "Samples", "Features",
"Genes", "Subsets", "PubMedID"]
)
progress(20)
for gds in info.values():
model.appendRow(gds_to_row(gds))
gds_list.append(gds)
progress(50)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model, info, gds_list
class OWPreprocess(widget.OWWidget):
name = "Preprocess"
description = "Construct a data preprocessing pipeline."
icon = "icons/Preprocess.svg"
priority = 2105
inputs = [("Data", Orange.data.Table, "set_data")]
outputs = [("Preprocessor", preprocess.preprocess.Preprocess),
("Preprocessed Data", Orange.data.Table)]
storedsettings = settings.Setting({})
autocommit = settings.Setting(True)
def __init__(self):
super().__init__()
self.data = None
self._invalidated = False
# List of available preprocessors (DescriptionRole : Description)
self.preprocessors = QStandardItemModel()
def mimeData(indexlist):
assert len(indexlist) == 1
index = indexlist[0]
qname = index.data(DescriptionRole).qualname
m = QMimeData()
m.setData("application/x-qwidget-ref", qname.encode("utf-8"))
return m
# TODO: Fix this (subclass even if just to pass a function
# for mimeData delegate)
self.preprocessors.mimeData = mimeData
box = gui.vBox(self.controlArea, "Preprocessors")
self.preprocessorsView = view = QListView(
selectionMode=QListView.SingleSelection,
dragEnabled=True,
dragDropMode=QListView.DragOnly)
view.setModel(self.preprocessors)
view.activated.connect(self.__activated)
box.layout().addWidget(view)
####
self._qname2ppdef = {ppdef.qualname: ppdef for ppdef in PREPROCESSORS}
# List of 'selected' preprocessors and their parameters.
self.preprocessormodel = None
self.flow_view = SequenceFlow()
self.controler = Controller(self.flow_view, parent=self)
self.overlay = OverlayWidget(self)
self.overlay.setAttribute(Qt.WA_TransparentForMouseEvents)
self.overlay.setWidget(self.flow_view)
self.overlay.setLayout(QVBoxLayout())
self.overlay.layout().addWidget(
QLabel("Drag items from the list on the left", wordWrap=True))
self.scroll_area = QScrollArea(
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn)
self.scroll_area.viewport().setAcceptDrops(True)
self.scroll_area.setWidget(self.flow_view)
self.scroll_area.setWidgetResizable(True)
self.mainArea.layout().addWidget(self.scroll_area)
self.flow_view.installEventFilter(self)
box = gui.vBox(self.controlArea, "Output")
gui.auto_commit(box, self, "autocommit", "Send", box=False)
self._initialize()
def _initialize(self):
for pp_def in PREPROCESSORS:
description = pp_def.description
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item = QStandardItem(icon, description.title)
item.setToolTip(description.summary or "")
item.setData(pp_def, DescriptionRole)
item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable
| Qt.ItemIsDragEnabled)
self.preprocessors.appendRow([item])
try:
model = self.load(self.storedsettings)
except Exception:
model = self.load({})
self.set_model(model)
if not model.rowCount():
# enforce default width constraint if no preprocessors
# are instantiated (if the model is not empty the constraints
# will be triggered by LayoutRequest event on the `flow_view`)
self.__update_size_constraint()
self.apply()
def load(self, saved):
"""Load a preprocessor list from a dict."""
name = saved.get("name", "")
preprocessors = saved.get("preprocessors", [])
model = StandardItemModel()
def dropMimeData(data, action, row, column, parent):
if data.hasFormat("application/x-qwidget-ref") and \
action == Qt.CopyAction:
qname = bytes(data.data("application/x-qwidget-ref")).decode()
ppdef = self._qname2ppdef[qname]
item = QStandardItem(ppdef.description.title)
item.setData({}, ParametersRole)
item.setData(ppdef.description.title, Qt.DisplayRole)
item.setData(ppdef, DescriptionRole)
self.preprocessormodel.insertRow(row, [item])
return True
else:
return False
model.dropMimeData = dropMimeData
for qualname, params in preprocessors:
pp_def = self._qname2ppdef[qualname]
description = pp_def.description
item = QStandardItem(description.title)
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item.setIcon(icon)
item.setToolTip(description.summary)
item.setData(pp_def, DescriptionRole)
item.setData(params, ParametersRole)
model.appendRow(item)
return model
def save(self, model):
"""Save the preprocessor list to a dict."""
d = {"name": ""}
preprocessors = []
for i in range(model.rowCount()):
item = model.item(i)
pp_def = item.data(DescriptionRole)
params = item.data(ParametersRole)
preprocessors.append((pp_def.qualname, params))
d["preprocessors"] = preprocessors
return d
def set_model(self, ppmodel):
if self.preprocessormodel:
self.preprocessormodel.dataChanged.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsInserted.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsMoved.disconnect(self.__on_modelchanged)
self.preprocessormodel.deleteLater()
self.preprocessormodel = ppmodel
self.controler.setModel(ppmodel)
if ppmodel is not None:
self.preprocessormodel.dataChanged.connect(self.__on_modelchanged)
self.preprocessormodel.rowsInserted.connect(self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.connect(self.__on_modelchanged)
self.preprocessormodel.rowsMoved.connect(self.__on_modelchanged)
self.__update_overlay()
def __update_overlay(self):
if self.preprocessormodel is None or \
self.preprocessormodel.rowCount() == 0:
self.overlay.setWidget(self.flow_view)
self.overlay.show()
else:
self.overlay.setWidget(None)
self.overlay.hide()
def __on_modelchanged(self):
self.__update_overlay()
self.commit()
@check_sql_input
def set_data(self, data=None):
"""Set the input data set."""
self.data = data
def handleNewSignals(self):
self.apply()
def __activated(self, index):
item = self.preprocessors.itemFromIndex(index)
action = item.data(DescriptionRole)
item = QStandardItem()
item.setData({}, ParametersRole)
item.setData(action.description.title, Qt.DisplayRole)
item.setData(action, DescriptionRole)
self.preprocessormodel.appendRow([item])
def buildpreproc(self):
plist = []
for i in range(self.preprocessormodel.rowCount()):
item = self.preprocessormodel.item(i)
desc = item.data(DescriptionRole)
params = item.data(ParametersRole)
if not isinstance(params, dict):
params = {}
create = desc.viewclass.createinstance
plist.append(create(params))
if len(plist) == 1:
return plist[0]
else:
return preprocess.preprocess.PreprocessorList(plist)
def apply(self):
# Sync the model into storedsettings on every apply.
self.storeSpecificSettings()
preprocessor = self.buildpreproc()
if self.data is not None:
self.error()
try:
data = preprocessor(self.data)
except (ValueError, ZeroDivisionError) as e:
self.error(str(e))
return
else:
data = None
self.send("Preprocessor", preprocessor)
self.send("Preprocessed Data", data)
def commit(self):
if not self._invalidated:
self._invalidated = True
QApplication.postEvent(self, QEvent(QEvent.User))
def customEvent(self, event):
if event.type() == QEvent.User and self._invalidated:
self._invalidated = False
self.apply()
def eventFilter(self, receiver, event):
if receiver is self.flow_view and event.type() == QEvent.LayoutRequest:
QTimer.singleShot(0, self.__update_size_constraint)
return super().eventFilter(receiver, event)
def storeSpecificSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().storeSpecificSettings()
def saveSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().saveSettings()
def onDeleteWidget(self):
self.data = None
self.set_model(None)
super().onDeleteWidget()
@Slot()
def __update_size_constraint(self):
# Update minimum width constraint on the scroll area containing
# the 'instantiated' preprocessor list (to avoid the horizontal
# scroll bar).
sh = self.flow_view.minimumSizeHint()
scroll_width = self.scroll_area.verticalScrollBar().width()
self.scroll_area.setMinimumWidth(
min(max(sh.width() + scroll_width + 2, self.controlArea.width()),
520))
def sizeHint(self):
sh = super().sizeHint()
return sh.expandedTo(QSize(sh.width() + 300, 500))
def send_report(self):
pp = [(self.controler.model().index(i, 0).data(Qt.DisplayRole), w)
for i, w in enumerate(self.controler.view.widgets())]
if len(pp):
self.report_items("Settings", pp)
def __set_index(self, f):
# type: (Future) -> None
# set results from `list_remote` query.
assert QThread.currentThread() is self.thread()
assert f.done()
self.setBlocking(False)
self.setStatusMessage("")
allinfolocal = self.list_local()
try:
res = f.result()
except Exception:
log.exception("Error while fetching updated index")
if not allinfolocal:
self.Error.no_remote_datasets()
else:
self.Warning.only_local_datasets()
res = {}
allinforemote = res # type: Dict[Tuple[str, str], dict]
allkeys = set(allinfolocal)
if allinforemote is not None:
allkeys = allkeys | set(allinforemote)
allkeys = sorted(allkeys)
def info(file_path):
if file_path in allinforemote:
info = allinforemote[file_path]
else:
info = allinfolocal[file_path]
islocal = file_path in allinfolocal
isremote = file_path in allinforemote
outdated = islocal and isremote and (
allinforemote[file_path].get('version', '') !=
allinfolocal[file_path].get('version', ''))
islocal &= not outdated
prefix = os.path.join('', *file_path[:-1])
filename = file_path[-1]
return namespace(
prefix=prefix, filename=filename,
title=info.get("title", filename),
datetime=info.get("datetime", None),
description=info.get("description", None),
references=info.get("references", []),
seealso=info.get("seealso", []),
source=info.get("source", None),
year=info.get("year", None),
instances=info.get("instances", None),
variables=info.get("variables", None),
target=info.get("target", None),
missing=info.get("missing", None),
tags=info.get("tags", []),
size=info.get("size", None),
islocal=islocal,
outdated=outdated
)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(HEADER)
current_index = -1
for i, file_path in enumerate(allkeys):
datainfo = info(file_path)
item1 = QStandardItem()
item1.setData(" " if datainfo.islocal else "", Qt.DisplayRole)
item1.setData(datainfo, Qt.UserRole)
item2 = QStandardItem(datainfo.title)
item3 = QStandardItem()
item3.setData(datainfo.size, Qt.DisplayRole)
item4 = QStandardItem()
item4.setData(datainfo.instances, Qt.DisplayRole)
item5 = QStandardItem()
item5.setData(datainfo.variables, Qt.DisplayRole)
item6 = QStandardItem()
item6.setData(datainfo.target, Qt.DisplayRole)
if datainfo.target:
item6.setIcon(variable_icon(datainfo.target))
item7 = QStandardItem()
item7.setData(", ".join(datainfo.tags) if datainfo.tags else "",
Qt.DisplayRole)
row = [item1, item2, item3, item4, item5, item6, item7]
model.appendRow(row)
if os.path.join(*file_path) == self.selected_id:
current_index = i
hs = self.view.header().saveState()
model_ = self.view.model().sourceModel()
self.view.model().setSourceModel(model)
self.view.header().restoreState(hs)
model_.deleteLater()
model_.setParent(None)
self.view.selectionModel().selectionChanged.connect(
self.__on_selection
)
# Update the info text
self.infolabel.setText(format_info(model.rowCount(), len(allinfolocal)))
if current_index != -1:
selmodel = self.view.selectionModel()
selmodel.select(
self.view.model().mapFromSource(model.index(current_index, 0)),
QItemSelectionModel.ClearAndSelect | QItemSelectionModel.Rows)
class OWBatchNorm(OWWidget):
name = "Batch Effect Removal"
description = "Batch effect normalization on Single Cell data set."
icon = "icons/BatchEffectRemoval.svg"
priority = 230
class Inputs:
data = Input("Data", Table)
class Outputs:
data = Output("Data", Table)
class Error(OWWidget.Error):
general_error = Msg({})
discrete_attributes = Msg("Data with discrete attributes "
"can not be processed.")
class Warning(OWWidget.Warning):
missing_values = Msg("Missing values have been replaced with 0.")
negative_values = Msg("Unable to use current settings due "
"to negative values in data.")
resizing_enabled = False
want_main_area = False
settingsHandler = PerfectDomainContextHandler()
batch_vars = ContextSetting([])
link_method = Setting(LinkMethod.IDENTITY_LINK)
skip_zeros = Setting(False)
auto_commit = Setting(True)
def __init__(self, parent=None):
super().__init__(parent)
self.data = None
# Info
infobox = gui.widgetBox(self.controlArea, "Info")
self.info_label = gui.widgetLabel(infobox, "No data on input.")
