class DropDownRadioBooleanFilter(QWidget, Control): """Container for multiple boolean filters """ def __init__(self, tree, dataset, master, parent=None): QWidget.__init__(self, parent) Control.__init__(self, tree, dataset, master) self.setLayout(QHBoxLayout()) self.cb = QComboBox(self) self.layout().addWidget(self.cb) rblayout = QVBoxLayout() self.radioButtons = [QRadioButton("Only", self), QRadioButton("Excluded", self) ] for b in self.radioButtons: rblayout.addWidget(b) self.radioButtons[0].setChecked(True) self.layout().addLayout(rblayout) self.options = [] self.setOptions(tree.subelements_top("Option")) def setOptions(self, options): self.cb.clear() self.options = [] for option in options: self.cb.addItem(option.displayName) self.options.append(option) for op, rb in zip(self.options[0].subelements_top("Option"), self.radioButtons): rb.setText(op.displayName) rb.setChecked(getattr(op, "default", "false") == "true") def value(self): return {"excluded": "0" if self.radioButtons[0].isChecked() else "1"} def query(self): filter = self.options[self.cb.currentIndex()] filter = biomart.FilterDescription( self.tree.registry, "FilterDescription", filter.attributes, filter.children) return [("Filter", filter, self.value())] def setControlValue(self, name, value): for i, option in enumerate(self.options): if option.internalName == name: self.cb.setCurrentIndex(i) if value == "Only": self.radioButtons[0].setChecked(True)
class DropDownRadioBooleanFilter(QWidget, Control): """Container for multiple boolean filters """ def __init__(self, tree, dataset, master, parent=None): QWidget.__init__(self, parent) Control.__init__(self, tree, dataset, master) self.setLayout(QHBoxLayout()) self.cb = QComboBox(self) self.layout().addWidget(self.cb) rblayout = QVBoxLayout() self.radioButtons = [QRadioButton("Only", self), QRadioButton("Excluded", self) ] for b in self.radioButtons: rblayout.addWidget(b) self.radioButtons[0].setChecked(True) self.layout().addLayout(rblayout) self.options = [] self.setOptions(tree.subelements_top("Option")) def setOptions(self, options): self.cb.clear() self.options = [] for option in options: self.cb.addItem(option.displayName) self.options.append(option) for op, rb in zip(self.options[0].subelements_top("Option"), self.radioButtons): rb.setText(op.displayName) rb.setChecked(getattr(op, "default", "false") == "true") def value(self): return {"excluded": "0" if self.radioButtons[0].isChecked() else "1"} def query(self): filter = self.options[self.cb.currentIndex()] filter = biomart.FilterDescription( self.tree.registry, "FilterDescription", filter.attributes, filter.children) return [("Filter", filter, self.value())] def setControlValue(self, name, value): for i, option in enumerate(self.options): if option.internalName == name: self.cb.setCurrentIndex(i) if value == "Only": self.radioButtons[0].setChecked(True)
class RecentPathsWComboMixin(RecentPathsWidgetMixin): """ Adds file combo handling to :obj:`RecentPathsWidgetMixin`. The mixin constructs a combo box `self.file_combo` and provides a method `set_file_list` for updating its content. The mixin also overloads the inherited `add_path` and `select_file` to call `set_file_list`. """ def __init__(self): super().__init__() self.file_combo = \ QComboBox(self, sizeAdjustPolicy=QComboBox.AdjustToContents) def add_path(self, filename): """Add (or move) a file name to the top of recent paths""" super().add_path(filename) self.set_file_list() def select_file(self, n): """Move the n-th file to the top of the list""" super().select_file(n) self.set_file_list() def set_file_list(self): """ Sets the items in the file list combo """ self._check_init() self.file_combo.clear() if not self.recent_paths: self.file_combo.addItem("(none)") self.file_combo.model().item(0).setEnabled(False) else: for i, recent in enumerate(self.recent_paths): self.file_combo.addItem(recent.basename) self.file_combo.model().item(i).setToolTip(recent.abspath) if not os.path.exists(recent.abspath): self.file_combo.setItemData(i, QBrush(Qt.red), Qt.TextColorRole) def workflowEnvChanged(self, key, value, oldvalue): super().workflowEnvChanged(key, value, oldvalue) if key == "basedir": self.set_file_list()
class DropDownIdListFilter(QWidget, Control): """Container for multiple id list filters """ def __init__(self, tree, dataset, master, parent=None): QWidget.__init__(self, parent) Control.__init__(self, tree, dataset, master) self.setLayout(QVBoxLayout()) self.setContentsMargins(0, 0, 0, 0) self.cb = QComboBox() self.idsEdit = QPlainTextEdit() self.layout().addWidget(self.cb) self.layout().addWidget(self.idsEdit) self.options = [] self.setOptions(tree.subelements_top("Option")) def setOptions(self, options): self.cb.clear() self.options = [] for option in options: self.cb.addItem(option.displayName) self.options.append(option) def value(self): return str(self.idsEdit.toPlainText()).split() def query(self): filter = self.options[self.cb.currentIndex()] filter = biomart.FilterDescription( self.tree.registry, "FilterDescription", filter.attributes, filter.children) return [("Filter", filter, self.value())] def setControlValue(self, name, value): if isinstance(value, list): value = "\n".join(value) for i, op in enumerate(self.options): if name == op.internalName: self.cb.setCurrentIndex(i) self.idsEdit.setPlainText(value)
class DropDownIdListFilter(QWidget, Control): """Container for multiple id list filters """ def __init__(self, tree, dataset, master, parent=None): QWidget.__init__(self, parent) Control.__init__(self, tree, dataset, master) self.setLayout(QVBoxLayout()) self.setContentsMargins(0, 0, 0, 0) self.cb = QComboBox() self.idsEdit = QPlainTextEdit() self.layout().addWidget(self.cb) self.layout().addWidget(self.idsEdit) self.options = [] self.setOptions(tree.subelements_top("Option")) def setOptions(self, options): self.cb.clear() self.options = [] for option in options: self.cb.addItem(option.displayName) self.options.append(option) def value(self): return str(self.idsEdit.toPlainText()).split() def query(self): filter = self.options[self.cb.currentIndex()] filter = biomart.FilterDescription( self.tree.registry, "FilterDescription", filter.attributes, filter.children) return [("Filter", filter, self.value())] def setControlValue(self, name, value): if isinstance(value, list): value = "\n".join(value) for i, op in enumerate(self.options): if name == op.internalName: self.cb.setCurrentIndex(i) self.idsEdit.setPlainText(value)
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 class Inputs: data = Input("Data", Orange.data.Table) learner = Input("Learner", Learner) class Outputs: data = Output("Data", Orange.data.Table) class Error(OWWidget.Error): imputation_failed = Msg("Imputation failed for '{}'") model_based_imputer_sparse = Msg("Model based imputer does not work for sparse data") DEFAULT_LEARNER = SimpleTreeLearner() METHODS = [AsDefault(), impute.DoNotImpute(), impute.Average(), impute.AsValue(), impute.Model(DEFAULT_LEARNER), impute.Random(), impute.DropInstances(), impute.Default()] DEFAULT, DO_NOT_IMPUTE, MODEL_BASED_IMPUTER, AS_INPUT = 0, 1, 4, 7 settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(DO_NOT_IMPUTE) variable_methods = settings.ContextSetting({}) autocommit = settings.Setting(True) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() # copy METHODS (some are modified by the widget) self.methods = copy.deepcopy(OWImpute.METHODS) main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, method in enumerate(self.methods): if not method.columns_only: button = QRadioButton(method.name) button.setChecked(i == self.default_method_index) button_group.addButton(button, i) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView( selectionMode=QListView.ExtendedSelection ) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed ) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for i, method in enumerate(self.methods): button = QRadioButton(text=method.name) button_group.addButton(button, i) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected ) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection ) method_layout.addStretch(2) reset_button = QPushButton( "Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_methods, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit( self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.layout().insertSpacing(0, 80) box.layout().insertWidget(0, self.report_button) self.data = None self.learner = None self.modified = False self.default_method = self.methods[self.default_method_index] self.executor = qconcurrent.ThreadExecutor(self) self.__task = None @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: self._default_method_index = index self.default_button_group.button(index).setChecked(True) self.default_method = self.methods[self.default_method_index] self.methods[self.DEFAULT].method = self.default_method # update variable view for index in map(self.varmodel.index, range(len(self.varmodel))): method = self.variable_methods.get( index.row(), self.methods[self.DEFAULT]) self.varmodel.setData(index, method, Qt.UserRole) self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @Inputs.data @check_sql_input def set_data(self, data): self.closeContext() self.varmodel[:] = [] self.variable_methods = {} self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) self.update_varview() self.unconditional_commit() @Inputs.learner def set_learner(self, learner): self.learner = learner or self.DEFAULT_LEARNER imputer = self.methods[self.MODEL_BASED_IMPUTER] imputer.learner = self.learner button = self.default_button_group.button(self.MODEL_BASED_IMPUTER) button.setText(imputer.name) variable_button = self.variable_button_group.button(self.MODEL_BASED_IMPUTER) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = self.MODEL_BASED_IMPUTER self.update_varview() self.commit() def get_method_for_column(self, column_index): """Returns the imputation method for column by its index. """ if not isinstance(column_index, int): column_index = column_index.row() return self.variable_methods.get(column_index, self.methods[self.DEFAULT]) def _invalidate(self): self.modified = True if self.__task is not None: self.cancel() self.commit() def commit(self): self.cancel() self.warning() self.Error.imputation_failed.clear() self.Error.model_based_imputer_sparse.clear() if self.data is None or len(self.data) == 0 or len(self.varmodel) == 0: self.Outputs.data.send(self.data) self.modified = False return data = self.data impute_state = [ (i, var, self.variable_methods.get(i, self.default_method)) for i, var in enumerate(self.varmodel) ] def impute_one(method, var, data): # type: (impute.BaseImputeMethod, Variable, Table) -> Any if isinstance(method, impute.Model) and data.is_sparse(): raise SparseNotSupported() elif isinstance(method, impute.DropInstances): return RowMask(method(data, var)) elif not method.supports_variable(var): raise VariableNotSupported(var) else: return method(data, var) futures = [] for _, var, method in impute_state: f = self.executor.submit( impute_one, copy.deepcopy(method), var, data) futures.append(f) w = qconcurrent.FutureSetWatcher(futures) w.doneAll.connect(self.__commit_finish) w.progressChanged.connect(self.__progress_changed) self.__task = Task(futures, w) self.progressBarInit(processEvents=False) self.setBlocking(True) @Slot() def __commit_finish(self): assert QThread.currentThread() is self.thread() assert self.__task is not None futures = self.__task.futures assert len(futures) == len(self.varmodel) assert self.data is not None self.__task = None self.setBlocking(False) self.progressBarFinished() data = self.data attributes = [] class_vars = [] drop_mask = np.zeros(len(self.data), bool) for i, (var, fut) in enumerate(zip(self.varmodel, futures)): assert fut.done() newvar = [] try: res = fut.result() except SparseNotSupported: self.Error.model_based_imputer_sparse() # ?? break except VariableNotSupported: self.warning("Default method can not handle '{}'". format(var.name)) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error for %s", var, exc_info=True) self.Error.imputation_failed(var.name) attributes = class_vars = None break else: if isinstance(res, RowMask): drop_mask |= res.mask newvar = var else: newvar = res if isinstance(newvar, Orange.data.Variable): newvar = [newvar] if i < len(data.domain.attributes): attributes.extend(newvar) else: class_vars.extend(newvar) if attributes is None: data = None else: domain = Orange.data.Domain(attributes, class_vars, data.domain.metas) try: data = self.data.from_table(domain, data[~drop_mask]) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error", exc_info=True) self.Error.imputation_failed("Unknown") data = None self.Outputs.data.send(data) self.modified = False @Slot(int, int) def __progress_changed(self, n, d): assert QThread.currentThread() is self.thread() assert self.__task is not None self.progressBarSet(100. * n / d) def cancel(self): if self.__task is not None: task, self.__task = self.__task, None task.cancel() task.watcher.doneAll.disconnect(self.__commit_finish) task.watcher.progressChanged.disconnect(self.