# Link method
method_box = gui.widgetBox(self.controlArea, "Method")
gui.comboBox(method_box,
self,
"link_method",
items=LinkMethod.items(),
callback=self.__link_method_changed)
gui.separator(method_box)
self.skip_zeros_check = gui.checkBox(
method_box,
self,
"skip_zeros",
"Skip zero expressions",
enabled=self.link_method != LinkMethod.LOG_LINK,
callback=lambda: self.commit())
# Batch Variable Selection
header_shema = (("selected", ""), ("variable", "Variable"),
("count", "#"), ("score", "Score"))
header_labels = labels = [label for _, label in header_shema]
header = namedtuple("header", [tag for tag, _ in header_shema])
self.Header = header(*[index for index, _ in enumerate(labels)])
batch_box = gui.widgetBox(self.controlArea, "Batch Variable Selection")
self.view = QTreeView()
self.model = QStandardItemModel()
self.model.itemChanged.connect(self.__selected_batch_vars_changed)
self.model.setHorizontalHeaderLabels(header_labels)
batch_box.layout().addWidget(self.view)
self._setup_view()
gui.auto_commit(self.controlArea, self, "auto_commit", "Apply",
"Apply Automatically")
def __link_method_changed(self):
enable = self.link_method != LinkMethod.LOG_LINK
self.skip_zeros_check.setEnabled(enable)
if not enable:
self.skip_zeros_check.setChecked(True)
self.commit()
def __selected_batch_vars_changed(self, item):
if item.checkState():
self.batch_vars.append(item.data(VariableRole))
else:
self.batch_vars.remove(item.data(VariableRole))
self.commit()
def _setup_view(self):
self.view.setModel(self.model)
self.view.setSelectionMode(QTreeView.NoSelection)
self.view.setSortingEnabled(True)
self.view.setRootIsDecorated(False)
self.view.setItemDelegateForColumn(self.Header.count,
IntegralDelegate(self))
self.view.setItemDelegateForColumn(self.Header.score,
RealDelegate(self))
self.view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.view.header().setStretchLastSection(False)
self.view.header().setSectionResizeMode(self.Header.variable,
QHeaderView.Stretch)
self.view.setFocus()
@Inputs.data
def set_data(self, data):
self.closeContext()
self.clear()
self.data = data
self._setup_info_label()
self._check_data()
self.openContext(data)
if self.data is not None:
self.batch_vars = [data.domain[v.name] for v in self.batch_vars]
self._setup_model()
self.commit()
def clear(self):
self.batch_vars = []
if self.model:
n_rows = self.model.rowCount()
self.model.removeRows(0, n_rows)
def _setup_info_label(self):
text = "No data on input."
if self.data is not None:
domain, attrs = self.data.domain, self.data.domain.attributes
text = "{} cells, {} genes\n".format(len(self.data), len(attrs))
text += "{} meta features".format(len(domain.metas)) \
if len(domain.metas) else "(no meta features)"
self.info_label.setText(text)
def _check_data(self):
self.clear_messages()
if self.data and self.data.domain.has_discrete_attributes():
self.data = None
self.Error.discrete_attributes()
if self.data and np.isnan(self.data.X).any():
self.data.X = np.nan_to_num(self.data.X)
self.Warning.missing_values()
def _setup_model(self):
estimator = ScBatchScorer()
for var in self.data.domain.class_vars + self.data.domain.metas:
if not var.is_primitive():
continue
try:
score = float(estimator.score_data(self.data, var))
except Exception:
score = np.nan
self.model.appendRow([
self.__selected_item(var),
self.__variable_item(var),
self.__count_item(var),
self.__score_item(score)
])
def __selected_item(self, var):
item = QStandardItem()
item.setData(var, VariableRole)
item.setCheckable(True)
select = var in self.batch_vars
item.setCheckState(Qt.Checked if select else Qt.Unchecked)
item.setEditable(False)
return item
def __variable_item(self, var):
item = QStandardItem()
item.setData(var.name, Qt.DisplayRole)
item.setData(gui.attributeIconDict[var], Qt.DecorationRole)
item.setEditable(False)
return item
def __count_item(self, var):
item = QStandardItem()
if var.is_discrete:
item.setData(len(var.values), Qt.DisplayRole)
item.setEditable(False)
return item
def __score_item(self, score):
item = QStandardItem()
item.setData(score, Qt.DisplayRole)
item.setEditable(False)
return item
def commit(self):
data = None
self.Error.general_error.clear()
self.Warning.negative_values.clear()
if self.data is not None:
if (self.data.X < 0).any() and self.skip_zeros:
self.Warning.negative_values()
data = self.data
else:
try:
data = SCBatchNormalizer(
LinkMethod.items()[self.link_method], self.skip_zeros,
self.batch_vars)(self.data)
except Exception as e:
self.Error.general_error(str(e))
data = None
self.Outputs.data.send(data)
def send_report(self):
method = LinkMethod.items()[self.link_method]
if self.skip_zeros:
method += " (Skip zero expressions)"
variables = ", ".join([v.name for v in self.batch_vars]) \
if self.batch_vars else "None"
self.report_items("", [("Method", method),
("Batch variable selection", variables)])
class OWCorpusViewer(OWWidget):
name = "Corpus Viewer"
description = "Display corpus contents."
icon = "icons/CorpusViewer.svg"
priority = 500
class Inputs:
corpus = Input("Corpus", Corpus, replaces=["Data"])
class Outputs:
matching_docs = Output("Matching Docs", Corpus, default=True)
other_docs = Output("Other Docs", Corpus)
settingsHandler = PerfectDomainContextHandler(
match_values=PerfectDomainContextHandler.MATCH_VALUES_ALL)
search_indices = ContextSetting(
[], exclude_metas=False) # features included in search
display_indices = ContextSetting(
[], exclude_metas=False) # features for display
display_features = ContextSetting([], exclude_metas=False)
regexp_filter = ContextSetting("")
selection = [0] # TODO: DataHashContextHandler
show_tokens = Setting(False)
autocommit = Setting(True)
class Warning(OWWidget.Warning):
no_feats_search = Msg('No features included in search.')
no_feats_display = Msg('No features selected for display.')
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.output_mask = [] # Output corpus indices
self.doc_webview = None # WebView for showing content
self.search_features = [
] # two copies are needed since Display allows drag & drop
self.display_list_indices = [0]
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Documents: %(n_documents)s')
gui.label(info_box, self, 'Preprocessed: %(is_preprocessed)s')
gui.label(info_box, self, ' ◦ Tokens: %(n_tokens)s')
gui.label(info_box, self, ' ◦ Types: %(n_types)s')
gui.label(info_box, self, 'POS tagged: %(is_pos_tagged)s')
gui.label(info_box, self, 'N-grams range: %(ngram_range)s')
gui.label(info_box, self, 'Matching: %(n_matching)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea,
self,
'search_indices',
'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features',
callback=self.search_features_changed)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box,
self,
'display_list_indices',
'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs,
enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box,
self,
'show_tokens',
'Show Tokens && Tags',
callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data',
'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea,
self,
'regexp_filter',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(
QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:')
self.filter_input.textChanged.connect(self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(self.show_docs)
# Document contents
self.doc_webview = gui.WebviewWidget(self.splitter, debug=False)
self.doc_webview.loadFinished.connect(self.highlight_docs)
self.mainArea.layout().addWidget(self.splitter)
def copy_to_clipboard(self):
text = self.doc_webview.selectedText()
QApplication.clipboard().setText(text)
@Inputs.corpus
def set_data(self, corpus=None):
self.closeContext()
self.reset_widget()
self.corpus = corpus
self.search_features = []
if corpus is not None:
domain = self.corpus.domain
# Enable/disable tokens checkbox
if not self.corpus.has_tokens():
self.show_tokens_checkbox.setCheckState(False)
self.show_tokens_checkbox.setEnabled(self.corpus.has_tokens())
self.search_features = list(
filter_visible(chain(domain.variables, domain.metas)))
self.display_features = list(
filter_visible(chain(domain.variables, domain.metas)))
self.search_indices = list(range(len(self.search_features)))
self.display_indices = list(range(len(self.display_features)))
self.selection = [0]
self.openContext(self.corpus)
self.display_list_indices = self.display_indices
self.regenerate_docs()
self.list_docs()
self.update_info()
self.set_selection()
self.show_docs()
self.commit()
def reset_widget(self):
# Corpus
self.corpus = None
self.corpus_docs = None
self.output_mask = []
self.display_features = []
# Widgets
self.search_listbox.clear()
self.display_listbox.clear()
self.filter_input.clear()
self.update_info()
# Models/vars
self.search_features.clear()
self.search_indices.clear()
self.display_indices.clear()
self.doc_list_model.clear()
# Warnings
self.Warning.clear()
# WebView
self.doc_webview.setHtml('')
def list_docs(self):
""" List documents into the left scrolling area """
if self.corpus_docs is None:
return
search_keyword = self.regexp_filter.strip('|')
try:
reg = re.compile(search_keyword, re.IGNORECASE)
except sre_constants.error:
return
def is_match(x):
return not bool(search_keyword) or reg.search(x)
self.output_mask.clear()
self.doc_list_model.clear()
for i, (doc, title, content) in enumerate(
zip(self.corpus, self.corpus.titles, self.corpus_docs)):
if is_match(content):
item = QStandardItem()
item.setData(title, Qt.DisplayRole)
item.setData(doc, Qt.UserRole)
self.doc_list_model.appendRow(item)
self.output_mask.append(i)
def reset_selection(self):
if self.doc_list_model.rowCount() > 0:
self.doc_list.selectRow(0) # Select the first document
else:
self.doc_webview.setHtml('')
def set_selection(self):
view = self.doc_list
if len(self.selection):
selection = QItemSelection()
for row in self.selection:
selection.append(
QItemSelectionRange(view.model().index(row, 0),
view.model().index(row, 0)))
view.selectionModel().select(selection,
QItemSelectionModel.ClearAndSelect)
def show_docs(self):
""" Show the selected documents in the right area """
HTML = '''
<!doctype html>
<html>
<head>
<script type="text/javascript" src="resources/jquery-3.1.1.min.js">
</script>
<script type="text/javascript" src="resources/jquery.mark.min.js">
</script>
<script type="text/javascript" src="resources/highlighter.js">
</script>
<meta charset='utf-8'>
<style>
table {{ border-collapse: collapse; }}
mark {{ background: #FFCD28; }}
tr > td {{
padding-bottom: 3px;
padding-top: 3px;
}}
body {{
font-family: Helvetica;
font-size: 10pt;
}}
.line {{ border-bottom: 1px solid #000; }}
.separator {{ height: 5px; }}
.variables {{
vertical-align: top;
padding-right: 10px;
}}
.token {{
padding: 3px;
border: 1px #B0B0B0 solid;
margin-right: 5px;
margin-bottom: 5px;
display: inline-block;
}}
img {{
max-width: 100%;
}}
</style>
</head>
<body>
{}
</body>
</html>
'''
self.display_indices = self.display_list_indices
if self.corpus is None:
return
self.Warning.no_feats_display.clear()
if len(self.display_indices) == 0:
self.Warning.no_feats_display()
if self.show_tokens:
tokens = list(self.corpus.ngrams_iterator(include_postags=True))
marked_search_features = [
f for i, f in enumerate(self.search_features)
if i in self.search_indices
]
html = '<table>'
selection = [
i.row() for i in self.doc_list.selectionModel().selectedRows()
]
if selection != []:
self.selection = selection
for doc_count, index in enumerate(
self.doc_list.selectionModel().selectedRows()):
if doc_count > 0: # add split
html += '<tr class="line separator"><td/><td/></tr>' \
'<tr class="separator"><td/><td/></tr>'
row_ind = index.data(Qt.UserRole).row_index
for ind in self.display_indices:
feature = self.display_features[ind]
mark = 'class="mark-area"' if feature in marked_search_features else ''
value = str(index.data(Qt.UserRole)[feature.name])
is_image = feature.attributes.get('type', '') == 'image'
if is_image and value != '?':
value = '<img src="{}"></img>'.format(value)
html += '<tr><td class="variables"><strong>{}:</strong></td>' \
'<td {}>{}</td></tr>'.format(
feature.name, mark, value)
if self.show_tokens:
html += '<tr><td class="variables"><strong>Tokens & Tags:</strong></td>' \
'<td>{}</td></tr>'.format(''.join('<span class="token">{}</span>'.format(
token) for token in tokens[row_ind]))
html += '</table>'
base = QUrl.fromLocalFile(__file__)
self.doc_webview.setHtml(HTML.format(html), base)
def search_features_changed(self):
self.regenerate_docs()
self.refresh_search()
def regenerate_docs(self):
self.corpus_docs = None
self.Warning.no_feats_search.clear()
if self.corpus is not None:
feats = [self.search_features[i] for i in self.search_indices]
if len(feats) == 0:
self.Warning.no_feats_search()
self.corpus_docs = self.corpus.documents_from_features(feats)
def refresh_search(self):
if self.corpus is not None:
self.list_docs()
self.reset_selection()
self.update_info()
self.commit()
@Slot()
def highlight_docs(self):
search_keyword = self.regexp_filter.\
strip('|').replace('\\', '\\\\') # escape one \ to two for mark.js
if search_keyword:
# mark is undefined when clearing the view (`setHtml('')`). Maybe
# set and template html with all the scripts, ... but no contents?
self.doc_webview.runJavaScript('''
if (typeof mark !== "undefined") {{
mark("{}");
}}
'''.format(search_keyword))
def update_info(self):
if self.corpus is not None:
self.n_documents = len(self.corpus)
self.n_matching = '{}/{}'.format(self.doc_list_model.rowCount(),
self.n_documents)
self.n_tokens = sum(
map(len,
self.corpus.tokens)) if self.corpus.has_tokens() else 'n/a'
self.n_types = len(
self.corpus.dictionary) if self.corpus.has_tokens() else 'n/a'
self.is_preprocessed = self.corpus.has_tokens()
self.is_pos_tagged = self.corpus.pos_tags is not None
self.ngram_range = '{}-{}'.format(*self.corpus.ngram_range)
else:
self.n_documents = ''
self.n_matching = ''
self.n_tokens = ''
self.n_types = ''
self.is_preprocessed = ''
self.is_pos_tagged = ''
self.ngram_range = ''
def commit(self):
if self.corpus is not None:
matched = self.corpus[self.output_mask]
output_mask = set(self.output_mask)
unmatched_mask = [
i for i in range(len(self.corpus)) if i not in output_mask
]
unmatched = self.corpus[unmatched_mask]
self.Outputs.matching_docs.send(matched)
self.Outputs.other_docs.send(unmatched)
else:
self.Outputs.matching_docs.send(None)
self.Outputs.other_docs.send(None)
def __set_index(self, f):
# type: (Future) -> None
# set results from `list_remote` query.
assert QThread.currentThread() is self.thread()
assert f.done()
self.setBlocking(False)
self.setStatusMessage("")
allinfolocal = list_local()
try:
res = f.result()
except Exception as er:
log = logging.getLogger(__name__)
log.exception("Error while fetching updated index")
if not allinfolocal:
self.error("Could not fetch data set list")
else:
self.warning("Could not fetch data sets list, only local "
"cached data sets are shown")
res = {}
allinforemote = res # type: Dict[Tuple[str, str], dict]
allkeys = set(allinfolocal)
if allinforemote is not None:
allkeys = allkeys | set(allinforemote)
allkeys = sorted(allkeys)
def info(prefix, filename):
if (prefix, filename) in allinforemote:
info = allinforemote[prefix, filename]
else:
info = allinfolocal[prefix, filename]
islocal = (prefix, filename) in allinfolocal
return namespace(prefix=prefix,
filename=filename,
title=info.get("title", filename),
datetime=info.get("datetime", None),
description=info.get("description", None),
reference=info.get("reference", None),
instances=info.get("instances", None),
variables=info.get("variables", None),
target=info.get("target", None),
missing=info.get("missing", None),
tags=info.get("tags", []),
size=info.get("size", None),
islocal=islocal)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(HEADER)
current_index = -1
for i, (prefix, filename) in enumerate(allkeys):
datainfo = info(prefix, filename)
item1 = QStandardItem()
item1.setData(" " if datainfo.islocal else "", Qt.DisplayRole)
item1.setData(datainfo, Qt.UserRole)
item2 = QStandardItem(datainfo.title)
item3 = QStandardItem()
item3.setData(datainfo.size, Qt.DisplayRole)
item4 = QStandardItem()
item4.setData(datainfo.instances, Qt.DisplayRole)
item5 = QStandardItem()
item5.setData(datainfo.variables, Qt.DisplayRole)
item6 = QStandardItem()
item6.setData(datainfo.target, Qt.DisplayRole)
item6.setIcon(variable_icon(datainfo.target))
item7 = QStandardItem()
item7.setData(", ".join(datainfo.tags), Qt.DisplayRole)
row = [item1, item2, item3, item4, item5, item6, item7]
model.appendRow(row)
if (prefix, filename) == self.selected_id:
current_index = i
hs = self.view.header().saveState()
model_ = self.view.model()
self.view.setModel(model)
self.view.header().restoreState(hs)
model_.deleteLater()
model_.setParent(None)
self.view.selectionModel().selectionChanged.connect(
self.__on_selection)
# Update the info text
self.infolabel.setText("{} datasets \n{} datasets cached".format(
model.rowCount(), len(allinfolocal)))
if current_index != -1:
selmodel = self.view.selectionModel()
selmodel.select(
model.index(current_index, 0),
QItemSelectionModel.ClearAndSelect | QItemSelectionModel.Rows)
class OWCorpusViewer(OWWidget):
name = "Corpus Viewer"
description = "Display corpus contents."
icon = "icons/CorpusViewer.svg"
priority = 500
class Inputs:
corpus = Input("Corpus", Corpus, replaces=["Data"])
class Outputs:
matching_docs = Output("Matching Docs", Corpus, default=True)
other_docs = Output("Other Docs", Corpus)
settingsHandler = PerfectDomainContextHandler(
match_values = PerfectDomainContextHandler.MATCH_VALUES_ALL
)
search_indices = ContextSetting([], exclude_metas=False) # features included in search
display_indices = ContextSetting([], exclude_metas=False) # features for display
display_features = ContextSetting([], exclude_metas=False)
regexp_filter = ContextSetting("")
selection = [0] # TODO: DataHashContextHandler
show_tokens = Setting(False)
autocommit = Setting(True)
class Warning(OWWidget.Warning):
no_feats_search = Msg('No features included in search.')
no_feats_display = Msg('No features selected for display.')
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.output_mask = [] # Output corpus indices
self.doc_webview = None # WebView for showing content
self.search_features = [] # two copies are needed since Display allows drag & drop
self.display_list_indices = [0]
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Documents: %(n_documents)s')
gui.label(info_box, self, 'Preprocessed: %(is_preprocessed)s')
gui.label(info_box, self, ' ◦ Tokens: %(n_tokens)s')
gui.label(info_box, self, ' ◦ Types: %(n_types)s')
gui.label(info_box, self, 'POS tagged: %(is_pos_tagged)s')
gui.label(info_box, self, 'N-grams range: %(ngram_range)s')
gui.label(info_box, self, 'Matching: %(n_matching)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea, self, 'search_indices', 'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features', callback=self.search_features_changed)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box, self, 'display_list_indices', 'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs, enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box, self, 'show_tokens',
'Show Tokens && Tags', callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data', 'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea, self, 'regexp_filter',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:')
self.filter_input.textChanged.connect(self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(self.show_docs)
# Document contents
self.doc_webview = gui.WebviewWidget(self.splitter, debug=False)
self.mainArea.layout().addWidget(self.splitter)
def copy_to_clipboard(self):
text = self.doc_webview.selectedText()
QApplication.clipboard().setText(text)
@Inputs.corpus
def set_data(self, corpus=None):
self.closeContext()
self.reset_widget()
self.corpus = corpus
self.search_features = []
if corpus is not None:
domain = self.corpus.domain
# Enable/disable tokens checkbox
if not self.corpus.has_tokens():
self.show_tokens_checkbox.setCheckState(False)
self.show_tokens_checkbox.setEnabled(self.corpus.has_tokens())
self.search_features = list(filter_visible(chain(domain.variables, domain.metas)))
self.display_features = list(filter_visible(chain(domain.variables, domain.metas)))
self.search_indices = list(range(len(self.search_features)))
self.display_indices = list(range(len(self.display_features)))
self.selection = [0]
self.openContext(self.corpus)
self.display_list_indices = self.display_indices
self.regenerate_docs()
self.list_docs()
self.update_info()
self.set_selection()
self.show_docs()
self.commit()
def reset_widget(self):
# Corpus
self.corpus = None
self.corpus_docs = None
self.output_mask = []
self.display_features = []
# Widgets
self.search_listbox.clear()
self.display_listbox.clear()
self.filter_input.clear()
self.update_info()
# Models/vars
self.search_features.clear()
self.search_indices.clear()
self.display_indices.clear()
self.doc_list_model.clear()
# Warnings
self.Warning.clear()
# WebView
self.doc_webview.setHtml('')
def list_docs(self):
""" List documents into the left scrolling area """
if self.corpus_docs is None:
return
search_keyword = self.regexp_filter.strip('|')
try:
reg = re.compile(search_keyword, re.IGNORECASE)
except sre_constants.error:
return
def is_match(x):
return not bool(search_keyword) or reg.search(x)
self.output_mask.clear()
self.doc_list_model.clear()
for i, (doc, title, content) in enumerate(zip(self.corpus, self.corpus.titles,
self.corpus_docs)):
if is_match(content):
item = QStandardItem()
item.setData(title, Qt.DisplayRole)
item.setData(doc, Qt.UserRole)
self.doc_list_model.appendRow(item)
self.output_mask.append(i)
def reset_selection(self):
if self.doc_list_model.rowCount() > 0:
self.doc_list.selectRow(0) # Select the first document
else:
self.doc_webview.setHtml('')
def set_selection(self):
view = self.doc_list
if len(self.selection):
selection = QItemSelection()
for row in self.selection:
selection.append(
QItemSelectionRange(
view.model().index(row, 0),
view.model().index(row, 0)
)
)
view.selectionModel().select(
selection, QItemSelectionModel.ClearAndSelect)
def show_docs(self):
""" Show the selected documents in the right area """
HTML = '''
<!doctype html>
<html>
<head>
<script type="text/javascript" src="resources/jquery-3.1.1.min.js">
</script>
<script type="text/javascript" src="resources/jquery.mark.min.js">
</script>
<script type="text/javascript" src="resources/highlighter.js">
</script>
<meta charset='utf-8'>
<style>
table {{ border-collapse: collapse; }}
mark {{ background: #FFCD28; }}
tr > td {{
padding-bottom: 3px;
padding-top: 3px;
}}
body {{
font-family: Helvetica;
font-size: 10pt;
}}
.line {{ border-bottom: 1px solid #000; }}
.separator {{ height: 5px; }}
.variables {{
vertical-align: top;
padding-right: 10px;
}}
.content {{
/* Adopted from https://css-tricks.com/snippets/css/prevent-long-urls-from-breaking-out-of-container/ */
/* These are technically the same, but use both */
overflow-wrap: break-word;
word-wrap: break-word;
-ms-word-break: break-all;
/* This is the dangerous one in WebKit, as it breaks things wherever */
word-break: break-all;
/* Instead use this non-standard one: */
word-break: break-word;
/* Adds a hyphen where the word breaks, if supported (No Blink) */
-ms-hyphens: auto;
-moz-hyphens: auto;
-webkit-hyphens: auto;
hyphens: auto;
}}
.token {{
padding: 3px;
border: 1px #B0B0B0 solid;
margin-right: 5px;
margin-bottom: 5px;
display: inline-block;
}}
img {{
max-width: 100%;
}}
</style>
</head>
<body>
{}
</body>
</html>
'''
self.display_indices = self.display_list_indices
if self.corpus is None:
return
self.Warning.no_feats_display.clear()
if len(self.display_indices) == 0:
self.Warning.no_feats_display()
if self.show_tokens:
tokens = list(self.corpus.ngrams_iterator(include_postags=True))
marked_search_features = [f for i, f in enumerate(self.search_features)
if i in self.search_indices]
html = '<table>'
selection = [i.row() for i in self.doc_list.selectionModel().selectedRows()]
if selection != []:
self.selection = selection
for doc_count, index in enumerate(self.doc_list.selectionModel().selectedRows()):
if doc_count > 0: # add split
html += '<tr class="line separator"><td/><td/></tr>' \
'<tr class="separator"><td/><td/></tr>'
row_ind = index.data(Qt.UserRole).row_index
for ind in self.display_indices:
feature = self.display_features[ind]
value = str(index.data(Qt.UserRole)[feature.name])
if feature in marked_search_features:
value = self.__mark_text(value)
value = value.replace('\n', '<br/>')
is_image = feature.attributes.get('type', '') == 'image'
if is_image and value != '?':
value = '<img src="{}"></img>'.format(value)
html += '<tr><td class="variables"><strong>{}:</strong></td>' \
'<td class="content">{}</td></tr>'.format(
feature.name, value)
if self.show_tokens:
html += '<tr><td class="variables"><strong>Tokens & Tags:</strong></td>' \
'<td>{}</td></tr>'.format(''.join('<span class="token">{}</span>'.format(
token) for token in tokens[row_ind]))
html += '</table>'
base = QUrl.fromLocalFile(__file__)
self.doc_webview.setHtml(HTML.format(html), base)
def __mark_text(self, text):
search_keyword = self.regexp_filter.strip('|')
if not search_keyword:
return text
try:
reg = re.compile(search_keyword, re.IGNORECASE | re.MULTILINE)
except sre_constants.error:
return text
matches = list(reg.finditer(text))
if not matches:
return text
text = list(text)
for m in matches[::-1]:
text[m.start():m.end()] = list('<mark data-markjs="true">{}</mark>'\
.format("".join(text[m.start():m.end()])))
return "".join(text)
def search_features_changed(self):
self.regenerate_docs()