__progress_changed) concurrent.futures.wait(task.futures) task.watcher.flush() self.progressBarFinished() self.setBlocking(False) def onDeleteWidget(self): self.cancel() super().onDeleteWidget() def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, None) if method is not None: specific.append("{} ({})".format(var.name, str(method))) default = self.default_method.name if specific: self.report_items(( ("Default method", default), ("Specific imputers", ", ".join(specific)) )) else: self.report_items((("Method", default),)) def _on_var_selection_changed(self): indexes = self.selection.selectedIndexes() methods = [self.get_method_for_column(i.row()) for i in indexes] def method_key(method): """ Decompose method into its type and parameters. """ # The return value should be hashable and __eq__ comparable if isinstance(method, AsDefault): return AsDefault, (method.method,) elif isinstance(method, impute.Model): return impute.Model, (method.learner,) elif isinstance(method, impute.Default): return impute.Default, (method.default,) else: return type(method), None methods = set(method_key(m) for m in methods) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) fixed_value = None value_stack_enabled = False current_value_widget = None if len(methods) == 1: method_type, parameters = methods.pop() for i, m in enumerate(self.methods): if method_type == type(m): self.variable_button_group.button(i).setChecked(True) if method_type is impute.Default: (fixed_value,) = parameters elif self.variable_button_group.checkedButton() is not None: # Uncheck the current button self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) assert self.variable_button_group.checkedButton() is None for method, button in zip(self.methods, self.variable_button_group.buttons()): enabled = all(method.supports_variable(var) for var in selected_vars) button.setEnabled(enabled) if not has_discrete: value_stack_enabled = True current_value_widget = self.value_double elif len(selected_vars) == 1: value_stack_enabled = True current_value_widget = self.value_combo self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) else: value_stack_enabled = False current_value_widget = None self.variable_button_group.button(self.AS_INPUT).setEnabled(False) self.value_stack.setEnabled(value_stack_enabled) if current_value_widget is not None: self.value_stack.setCurrentWidget(current_value_widget) if fixed_value is not None: if current_value_widget is self.value_combo: self.value_combo.setCurrentIndex(fixed_value) elif current_value_widget is self.value_double: self.value_double.setValue(fixed_value) else: assert False def set_method_for_current_selection(self, method_index): indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): if method_index == self.DEFAULT: for index in indexes: self.variable_methods.pop(index.row(), None) elif method_index == OWImpute.AS_INPUT: current = self.value_stack.currentWidget() if current is self.value_combo: value = self.value_combo.currentIndex() else: value = self.value_double.value() for index in indexes: method = impute.Default(default=value) self.variable_methods[index.row()] = method else: method = self.methods[method_index] for index in indexes: self.variable_methods[index.row()] = method self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData(index, self.get_method_for_column(index.row()), Qt.UserRole) def _on_value_selected(self): # The fixed 'Value' in the widget has been changed by the user. self.variable_button_group.button(self.AS_INPUT).setChecked(True) self.set_method_for_current_selection(self.AS_INPUT) def reset_variable_methods(self): indexes = list(map(self.varmodel.index, range(len(self.varmodel)))) self.set_method_for_indexes(indexes, self.DEFAULT) self.variable_button_group.button(self.DEFAULT).setChecked(True)
class ControlCombo(ControlBase, QWidget): """This class represents a wrapper to the combo box""" def __init__(self, label='', default=None, helptext=None): QWidget.__init__(self) ControlBase.__init__(self, label, default, helptext) ########################################################################## ############ Functions ################################################### ########################################################################## def init_form(self): self._layout = QHBoxLayout() self._combo = QComboBox(self.form) if self._label is not None: self._combolabel = QLabel(self.form) self._layout.addWidget(self._combolabel) self._combolabel.setAccessibleName('ControlCombo-label') self.label = self._label else: self._combolabel = None self._layout.addWidget(self._combo) self.form.setLayout(self._layout) self._combo.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed) self._layout.setContentsMargins(0, 0, 0, 0) self.form.setContentsMargins(0, 0, 0, 0) self.form.setMinimumHeight(38) self.form.setMaximumHeight(38) self.form.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Fixed) self._combo.currentIndexChanged.connect(self._currentIndexChanged) self._combo.activated.connect(self._activated) self._combo.highlighted.connect(self._highlighted) self._combo.editTextChanged.connect(self._editTextChanged) self._items = {} self._addingItem = False def clear(self): self._items = {} self._value = None self._combo.clear() def add_item(self, label, value=None): self._addingItem = True if value is not None: if not (value in self._items.values()): self._combo.addItem(label) else: if not (label in self._items.keys()): self._combo.addItem(label) firstValue = False if self._items == {}: firstValue = True if value is None: self._items[str(label)] = label else: self._items[str(label)] = value self._addingItem = False if firstValue: self.value = self._items[label] def __add__(self, val): if isinstance(val, tuple): self.add_item(val[0], val[1]) else: self.add_item(val) return self def get_item_index_by_name(self, item_name): """ Returns the index of the item containing the given name :param item_name: item name in combo box :type item_name: string """ return self._combo.findText(item_name) def count(self): return self._combo.count() def show(self): """ Show the control """ QWidget.show(self) def hide(self): """ Hide the control """ QWidget.hide(self) ########################################################################## ############ Events ###################################################### ########################################################################## def current_index_changed_event(self, index): """Called when the user chooses an item in the combobox and the selected choice is different from the last one selected. @index: item's index """ pass def activated_event(self, index): """Called when the user chooses an item in the combobox. Note that this signal happens even when the choice is not changed @index: item's index """ pass def highlighted_event(self, index): pass def edittext_changed_event(self, text): pass ########################################################################## ############ PROPERTIES ################################################## ########################################################################## @property def form(self): return self @property def current_index(self): return self._combo.currentIndex() @current_index.setter def current_index(self, value): self._combo.setCurrentIndex(value) @property def items(self): return self._items.items() @property def value(self): return self._value @value.setter def value(self, value): for key, val in self.items: if value == val: index = self._combo.findText(key) self._combo.setCurrentIndex(index) if self._value != value: self.changed_event() self._value = val @property def text(self): return str(self._combo.currentText()) @text.setter def text(self, value): for key, val in self.items: if value == key: self.value = val break @property def label(self): if self._combolabel: return self._combolabel.text() else: return None @label.setter def label(self, value): """ Label of the control, if applies @type value: string """ if self._combolabel: self._combolabel.setText(value) ########################################################################## ############ Private functions ########################################### ########################################################################## def _activated(self, index): if not self._addingItem: item = self._combo.currentText() if len(item) >= 1: ControlBase.value.fset(self, self._items[str(item)]) self.activated_event(index) def _highlighted(self, index): """Called when an item in the combobox popup list is highlighted by the user. @index: item's index """ self.highlighted_event(index) def _editTextChanged(self, text): self.edittext_changed_event(text) def _currentIndexChanged(self, index): if not self._addingItem: item = self._combo.currentText() if len(item) >= 1: ControlBase.value.fset(self, self._items[str(item)]) self.current_index_changed_event(index)
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 class Inputs: data = Input("Data", Orange.data.Table) learner = Input("Learner", Learner) class Outputs: data = Output("Data", Orange.data.Table) class Error(OWWidget.Error): imputation_failed = Msg("Imputation failed for '{}'") model_based_imputer_sparse = Msg("Model based imputer does not work for sparse data") settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(int(Method.Leave)) # type: int # Per-variable imputation state (synced in storeSpecificSettings) _variable_imputation_state = settings.ContextSetting({}) # type: VariableState autocommit = settings.Setting(True) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() self.data = None # type: Optional[Orange.data.Table] self.learner = None # type: Optional[Learner] self.default_learner = SimpleTreeLearner() self.modified = False self.executor = qconcurrent.ThreadExecutor(self) self.__task = None main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for method, _ in list(METHODS.items())[1:-1]: imputer = self.create_imputer(method) button = QRadioButton(imputer.name) button.setChecked(method == self.default_method_index) button_group.addButton(button, method) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView( selectionMode=QListView.ExtendedSelection, uniformItemSizes=True ) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed ) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for method in Method: imputer = self.create_imputer(method) button = QRadioButton(text=imputer.name) button_group.addButton(button, method) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected ) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection ) method_layout.addStretch(2) reset_button = QPushButton( "Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_state, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit( self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.button.setFixedWidth(180) box.layout().insertStretch(0) def create_imputer(self, method, *args): # type: (Method, ...) -> impute.BaseImputeMethod if method == Method.Model: if self.learner is not None: return impute.Model(self.learner) else: return impute.Model(self.default_learner) elif method == Method.AsAboveSoBelow: assert self.default_method_index != Method.AsAboveSoBelow default = self.create_imputer(Method(self.default_method_index)) m = AsDefault() m.method = default return m else: return METHODS[method](*args) @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: assert index != Method.AsAboveSoBelow self._default_method_index = index self.default_button_group.button(index).setChecked(True) # update variable view self.update_varview() self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @Inputs.data @check_sql_input def set_data(self, data): self.closeContext() self.varmodel[:] = [] self._variable_imputation_state = {} # type: VariableState self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) # restore per variable imputation state self._restore_state(self._variable_imputation_state) self.update_varview() self.unconditional_commit() @Inputs.learner def set_learner(self, learner): self.learner = learner or self.default_learner imputer = self.create_imputer(Method.Model) button = self.default_button_group.button(Method.Model) button.setText(imputer.name) variable_button = self.variable_button_group.button(Method.Model) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = Method.Model self.update_varview() self.commit() def get_method_for_column(self, column_index): # type: (int) -> impute.BaseImputeMethod """ Return the imputation method for column by its index. """ assert 0 <= column_index < len(self.varmodel) idx = self.varmodel.index(column_index, 0) state = idx.data(StateRole) if state is None: state = (Method.AsAboveSoBelow, ()) return self.create_imputer(state[0], *state[1]) def _invalidate(self): self.modified = True if self.__task is not None: self.cancel() self.commit() def commit(self): self.cancel() self.warning() self.Error.imputation_failed.clear() self.Error.model_based_imputer_sparse.clear() if self.data is None or len(self.data) == 0 or len(self.varmodel) == 0: self.Outputs.data.send(self.data) self.modified = False return data = self.data impute_state = [ (i, var, self.get_method_for_column(i)) for i, var in enumerate(self.varmodel) ] # normalize to the effective method bypasing AsDefault impute_state = [ (i, var, m.method if isinstance(m, AsDefault) else m) for i, var, m in impute_state ] def impute_one(method, var, data): # type: (impute.BaseImputeMethod, Variable, Table) -> Any if isinstance(method, impute.Model) and data.is_sparse(): raise SparseNotSupported() elif isinstance(method, impute.DropInstances): return RowMask(method(data, var)) elif not method.supports_variable(var): raise VariableNotSupported(var) else: return method(data, var) futures = [] for _, var, method in impute_state: f = self.executor.submit( impute_one, copy.deepcopy(method), var, data) futures.append(f) w = qconcurrent.FutureSetWatcher(futures) w.doneAll.connect(self.__commit_finish) w.progressChanged.connect(self.__progress_changed) self.__task = Task(futures, w) self.progressBarInit(processEvents=False) self.setBlocking(True) @Slot() def __commit_finish(self): assert QThread.currentThread() is self.thread() assert self.__task is not None futures = self.__task.futures assert len(futures) == len(self.varmodel) assert self.data is not None self.__task = None self.setBlocking(False) self.progressBarFinished() data = self.data attributes = [] class_vars = [] drop_mask = np.zeros(len(self.data), bool) for i, (var, fut) in enumerate(zip(self.varmodel, futures)): assert fut.done() newvar = [] try: res = fut.result() except SparseNotSupported: self.Error.model_based_imputer_sparse() # ?? break except VariableNotSupported: self.warning("Default method can not handle '{}'". format(var.name)) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error for %s", var, exc_info=True) self.Error.imputation_failed(var.name) attributes = class_vars = None break else: if isinstance(res, RowMask): drop_mask |= res.mask newvar = var else: newvar = res if isinstance(newvar, Orange.data.Variable): newvar = [newvar] if i < len(data.domain.attributes): attributes.extend(newvar) else: class_vars.extend(newvar) if attributes is None: data = None else: domain = Orange.data.Domain(attributes, class_vars, data.domain.metas) try: data = self.data.from_table(domain, data[~drop_mask]) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error", exc_info=True) self.Error.imputation_failed("Unknown") data = None self.Outputs.data.send(data) self.modified = False @Slot(int, int) def __progress_changed(self, n, d): assert QThread.currentThread() is self.thread() assert self.__task is not None self.progressBarSet(100. * n / d) def cancel(self): if self.__task is not None: task, self.__task = self.__task, None task.cancel() task.watcher.doneAll.disconnect(self.__commit_finish) task.watcher.progressChanged.disconnect(self.__progress_changed) concurrent.futures.wait(task.futures) task.watcher.flush() self.progressBarFinished() self.setBlocking(False) def onDeleteWidget(self): self.cancel() super().onDeleteWidget() def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.get_method_for_column(i) if not isinstance(method, AsDefault): specific.append("{} ({})".format(var.name, str(method))) default = self.create_imputer(Method.AsAboveSoBelow) if specific: self.report_items(( ("Default method", default.name), ("Specific imputers", ", ".join(specific)) )) else: self.report_items((("Method", default.name),)) def _on_var_selection_changed(self): indexes = self.selection.selectedIndexes() defmethod = (Method.AsAboveSoBelow, ()) methods = [index.data(StateRole) for index in indexes] methods = [m if m is not None else defmethod for m in methods] methods = set(methods) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) fixed_value = None value_stack_enabled = False current_value_widget = None if len(methods) == 1: method_type, parameters = methods.pop() for m in Method: if method_type == m: self.variable_button_group.button(m).setChecked(True) if method_type == Method.Default: (fixed_value,) = parameters elif self.variable_button_group.checkedButton() is not None: # Uncheck the current button self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) assert self.variable_button_group.checkedButton() is None # Update variable methods GUI enabled state based on selection. for method in Method: # use a default constructed imputer to query support imputer = self.create_imputer(method) enabled = all(imputer.supports_variable(var) for var in selected_vars) button = self.variable_button_group.button(method) button.setEnabled(enabled) # Update the "Value" edit GUI. if not has_discrete: # no discrete variables -> allow mass edit for all (continuous vars) value_stack_enabled = True current_value_widget = self.value_double elif len(selected_vars) == 1: # single discrete var -> enable and fill the values combo value_stack_enabled = True current_value_widget = self.value_combo self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) else: # mixed type selection -> disable value_stack_enabled = False current_value_widget = None self.variable_button_group.button(Method.Default).setEnabled(False) self.value_stack.setEnabled(value_stack_enabled) if current_value_widget is not None: self.value_stack.setCurrentWidget(current_value_widget) if fixed_value is not None: # set current value if current_value_widget is self.value_combo: self.value_combo.setCurrentIndex(fixed_value) elif current_value_widget is self.value_double: self.value_double.setValue(fixed_value) else: assert False def set_method_for_current_selection(self, method_index): # type: (Method) -> None indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): # type: (List[QModelIndex], Method) -> None if method_index == Method.AsAboveSoBelow: for index in indexes: self.varmodel.setData(index, None, StateRole) elif method_index == Method.Default: current = self.value_stack.currentWidget() if current is self.value_combo: value = self.value_combo.currentIndex() else: value = self.value_double.value() for index in indexes: state = (int(Method.Default), (value,)) self.varmodel.setData(index, state, StateRole) else: state = (int(method_index), ()) for index in indexes: self.varmodel.setData(index, state, StateRole) self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData( index, self.get_method_for_column(index.row()), DisplayMethodRole) def _on_value_selected(self): # The fixed 'Value' in the widget has been changed by the user. self.variable_button_group.button(Method.Default).setChecked(True) self.set_method_for_current_selection(Method.Default) def reset_variable_state(self): indexes = list(map(self.varmodel.index, range(len(self.varmodel)))) self.set_method_for_indexes(indexes, Method.AsAboveSoBelow) self.variable_button_group.button(Method.AsAboveSoBelow).setChecked(True) def _store_state(self): # type: () -> VariableState """ Save the current variable imputation state """ state = {} # type: VariableState for i, var in enumerate(self.varmodel): index = self.varmodel.index(i) m = index.data(StateRole) if m is not None: state[var_key(var)] = m return state def _restore_state(self, state): # type: (VariableState) -> None """ Restore the variable imputation state from the saved state """ def check(state): # check if state is a proper State if isinstance(state, tuple) and len(state) == 2: m, p = state if isinstance(m, int) and isinstance(p, tuple) and \ 0 <= m < len(Method): return True return False for i, var in enumerate(self.varmodel): m = state.get(var_key(var), None) if check(m): self.varmodel.setData(self.varmodel.index(i), m, StateRole) def storeSpecificSettings(self): self._variable_imputation_state = self._store_state() super().storeSpecificSettings()
class OWSql(OWWidget): name = "SQL Table" id = "orange.widgets.data.sql" description = "Load data set from SQL." icon = "icons/SQLTable.svg" priority = 10 category = "Data" keywords = ["data", "file", "load", "read"] class Outputs: data = Output( "Data", Table, doc="Attribute-valued data set read from the input file.") settings_version = 2 want_main_area = False resizing_enabled = False host = Setting(None) port = Setting(None) database = Setting(None) schema = Setting(None) username = "" password = "" table = Setting(None) sql = Setting("") guess_values = Setting(True) download = Setting(False) materialize = Setting(False) materialize_table_name = Setting("") class Information(OWWidget.Information): data_sampled = Msg("Data description was generated from a sample.") class Error(OWWidget.Error): connection = Msg("{}") no_backends = Msg("Please install a backend to use this widget") missing_extension = Msg("Database is missing extension{}: {}") def __init__(self): super().__init__() self.backend = None self.data_desc_table = None self.database_desc = None vbox = gui.vBox(self.controlArea, "Server", addSpace=True) box = gui.vBox(vbox) self.backendmodel = BackendModel(Backend.available_backends()) self.backendcombo = QComboBox(box) if len(self.backendmodel): self.backendcombo.setModel(self.backendmodel) else: self.Error.no_backends() box.setEnabled(False) box.layout().addWidget(self.backendcombo) self.servertext = QLineEdit(box) self.servertext.setPlaceholderText('Server') self.servertext.setToolTip('Server') self.servertext.editingFinished.connect(self._load_credentials) if self.host: self.servertext.setText(self.host if not self.port else '{}:{}'. format(self.host, self.port)) box.layout().addWidget(self.servertext) self.databasetext = QLineEdit(box) self.databasetext.setPlaceholderText('Database[/Schema]') self.databasetext.setToolTip('Database or optionally Database/Schema') if self.database: self.databasetext.setText( self.database if not self.schema else '{}/{}'. format(self.database, self.schema)) box.layout().addWidget(self.databasetext) self.usernametext = QLineEdit(box) self.usernametext.setPlaceholderText('Username') self.usernametext.setToolTip('Username') box.layout().addWidget(self.usernametext) self.passwordtext = QLineEdit(box) self.passwordtext.setPlaceholderText('Password') self.passwordtext.setToolTip('Password') self.passwordtext.setEchoMode(QLineEdit.Password) box.layout().addWidget(self.passwordtext) self._load_credentials() tables = gui.hBox(box) self.tablemodel = TableModel() self.tablecombo = QComboBox( minimumContentsLength=35, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength) self.tablecombo.setModel(self.tablemodel) self.tablecombo.setToolTip('table') tables.layout().addWidget(self.tablecombo) self.tablecombo.activated[int].connect(self.select_table) self.connectbutton = gui.button(tables, self, '↻', callback=self.connect) self.connectbutton.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) tables.layout().addWidget(self.connectbutton) self.custom_sql = gui.vBox(box) self.custom_sql.setVisible(False) self.sqltext = QTextEdit(self.custom_sql) self.sqltext.setPlainText(self.sql) self.custom_sql.layout().addWidget(self.sqltext) mt = gui.hBox(self.custom_sql) cb = gui.checkBox(mt, self, 'materialize', 'Materialize to table ') cb.setToolTip('Save results of the query in a table') le = gui.lineEdit(mt, self, 'materialize_table_name') le.setToolTip('Save results of the query in a table') self.executebtn = gui.button(self.custom_sql, self, 'Execute', callback=self.open_table) box.layout().addWidget(self.custom_sql) gui.checkBox(box, self, "guess_values", "Auto-discover discrete variables", callback=self.open_table) gui.checkBox(box, self, "download", "Download data to local memory", callback=self.open_table) gui.rubber(self.buttonsArea) QTimer.singleShot(0, self.connect) def _load_credentials(self): self._parse_host_port() cm = self._credential_manager(self.host, self.port) self.username = cm.username self.password = cm.password if self.username: self.usernametext.setText(self.username) if self.password: self.passwordtext.setText(self.password) def _save_credentials(self): cm = self._credential_manager(self.host, self.port) cm.username = self.username cm.password = self.password def _credential_manager(self, host, port): return CredentialManager("SQL Table: {}:{}".format(host, port)) def error(self, id=0, text=""): super().error(id, text) err_style = 'QLineEdit {border: 2px solid red;}' if 'server' in text or 'host' in text: self.servertext.setStyleSheet(err_style) else: self.servertext.setStyleSheet('') if 'role' in text: self.usernametext.setStyleSheet(err_style) else: self.usernametext.setStyleSheet('') if 'database' in text: self.databasetext.setStyleSheet(err_style) else: self.databasetext.setStyleSheet('') def _parse_host_port(self): hostport = self.servertext.text().split(':') self.host = hostport[0] self.port = hostport[1] if len(hostport) == 2 else None def connect(self): self._parse_host_port() self.database, _, self.schema = self.databasetext.text().partition('/') self.username = self.usernametext.text() or None self.password = self.passwordtext.text() or None try: if self.backendcombo.currentIndex() < 0: return backend = self.backendmodel[self.backendcombo.currentIndex()] self.backend = backend( dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password)) self.Error.connection.clear() self._save_credentials() self.database_desc = OrderedDict( (("Host", self.host), ("Port", self.port), ("Database", self.database), ("User name", self.username))) self.refresh_tables() self.select_table() except BackendError as err: error = str(err).split('\n')[0] self.Error.connection(error) self.database_desc = self.data_desc_table = None self.tablecombo.clear() def refresh_tables(self): self.tablemodel.clear() self.Error.missing_extension.clear() if self.backend is None: self.data_desc_table = None return self.tablemodel.append("Select a table") self.tablemodel.extend(self.backend.list_tables(self.schema)) self.tablemodel.append("Custom SQL") def select_table(self): curIdx = self.tablecombo.currentIndex() if self.tablecombo.itemText(curIdx) != "Custom SQL": self.custom_sql.setVisible(False) return self.open_table() else: self.custom_sql.setVisible(True) self.data_desc_table = None self.database_desc["Table"] = "(None)" self.table = None #self.Error.missing_extension( # 's' if len(missing) > 1 else '', # ', '.join(missing), # shown=missing) def open_table(self): table = self.get_table() self.data_desc_table = table self.Outputs.data.send(table) def get_table(self): if self.tablecombo.currentIndex() <= 0: if self.database_desc: self.database_desc["Table"] = "(None)" self.data_desc_table = None return if self.tablecombo.currentIndex() < self.tablecombo.count() - 1: self.table = self.tablemodel[self.tablecombo.currentIndex()] self.database_desc["Table"] = self.table if "Query" in self.database_desc: del self.database_desc["Query"] else: self.sql = self.table = self.sqltext.toPlainText() if self.materialize: import psycopg2 if not self.materialize_table_name: self.Error.connection( "Specify a table name to materialize the query") return try: with self.backend.execute_sql_query( "DROP TABLE IF EXISTS " + self.materialize_table_name): pass with self.backend.execute_sql_query( "CREATE TABLE " + self.materialize_table_name + " AS " + self.table): pass with self.backend.execute_sql_query( "ANALYZE " + self.materialize_table_name): pass self.table = self.materialize_table_name except (psycopg2.ProgrammingError, BackendError) as ex: self.Error.connection(str(ex)) return try: table = SqlTable(dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password), self.table, backend=type(self.backend), inspect_values=False) except BackendError as ex: self.Error.connection(str(ex)) return self.Error.connection.clear() sample = False if table.approx_len() > LARGE_TABLE and self.guess_values: confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Attribute discovery might take " "a long time on large tables.