self.refresh_search()
def regenerate_docs(self):
self.corpus_docs = None
self.Warning.no_feats_search.clear()
if self.corpus is not None:
feats = [self.search_features[i] for i in self.search_indices]
if len(feats) == 0:
self.Warning.no_feats_search()
self.corpus_docs = self.corpus.documents_from_features(feats)
def refresh_search(self):
if self.corpus is not None:
self.list_docs()
self.reset_selection()
self.update_info()
self.commit()
def update_info(self):
if self.corpus is not None:
self.n_documents = len(self.corpus)
self.n_matching = '{}/{}'.format(self.doc_list_model.rowCount(), self.n_documents)
self.n_tokens = sum(map(len, self.corpus.tokens)) if self.corpus.has_tokens() else 'n/a'
self.n_types = len(self.corpus.dictionary) if self.corpus.has_tokens() else 'n/a'
self.is_preprocessed = self.corpus.has_tokens()
self.is_pos_tagged = self.corpus.pos_tags is not None
self.ngram_range = '{}-{}'.format(*self.corpus.ngram_range)
else:
self.n_documents = ''
self.n_matching = ''
self.n_tokens = ''
self.n_types = ''
self.is_preprocessed = ''
self.is_pos_tagged = ''
self.ngram_range = ''
def commit(self):
if self.corpus is not None:
matched = self.corpus[self.output_mask]
output_mask = set(self.output_mask)
unmatched_mask = [i for i in range(len(self.corpus)) if i not in output_mask]
unmatched = self.corpus[unmatched_mask]
self.Outputs.matching_docs.send(matched)
self.Outputs.other_docs.send(unmatched)
else:
self.Outputs.matching_docs.send(None)
self.Outputs.other_docs.send(None)
def send_report(self):
self.report_items((
("Query", self.regexp_filter),
("Matching documents", self.n_matching),
))
def __on_enrichment_finished(self, results):
assert QThread.currentThread() is self.thread()
self.__state &= ~OWSetEnrichment.RunningEnrichment
query, reference, results = results
if self.annotationsChartView.model():
self.annotationsChartView.model().clear()
nquery = len(query)
nref = len(reference)
maxcount = max((len(e.query_mapped) for _, e in results), default=1)
maxrefcount = max((len(e.reference_mapped) for _, e in results),
default=1)
nspaces = int(math.ceil(math.log10(maxcount or 1)))
refspaces = int(math.ceil(math.log(maxrefcount or 1)))
query_fmt = "%" + str(nspaces) + "s (%.2f%%)"
ref_fmt = "%" + str(refspaces) + "s (%.2f%%)"
def fmt_count(fmt, count, total):
return fmt % (count, 100.0 * count / (total or 1))
fmt_query_count = partial(fmt_count, query_fmt)
fmt_ref_count = partial(fmt_count, ref_fmt)
linkFont = QFont(self.annotationsChartView.viewOptions().font)
linkFont.setUnderline(True)
def item(value=None, tooltip=None, user=None):
si = QStandardItem()
if value is not None:
si.setData(value, Qt.DisplayRole)
if tooltip is not None:
si.setData(tooltip, Qt.ToolTipRole)
if user is not None:
si.setData(user, Qt.UserRole)
else:
si.setData(value, Qt.UserRole)
return si
model = QStandardItemModel()
model.setSortRole(Qt.UserRole)
model.setHorizontalHeaderLabels([
"Category", "Term", "Count", "Reference count", "p-value", "FDR",
"Enrichment"
])
for i, (gset, enrich) in enumerate(results):
if len(enrich.query_mapped) == 0:
continue
nquery_mapped = len(enrich.query_mapped)
nref_mapped = len(enrich.reference_mapped)
row = [
item(", ".join(gset.hierarchy)),
item(gsname(gset), tooltip=gset.link),
item(fmt_query_count(nquery_mapped, nquery),
tooltip=nquery_mapped,
user=nquery_mapped),
item(fmt_ref_count(nref_mapped, nref),
tooltip=nref_mapped,
user=nref_mapped),
item(fmtp(enrich.p_value), user=enrich.p_value),
item(
), # column 5, FDR, is computed in filterAnnotationsChartView
item(enrich.enrichment_score,
tooltip="%.3f" % enrich.enrichment_score,
user=enrich.enrichment_score)
]
row[0].geneset = gset
row[0].enrichment = enrich
row[1].setData(gset.link, gui.LinkRole)
row[1].setFont(linkFont)
row[1].setForeground(QColor(Qt.blue))
model.appendRow(row)
self.annotationsChartView.setModel(model)
self.annotationsChartView.selectionModel().selectionChanged.connect(
self.commit)
if not model.rowCount():
self.warning(0, "No enriched sets found.")
else:
self.warning(0)
allnames = set(
gsname(geneset) for geneset, (count, _, _, _) in results if count)
allnames |= reduce(operator.ior,
(set(word_split(name)) for name in allnames), set())
self.filterCompleter.setModel(None)
self.completerModel = QStringListModel(sorted(allnames))
self.filterCompleter.setModel(self.completerModel)
if results:
max_score = max(
(e.enrichment_score
for _, e in results if np.isfinite(e.enrichment_score)),
default=1)
self.annotationsChartView.setItemDelegateForColumn(
6, BarItemDelegate(self, scale=(0.0, max_score)))
self.annotationsChartView.setItemDelegateForColumn(
1, gui.LinkStyledItemDelegate(self.annotationsChartView))
header = self.annotationsChartView.header()
for i in range(model.columnCount()):
sh = self.annotationsChartView.sizeHintForColumn(i)
sh = max(sh, header.sectionSizeHint(i))
self.annotationsChartView.setColumnWidth(i, max(min(sh, 300), 30))
# self.annotationsChartView.resizeColumnToContents(i)
self.filterAnnotationsChartView()
self.progressBarFinished()
self.setStatusMessage("")
def __setupUi(self):
"""Set up the UI.
"""
if self.__macUnified:
self.tab = QToolBar(
floatable=False, movable=False, allowedAreas=Qt.TopToolBarArea,
)
self.addToolBar(Qt.TopToolBarArea, self.tab)
self.setUnifiedTitleAndToolBarOnMac(True)
# This does not seem to work
self.setWindowFlags(self.windowFlags() & \
~Qt.MacWindowToolBarButtonHint)
self.tab.actionTriggered[QAction].connect(
self.__macOnToolBarAction
)
central = QStackedWidget()
central.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
else:
self.tab = central = QTabWidget(self)
# Add a close button to the bottom of the dialog
# (to satisfy GNOME 3 which shows the dialog without a title bar).
container = container_widget_helper()
container.layout().addWidget(central)
buttonbox = QDialogButtonBox(QDialogButtonBox.Close)
buttonbox.rejected.connect(self.close)
container.layout().addWidget(buttonbox)
self.setCentralWidget(container)
self.stack = central
# General Tab
tab = QWidget()
self.addTab(tab, self.tr("General"),
toolTip=self.tr("General Options"))
form = QFormLayout()
tab.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
nodes = QWidget(self, objectName="nodes")
nodes.setLayout(QVBoxLayout())
nodes.layout().setContentsMargins(0, 0, 0, 0)
cb_anim = QCheckBox(
self.tr("Enable node animations"),
objectName="enable-node-animations",
toolTip=self.tr("Enable shadow and ping animations for nodes "
"in the workflow.")
)
self.bind(cb_anim, "checked", "schemeedit/enable-node-animations")
nodes.layout().addWidget(cb_anim)
form.addRow(self.tr("Nodes"), nodes)
links = QWidget(self, objectName="links")
links.setLayout(QVBoxLayout())
links.layout().setContentsMargins(0, 0, 0, 0)
cb_show = QCheckBox(
self.tr("Show channel names between widgets"),
objectName="show-channel-names",
toolTip=self.tr("Show source and sink channel names "
"over the links.")
)
self.bind(cb_show, "checked", "schemeedit/show-channel-names")
links.layout().addWidget(cb_show)
form.addRow(self.tr("Links"), links)
quickmenu = QWidget(self, objectName="quickmenu-options")
quickmenu.setLayout(QVBoxLayout())
quickmenu.layout().setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("On double click"),
toolTip=self.tr("Open quick menu on a double click "
"on an empty spot in the canvas"))
cb2 = QCheckBox(self.tr("On right click"),
toolTip=self.tr("Open quick menu on a right click "
"on an empty spot in the canvas"))
cb3 = QCheckBox(self.tr("On space key press"),
toolTip=self.tr("On Space key press while the mouse"
"is hovering over the canvas."))
cb4 = QCheckBox(self.tr("On any key press"),
toolTip=self.tr("On any key press while the mouse"
"is hovering over the canvas."))
self.bind(cb1, "checked", "quickmenu/trigger-on-double-click")
self.bind(cb2, "checked", "quickmenu/trigger-on-right-click")
self.bind(cb3, "checked", "quickmenu/trigger-on-space-key")
self.bind(cb4, "checked", "quickmenu/trigger-on-any-key")
quickmenu.layout().addWidget(cb1)
quickmenu.layout().addWidget(cb2)
quickmenu.layout().addWidget(cb3)
quickmenu.layout().addWidget(cb4)
form.addRow(self.tr("Open quick menu on"), quickmenu)
startup = QWidget(self, objectName="startup-group")
startup.setLayout(QVBoxLayout())
startup.layout().setContentsMargins(0, 0, 0, 0)
cb_splash = QCheckBox(self.tr("Show splash screen"), self,
objectName="show-splash-screen")
cb_welcome = QCheckBox(self.tr("Show welcome screen"), self,
objectName="show-welcome-screen")
self.bind(cb_splash, "checked", "startup/show-splash-screen")
self.bind(cb_welcome, "checked", "startup/show-welcome-screen")
startup.layout().addWidget(cb_splash)
startup.layout().addWidget(cb_welcome)
form.addRow(self.tr("On startup"), startup)
toolbox = QWidget(self, objectName="toolbox-group")
toolbox.setLayout(QVBoxLayout())
toolbox.layout().setContentsMargins(0, 0, 0, 0)
exclusive = QCheckBox(self.tr("Only one tab can be open at a time"))
self.bind(exclusive, "checked", "mainwindow/toolbox-dock-exclusive")
toolbox.layout().addWidget(exclusive)
form.addRow(self.tr("Tool box"), toolbox)
tab.setLayout(form)
# Output Tab
tab = QWidget()
self.addTab(tab, self.tr("Output"),
toolTip="Output Redirection")
form = QFormLayout()
box = QWidget()
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
combo = QComboBox()
combo.addItems([self.tr("Critical"),
self.tr("Error"),
self.tr("Warn"),
self.tr("Info"),
self.tr("Debug")])
self.bind(combo, "currentIndex", "logging/level")
layout.addWidget(combo)
box.setLayout(layout)
form.addRow(self.tr("Logging"), box)
box = QWidget()
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("Open in external browser"),
objectName="open-in-external-browser")
self.bind(cb1, "checked", "help/open-in-external-browser")
layout.addWidget(cb1)
box.setLayout(layout)
form.addRow(self.tr("Help window"), box)
tab.setLayout(form)
# Categories Tab
tab = QWidget()
layout = QVBoxLayout()
view = QListView(
editTriggers=QListView.NoEditTriggers
)
from .. import registry
reg = registry.global_registry()
model = QStandardItemModel()
settings = QSettings()
for cat in reg.categories():
item = QStandardItem()
item.setText(cat.name)
item.setCheckable(True)
visible, _ = category_state(cat, settings)
item.setCheckState(Qt.Checked if visible else Qt.Unchecked)
model.appendRow([item])
view.setModel(model)
layout.addWidget(view)
tab.setLayout(layout)
model.itemChanged.connect(
lambda item:
save_category_state(
reg.category(str(item.text())),
_State(item.checkState() == Qt.Checked, -1),
settings
)
)
self.addTab(tab, "Categories")
# Add-ons Tab
tab = QWidget()
self.addTab(tab, self.tr("Add-ons"),
toolTip="Settings related to add-on installation")
form = QFormLayout()
conda = QWidget(self, objectName="conda-group")
conda.setLayout(QVBoxLayout())
conda.layout().setContentsMargins(0, 0, 0, 0)
cb_conda_install = QCheckBox(self.tr("Install add-ons with conda"), self,
objectName="allow-conda-experimental")
self.bind(cb_conda_install, "checked", "add-ons/allow-conda-experimental")
conda.layout().addWidget(cb_conda_install)
form.addRow(self.tr("Conda"), conda)
form.addRow(self.tr("Pip"), QLabel("Pip install arguments:"))
line_edit_pip = QLineEdit()
self.bind(line_edit_pip, "text", "add-ons/pip-install-arguments")
form.addRow("", line_edit_pip)
tab.setLayout(form)
# Network Tab
tab = QWidget()
self.addTab(tab, self.tr("Network"),
toolTip="Settings related to networking")
form = QFormLayout()
line_edit_http_proxy = QLineEdit()
self.bind(line_edit_http_proxy, "text", "network/http-proxy")
form.addRow("HTTP proxy:", line_edit_http_proxy)
line_edit_https_proxy = QLineEdit()
self.bind(line_edit_https_proxy, "text", "network/https-proxy")
form.addRow("HTTPS proxy:", line_edit_https_proxy)
tab.setLayout(form)
if self.__macUnified:
# Need some sensible size otherwise mac unified toolbar 'takes'
# the space that should be used for layout of the contents
self.adjustSize()
class OWOntology(OWWidget, ConcurrentWidgetMixin):
name = "Ontology"
description = ""
icon = "icons/Ontology.svg"
priority = 1110
keywords = []
CACHED, LIBRARY = range(2) # library list modification types
RUN_BUTTON, INC_BUTTON = "Generate", "Include"
settingsHandler = DomainContextHandler()
ontology_library: List[Dict] = Setting([
{"name": Ontology.generate_name([]), "ontology": {}},
])
ontology_index: int = Setting(0)
ontology: OntoType = Setting((), schema_only=True)
include_children = Setting(True)
auto_commit = Setting(True)
class Inputs:
words = Input("Words", Table)
class Outputs:
words = Output("Words", Table, dynamic=False)
class Warning(OWWidget.Warning):
no_words_column = Msg("Input is missing 'Words' column.")