\n" "Do you want to auto discover attributes?") confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) sample_button = confirm.addButton("Yes, on a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: self.guess_values = False elif confirm.clickedButton() == sample_button: sample = True self.Information.clear() if self.guess_values: QApplication.setOverrideCursor(QCursor(Qt.WaitCursor)) if sample: s = table.sample_time(1) domain = s.get_domain(inspect_values=True) self.Information.data_sampled() else: domain = table.get_domain(inspect_values=True) QApplication.restoreOverrideCursor() table.domain = domain if self.download: if table.approx_len() > MAX_DL_LIMIT: QMessageBox.warning( self, 'Warning', "Data is too big to download.\n" "Consider using the Data Sampler widget to download " "a sample instead.") self.download = False elif table.approx_len() > AUTO_DL_LIMIT: confirm = QMessageBox.question( self, 'Question', "Data appears to be big. Do you really " "want to download it to local memory?", QMessageBox.Yes | QMessageBox.No, QMessageBox.No) if confirm == QMessageBox.No: self.download = False if self.download: table.download_data(MAX_DL_LIMIT) table = Table(table) return table def send_report(self): if not self.database_desc: self.report_paragraph("No database connection.") return self.report_items("Database", self.database_desc) if self.data_desc_table: self.report_items("Data", report.describe_data(self.data_desc_table)) @classmethod def migrate_settings(cls, settings, version): if version < 2: # Until Orange version 3.4.4 username and password had been stored # in Settings. cm = cls._credential_manager(settings["host"], settings["port"]) cm.username = settings["username"] cm.password = settings["password"]
class OWSql(OWWidget): name = "SQL Table" id = "orange.widgets.data.sql" description = "Load data set from SQL." icon = "icons/SQLTable.svg" priority = 30 category = "Data" keywords = ["data", "file", "load", "read", "SQL"] class Outputs: data = Output("Data", Table, doc="Attribute-valued data set read from the input file.") settings_version = 2 want_main_area = False resizing_enabled = False host = Setting(None) port = Setting(None) database = Setting(None) schema = Setting(None) username = "" password = "" table = Setting(None) sql = Setting("") guess_values = Setting(True) download = Setting(False) materialize = Setting(False) materialize_table_name = Setting("") class Information(OWWidget.Information): data_sampled = Msg("Data description was generated from a sample.") class Error(OWWidget.Error): connection = Msg("{}") no_backends = Msg("Please install a backend to use this widget") missing_extension = Msg("Database is missing extension{}: {}") def __init__(self): super().__init__() self.backend = None self.data_desc_table = None self.database_desc = None vbox = gui.vBox(self.controlArea, "Server", addSpace=True) box = gui.vBox(vbox) self.backends = BackendModel(Backend.available_backends()) self.backendcombo = QComboBox(box) if len(self.backends): self.backendcombo.setModel(self.backends) else: self.Error.no_backends() box.setEnabled(False) box.layout().addWidget(self.backendcombo) self.servertext = QLineEdit(box) self.servertext.setPlaceholderText('Server') self.servertext.setToolTip('Server') self.servertext.editingFinished.connect(self._load_credentials) if self.host: self.servertext.setText(self.host if not self.port else '{}:{}'.format(self.host, self.port)) box.layout().addWidget(self.servertext) self.databasetext = QLineEdit(box) self.databasetext.setPlaceholderText('Database[/Schema]') self.databasetext.setToolTip('Database or optionally Database/Schema') if self.database: self.databasetext.setText( self.database if not self.schema else '{}/{}'.format(self.database, self.schema)) box.layout().addWidget(self.databasetext) self.usernametext = QLineEdit(box) self.usernametext.setPlaceholderText('Username') self.usernametext.setToolTip('Username') box.layout().addWidget(self.usernametext) self.passwordtext = QLineEdit(box) self.passwordtext.setPlaceholderText('Password') self.passwordtext.setToolTip('Password') self.passwordtext.setEchoMode(QLineEdit.Password) box.layout().addWidget(self.passwordtext) self._load_credentials() self.tables = TableModel() tables = gui.hBox(box) self.tablecombo = QComboBox( minimumContentsLength=35, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength ) self.tablecombo.setModel(self.tables) self.tablecombo.setToolTip('table') tables.layout().addWidget(self.tablecombo) self.connect() index = self.tablecombo.findText(str(self.table)) if index != -1: self.tablecombo.setCurrentIndex(index) # set up the callback to select_table in case of selection change self.tablecombo.activated[int].connect(self.select_table) self.connectbutton = gui.button( tables, self, '↻', callback=self.connect) self.connectbutton.setSizePolicy( QSizePolicy.Fixed, QSizePolicy.Fixed) tables.layout().addWidget(self.connectbutton) self.custom_sql = gui.vBox(box) self.custom_sql.setVisible(False) self.sqltext = QTextEdit(self.custom_sql) self.sqltext.setPlainText(self.sql) self.custom_sql.layout().addWidget(self.sqltext) mt = gui.hBox(self.custom_sql) cb = gui.checkBox(mt, self, 'materialize', 'Materialize to table ') cb.setToolTip('Save results of the query in a table') le = gui.lineEdit(mt, self, 'materialize_table_name') le.setToolTip('Save results of the query in a table') self.executebtn = gui.button( self.custom_sql, self, 'Execute', callback=self.open_table) box.layout().addWidget(self.custom_sql) gui.checkBox(box, self, "guess_values", "Auto-discover categorical variables", callback=self.open_table) gui.checkBox(box, self, "download", "Download data to local memory", callback=self.open_table) gui.rubber(self.buttonsArea) QTimer.singleShot(0, self.select_table) def _load_credentials(self): self._parse_host_port() cm = self._credential_manager(self.host, self.port) self.username = cm.username self.password = cm.password if self.username: self.usernametext.setText(self.username) if self.password: self.passwordtext.setText(self.password) def _save_credentials(self): cm = self._credential_manager(self.host, self.port) cm.username = self.username or '' cm.password = self.password or '' def _credential_manager(self, host, port): return CredentialManager("SQL Table: {}:{}".format(host, port)) def error(self, id=0, text=""): super().error(id, text) err_style = 'QLineEdit {border: 2px solid red;}' if 'server' in text or 'host' in text: self.servertext.setStyleSheet(err_style) else: self.servertext.setStyleSheet('') if 'role' in text: self.usernametext.setStyleSheet(err_style) else: self.usernametext.setStyleSheet('') if 'database' in text: self.databasetext.setStyleSheet(err_style) else: self.databasetext.setStyleSheet('') def _parse_host_port(self): hostport = self.servertext.text().split(':') self.host = hostport[0] self.port = hostport[1] if len(hostport) == 2 else None def connect(self): self._parse_host_port() self.database, _, self.schema = self.databasetext.text().partition('/') self.username = self.usernametext.text() or None self.password = self.passwordtext.text() or None try: if self.backendcombo.currentIndex() < 0: return backend = self.backends[self.backendcombo.currentIndex()] self.backend = backend(dict( host=self.host, port=self.port, database=self.database, user=self.username, password=self.password )) self.Error.connection.clear() self._save_credentials() self.database_desc = OrderedDict(( ("Host", self.host), ("Port", self.port), ("Database", self.database), ("User name", self.username) )) self.refresh_tables() except BackendError as err: error = str(err).split('\n')[0] self.Error.connection(error) self.database_desc = self.data_desc_table = None self.tablecombo.clear() def refresh_tables(self): self.tables.clear() self.Error.missing_extension.clear() if self.backend is None: self.data_desc_table = None return self.tables.append("Select a table") self.tables.append("Custom SQL") self.tables.extend(self.backend.list_tables(self.schema)) # Called on tablecombo selection change: def select_table(self): curIdx = self.tablecombo.currentIndex() if self.tablecombo.itemText(curIdx) != "Custom SQL": self.custom_sql.setVisible(False) return self.open_table() else: self.custom_sql.setVisible(True) self.data_desc_table = None self.database_desc["Table"] = "(None)" self.table = None if len(str(self.sql)) > 14: return self.open_table() #self.Error.missing_extension( # 's' if len(missing) > 1 else '', # ', '.join(missing), # shown=missing) def open_table(self): table = self.get_table() self.data_desc_table = table self.Outputs.data.send(table) def get_table(self): curIdx = self.tablecombo.currentIndex() if curIdx <= 0: if self.database_desc: self.database_desc["Table"] = "(None)" self.data_desc_table = None return if self.tablecombo.itemText(curIdx) != "Custom SQL": self.table = self.tables[self.tablecombo.currentIndex()] self.database_desc["Table"] = self.table if "Query" in self.database_desc: del self.database_desc["Query"] what = self.table else: what = self.sql = self.sqltext.toPlainText() self.table = "Custom SQL" if self.materialize: import psycopg2 if not self.materialize_table_name: self.Error.connection( "Specify a table name to materialize the query") return try: with self.backend.execute_sql_query("DROP TABLE IF EXISTS " + self.materialize_table_name): pass with self.backend.execute_sql_query("CREATE TABLE " + self.materialize_table_name + " AS " + self.sql): pass with self.backend.execute_sql_query("ANALYZE " + self.materialize_table_name): pass except (psycopg2.ProgrammingError, BackendError) as ex: self.Error.connection(str(ex)) return try: table = SqlTable(dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password), what, backend=type(self.backend), inspect_values=False) except BackendError as ex: self.Error.connection(str(ex)) return self.Error.connection.clear() sample = False if table.approx_len() > LARGE_TABLE and self.guess_values: confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Attribute discovery might take " "a long time on large tables.\n" "Do you want to auto discover attributes?") confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) sample_button = confirm.addButton("Yes, on a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: self.guess_values = False elif confirm.clickedButton() == sample_button: sample = True self.Information.clear() if self.guess_values: QApplication.setOverrideCursor(QCursor(Qt.WaitCursor)) if sample: s = table.sample_time(1) domain = s.get_domain(inspect_values=True) self.Information.data_sampled() else: domain = table.get_domain(inspect_values=True) QApplication.restoreOverrideCursor() table.domain = domain if self.download: if table.approx_len() > MAX_DL_LIMIT: QMessageBox.warning( self, 'Warning', "Data is too big to download.\n" "Consider using the Data Sampler widget to download " "a sample instead.") self.download = False elif table.approx_len() > AUTO_DL_LIMIT: confirm = QMessageBox.question( self, 'Question', "Data appears to be big. Do you really " "want to download it to local memory?", QMessageBox.Yes | QMessageBox.No, QMessageBox.No) if confirm == QMessageBox.No: self.download = False if self.download: table.download_data(MAX_DL_LIMIT) table = Table(table) return table def send_report(self): if not self.database_desc: self.report_paragraph("No database connection.") return self.report_items("Database", self.database_desc) if self.data_desc_table: self.report_items("Data", report.describe_data(self.data_desc_table)) @classmethod def migrate_settings(cls, settings, version): if version < 2: # Until Orange version 3.4.4 username and password had been stored # in Settings. cm = cls._credential_manager(settings["host"], settings["port"]) cm.username = settings["username"] cm.password = settings["password"]