class Error(OWWidget.Error):
load_error = Msg("{}")
def __init__(self):
OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
self.__onto_handler = OntologyHandler()
flags = Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsEditable
self.__model = PyListModel([], self, flags=flags)
self.__input_model = QStandardItemModel()
self.__library_view: QListView = None
self.__input_view: ListViewSearch = None
self.__ontology_view: EditableTreeView = None
self.ontology_info = ""
self._setup_gui()
self._restore_state()
self.settingsAboutToBePacked.connect(self._save_state)
def _setup_gui(self):
# control area
library_box: QGroupBox = gui.vBox(self.controlArea, "Library")
library_box.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Maximum)
edit_triggers = QListView.DoubleClicked | QListView.EditKeyPressed
self.__library_view = QListView(
editTriggers=int(edit_triggers),
minimumWidth=200,
sizePolicy=QSizePolicy(QSizePolicy.Ignored, QSizePolicy.Expanding),
)
self.__library_view.setFixedHeight(100)
self.__library_view.setItemDelegate(LibraryItemDelegate(self))
self.__library_view.setModel(self.__model)
self.__library_view.selectionModel().selectionChanged.connect(
self.__on_selection_changed
)
actions_widget = ModelActionsWidget()
actions_widget.layout().setSpacing(1)
tool_tip = "Add a new ontology to the library"
action = QAction("+", self, toolTip=tool_tip)
action.triggered.connect(self.__on_add)
actions_widget.addAction(action)
tool_tip = "Remove the ontology from the library"
action = QAction("\N{MINUS SIGN}", self, toolTip=tool_tip)
action.triggered.connect(self.__on_remove)
actions_widget.addAction(action)
tool_tip = "Save changes in the editor to the library"
action = QAction("Update", self, toolTip=tool_tip)
action.triggered.connect(self.__on_update)
actions_widget.addAction(action)
gui.rubber(actions_widget)
action = QAction("More", self, toolTip="More actions")
new_from_file = QAction("Import Ontology from File", self)
new_from_file.triggered.connect(self.__on_import_file)
new_from_url = QAction("Import Ontology from URL", self)
new_from_url.triggered.connect(self.__on_import_url)
save_to_file = QAction("Save Ontology to File", self)
save_to_file.triggered.connect(self.__on_save)
menu = QMenu(actions_widget)
menu.addAction(new_from_file)
menu.addAction(new_from_url)
menu.addAction(save_to_file)
action.setMenu(menu)
button = actions_widget.addAction(action)
button.setPopupMode(QToolButton.InstantPopup)
vlayout = QVBoxLayout()
vlayout.setSpacing(1)
vlayout.setContentsMargins(0, 0, 0, 0)
vlayout.addWidget(self.__library_view)
vlayout.addWidget(actions_widget)
library_box.layout().setSpacing(1)
library_box.layout().addLayout(vlayout)
input_box: QGroupBox = gui.vBox(self.controlArea, "Input")
self.__input_view = ListViewSearch(
sizePolicy=QSizePolicy(QSizePolicy.Ignored, QSizePolicy.Expanding),
selectionMode=QListView.ExtendedSelection,
dragEnabled=True,
)
self.__input_view.setModel(self.__input_model)
self.__input_view.selectionModel().selectionChanged.connect(
self._enable_include_button
)
self.__inc_button = gui.button(
None, self, self.INC_BUTTON, enabled=False,
toolTip="Include selected words into the ontology",
autoDefault=False, callback=self.__on_toggle_include
)
input_box.layout().setSpacing(1)
input_box.layout().addWidget(self.__input_view)
input_box.layout().addWidget(self.__inc_button)
self.__run_button = gui.button(
self.controlArea, self, self.RUN_BUTTON,
callback=self.__on_toggle_run
)
gui.checkBox(
self.controlArea, self, "include_children", "Include subtree",
box="Output", callback=self.commit.deferred
)
box = gui.vBox(self.controlArea, "Ontology info")
gui.label(box, self, "%(ontology_info)s")
gui.auto_send(self.buttonsArea, self, "auto_commit")
# main area
ontology_box: QGroupBox = gui.vBox(self.mainArea, box=True)
self.__ontology_view = EditableTreeView(self)
self.__ontology_view.dataChanged.connect(
self.__on_ontology_data_changed
)
self.__ontology_view.selectionChanged.connect(self.commit.deferred)
ontology_box.layout().setSpacing(1)
ontology_box.layout().addWidget(self.__ontology_view)
self._enable_include_button()
def __on_selection_changed(self, selection: QItemSelection, *_):
self.Error.load_error.clear()
if selection.indexes():
self.ontology_index = row = selection.indexes()[0].row()
data = self.__model[row].cached_word_tree
self.__ontology_view.set_data(data)
self.__update_score()
error_msg = self.__model[row].error_msg
if error_msg:
self.Error.load_error(error_msg)
def __on_add(self):
name = Ontology.generate_name([l.name for l in self.__model])
data = self.__ontology_view.get_data()
self.__model.append(Ontology(name, data))
self.__set_selected_row(len(self.__model) - 1)
def __on_remove(self):
index = self.__get_selected_row()
if index is not None:
del self.__model[index]
self.__set_selected_row(max(index - 1, 0))
def __on_update(self):
self.__set_current_modified(self.LIBRARY)
def __on_import_file(self):
ontology = read_from_file(self)
self._import_ontology(ontology)
def __on_import_url(self):
ontology = read_from_url(self)
self._import_ontology(ontology)
def __on_save(self):
index = self.__get_selected_row()
if index is not None:
filename = self.__model[index].filename
if filename:
filename, _ = os.path.splitext(filename)
else:
filename = os.path.expanduser("~/")
save_ontology(self, filename, self.__ontology_view.get_data())
QApplication.setActiveWindow(self)
def __on_toggle_include(self):
if self.task is not None:
self._cancel_tasks()
else:
self._run_insert()
def __on_toggle_run(self):
if self.task is not None:
self._cancel_tasks()
else:
self._run()
def __on_ontology_data_changed(self):
self.__set_current_modified(self.CACHED)
self.__update_score()
self._enable_include_button()
self.commit.deferred()
@Inputs.words
def set_words(self, words: Optional[Table]):
self.Warning.no_words_column.clear()
self.__input_model.clear()
if words:
if WORDS_COLUMN_NAME in words.domain and words.domain[
WORDS_COLUMN_NAME].attributes.get("type") == "words":
for word in words.get_column_view(WORDS_COLUMN_NAME)[0]:
self.__input_model.appendRow(QStandardItem(word))
else:
self.Warning.no_words_column()
@gui.deferred
def commit(self):
if self.include_children:
words = self.__ontology_view.get_selected_words_with_children()
else:
words = self.__ontology_view.get_selected_words()
words_table = self._create_output_table(sorted(words))
self.Outputs.words.send(words_table)
@staticmethod
def _create_output_table(words: List[str]) -> Optional[Table]:
if not words:
return None
return create_words_table(words)
def _cancel_tasks(self):
self.cancel()
self.__inc_button.setText(self.INC_BUTTON)
self.__run_button.setText(self.RUN_BUTTON)
def _run(self):
self.__run_button.setText("Stop")
words = self.__ontology_view.get_words()
handler = self.__onto_handler.generate
self.start(_run, handler, (words,))
def _run_insert(self):
self.__inc_button.setText("Stop")
tree = self.__ontology_view.get_data()
words = self.__get_selected_input_words()
handler = self.__onto_handler.insert
self.start(_run, handler, (tree, words))
def on_done(self, data: Dict):
self.__inc_button.setText(self.INC_BUTTON)
self.__run_button.setText(self.RUN_BUTTON)
self.__ontology_view.set_data(data, keep_history=True)
self.__set_current_modified(self.CACHED)
self.__update_score()
def __update_score(self):
tree = self.__ontology_view.get_data()
score = round(self.__onto_handler.score(tree), 2) \
if len(tree) == 1 and list(tree.values())[0] else "/"
self.ontology_info = f"Score: {score}"
def on_exception(self, ex: Exception):
raise ex
def on_partial_result(self, _: Any):
pass
def onDeleteWidget(self):
self.shutdown()
super().onDeleteWidget()
def __set_selected_row(self, row: int):
self.__library_view.selectionModel().select(
self.__model.index(row, 0), QItemSelectionModel.ClearAndSelect
)
def __get_selected_row(self) -> Optional[int]:
rows = self.__library_view.selectionModel().selectedRows()
return rows[0].row() if rows else None
def __set_current_modified(self, mod_type: int):
index = self.__get_selected_row()
if index is not None:
if mod_type == self.LIBRARY:
ontology = self.__ontology_view.get_data()
self.__model[index].word_tree = ontology
self.__model[index].cached_word_tree = ontology
self.__model[index].update_rule_flag = Ontology.NotModified
elif mod_type == self.CACHED:
ontology = self.__ontology_view.get_data()
self.__model[index].cached_word_tree = ontology
else:
raise NotImplementedError
self.__model.emitDataChanged(index)
self.__library_view.repaint()
def __get_selected_input_words(self) -> List[str]:
return [self.__input_view.model().data(index) for index in
self.__input_view.selectedIndexes()]
def _import_ontology(self, ontology: Ontology):
if ontology is not None:
self.__model.append(ontology)
self.__set_selected_row(len(self.__model) - 1)
QApplication.setActiveWindow(self)
def _restore_state(self):
source = [Ontology.from_dict(s) for s in self.ontology_library]
self.__model.wrap(source)
self.__set_selected_row(self.ontology_index)
if self.ontology:
self.__ontology_view.set_data(self.ontology)
self.__set_current_modified(self.CACHED)
self.__update_score()
self.commit.now()
def _save_state(self):
self.ontology_library = [s.as_dict() for s in self.__model]
self.ontology = self.__ontology_view.get_data(with_selection=True)
def _enable_include_button(self):
tree = self.__ontology_view.get_data()
words = self.__get_selected_input_words()
enabled = len(tree) == 1 and len(words) > 0
self.__inc_button.setEnabled(enabled)
def send_report(self):
model = self.__model
library = model[self.ontology_index].name if model else "/"
self.report_items("Settings", [("Library", library)])
ontology = self.__ontology_view.get_data()
style = """
<style>
ul {
padding-top: 0px;
padding-right: 0px;
padding-bottom: 0px;
padding-left: 20px;
}
</style>
"""
self.report_raw("Ontology", style + _tree_to_html(ontology))
def __setupUi(self):
"""Set up the UI.