class FileWidget(QWidget): on_open = pyqtSignal(str) # TODO consider removing directory_aliases since it is not used any more def __init__(self, dialog_title='', dialog_format='', start_dir=os.path.expanduser('~/'), icon_size=(12, 20), minimal_width=200, browse_label='Browse', on_open=None, reload_button=True, reload_label='Reload', recent_files=None, directory_aliases=None, allow_empty=True, empty_file_label='(none)'): """ Creates a widget with a button for file loading and an optional combo box for recent files and reload buttons. Args: dialog_title (str): The title of the dialog. dialog_format (str): Formats for the dialog. start_dir (str): A directory to start from. icon_size (int, int): The size of buttons' icons. on_open (callable): A callback function that accepts filepath as the only argument. reload_button (bool): Whether to show reload button. reload_label (str): The text displayed on the reload button. recent_files (List[str]): List of recent files. directory_aliases (dict): An {alias: dir} dictionary for fast directories' access. allow_empty (bool): Whether empty path is allowed. """ super().__init__() self.dialog_title = dialog_title self.dialog_format = dialog_format self.start_dir = start_dir # Recent files should also contain `empty_file_label` so # when (none) is selected this is stored in settings. self.recent_files = recent_files if recent_files is not None else [] self.directory_aliases = directory_aliases or {} self.allow_empty = allow_empty self.empty_file_label = empty_file_label if self.empty_file_label not in self.recent_files \ and (self.allow_empty or not self.recent_files): self.recent_files.append(self.empty_file_label) self.check_existence() self.on_open.connect(on_open) layout = QHBoxLayout(self) layout.setContentsMargins(0, 0, 0, 0) if recent_files is not None: self.file_combo = QComboBox() self.file_combo.setMinimumWidth(minimal_width) self.file_combo.activated[int].connect(self.select) self.update_combo() layout.addWidget(self.file_combo) self.browse_button = QPushButton(browse_label) self.browse_button.setFocusPolicy(Qt.NoFocus) self.browse_button.clicked.connect(self.browse) self.browse_button.setIcon(self.style() .standardIcon(QStyle.SP_DirOpenIcon)) self.browse_button.setIconSize(QSize(*icon_size)) self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) layout.addWidget(self.browse_button) if reload_button: self.reload_button = QPushButton(reload_label) self.reload_button.setFocusPolicy(Qt.NoFocus) self.reload_button.clicked.connect(self.reload) self.reload_button.setIcon(self.style() .standardIcon(QStyle.SP_BrowserReload)) self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) self.reload_button.setIconSize(QSize(*icon_size)) layout.addWidget(self.reload_button) def browse(self, start_dir=None): start_dir = start_dir or self.start_dir path, _ = QFileDialog().getOpenFileName(self, self.dialog_title, start_dir, self.dialog_format) if path and self.recent_files is not None: if path in self.recent_files: self.recent_files.remove(path) self.recent_files.insert(0, path) self.update_combo() if path: self.open_file(path) def select(self, n): name = self.file_combo.currentText() if name == self.empty_file_label: del self.recent_files[n] self.recent_files.insert(0, self.empty_file_label) self.update_combo() self.open_file(self.empty_file_label) elif name in self.directory_aliases: self.browse(self.directory_aliases[name]) elif n < len(self.recent_files): name = self.recent_files[n] del self.recent_files[n] self.recent_files.insert(0, name) self.update_combo() self.open_file(self.recent_files[0]) def update_combo(self): """ Sync combo values to the changes in self.recent_files. """ if self.recent_files is not None: self.file_combo.clear() for i, file in enumerate(self.recent_files): # remove (none) when we have some files and allow_empty=False if file == self.empty_file_label and \ not self.allow_empty and len(self.recent_files) > 1: del self.recent_files[i] else: self.file_combo.addItem(os.path.split(file)[1]) for alias in self.directory_aliases.keys(): self.file_combo.addItem(alias) def reload(self): if self.recent_files: self.select(0) def check_existence(self): if self.recent_files: to_remove = [] for file in self.recent_files: doc_path = os.path.join(get_sample_corpora_dir(), file) exists = any(os.path.exists(f) for f in [file, doc_path]) if file != self.empty_file_label and not exists: to_remove.append(file) for file in to_remove: self.recent_files.remove(file) def open_file(self, path): self.on_open.emit(path if path != self.empty_file_label else '') def get_selected_filename(self): if self.recent_files: return self.recent_files[0] else: return self.empty_file_label
class OWPubmed(OWWidget): name = 'Pubmed' description = 'Fetch data from Pubmed.' icon = 'icons/Pubmed.svg' priority = 20 outputs = [(Output.CORPUS, Corpus)] want_main_area = False resizing_enabled = False QT_DATE_FORMAT = 'yyyy-MM-dd' PY_DATE_FORMAT = '%Y-%m-%d' MIN_DATE = date(1800, 1, 1) # Settings. recent_emails = Setting([]) author = Setting('') pub_date_from = Setting('') pub_date_to = Setting('') recent_keywords = Setting([]) last_advanced_query = Setting('') num_records = Setting(1000) # Text includes checkboxes. includes_authors = Setting(True) includes_title = Setting(True) includes_mesh = Setting(True) includes_abstract = Setting(True) includes_url = Setting(True) class Warning(OWWidget.Warning): no_query = Msg('Please specify the keywords for this query.') class Error(OWWidget.Error): api_error = Msg('API error: {}.') def __init__(self): super().__init__() self.output_corpus = None self.pubmed_api = None self.progress = None self.email_is_valid = False self.record_count = 0 self.download_running = False # To hold all the controls. Makes access easier. self.pubmed_controls = [] h_box = gui.hBox(self.controlArea) label = gui.label(h_box, self, 'Email:') label.setMaximumSize(label.sizeHint()) # Drop-down for recent emails. self.email_combo = QComboBox(h_box) self.email_combo.setMinimumWidth(150) self.email_combo.setEditable(True) self.email_combo.lineEdit().textChanged.connect(self.sync_email) h_box.layout().addWidget(self.email_combo) self.email_combo.activated[int].connect(self.select_email) # RECORD SEARCH self.search_tabs = gui.tabWidget(self.controlArea) # --- Regular search --- regular_search_box = gui.widgetBox(self.controlArea, addSpace=True) # Author self.author_input = gui.lineEdit(regular_search_box, self, 'author', 'Author:', orientation=Qt.Horizontal) self.pubmed_controls.append(self.author_input) h_box = gui.hBox(regular_search_box) year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal) min_date = QDate.fromString( self.MIN_DATE.strftime(self.PY_DATE_FORMAT), self.QT_DATE_FORMAT ) if not self.pub_date_from: self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT) if not self.pub_date_to: self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT) self.date_from = QDateEdit( QDate.fromString(self.pub_date_from, self.QT_DATE_FORMAT), displayFormat=self.QT_DATE_FORMAT, minimumDate=min_date, calendarPopup=True ) self.date_to = QDateEdit( QDate.fromString(self.pub_date_to, self.QT_DATE_FORMAT), displayFormat=self.QT_DATE_FORMAT, minimumDate=min_date, calendarPopup=True ) self.date_from.dateChanged.connect( lambda date: setattr(self, 'pub_date_from', date.toString(self.QT_DATE_FORMAT))) self.date_to.dateChanged.connect( lambda date: setattr(self, 'pub_date_to', date.toString(self.QT_DATE_FORMAT))) self.pubmed_controls.append(self.date_from) self.pubmed_controls.append(self.date_to) gui.label(year_box, self, 'From:') year_box.layout().addWidget(self.date_from) gui.label(year_box, self, 'to:') year_box.layout().addWidget(self.date_to) # Keywords. h_box = gui.hBox(regular_search_box) label = gui.label(h_box, self, 'Query:') label.setMaximumSize(label.sizeHint()) self.keyword_combo = QComboBox(h_box) self.keyword_combo.setMinimumWidth(150) self.keyword_combo.setEditable(True) h_box.layout().addWidget(self.keyword_combo) self.keyword_combo.activated[int].connect(self.select_keywords) self.pubmed_controls.append(self.keyword_combo) tab_height = regular_search_box.sizeHint() regular_search_box.setMaximumSize(tab_height) # --- Advanced search --- advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True) # Advanced search query. h_box = gui.hBox(advanced_search_box) self.advanced_query_input = QTextEdit(h_box) h_box.layout().addWidget(self.advanced_query_input) self.advanced_query_input.setMaximumSize(tab_height) self.pubmed_controls.append(self.advanced_query_input) gui.createTabPage(self.search_tabs, 'Regular search', regular_search_box) gui.createTabPage(self.search_tabs, 'Advanced search', advanced_search_box) # Search info label. self.search_info_label = gui.label( self.controlArea, self, 'Number of records found: /') # Search for records button. self.run_search_button = gui.button( self.controlArea, self, 'Find records', callback=self.run_search, tooltip='Performs a search for articles that fit the ' 'specified parameters.') self.pubmed_controls.append(self.run_search_button) h_line = QFrame() h_line.setFrameShape(QFrame.HLine) h_line.setFrameShadow(QFrame.Sunken) self.controlArea.layout().addWidget(h_line) # RECORD RETRIEVAL # Text includes box. text_includes_box = gui.widgetBox(self.controlArea, 'Text includes', addSpace=True) self.authors_checkbox = gui.checkBox(text_includes_box, self, 'includes_authors', 'Authors') self.title_checkbox = gui.checkBox(text_includes_box, self, 'includes_title', 'Article title') self.mesh_checkbox = gui.checkBox(text_includes_box, self, 'includes_mesh', 'Mesh headings') self.abstract_checkbox = gui.checkBox(text_includes_box, self, 'includes_abstract', 'Abstract') self.url_checkbox = gui.checkBox(text_includes_box, self, 'includes_url', 'URL') self.pubmed_controls.append(self.authors_checkbox) self.pubmed_controls.append(self.title_checkbox) self.pubmed_controls.append(self.mesh_checkbox) self.pubmed_controls.append(self.abstract_checkbox) self.pubmed_controls.append(self.url_checkbox) # Num. records. h_box = gui.hBox(self.controlArea) label = gui.label(h_box, self, 'Retrieve') label.setMaximumSize(label.sizeHint()) self.num_records_input = gui.spin(h_box, self, 'num_records', minv=1, maxv=100000) self.max_records_label = gui.label(h_box, self, 'records from /.') self.max_records_label.setMaximumSize(self.max_records_label .sizeHint()) self.pubmed_controls.append(self.num_records_input) # Download articles. # Search for records button. self.retrieve_records_button = gui.button( self.controlArea, self, 'Retrieve records', callback=self.retrieve_records, tooltip='Retrieves the specified documents.') self.pubmed_controls.append(self.retrieve_records_button) # Num. retrieved records info label. self.retrieval_info_label = gui.label( self.controlArea, self, 'Number of records retrieved: /') # Load the most recent emails. self.set_email_list() # Load the most recent queries. self.set_keyword_list() # Check the email and enable controls accordingly. if self.recent_emails: email = self.recent_emails[0] self.email_is_valid = validate_email(email) self.enable_controls() def sync_email(self): email = self.email_combo.currentText() self.email_is_valid = validate_email(email) self.enable_controls() def enable_controls(self): # Enable/disable controls accordingly. for control in self.pubmed_controls: control.setEnabled(self.email_is_valid) if self.pubmed_api is None or self.pubmed_api.search_record_count == 0: self.retrieve_records_button.setEnabled(False) if not self.email_is_valid: self.email_combo.setFocus() def run_search(self): self.Error.clear() self.Warning.clear() self.run_search_button.setEnabled(False) self.retrieve_records_button.setEnabled(False) # Add the email to history. email = self.email_combo.currentText() if email not in self.recent_emails: self.recent_emails.insert(0, email) # Check if the PubMed object is present. if self.pubmed_api is None: self.pubmed_api = Pubmed( email=email, progress_callback=self.api_progress_callback, error_callback=self.api_error_callback, ) if self.search_tabs.currentIndex() == 0: # Get query parameters. terms = self.keyword_combo.currentText().split() authors = self.author_input.text().split() error = self.pubmed_api._search_for_records( terms, authors, self.pub_date_from, self.pub_date_to ) if error is not None: self.Error.api_error(str(error)) return if self.keyword_combo.currentText() not in self.recent_keywords: self.recent_keywords.insert( 0, self.keyword_combo.currentText() ) else: query = self.advanced_query_input.toPlainText() if not query: self.Warning.no_query() self.run_search_button.setEnabled(True) self.retrieve_records_button.setEnabled(True) return error = self.pubmed_api._search_for_records(advanced_query=query) if error is not None: self.Error.api_error(str(error)) return self.last_advanced_query = query self.enable_controls() self.update_search_info() def retrieve_records(self): self.Warning.clear() self.Error.clear() if self.pubmed_api is None: return if self.download_running: self.download_running = False self.run_search_button.setEnabled(True) self.retrieve_records_button.setText('Retrieve records') self.pubmed_api.stop_retrieving() return self.download_running = True self.run_search_button.setEnabled(False) self.output_corpus = None # Clear the old records. # Change the button label. self.retrieve_records_button.setText('Stop retrieving') # Text fields. text_includes_params = [ self.includes_authors, self.includes_title, self.includes_mesh, self.includes_abstract, self.includes_url, True, # Publication date field; included always. ] required_text_fields = [ field for field_name, field in zip(text_includes_params, PUBMED_TEXT_FIELDS) if field_name ] batch_size = min(Pubmed.MAX_BATCH_SIZE, self.num_records) + 1 with self.progressBar(self.num_records/batch_size) as progress: self.progress = progress self.output_corpus = self.pubmed_api._retrieve_records( self.num_records, required_text_fields ) self.retrieve_records_button.setText('Retrieve records') self.download_running = False self.send(Output.CORPUS, self.output_corpus) self.update_retrieval_info() self.run_search_button.setEnabled(True) def api_progress_callback(self, start_at=None): if start_at is not None: self.progress.count = start_at else: self.progress.advance() def api_error_callback(self, error): self.Error.api_error(str(error)) if self.progress is not None: self.progress.finish() def update_search_info(self): max_records_count = min( self.pubmed_api.MAX_RECORDS, self.pubmed_api.search_record_count ) self.search_info_label.setText( 'Number of retrievable records for ' 'this search query: {} '.format(max_records_count) ) self.max_records_label.setText( 'records from {}.'.format(max_records_count) ) self.max_records_label.setMaximumSize(self.max_records_label .sizeHint()) self.num_records_input.setMaximum(max_records_count) self.retrieve_records_button.setFocus() def update_retrieval_info(self): document_count = 0 if self.output_corpus is not None: document_count = len(self.output_corpus) self.retrieval_info_label.setText( 'Number of records retrieved: {} '.format(document_count) ) self.retrieval_info_label.setMaximumSize( self.retrieval_info_label.sizeHint() ) def select_email(self, n): if n < len(self.recent_emails): email = self.recent_emails[n] del self.recent_emails[n] self.recent_emails.insert(0, email) if len(self.recent_emails) > 0: self.set_email_list() def set_email_list(self): self.email_combo.clear() for email in self.recent_emails: self.email_combo.addItem(email) def select_keywords(self, n): if n < len(self.recent_keywords): keywords = self.recent_keywords[n] del self.recent_keywords[n] self.recent_keywords.insert(0, keywords) if len(self.recent_keywords) > 0: self.set_keyword_list() def set_keyword_list(self): self.keyword_combo.clear() if not self.recent_keywords: # Sample queries. self.recent_keywords.append('orchid') self.recent_keywords.append('hypertension') self.recent_keywords.append('blood pressure') self.recent_keywords.append('radiology') for keywords in self.recent_keywords: self.keyword_combo.addItem(keywords) def open_calendar(self, widget): cal_dlg = CalendarDialog(self, 'Date picker') if cal_dlg.exec_(): widget.setText(cal_dlg.picked_date)