"""
if self.__macUnified:
self.tab = QToolBar(
floatable=False,
movable=False,
allowedAreas=Qt.TopToolBarArea,
)
self.addToolBar(Qt.TopToolBarArea, self.tab)
self.setUnifiedTitleAndToolBarOnMac(True)
# This does not seem to work
self.setWindowFlags(self.windowFlags() & \
~Qt.MacWindowToolBarButtonHint)
self.tab.actionTriggered[QAction].connect(
self.__macOnToolBarAction)
central = QStackedWidget()
central.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
else:
self.tab = central = QTabWidget(self)
# Add a close button to the bottom of the dialog
# (to satisfy GNOME 3 which shows the dialog without a title bar).
container = container_widget_helper()
container.layout().addWidget(central)
buttonbox = QDialogButtonBox(QDialogButtonBox.Close)
buttonbox.rejected.connect(self.close)
container.layout().addWidget(buttonbox)
self.setCentralWidget(container)
self.stack = central
# General Tab
tab = QWidget()
self.addTab(tab,
self.tr("General"),
toolTip=self.tr("General Options"))
form = FormLayout()
tab.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
nodes = QWidget(self, objectName="nodes")
nodes.setLayout(QVBoxLayout())
nodes.layout().setContentsMargins(0, 0, 0, 0)
cb_anim = QCheckBox(self.tr("Enable node animations"),
objectName="enable-node-animations",
toolTip=self.tr(
"Enable shadow and ping animations for nodes "
"in the workflow."))
self.bind(cb_anim, "checked", "schemeedit/enable-node-animations")
nodes.layout().addWidget(cb_anim)
form.addRow(self.tr("Nodes"), nodes)
links = QWidget(self, objectName="links")
links.setLayout(QVBoxLayout())
links.layout().setContentsMargins(0, 0, 0, 0)
cb_show = QCheckBox(self.tr("Show channel names between widgets"),
objectName="show-channel-names",
toolTip=self.tr(
"Show source and sink channel names "
"over the links."))
self.bind(cb_show, "checked", "schemeedit/show-channel-names")
links.layout().addWidget(cb_show)
form.addRow(self.tr("Links"), links)
quickmenu = QWidget(self, objectName="quickmenu-options")
quickmenu.setLayout(QVBoxLayout())
quickmenu.layout().setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("Open on double click"),
toolTip=self.tr("Open quick menu on a double click "
"on an empty spot in the canvas"))
cb2 = QCheckBox(self.tr("Open on right click"),
toolTip=self.tr("Open quick menu on a right click "
"on an empty spot in the canvas"))
cb3 = QCheckBox(self.tr("Open on space key press"),
toolTip=self.tr(
"Open quick menu on Space key press "
"while the mouse is hovering over the canvas."))
cb4 = QCheckBox(self.tr("Open on any key press"),
toolTip=self.tr(
"Open quick menu on any key press "
"while the mouse is hovering over the canvas."))
cb5 = QCheckBox(self.tr("Show categories"),
toolTip=self.tr(
"In addition to searching, allow filtering "
"by categories."))
self.bind(cb1, "checked", "quickmenu/trigger-on-double-click")
self.bind(cb2, "checked", "quickmenu/trigger-on-right-click")
self.bind(cb3, "checked", "quickmenu/trigger-on-space-key")
self.bind(cb4, "checked", "quickmenu/trigger-on-any-key")
self.bind(cb5, "checked", "quickmenu/show-categories")
quickmenu.layout().addWidget(cb1)
quickmenu.layout().addWidget(cb2)
quickmenu.layout().addWidget(cb3)
quickmenu.layout().addWidget(cb4)
quickmenu.layout().addWidget(cb5)
form.addRow(self.tr("Quick menu"), quickmenu)
startup = QWidget(self, objectName="startup-group")
startup.setLayout(QVBoxLayout())
startup.layout().setContentsMargins(0, 0, 0, 0)
cb_splash = QCheckBox(self.tr("Show splash screen"),
self,
objectName="show-splash-screen")
cb_welcome = QCheckBox(self.tr("Show welcome screen"),
self,
objectName="show-welcome-screen")
cb_crash = QCheckBox(self.tr("Load crashed scratch workflows"),
self,
objectName="load-crashed-workflows")
self.bind(cb_splash, "checked", "startup/show-splash-screen")
self.bind(cb_welcome, "checked", "startup/show-welcome-screen")
self.bind(cb_crash, "checked", "startup/load-crashed-workflows")
startup.layout().addWidget(cb_splash)
startup.layout().addWidget(cb_welcome)
startup.layout().addWidget(cb_crash)
form.addRow(self.tr("On startup"), startup)
toolbox = QWidget(self, objectName="toolbox-group")
toolbox.setLayout(QVBoxLayout())
toolbox.layout().setContentsMargins(0, 0, 0, 0)
exclusive = QCheckBox(self.tr("Only one tab can be open at a time"))
self.bind(exclusive, "checked", "mainwindow/toolbox-dock-exclusive")
toolbox.layout().addWidget(exclusive)
form.addRow(self.tr("Tool box"), toolbox)
tab.setLayout(form)
# Style tab
tab = StyleConfigWidget()
self.addTab(tab, self.tr("&Style"), toolTip="Application style")
self.bind(tab, "selectedStyle_", "application-style/style-name")
self.bind(tab, "selectedPalette_", "application-style/palette")
# Output Tab
tab = QWidget()
self.addTab(tab, self.tr("Output"), toolTip="Output Redirection")
form = FormLayout()
combo = QComboBox()
combo.addItems([
self.tr("Critical"),
self.tr("Error"),
self.tr("Warn"),
self.tr("Info"),
self.tr("Debug")
])
self.bind(combo, "currentIndex", "logging/level")
form.addRow(self.tr("Logging"), combo)
box = QWidget()
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("Open in external browser"),
objectName="open-in-external-browser")
self.bind(cb1, "checked", "help/open-in-external-browser")
layout.addWidget(cb1)
box.setLayout(layout)
form.addRow(self.tr("Help window"), box)
tab.setLayout(form)
# Categories Tab
tab = QWidget()
layout = QVBoxLayout()
view = QListView(editTriggers=QListView.NoEditTriggers)
from .. import registry
reg = registry.global_registry()
model = QStandardItemModel()
settings = QSettings()
for cat in reg.categories():
item = QStandardItem()
item.setText(cat.name)
item.setCheckable(True)
visible, _ = category_state(cat, settings)
item.setCheckState(Qt.Checked if visible else Qt.Unchecked)
model.appendRow([item])
view.setModel(model)
layout.addWidget(view)
tab.setLayout(layout)
model.itemChanged.connect(lambda item: save_category_state(
reg.category(str(item.text())),
_State(item.checkState() == Qt.Checked, -1), settings))
self.addTab(tab, "Categories")
# Add-ons Tab
tab = QWidget()
self.addTab(tab,
self.tr("Add-ons"),
toolTip="Settings related to add-on installation")
form = FormLayout()
conda = QWidget(self, objectName="conda-group")
conda.setLayout(QVBoxLayout())
conda.layout().setContentsMargins(0, 0, 0, 0)
cb_conda_install = QCheckBox(self.tr("Install add-ons with conda"),
self,
objectName="allow-conda")
self.bind(cb_conda_install, "checked", "add-ons/allow-conda")
conda.layout().addWidget(cb_conda_install)
form.addRow(self.tr("Conda"), conda)
form.addRow(self.tr("Pip"), QLabel("Pip install arguments:"))
line_edit_pip = QLineEdit()
self.bind(line_edit_pip, "text", "add-ons/pip-install-arguments")
form.addRow("", line_edit_pip)
tab.setLayout(form)
# Network Tab
tab = QWidget()
self.addTab(tab,
self.tr("Network"),
toolTip="Settings related to networking")
form = FormLayout()
line_edit_http_proxy = QLineEdit()
self.bind(line_edit_http_proxy, "text", "network/http-proxy")
form.addRow("HTTP proxy:", line_edit_http_proxy)
line_edit_https_proxy = QLineEdit()
self.bind(line_edit_https_proxy, "text", "network/https-proxy")
form.addRow("HTTPS proxy:", line_edit_https_proxy)
tab.setLayout(form)
if self.__macUnified:
# Need some sensible size otherwise mac unified toolbar 'takes'
# the space that should be used for layout of the contents
self.adjustSize()
class ResolweDataWidget(QWidget):
def __init__(self, data_objects, descriptor_schema, *args, **kwargs):
super().__init__(*args, **kwargs)
self.ow = kwargs.get('parent', None)
self._data_objects = data_objects
self.descriptor_schema = descriptor_schema
self.header_schema = None
self.header = None
# set layout
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.view = QTreeView()
self.view.setSortingEnabled(False)
self.view.setAlternatingRowColors(True)
self.view.setEditTriggers(QTreeView.NoEditTriggers)
self.view.setSelectionMode(QTreeView.SingleSelection)
self.model = QStandardItemModel()
self.display_data_objects()
self.layout().addWidget(self.view)
def __set_header_values(self):
if self.header_schema:
labels = [val.get('label', '?') for val in self.header_schema]
self.model.setHorizontalHeaderLabels(labels)
def __create_row(self, obj):
row_items = []
tabular_data = obj.descriptor.get('tabular', None)
output_data = obj.output.get('table', None)
# TODO: refactor this. Use file_name and size from obj.output instead of desc. schema
for schema_value in self.header_schema:
item = QStandardItem()
schema_key = schema_value['name']
data_info = tabular_data.get(schema_key,
'?') if tabular_data else '?'
if schema_key == 'file_name' and data_info == '?':
data_info = output_data.get('file',
'?') if output_data else '?'
elif schema_key == 'file_size' and data_info == '?':
data_info = output_data.get('size',
'?') if output_data else '?'
item.setData(data_info, Qt.DisplayRole)
row_items.append(item)
return row_items
def __populate_data_model(self):
if self.model:
self.model.clear()
for data_object in self.data_objects:
self.model.appendRow(self.__create_row(data_object))
def __parse_description_schema(self):
self.header_schema = []
if self.descriptor_schema:
for schema_value in self.descriptor_schema.schema:
if schema_value['name'] == 'tabular':
[
self.header_schema.append(value)
for value in schema_value['group']
]
if self.header_schema:
keys = [val.get('name', '?') for val in self.header_schema]
header_index = namedtuple('header_index',
[label for label in keys])
self.header = header_index(
*[index for index, _ in enumerate(keys)])
@property
def data_objects(self):
return self._data_objects
@data_objects.setter
def data_objects(self, data_objects):
self._data_objects = data_objects
self.display_data_objects()
def display_data_objects(self):
self.__parse_description_schema()
self.__populate_data_model()
self.__set_header_values()
self.view.setModel(self.model)
def set_target_column(self, target_column):
# type: (int) -> None
for row in range(self.model.rowCount()):
item = self.model.item(row, target_column)
item_data = item.data(role=Qt.DisplayRole)
if item_data:
item.setIcon(variable_icon(item_data))
def selected_data_object(self):
# type: () -> Data
rows = self.view.selectionModel().selectedRows()
assert 0 <= len(rows) <= 1
sel_row_index = rows[0].row() if rows else None
obj_range = range(len(self._data_objects))
assert sel_row_index in obj_range
try:
return self._data_objects[sel_row_index]
except IndexError:
# can this happen? self._data_objects can't
# be empty if model is constructed
pass
def __setupUi(self):
"""Set up the UI.