class OWPubmed(OWWidget): name = 'Pubmed' description = 'Fetch data from Pubmed.' icon = 'icons/Pubmed.svg' priority = 140 outputs = [(Output.CORPUS, Corpus)] want_main_area = False resizing_enabled = False QT_DATE_FORMAT = 'yyyy-MM-dd' PY_DATE_FORMAT = '%Y-%m-%d' MIN_DATE = date(1800, 1, 1) # Settings. recent_emails = Setting([]) author = Setting('') pub_date_from = Setting('') pub_date_to = Setting('') recent_keywords = Setting([]) last_advanced_query = Setting('') num_records = Setting(1000) # Text includes checkboxes. includes_authors = Setting(True) includes_title = Setting(True) includes_mesh = Setting(True) includes_abstract = Setting(True) includes_url = Setting(True) class Warning(OWWidget.Warning): no_query = Msg('Please specify the keywords for this query.') class Error(OWWidget.Error): api_error = Msg('API error: {}.') def __init__(self): super().__init__() self.output_corpus = None self.pubmed_api = None self.progress = None self.email_is_valid = False self.record_count = 0 self.download_running = False # To hold all the controls. Makes access easier. self.pubmed_controls = [] h_box = gui.hBox(self.controlArea) label = gui.label(h_box, self, 'Email:') label.setMaximumSize(label.sizeHint()) # Drop-down for recent emails. self.email_combo = QComboBox(h_box) self.email_combo.setMinimumWidth(150) self.email_combo.setEditable(True) self.email_combo.lineEdit().textChanged.connect(self.sync_email) h_box.layout().addWidget(self.email_combo) self.email_combo.activated[int].connect(self.select_email) # RECORD SEARCH self.search_tabs = gui.tabWidget(self.controlArea) # --- Regular search --- regular_search_box = gui.widgetBox(self.controlArea, addSpace=True) # Author self.author_input = gui.lineEdit(regular_search_box, self, 'author', 'Author:', orientation=Qt.Horizontal) self.pubmed_controls.append(self.author_input) h_box = gui.hBox(regular_search_box) year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal) min_date = QDate.fromString( self.MIN_DATE.strftime(self.PY_DATE_FORMAT), self.QT_DATE_FORMAT) if not self.pub_date_from: self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT) if not self.pub_date_to: self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT) self.date_from = QDateEdit(QDate.fromString(self.pub_date_from, self.QT_DATE_FORMAT), displayFormat=self.QT_DATE_FORMAT, minimumDate=min_date, calendarPopup=True) self.date_to = QDateEdit(QDate.fromString(self.pub_date_to, self.QT_DATE_FORMAT), displayFormat=self.QT_DATE_FORMAT, minimumDate=min_date, calendarPopup=True) self.date_from.dateChanged.connect(lambda date: setattr( self, 'pub_date_from', date.toString(self.QT_DATE_FORMAT))) self.date_to.dateChanged.connect(lambda date: setattr( self, 'pub_date_to', date.toString(self.QT_DATE_FORMAT))) self.pubmed_controls.append(self.date_from) self.pubmed_controls.append(self.date_to) gui.label(year_box, self, 'From:') year_box.layout().addWidget(self.date_from) gui.label(year_box, self, 'to:') year_box.layout().addWidget(self.date_to) # Keywords. h_box = gui.hBox(regular_search_box) label = gui.label(h_box, self, 'Query:') label.setMaximumSize(label.sizeHint()) self.keyword_combo = QComboBox(h_box) self.keyword_combo.setMinimumWidth(150) self.keyword_combo.setEditable(True) h_box.layout().addWidget(self.keyword_combo) self.keyword_combo.activated[int].connect(self.select_keywords) self.pubmed_controls.append(self.keyword_combo) tab_height = regular_search_box.sizeHint() regular_search_box.setMaximumSize(tab_height) # --- Advanced search --- advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True) # Advanced search query. h_box = gui.hBox(advanced_search_box) self.advanced_query_input = QTextEdit(h_box) h_box.layout().addWidget(self.advanced_query_input) self.advanced_query_input.setMaximumSize(tab_height) self.pubmed_controls.append(self.advanced_query_input) gui.createTabPage(self.search_tabs, 'Regular search', regular_search_box) gui.createTabPage(self.search_tabs, 'Advanced search', advanced_search_box) # Search info label. self.search_info_label = gui.label(self.controlArea, self, 'Number of records found: /') # Search for records button. self.run_search_button = gui.button( self.controlArea, self, 'Find records', callback=self.run_search, tooltip='Performs a search for articles that fit the ' 'specified parameters.') self.pubmed_controls.append(self.run_search_button) h_line = QFrame() h_line.setFrameShape(QFrame.HLine) h_line.setFrameShadow(QFrame.Sunken) self.controlArea.layout().addWidget(h_line) # RECORD RETRIEVAL # Text includes box. text_includes_box = gui.widgetBox(self.controlArea, 'Text includes', addSpace=True) self.authors_checkbox = gui.checkBox(text_includes_box, self, 'includes_authors', 'Authors') self.title_checkbox = gui.checkBox(text_includes_box, self, 'includes_title', 'Article title') self.mesh_checkbox = gui.checkBox(text_includes_box, self, 'includes_mesh', 'Mesh headings') self.abstract_checkbox = gui.checkBox(text_includes_box, self, 'includes_abstract', 'Abstract') self.url_checkbox = gui.checkBox(text_includes_box, self, 'includes_url', 'URL') self.pubmed_controls.append(self.authors_checkbox) self.pubmed_controls.append(self.title_checkbox) self.pubmed_controls.append(self.mesh_checkbox) self.pubmed_controls.append(self.abstract_checkbox) self.pubmed_controls.append(self.url_checkbox) # Num. records. h_box = gui.hBox(self.controlArea) label = gui.label(h_box, self, 'Retrieve') label.setMaximumSize(label.sizeHint()) self.num_records_input = gui.spin(h_box, self, 'num_records', minv=1, maxv=10000) self.max_records_label = gui.label(h_box, self, 'records from /.') self.max_records_label.setMaximumSize( self.max_records_label.sizeHint()) self.pubmed_controls.append(self.num_records_input) # Download articles. # Search for records button. self.retrieve_records_button = gui.button( self.controlArea, self, 'Retrieve records', callback=self.retrieve_records, tooltip='Retrieves the specified documents.') self.pubmed_controls.append(self.retrieve_records_button) # Num. retrieved records info label. self.retrieval_info_label = gui.label( self.controlArea, self, 'Number of records retrieved: /') # Load the most recent emails. self.set_email_list() # Load the most recent queries. self.set_keyword_list() # Check the email and enable controls accordingly. if self.recent_emails: email = self.recent_emails[0] self.email_is_valid = validate_email(email) self.enable_controls() def sync_email(self): email = self.email_combo.currentText() self.email_is_valid = validate_email(email) self.enable_controls() def enable_controls(self): # Enable/disable controls accordingly. for control in self.pubmed_controls: control.setEnabled(self.email_is_valid) if self.pubmed_api is None or self.pubmed_api.search_record_count == 0: self.retrieve_records_button.setEnabled(False) if not self.email_is_valid: self.email_combo.setFocus() def run_search(self): self.Error.clear() self.Warning.clear() self.run_search_button.setEnabled(False) self.retrieve_records_button.setEnabled(False) # Add the email to history. email = self.email_combo.currentText() if email not in self.recent_emails: self.recent_emails.insert(0, email) # Check if the PubMed object is present. if self.pubmed_api is None: self.pubmed_api = Pubmed( email=email, progress_callback=self.api_progress_callback, error_callback=self.api_error_callback, ) if self.search_tabs.currentIndex() == 0: # Get query parameters. terms = self.keyword_combo.currentText().split() authors = self.author_input.text().split() error = self.pubmed_api._search_for_records( terms, authors, self.pub_date_from, self.pub_date_to) if error is not None: self.Error.api_error(str(error)) return if self.keyword_combo.currentText() not in self.recent_keywords: self.recent_keywords.insert(0, self.keyword_combo.currentText()) else: query = self.advanced_query_input.toPlainText() if not query: self.Warning.no_query() self.run_search_button.setEnabled(True) self.retrieve_records_button.setEnabled(True) return error = self.pubmed_api._search_for_records(advanced_query=query) if error is not None: self.Error.api_error(str(error)) return self.last_advanced_query = query self.enable_controls() self.update_search_info() def retrieve_records(self): self.Warning.clear() self.Error.clear() if self.pubmed_api is None: return if self.download_running: self.download_running = False self.run_search_button.setEnabled(True) self.retrieve_records_button.setText('Retrieve records') self.pubmed_api.stop_retrieving() return self.download_running = True self.run_search_button.setEnabled(False) self.output_corpus = None # Clear the old records. # Change the button label. self.retrieve_records_button.setText('Stop retrieving') # Text fields. text_includes_params = [ self.includes_authors, self.includes_title, self.includes_mesh, self.includes_abstract, self.includes_url, True, # Publication date field; included always. ] required_text_fields = [ field for field_name, field in zip( text_includes_params, PUBMED_TEXT_FIELDS) if field_name ] batch_size = min(Pubmed.MAX_BATCH_SIZE, self.num_records) + 1 with self.progressBar(self.num_records / batch_size) as progress: self.progress = progress self.output_corpus = self.pubmed_api._retrieve_records( self.num_records, required_text_fields) self.retrieve_records_button.setText('Retrieve records') self.download_running = False self.send(Output.CORPUS, self.output_corpus) self.update_retrieval_info() self.run_search_button.setEnabled(True) def api_progress_callback(self, start_at=None): if start_at is not None: self.progress.count = start_at else: self.progress.advance() def api_error_callback(self, error): self.Error.api_error(str(error)) if self.progress is not None: self.progress.finish() def update_search_info(self): max_records_count = min(self.pubmed_api.MAX_RECORDS, self.pubmed_api.search_record_count) self.search_info_label.setText( 'Number of retrievable records for ' 'this search query: {} '.format(max_records_count)) self.max_records_label.setText( 'records from {}.'.format(max_records_count)) self.max_records_label.setMaximumSize( self.max_records_label.sizeHint()) self.num_records_input.setMaximum(max_records_count) self.retrieve_records_button.setFocus() def update_retrieval_info(self): document_count = 0 if self.output_corpus is not None: document_count = len(self.output_corpus) self.retrieval_info_label.setText( 'Number of records retrieved: {} '.format(document_count)) self.retrieval_info_label.setMaximumSize( self.retrieval_info_label.sizeHint()) def select_email(self, n): if n < len(self.recent_emails): email = self.recent_emails[n] del self.recent_emails[n] self.recent_emails.insert(0, email) if len(self.recent_emails) > 0: self.set_email_list() def set_email_list(self): self.email_combo.clear() for email in self.recent_emails: self.email_combo.addItem(email) def select_keywords(self, n): if n < len(self.recent_keywords): keywords = self.recent_keywords[n] del self.recent_keywords[n] self.recent_keywords.insert(0, keywords) if len(self.recent_keywords) > 0: self.set_keyword_list() def set_keyword_list(self): self.keyword_combo.clear() if not self.recent_keywords: # Sample queries. self.recent_keywords.append('orchid') self.recent_keywords.append('hypertension') self.recent_keywords.append('blood pressure') self.recent_keywords.append('radiology') for keywords in self.recent_keywords: self.keyword_combo.addItem(keywords) def open_calendar(self, widget): cal_dlg = CalendarDialog(self, 'Date picker') if cal_dlg.exec_(): widget.setText(cal_dlg.picked_date) def send_report(self): if not self.pubmed_api: return max_records_count = min(self.pubmed_api.MAX_RECORDS, self.pubmed_api.search_record_count) if self.search_tabs.currentIndex() == 0: terms = self.keyword_combo.currentText() authors = self.author_input.text() self.report_items( (('Query', terms if terms else None), ('Authors', authors if authors else None), ('Date', 'from {} to {}'.format(self.pub_date_from, self.pub_date_to)), ('Number of records retrieved', '{}/{}'.format( len(self.output_corpus) if self.output_corpus else 0, max_records_count)))) else: query = self.advanced_query_input.toPlainText() self.report_items( (('Query', query if query else None), ('Number of records retrieved', '{}/{}'.format( len(self.output_corpus) if self.output_corpus else 0, max_records_count))))