"""
if self.__macUnified:
self.tab = QToolBar(
floatable=False, movable=False, allowedAreas=Qt.TopToolBarArea,
)
self.addToolBar(Qt.TopToolBarArea, self.tab)
self.setUnifiedTitleAndToolBarOnMac(True)
# This does not seem to work
self.setWindowFlags(self.windowFlags() & \
~Qt.MacWindowToolBarButtonHint)
self.tab.actionTriggered[QAction].connect(
self.__macOnToolBarAction
)
central = QStackedWidget()
central.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
else:
self.tab = central = QTabWidget(self)
# Add a close button to the bottom of the dialog
# (to satisfy GNOME 3 which shows the dialog without a title bar).
container = container_widget_helper()
container.layout().addWidget(central)
buttonbox = QDialogButtonBox(QDialogButtonBox.Close)
buttonbox.rejected.connect(self.close)
container.layout().addWidget(buttonbox)
self.setCentralWidget(container)
self.stack = central
# General Tab
tab = QWidget()
self.addTab(tab, self.tr("常规"),
toolTip=self.tr("常规选项"))
form = FormLayout()
tab.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
nodes = QWidget(self, objectName="nodes")
nodes.setLayout(QVBoxLayout())
nodes.layout().setContentsMargins(0, 0, 0, 0)
cb_anim = QCheckBox(
self.tr("启用节点动画"),
objectName="enable-node-animations",
toolTip=self.tr("为工作流中的节点启用阴影和ping动画。")
)
self.bind(cb_anim, "checked", "schemeedit/enable-node-animations")
nodes.layout().addWidget(cb_anim)
form.addRow(self.tr("结点"), nodes)
links = QWidget(self, objectName="links")
links.setLayout(QVBoxLayout())
links.layout().setContentsMargins(0, 0, 0, 0)
cb_show = QCheckBox(
self.tr("在窗口小部件之间显示通道名称"),
objectName="show-channel-names",
toolTip=self.tr("在链接上显示源和接收器通道名称。")
)
self.bind(cb_show, "checked", "schemeedit/show-channel-names")
links.layout().addWidget(cb_show)
form.addRow(self.tr("链接"), links)
quickmenu = QWidget(self, objectName="quickmenu-options")
quickmenu.setLayout(QVBoxLayout())
quickmenu.layout().setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("双击时打开"),
toolTip=self.tr("双击画布中的空白位置打开快捷菜单"))
cb2 = QCheckBox(self.tr("单击鼠标右键时打开"),
toolTip=self.tr("右键单击画布中的空白处打开快捷菜单"))
cb3 = QCheckBox(self.tr("按空格键时打开"),
toolTip=self.tr("当鼠标悬停在画布上时，按空格键。"))
cb4 = QCheckBox(self.tr("按任意按键时打开"),
toolTip=self.tr("当鼠标悬停在画布上时，按任意键。"))
cb5 = QCheckBox(self.tr("显示分类"),
toolTip=self.tr("In addition to searching, allow filtering "
"by categories."))
self.bind(cb1, "checked", "quickmenu/trigger-on-double-click")
self.bind(cb2, "checked", "quickmenu/trigger-on-right-click")
self.bind(cb3, "checked", "quickmenu/trigger-on-space-key")
self.bind(cb4, "checked", "quickmenu/trigger-on-any-key")
self.bind(cb5, "checked", "quickmenu/show-categories")
quickmenu.layout().addWidget(cb1)
quickmenu.layout().addWidget(cb2)
quickmenu.layout().addWidget(cb3)
quickmenu.layout().addWidget(cb4)
quickmenu.layout().addWidget(cb5)
form.addRow(self.tr("快捷菜单"), quickmenu)
startup = QWidget(self, objectName="startup-group")
startup.setLayout(QVBoxLayout())
startup.layout().setContentsMargins(0, 0, 0, 0)
cb_splash = QCheckBox(self.tr("显示启动画面"), self,
objectName="show-splash-screen")
cb_welcome = QCheckBox(self.tr("显示欢迎界面"), self,
objectName="show-welcome-screen")
cb_crash = QCheckBox(self.tr("加载崩溃的工作流"), self,
objectName="load-crashed-workflows")
self.bind(cb_splash, "checked", "startup/show-splash-screen")
self.bind(cb_welcome, "checked", "startup/show-welcome-screen")
self.bind(cb_crash, "checked", "startup/load-crashed-workflows")
startup.layout().addWidget(cb_splash)
startup.layout().addWidget(cb_welcome)
startup.layout().addWidget(cb_crash)
form.addRow(self.tr("启动时"), startup)
toolbox = QWidget(self, objectName="toolbox-group")
toolbox.setLayout(QVBoxLayout())
toolbox.layout().setContentsMargins(0, 0, 0, 0)
exclusive = QCheckBox(self.tr("一次只能打开一个选项卡"))
self.bind(exclusive, "checked", "mainwindow/toolbox-dock-exclusive")
toolbox.layout().addWidget(exclusive)
form.addRow(self.tr("工具箱"), toolbox)
tab.setLayout(form)
# Style tab
tab = StyleConfigWidget()
self.addTab(tab, self.tr("&Style"), toolTip="Application style")
self.bind(tab, "selectedStyle_", "application-style/style-name")
self.bind(tab, "selectedPalette_", "application-style/palette")
# Output Tab
tab = QWidget()
self.addTab(tab, self.tr("输出"),
toolTip="输出重定向")
form = FormLayout()
combo = QComboBox()
combo.addItems([self.tr("关键"),
self.tr("错误"),
self.tr("警告"),
self.tr("信息"),
self.tr("调试")])
self.bind(combo, "currentIndex", "logging/level")
form.addRow(self.tr("记录"), combo)
box = QWidget()
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
cb1 = QCheckBox(self.tr("在外部浏览器中打开"),
objectName="open-in-external-browser")
self.bind(cb1, "checked", "help/open-in-external-browser")
layout.addWidget(cb1)
box.setLayout(layout)
form.addRow(self.tr("帮助窗口"), box)
tab.setLayout(form)
# Categories Tab
tab = QWidget()
layout = QVBoxLayout()
view = QListView(
editTriggers=QListView.NoEditTriggers
)
from .. import registry
reg = registry.global_registry()
model = QStandardItemModel()
settings = QSettings()
for cat in reg.categories():
item = QStandardItem()
item.setText(cat.name)
item.setCheckable(True)
visible, _ = category_state(cat, settings)
item.setCheckState(Qt.Checked if visible else Qt.Unchecked)
model.appendRow([item])
view.setModel(model)
layout.addWidget(view)
tab.setLayout(layout)
model.itemChanged.connect(
lambda item:
save_category_state(
reg.category(str(item.text())),
_State(item.checkState() == Qt.Checked, -1),
settings
)
)
self.addTab(tab, "类别")
# Add-ons Tab
tab = QWidget()
self.addTab(tab, self.tr("插件"),
toolTip="与插件安装相关的设置")
form = FormLayout()
conda = QWidget(self, objectName="conda-group")
conda.setLayout(QVBoxLayout())
conda.layout().setContentsMargins(0, 0, 0, 0)
mirror_install = QCheckBox(self.tr("使用国内镜像安装"), self,
objectName="allow-conda")
self.bind(mirror_install, "checked", "add-ons/allow-conda")
conda.layout().addWidget(mirror_install)
form.addRow(self.tr("镜像"), conda)
form.addRow(self.tr("Pip"), QLabel("Pip 安装参数:"))
line_edit_pip = QLineEdit()
# line_edit_pip.setText('-i https://mirrors.aliyun.com/pypi/simple')
self.bind(line_edit_pip, "text", "add-ons/pip-install-arguments")
form.addRow("", line_edit_pip)
tab.setLayout(form)
# Network Tab
tab = QWidget()
self.addTab(tab, self.tr("网络"),
toolTip="与网络相关的设置")
form = FormLayout()
line_edit_http_proxy = QLineEdit()
self.bind(line_edit_http_proxy, "text", "network/http-proxy")
form.addRow("HTTP 代理:", line_edit_http_proxy)
line_edit_https_proxy = QLineEdit()
self.bind(line_edit_https_proxy, "text", "network/https-proxy")
form.addRow("HTTPS 代理:", line_edit_https_proxy)
tab.setLayout(form)
if self.__macUnified:
# Need some sensible size otherwise mac unified toolbar 'takes'
# the space that should be used for layout of the contents
self.adjustSize()
def find_rules(self):
if self.data is None or not len(self.data):
return
if self._is_running:
self._is_running = False
return
self.button.button.setText('Cancel')
self._is_running = True
data = self.data
self.table.model().clear()
n_examples = len(data)
NumericItem = self.NumericItem
StandardItem = self.StandardItem
filterSearch = self.filterSearch
itemsetMin = self.filterAntecedentMin + self.filterConsequentMin
itemsetMax = self.filterAntecedentMax + self.filterConsequentMax
isSizeMatch = self.isSizeMatch
isRegexMatch = self.isRegexMatch
X, mapping = OneHot.encode(data, self.classify)
self.Error.need_discrete_data.clear()
if X is None:
self.Error.need_discrete_data()
self.onehot_mapping = mapping
ITEM_FMT = '{}' if issparse(data.X) else '{}={}'
names = {
item:
('{}={}' if var is data.domain.class_var else ITEM_FMT).format(
var.name, val)
for item, var, val in OneHot.decode(mapping, data, mapping)
}
# Items that consequent must include if classifying
class_items = {
item
for item, var, val in OneHot.decode(mapping, data, mapping)
if var is data.domain.class_var
} if self.classify else set()
assert bool(class_items) == bool(self.classify)
model = QStandardItemModel(self.table)
for col, (label, tooltip) in enumerate([
("Supp", "Support"),
("Conf", "Confidence (support / antecedent support)"),
("Covr", "Coverage (antecedent support / number of examples)"),
("Strg", "Strength (consequent support / antecedent support)"),
("Lift",
"Lift (number of examples * confidence / consequent support)"),
("Levr",
"Leverage ((support * number of examples - antecedent support * consequent support) / (number of examples)²)"
), ("Antecedent", None), ("", None), ("Consequent", None)
]):
item = QStandardItem(label)
item.setToolTip(tooltip)
model.setHorizontalHeaderItem(col, item)
#~ # Aggregate rules by common (support,confidence) for scatterplot
#~ scatter_agg = defaultdict(list)
# Find itemsets
nRules = 0
itemsets = {}
ARROW_ITEM = StandardItem('→')
ARROW_ITEM.setTextAlignment(Qt.AlignCenter)
with self.progressBar(self.maxRules + 1) as progress:
for itemset, support in frequent_itemsets(X,
self.minSupport / 100):
itemsets[itemset] = support
if class_items and not class_items & itemset:
continue
# Filter itemset by joined filters before descending into it
itemset_str = ' '.join(names[i] for i in itemset)
if (filterSearch and
(len(itemset) < itemsetMin or itemsetMax < len(itemset)
or not isRegexMatch(itemset_str, itemset_str))):
continue
for rule in association_rules(itemsets,
self.minConfidence / 100,
itemset):
left, right, support, confidence = rule
if class_items and right - class_items:
continue
if filterSearch and not isSizeMatch(len(left), len(right)):
continue
left_str = ', '.join(names[i] for i in sorted(left))
right_str = ', '.join(names[i] for i in sorted(right))
if filterSearch and not isRegexMatch(left_str, right_str):
continue
# All filters matched, calculate stats and add table row
_, _, _, _, coverage, strength, lift, leverage = next(
rules_stats((rule, ), itemsets, n_examples))
support_item = NumericItem(support / n_examples)
# Set row data on first column
support_item.setData(
(itemset - class_items, class_items and
(class_items & itemset).pop()), self.ROW_DATA_ROLE)
left_item = StandardItem(left_str, len(left))
left_item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
model.appendRow([
support_item,
NumericItem(confidence),
NumericItem(coverage),
NumericItem(strength),
NumericItem(lift),
NumericItem(leverage), left_item,
ARROW_ITEM.clone(),
StandardItem(right_str, len(right))
])
#~ scatter_agg[(round(support / n_examples, 2), round(confidence, 2))].append((left, right))
nRules += 1
progress.advance()
if not self._is_running or nRules >= self.maxRules:
break
qApp.processEvents()
if not self._is_running or nRules >= self.maxRules:
break
# Populate the TableView
table = self.table
table.setHidden(True)
table.setSortingEnabled(False)
proxy_model = self.proxy_model
proxy_model.setSourceModel(model)
table.setModel(proxy_model)
for i in range(model.columnCount()):
table.resizeColumnToContents(i)
table.setSortingEnabled(True)
table.setHidden(False)
self.button.button.setText('Find Rules')
self.nRules = nRules
self.nFilteredRules = proxy_model.rowCount(
) # TODO: continue; also add in owitemsets
self.nSelectedRules = 0
self.nSelectedExamples = 0
self._is_running = False
class OWPreprocess(widget.OWWidget, openclass=True):
name = "Preprocess"
description = "Construct a data preprocessing pipeline."