class FileWidget(QWidget): on_open = pyqtSignal(str) # TODO consider removing directory_aliases since it is not used any more def __init__(self, dialog_title='', dialog_format='', start_dir=os.path.expanduser('~/'), icon_size=(12, 20), minimal_width=200, browse_label='Browse', on_open=None, reload_button=True, reload_label='Reload', recent_files=None, directory_aliases=None, allow_empty=True, empty_file_label='(none)'): """ Creates a widget with a button for file loading and an optional combo box for recent files and reload buttons. Args: dialog_title (str): The title of the dialog. dialog_format (str): Formats for the dialog. start_dir (str): A directory to start from. icon_size (int, int): The size of buttons' icons. on_open (callable): A callback function that accepts filepath as the only argument. reload_button (bool): Whether to show reload button. reload_label (str): The text displayed on the reload button. recent_files (List[str]): List of recent files. directory_aliases (dict): An {alias: dir} dictionary for fast directories' access. allow_empty (bool): Whether empty path is allowed. """ super().__init__() self.dialog_title = dialog_title self.dialog_format = dialog_format self.start_dir = start_dir # Recent files should also contain `empty_file_label` so # when (none) is selected this is stored in settings. self.recent_files = recent_files if recent_files is not None else [] self.directory_aliases = directory_aliases or {} self.allow_empty = allow_empty self.empty_file_label = empty_file_label if self.empty_file_label not in self.recent_files \ and (self.allow_empty or not self.recent_files): self.recent_files.append(self.empty_file_label) self.check_existence() self.on_open.connect(on_open) layout = QHBoxLayout(self) layout.setContentsMargins(0, 0, 0, 0) if recent_files is not None: self.file_combo = QComboBox() self.file_combo.setMinimumWidth(minimal_width) self.file_combo.activated[int].connect(self.select) self.update_combo() layout.addWidget(self.file_combo) self.browse_button = QPushButton(browse_label) self.browse_button.setFocusPolicy(Qt.NoFocus) self.browse_button.clicked.connect(self.browse) self.browse_button.setIcon(self.style().standardIcon( QStyle.SP_DirOpenIcon)) self.browse_button.setIconSize(QSize(*icon_size)) self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) layout.addWidget(self.browse_button) if reload_button: self.reload_button = QPushButton(reload_label) self.reload_button.setFocusPolicy(Qt.NoFocus) self.reload_button.clicked.connect(self.reload) self.reload_button.setIcon(self.style().standardIcon( QStyle.SP_BrowserReload)) self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) self.reload_button.setIconSize(QSize(*icon_size)) layout.addWidget(self.reload_button) def browse(self, start_dir=None): start_dir = start_dir or self.start_dir path, _ = QFileDialog().getOpenFileName(self, self.dialog_title, start_dir, self.dialog_format) if path and self.recent_files is not None: if path in self.recent_files: self.recent_files.remove(path) self.recent_files.insert(0, path) self.update_combo() if path: self.open_file(path) def select(self, n): name = self.file_combo.currentText() if name == self.empty_file_label: del self.recent_files[n] self.recent_files.insert(0, self.empty_file_label) self.update_combo() self.open_file(self.empty_file_label) elif name in self.directory_aliases: self.browse(self.directory_aliases[name]) elif n < len(self.recent_files): name = self.recent_files[n] del self.recent_files[n] self.recent_files.insert(0, name) self.update_combo() self.open_file(self.recent_files[0]) def update_combo(self): """ Sync combo values to the changes in self.recent_files. """ if self.recent_files is not None: self.file_combo.clear() for i, file in enumerate(self.recent_files): # remove (none) when we have some files and allow_empty=False if file == self.empty_file_label and \ not self.allow_empty and len(self.recent_files) > 1: del self.recent_files[i] else: self.file_combo.addItem(os.path.split(file)[1]) for alias in self.directory_aliases.keys(): self.file_combo.addItem(alias) def reload(self): if self.recent_files: self.select(0) def check_existence(self): if self.recent_files: to_remove = [] for file in self.recent_files: doc_path = os.path.join(get_sample_corpora_dir(), file) exists = any(os.path.exists(f) for f in [file, doc_path]) if file != self.empty_file_label and not exists: to_remove.append(file) for file in to_remove: self.recent_files.remove(file) def open_file(self, path): self.on_open.emit(path if path != self.empty_file_label else '') def get_selected_filename(self): if self.recent_files: return self.recent_files[0] else: return self.empty_file_label
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 class Inputs: data = Input("Data", Orange.data.Table) learner = Input("Learner", Learner) class Outputs: data = Output("Data", Orange.data.Table) class Error(OWWidget.Error): imputation_failed = Msg("Imputation failed for '{}'") model_based_imputer_sparse = Msg("Model based imputer does not work for sparse data") DEFAULT_LEARNER = SimpleTreeLearner() METHODS = [AsDefault(), impute.DoNotImpute(), impute.Average(), impute.AsValue(), impute.Model(DEFAULT_LEARNER), impute.Random(), impute.DropInstances(), impute.Default()] DEFAULT, DO_NOT_IMPUTE, MODEL_BASED_IMPUTER, AS_INPUT = 0, 1, 4, 7 settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(DO_NOT_IMPUTE) variable_methods = settings.ContextSetting({}) autocommit = settings.Setting(True) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() # copy METHODS (some are modified by the widget) self.methods = copy.deepcopy(OWImpute.METHODS) main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, method in enumerate(self.methods): if not method.columns_only: button = QRadioButton(method.name) button.setChecked(i == self.default_method_index) button_group.addButton(button, i) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView( selectionMode=QListView.ExtendedSelection ) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed ) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for i, method in enumerate(self.methods): button = QRadioButton(text=method.name) button_group.addButton(button, i) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected ) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection ) method_layout.addStretch(2) reset_button = QPushButton( "Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_methods, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit( self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.button.setFixedWidth(180) box.layout().insertStretch(0) self.data = None self.learner = None self.modified = False self.default_method = self.methods[self.default_method_index] self.executor = qconcurrent.ThreadExecutor(self) self.__task = None @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: self._default_method_index = index self.default_button_group.button(index).setChecked(True) self.default_method = self.methods[self.default_method_index] self.methods[self.DEFAULT].method = self.default_method # update variable view for index in map(self.varmodel.index, range(len(self.varmodel))): method = self.variable_methods.get( index.row(), self.methods[self.DEFAULT]) self.varmodel.setData(index, method, Qt.UserRole) self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @Inputs.data @check_sql_input def set_data(self, data): self.closeContext() self.varmodel[:] = [] self.variable_methods = {} self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) self.update_varview() self.unconditional_commit() @Inputs.learner def set_learner(self, learner): self.learner = learner or self.DEFAULT_LEARNER imputer = self.methods[self.MODEL_BASED_IMPUTER] imputer.learner = self.learner button = self.default_button_group.button(self.MODEL_BASED_IMPUTER) button.setText(imputer.name) variable_button = self.variable_button_group.button(self.MODEL_BASED_IMPUTER) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = self.MODEL_BASED_IMPUTER self.update_varview() self.commit() def get_method_for_column(self, column_index): """Returns the imputation method for column by its index. """ if not isinstance(column_index, int): column_index = column_index.row() return self.variable_methods.get(column_index, self.methods[self.DEFAULT]) def _invalidate(self): self.modified = True if self.__task is not None: self.cancel() self.commit() def commit(self): self.cancel() self.warning() self.Error.imputation_failed.clear() self.Error.model_based_imputer_sparse.clear() if self.data is None or len(self.data) == 0 or len(self.varmodel) == 0: self.Outputs.data.send(self.data) self.modified = False return data = self.data impute_state = [ (i, var, self.variable_methods.get(i, self.default_method)) for i, var in enumerate(self.varmodel) ] def impute_one(method, var, data): # type: (impute.BaseImputeMethod, Variable, Table) -> Any if isinstance(method, impute.Model) and data.is_sparse(): raise SparseNotSupported() elif isinstance(method, impute.DropInstances): return RowMask(method(data, var)) elif not method.supports_variable(var): raise VariableNotSupported(var) else: return method(data, var) futures = [] for _, var, method in impute_state: f = self.executor.submit( impute_one, copy.deepcopy(method), var, data) futures.append(f) w = qconcurrent.FutureSetWatcher(futures) w.doneAll.connect(self.__commit_finish) w.progressChanged.connect(self.__progress_changed) self.__task = Task(futures, w) self.progressBarInit(processEvents=False) self.setBlocking(True) @Slot() def __commit_finish(self): assert QThread.currentThread() is self.thread() assert self.__task is not None futures = self.__task.futures assert len(futures) == len(self.varmodel) assert self.data is not None self.__task = None self.setBlocking(False) self.progressBarFinished() data = self.data attributes = [] class_vars = [] drop_mask = np.zeros(len(self.data), bool) for i, (var, fut) in enumerate(zip(self.varmodel, futures)): assert fut.done() newvar = [] try: res = fut.result() except SparseNotSupported: self.Error.model_based_imputer_sparse() # ?? break except VariableNotSupported: self.warning("Default method can not handle '{}'". format(var.name)) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error for %s", var, exc_info=True) self.Error.imputation_failed(var.name) attributes = class_vars = None break else: if isinstance(res, RowMask): drop_mask |= res.mask newvar = var else: newvar = res if isinstance(newvar, Orange.data.Variable): newvar = [newvar] if i < len(data.domain.attributes): attributes.extend(newvar) else: class_vars.extend(newvar) if attributes is None: data = None else: domain = Orange.data.Domain(attributes, class_vars, data.domain.metas) try: data = self.data.from_table(domain, data[~drop_mask]) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error", exc_info=True) self.Error.imputation_failed("Unknown") data = None self.Outputs.data.send(data) self.modified = False @Slot(int, int) def __progress_changed(self, n, d): assert QThread.currentThread() is self.thread() assert self.__task is not None self.progressBarSet(100. * n / d) def cancel(self): if self.__task is not None: task, self.__task = self.__task, None task.cancel() task.watcher.doneAll.disconnect(self.__commit_finish) task.watcher.progressChanged.disconnect(self.__progress_changed) concurrent.futures.wait(task.futures) task.watcher.flush() self.progressBarFinished() self.setBlocking(False) def onDeleteWidget(self): self.cancel() super().onDeleteWidget() def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, None) if method is not None: specific.append("{} ({})".format(var.name, str(method))) default = self.default_method.name if specific: self.report_items(( ("Default method", default), ("Specific imputers", ", ".join(specific)) )) else: self.report_items((("Method", default),)) def _on_var_selection_changed(self): indexes = self.selection.selectedIndexes() methods = [self.get_method_for_column(i.row()) for i in indexes] def method_key(method): """ Decompose method into its type and parameters. """ # The return value should be hashable and __eq__ comparable if isinstance(method, AsDefault): return AsDefault, (method.method,) elif isinstance(method, impute.Model): return impute.Model, (method.learner,) elif isinstance(method, impute.Default): return impute.Default, (method.default,) else: return type(method), None methods = set(method_key(m) for m in methods) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) fixed_value = None value_stack_enabled = False current_value_widget = None if len(methods) == 1: method_type, parameters = methods.pop() for i, m in enumerate(self.methods): if method_type == type(m): self.variable_button_group.button(i).setChecked(True) if method_type is impute.Default: (fixed_value,) = parameters elif self.variable_button_group.checkedButton() is not None: # Uncheck the current button self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) assert self.variable_button_group.checkedButton() is None for method, button in zip(self.methods, self.variable_button_group.buttons()): enabled = all(method.supports_variable(var) for var in selected_vars) button.setEnabled(enabled) if not has_discrete: value_stack_enabled = True current_value_widget = self.value_double elif len(selected_vars) == 1: value_stack_enabled = True current_value_widget = self.value_combo self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) else: value_stack_enabled = False current_value_widget = None self.variable_button_group.button(self.AS_INPUT).setEnabled(False) self.value_stack.setEnabled(value_stack_enabled) if current_value_widget is not None: self.value_stack.setCurrentWidget(current_value_widget) if fixed_value is not None: if current_value_widget is self.value_combo: self.value_combo.setCurrentIndex(fixed_value) elif current_value_widget is self.value_double: self.value_double.setValue(fixed_value) else: assert False def set_method_for_current_selection(self, method_index): indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): if method_index == self.DEFAULT: for index in indexes: self.variable_methods.pop(index.row(), None) elif method_index == OWImpute.AS_INPUT: current = self.value_stack.currentWidget() if current is self.value_combo: value = self.value_combo.currentIndex() else: value = self.value_double.value() for index in indexes: method = impute.Default(default=value) self.variable_methods[index.row()] = method else: method = self.methods[method_index] for index in indexes: self.variable_methods[index.row()] = method self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData(index, self.get_method_for_column(index.row()), Qt.UserRole) def _on_value_selected(self): # The fixed 'Value' in the widget has been changed by the user. self.variable_button_group.button(self.AS_INPUT).setChecked(True) self.set_method_for_current_selection(self.AS_INPUT) def reset_variable_methods(self): indexes = list(map(self.varmodel.index, range(len(self.varmodel)))) self.set_method_for_indexes(indexes, self.DEFAULT) self.variable_button_group.button(self.DEFAULT).setChecked(True)