icon = "icons/Preprocess.svg"
priority = 2105
keywords = ["process"]
settings_version = 2
class Inputs:
data = Input("Data", Orange.data.Table)
class Outputs:
preprocessor = Output("Preprocessor",
preprocess.preprocess.Preprocess,
dynamic=False)
preprocessed_data = Output("Preprocessed Data", Orange.data.Table)
storedsettings = Setting({})
autocommit = Setting(True)
PREPROCESSORS = PREPROCESS_ACTIONS
CONTROLLER = Controller
def __init__(self):
super().__init__()
self.data = None
self._invalidated = False
# List of available preprocessors (DescriptionRole : Description)
self.preprocessors = QStandardItemModel()
def mimeData(indexlist):
assert len(indexlist) == 1
index = indexlist[0]
qname = index.data(DescriptionRole).qualname
m = QMimeData()
m.setData("application/x-qwidget-ref", qname.encode("utf-8"))
return m
# TODO: Fix this (subclass even if just to pass a function
# for mimeData delegate)
self.preprocessors.mimeData = mimeData
box = gui.vBox(self.controlArea, "Preprocessors")
gui.rubber(self.controlArea)
# we define a class that lets us set the vertical sizeHint
# based on the height and number of items in the list
# see self.__update_list_sizeHint
class ListView(QListView):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.vertical_hint = None
def sizeHint(self):
sh = super().sizeHint()
if self.vertical_hint:
return QSize(sh.width(), self.vertical_hint)
return sh
self.preprocessorsView = view = ListView(
selectionMode=QListView.SingleSelection,
dragEnabled=True,
dragDropMode=QListView.DragOnly)
view.setModel(self.preprocessors)
view.activated.connect(self.__activated)
box.layout().addWidget(view)
####
self._qname2ppdef = {
ppdef.qualname: ppdef
for ppdef in self.PREPROCESSORS
}
# List of 'selected' preprocessors and their parameters.
self.preprocessormodel = None
self.flow_view = SequenceFlow()
self.controler = self.CONTROLLER(self.flow_view, parent=self)
self.overlay = OverlayWidget(self)
self.overlay.setAttribute(Qt.WA_TransparentForMouseEvents)
self.overlay.setWidget(self.flow_view)
self.overlay.setLayout(QVBoxLayout())
self.overlay.layout().addWidget(
QLabel("Drag items from the list on the left", wordWrap=True))
self.scroll_area = QScrollArea(
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn)
self.scroll_area.viewport().setAcceptDrops(True)
self.scroll_area.setWidget(self.flow_view)
self.scroll_area.setWidgetResizable(True)
self.mainArea.layout().addWidget(self.scroll_area)
self.flow_view.installEventFilter(self)
gui.auto_apply(self.buttonsArea, self, "autocommit")
self._initialize()
def _initialize(self):
for pp_def in self.PREPROCESSORS:
description = pp_def.description
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item = QStandardItem(icon, description.title)
item.setToolTip(description.summary or "")
item.setData(pp_def, DescriptionRole)
item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable
| Qt.ItemIsDragEnabled)
self.preprocessors.appendRow([item])
self.__update_list_sizeHint()
model = self.load(self.storedsettings)
self.set_model(model)
if not model.rowCount():
# enforce default width constraint if no preprocessors
# are instantiated (if the model is not empty the constraints
# will be triggered by LayoutRequest event on the `flow_view`)
self.__update_size_constraint()
self.apply()
def __update_list_sizeHint(self):
view = self.preprocessorsView
h = view.sizeHintForRow(0)
n = self.preprocessors.rowCount()
view.vertical_hint = n * h + 2 # only on Mac?
view.updateGeometry()
def load(self, saved):
"""Load a preprocessor list from a dict."""
preprocessors = saved.get("preprocessors", [])
model = StandardItemModel()
def dropMimeData(data, action, row, _column, _parent):
if data.hasFormat("application/x-qwidget-ref") and \
action == Qt.CopyAction:
qname = bytes(data.data("application/x-qwidget-ref")).decode()
ppdef = self._qname2ppdef[qname]
item = QStandardItem(ppdef.description.title)
item.setData({}, ParametersRole)
item.setData(ppdef.description.title, Qt.DisplayRole)
item.setData(ppdef, DescriptionRole)
self.preprocessormodel.insertRow(row, [item])
return True
else:
return False
model.dropMimeData = dropMimeData
for qualname, params in preprocessors:
pp_def = self._qname2ppdef[qualname]
description = pp_def.description
item = QStandardItem(description.title)
if description.icon:
icon = QIcon(description.icon)
else:
icon = QIcon()
item.setIcon(icon)
item.setToolTip(description.summary)
item.setData(pp_def, DescriptionRole)
item.setData(params, ParametersRole)
model.appendRow(item)
return model
@staticmethod
def save(model):
"""Save the preprocessor list to a dict."""
d = {"name": ""}
preprocessors = []
for i in range(model.rowCount()):
item = model.item(i)
pp_def = item.data(DescriptionRole)
params = item.data(ParametersRole)
preprocessors.append((pp_def.qualname, params))
d["preprocessors"] = preprocessors
return d
def set_model(self, ppmodel):
if self.preprocessormodel:
self.preprocessormodel.dataChanged.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsInserted.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.disconnect(
self.__on_modelchanged)
self.preprocessormodel.rowsMoved.disconnect(self.__on_modelchanged)
self.preprocessormodel.deleteLater()
self.preprocessormodel = ppmodel
self.controler.setModel(ppmodel)
if ppmodel is not None:
self.preprocessormodel.dataChanged.connect(self.__on_modelchanged)
self.preprocessormodel.rowsInserted.connect(self.__on_modelchanged)
self.preprocessormodel.rowsRemoved.connect(self.__on_modelchanged)
self.preprocessormodel.rowsMoved.connect(self.__on_modelchanged)
self.__update_overlay()
def __update_overlay(self):
if self.preprocessormodel is None or \
self.preprocessormodel.rowCount() == 0:
self.overlay.setWidget(self.flow_view)
self.overlay.show()
else:
self.overlay.setWidget(None)
self.overlay.hide()
def __on_modelchanged(self):
self.__update_overlay()
self.commit()
@Inputs.data
@check_sql_input
def set_data(self, data=None):
"""Set the input dataset."""
self.data = data
def handleNewSignals(self):
self.apply()
def __activated(self, index):
item = self.preprocessors.itemFromIndex(index)
action = item.data(DescriptionRole)
item = QStandardItem()
item.setData({}, ParametersRole)
item.setData(action.description.title, Qt.DisplayRole)
item.setData(action, DescriptionRole)
self.preprocessormodel.appendRow([item])
def buildpreproc(self):
plist = []
for i in range(self.preprocessormodel.rowCount()):
item = self.preprocessormodel.item(i)
desc = item.data(DescriptionRole)
params = item.data(ParametersRole)
if not isinstance(params, dict):
params = {}
create = desc.viewclass.createinstance
plist.append(create(params))
if len(plist) == 1:
return plist[0]
else:
return preprocess.preprocess.PreprocessorList(plist)
def apply(self):
# Sync the model into storedsettings on every apply.
self.storeSpecificSettings()
preprocessor = self.buildpreproc()
if self.data is not None:
self.error()
try:
data = preprocessor(self.data)
except (ValueError, ZeroDivisionError) as e:
self.error(str(e))
return
else:
data = None
self.Outputs.preprocessor.send(preprocessor)
self.Outputs.preprocessed_data.send(data)
def commit(self):
if not self._invalidated:
self._invalidated = True
QApplication.postEvent(self, QEvent(QEvent.User))
def customEvent(self, event):
if event.type() == QEvent.User and self._invalidated:
self._invalidated = False
self.apply()
def eventFilter(self, receiver, event):
if receiver is self.flow_view and event.type() == QEvent.LayoutRequest:
QTimer.singleShot(0, self.__update_size_constraint)
return super().eventFilter(receiver, event)
def storeSpecificSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().storeSpecificSettings()
def saveSettings(self):
"""Reimplemented."""
self.storedsettings = self.save(self.preprocessormodel)
super().saveSettings()
@classmethod
def migrate_settings(cls, settings, version):
if version < 2:
for action, params in settings["storedsettings"]["preprocessors"]:
if action == "orange.preprocess.scale":
scale = center = None
if "center" in params:
center = params.pop("center").name
if "scale" in params:
scale = params.pop("scale").name
migratable = {
("Mean", "NoScaling"): Scale.CenterByMean,
("NoCentering", "Std"): Scale.ScaleBySD,
("Mean", "Std"): Scale.NormalizeBySD,
("NoCentering", "Span"):
Scale.NormalizeBySpan_ZeroBased
}
params["method"] = \
migratable.get((center, scale), Scale.NormalizeBySD)
def onDeleteWidget(self):
self.data = None
self.set_model(None)
super().onDeleteWidget()
@Slot()
def __update_size_constraint(self):
# Update minimum width constraint on the scroll area containing
# the 'instantiated' preprocessor list (to avoid the horizontal
# scroll bar).
sh = self.flow_view.minimumSizeHint()
scroll_width = self.scroll_area.verticalScrollBar().width()
self.scroll_area.setMinimumWidth(
min(max(sh.width() + scroll_width + 2, self.controlArea.width()),
520))
def send_report(self):
pp = [(self.controler.model().index(i, 0).data(Qt.DisplayRole), w)
for i, w in enumerate(self.controler.view.widgets())]
if pp:
self.report_items("Settings", pp)
def __on_enrichment_finished(self, results):
assert QThread.currentThread() is self.thread()
self.__state &= ~OWSetEnrichment.RunningEnrichment
query, reference, results = results
if self.annotationsChartView.model():
self.annotationsChartView.model().clear()
nquery = len(query)
nref = len(reference)
maxcount = max((len(e.query_mapped) for _, e in results),
default=1)
maxrefcount = max((len(e.reference_mapped) for _, e in results),
default=1)
nspaces = int(math.ceil(math.log10(maxcount or 1)))
refspaces = int(math.ceil(math.log(maxrefcount or 1)))
query_fmt = "%" + str(nspaces) + "s (%.2f%%)"
ref_fmt = "%" + str(refspaces) + "s (%.2f%%)"
def fmt_count(fmt, count, total):
return fmt % (count, 100.0 * count / (total or 1))
fmt_query_count = partial(fmt_count, query_fmt)
fmt_ref_count = partial(fmt_count, ref_fmt)
linkFont = QFont(self.annotationsChartView.viewOptions().font)
linkFont.setUnderline(True)
def item(value=None, tooltip=None, user=None):
si = QStandardItem()
if value is not None:
si.setData(value, Qt.DisplayRole)
if tooltip is not None:
si.setData(tooltip, Qt.ToolTipRole)
if user is not None:
si.setData(user, Qt.UserRole)
else:
si.setData(value, Qt.UserRole)
return si
model = QStandardItemModel()
model.setSortRole(Qt.UserRole)
model.setHorizontalHeaderLabels(
["Category", "Term", "Count", "Reference count", "p-value",
"FDR", "Enrichment"])
for i, (gset, enrich) in enumerate(results):
if len(enrich.query_mapped) == 0:
continue
nquery_mapped = len(enrich.query_mapped)
nref_mapped = len(enrich.reference_mapped)
row = [
item(", ".join(gset.hierarchy)),
item(gsname(gset), tooltip=gset.link),
item(fmt_query_count(nquery_mapped, nquery),
tooltip=nquery_mapped, user=nquery_mapped),
item(fmt_ref_count(nref_mapped, nref),
tooltip=nref_mapped, user=nref_mapped),
item(fmtp(enrich.p_value), user=enrich.p_value),
item(), # column 5, FDR, is computed in filterAnnotationsChartView
item(enrich.enrichment_score,
tooltip="%.3f" % enrich.enrichment_score,
user=enrich.enrichment_score)
]
row[0].geneset = gset
row[0].enrichment = enrich
row[1].setData(gset.link, gui.LinkRole)
row[1].setFont(linkFont)
row[1].setForeground(QColor(Qt.blue))
model.appendRow(row)
self.annotationsChartView.setModel(model)
self.annotationsChartView.selectionModel().selectionChanged.connect(
self.commit
)
if not model.rowCount():
self.warning(0, "No enriched sets found.")
else:
self.warning(0)
allnames = set(gsname(geneset)
for geneset, (count, _, _, _) in results if count)
allnames |= reduce(operator.ior,
(set(word_split(name)) for name in allnames),
set())
self.filterCompleter.setModel(None)
self.completerModel = QStringListModel(sorted(allnames))
self.filterCompleter.setModel(self.completerModel)
if results:
max_score = max((e.enrichment_score for _, e in results
if np.isfinite(e.enrichment_score)),
default=1)
self.annotationsChartView.setItemDelegateForColumn(
6, BarItemDelegate(self, scale=(0.0, max_score))
)
self.annotationsChartView.setItemDelegateForColumn(
1, gui.LinkStyledItemDelegate(self.annotationsChartView)
)
header = self.annotationsChartView.header()
for i in range(model.columnCount()):
sh = self.annotationsChartView.sizeHintForColumn(i)
sh = max(sh, header.sectionSizeHint(i))
self.annotationsChartView.setColumnWidth(i, max(min(sh, 300), 30))
# self.annotationsChartView.resizeColumnToContents(i)
self.filterAnnotationsChartView()
self.progressBarFinished()
self.setStatusMessage("")