class FileWidget(QWidget): on_open = pyqtSignal(str) def __init__(self, dialog_title='', dialog_format='', start_dir=os.path.expanduser('~/'), icon_size=(12, 20), minimal_width=200, browse_label='Browse', on_open=None, reload_button=True, reload_label='Reload', recent_files=None, directory_aliases=None, allow_empty=True, empty_file_label='(none)'): """ Creates a widget with a button for file loading and an optional combo box for recent files and reload buttons. Args: dialog_title (str): The title of the dialog. dialog_format (str): Formats for the dialog. start_dir (str): A directory to start from. icon_size (int, int): The size of buttons' icons. on_open (callable): A callback function that accepts filepath as the only argument. reload_button (bool): Whether to show reload button. reload_label (str): The text displayed on the reload button. recent_files (List[str]): List of recent files. directory_aliases (dict): An {alias: dir} dictionary for fast directories' access. allow_empty (bool): Whether empty path is allowed. """ super().__init__() self.dialog_title = dialog_title self.dialog_format = dialog_format self.start_dir = start_dir self.recent_files = recent_files self.directory_aliases = directory_aliases or {} self.check_existence() self.on_open.connect(on_open) self.allow_empty = allow_empty self.empty_file_label = empty_file_label layout = QHBoxLayout(self) layout.setContentsMargins(0, 0, 0, 0) if recent_files is not None: self.file_combo = QComboBox() self.file_combo.setMinimumWidth(minimal_width) self.file_combo.activated[int].connect(self.select) self.update_combo() layout.addWidget(self.file_combo) self.browse_button = QPushButton(browse_label) self.browse_button.setFocusPolicy(Qt.NoFocus) self.browse_button.clicked.connect(self.browse) self.browse_button.setIcon(self.style() .standardIcon(QStyle.SP_DirOpenIcon)) self.browse_button.setIconSize(QSize(*icon_size)) self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) layout.addWidget(self.browse_button) if reload_button: self.reload_button = QPushButton(reload_label) self.reload_button.setFocusPolicy(Qt.NoFocus) self.reload_button.clicked.connect(self.reload) self.reload_button.setIcon(self.style() .standardIcon(QStyle.SP_BrowserReload)) self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) self.reload_button.setIconSize(QSize(*icon_size)) layout.addWidget(self.reload_button) def browse(self, start_dir=None): start_dir = start_dir or self.start_dir path, _ = QFileDialog().getOpenFileName(self, self.dialog_title, start_dir, self.dialog_format) if path and self.recent_files is not None: if path in self.recent_files: self.recent_files.remove(path) self.recent_files.insert(0, path) self.update_combo() self.open_file(path) def select(self, n): name = self.file_combo.currentText() if n < len(self.recent_files): name = self.recent_files[n] del self.recent_files[n] self.recent_files.insert(0, name) self.open_file(self.recent_files[0]) self.update_combo() elif name == self.empty_file_label: self.open_file(self.empty_file_label) elif name in self.directory_aliases: self.browse(self.directory_aliases[name]) def update_combo(self): if self.recent_files is not None: self.file_combo.clear() for file in self.recent_files: self.file_combo.addItem(os.path.split(file)[1]) if self.allow_empty or not self.recent_files: self.file_combo.addItem(self.empty_file_label) for alias in self.directory_aliases.keys(): self.file_combo.addItem(alias) def reload(self): if self.recent_files: self.select(0) def check_existence(self): if self.recent_files: to_remove = [ file for file in self.recent_files if not os.path.exists(file) ] for file in to_remove: self.recent_files.remove(file) def open_file(self, path): try: self.on_open.emit(path if path != self.empty_file_label else '') except (OSError, IOError): self.loading_error_signal.emit('Could not open "{}".' .format(path))
class FileWidget(QWidget): on_open = pyqtSignal(str) def __init__(self, dialog_title='', dialog_format='', start_dir=os.path.expanduser('~/'), icon_size=(12, 20), minimal_width=200, browse_label='Browse', on_open=None, reload_button=True, reload_label='Reload', recent_files=None, directory_aliases=None, allow_empty=True, empty_file_label='(none)'): """ Creates a widget with a button for file loading and an optional combo box for recent files and reload buttons. Args: dialog_title (str): The title of the dialog. dialog_format (str): Formats for the dialog. start_dir (str): A directory to start from. icon_size (int, int): The size of buttons' icons. on_open (callable): A callback function that accepts filepath as the only argument. reload_button (bool): Whether to show reload button. reload_label (str): The text displayed on the reload button. recent_files (List[str]): List of recent files. directory_aliases (dict): An {alias: dir} dictionary for fast directories' access. allow_empty (bool): Whether empty path is allowed. """ super().__init__() self.dialog_title = dialog_title self.dialog_format = dialog_format self.start_dir = start_dir self.recent_files = recent_files self.directory_aliases = directory_aliases or {} self.check_existence() self.on_open.connect(on_open) self.allow_empty = allow_empty self.empty_file_label = empty_file_label layout = QHBoxLayout(self) layout.setContentsMargins(0, 0, 0, 0) if recent_files is not None: self.file_combo = QComboBox() self.file_combo.setMinimumWidth(minimal_width) self.file_combo.activated[int].connect(self.select) self.update_combo() layout.addWidget(self.file_combo) self.browse_button = QPushButton(browse_label) self.browse_button.setFocusPolicy(Qt.NoFocus) self.browse_button.clicked.connect(self.browse) self.browse_button.setIcon(self.style().standardIcon( QStyle.SP_DirOpenIcon)) self.browse_button.setIconSize(QSize(*icon_size)) self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) layout.addWidget(self.browse_button) if reload_button: self.reload_button = QPushButton(reload_label) self.reload_button.setFocusPolicy(Qt.NoFocus) self.reload_button.clicked.connect(self.reload) self.reload_button.setIcon(self.style().standardIcon( QStyle.SP_BrowserReload)) self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) self.reload_button.setIconSize(QSize(*icon_size)) layout.addWidget(self.reload_button) def browse(self, start_dir=None): start_dir = start_dir or self.start_dir path, _ = QFileDialog().getOpenFileName(self, self.dialog_title, start_dir, self.dialog_format) if path and self.recent_files is not None: if path in self.recent_files: self.recent_files.remove(path) self.recent_files.insert(0, path) self.update_combo() self.open_file(path) def select(self, n): name = self.file_combo.currentText() if n < len(self.recent_files): name = self.recent_files[n] del self.recent_files[n] self.recent_files.insert(0, name) self.open_file(self.recent_files[0]) self.update_combo() elif name == self.empty_file_label: self.open_file(self.empty_file_label) elif name in self.directory_aliases: self.browse(self.directory_aliases[name]) def update_combo(self): if self.recent_files is not None: self.file_combo.clear() for file in self.recent_files: self.file_combo.addItem(os.path.split(file)[1]) if self.allow_empty or not self.recent_files: self.file_combo.addItem(self.empty_file_label) for alias in self.directory_aliases.keys(): self.file_combo.addItem(alias) def reload(self): if self.recent_files: self.select(0) def check_existence(self): if self.recent_files: to_remove = [ file for file in self.recent_files if not os.path.exists(file) ] for file in to_remove: self.recent_files.remove(file) def open_file(self, path): try: self.on_open.emit(path if path != self.empty_file_label else '') except (OSError, IOError): self.loading_error_signal.emit('Could not open "{}".'.format(path))
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 keywords = ["substitute", "missing"] class Inputs: data = Input("Data", Orange.data.Table) learner = Input("Learner", Learner) class Outputs: data = Output("Data", Orange.data.Table) class Error(OWWidget.Error): imputation_failed = Msg("Imputation failed for '{}'") model_based_imputer_sparse = \ Msg("Model based imputer does not work for sparse data") class Warning(OWWidget.Warning): cant_handle_var = Msg("Default method can not handle '{}'") settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(int(Method.Leave)) # type: int # Per-variable imputation state (synced in storeSpecificSettings) _variable_imputation_state = settings.ContextSetting( {}) # type: VariableState autocommit = settings.Setting(True) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() self.data = None # type: Optional[Orange.data.Table] self.learner = None # type: Optional[Learner] self.default_learner = SimpleTreeLearner(min_instances=10, max_depth=10) self.modified = False self.executor = qconcurrent.ThreadExecutor(self) self.__task = None main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QGridLayout(box) box_layout.setContentsMargins(5, 0, 0, 0) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, (method, _) in enumerate(list(METHODS.items())[1:-1]): imputer = self.create_imputer(method) button = QRadioButton(imputer.name) button.setChecked(method == self.default_method_index) button_group.addButton(button, method) box_layout.addWidget(button, i % 3, i // 3) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = ListViewSearch( selectionMode=QListView.ExtendedSelection, uniformItemSizes=True) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for method in Method: imputer = self.create_imputer(method) button = QRadioButton(text=imputer.name) button_group.addButton(button, method) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection) method_layout.addStretch(2) reset_button = QPushButton("Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_state, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_apply(self.controlArea, self, "autocommit") box.button.setFixedWidth(180) box.layout().insertStretch(0) self.info.set_input_summary(self.info.NoInput) self.info.set_output_summary(self.info.NoOutput) def create_imputer(self, method, *args): # type: (Method, ...) -> impute.BaseImputeMethod if method == Method.Model: if self.learner is not None: return impute.Model(self.learner) else: return impute.Model(self.default_learner) elif method == Method.AsAboveSoBelow: assert self.default_method_index != Method.AsAboveSoBelow default = self.create_imputer(Method(self.default_method_index)) m = AsDefault() m.method = default return m else: return METHODS[method](*args) @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: assert index != Method.AsAboveSoBelow self._default_method_index = index self.default_button_group.button(index).setChecked(True) # update variable view self.update_varview() self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @Inputs.data @check_sql_input def set_data(self, data): self.cancel() self.closeContext() self.varmodel[:] = [] self._variable_imputation_state = {} # type: VariableState self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) # restore per variable imputation state self._restore_state(self._variable_imputation_state) summary = len(data) if data else self.info.NoInput details = format_summary_details(data) if data else "" self.info.set_input_summary(summary, details) self.update_varview() self.unconditional_commit() @Inputs.learner def set_learner(self, learner): self.cancel() self.learner = learner or self.default_learner imputer = self.create_imputer(Method.Model) button = self.default_button_group.button(Method.Model) button.setText(imputer.name) variable_button = self.variable_button_group.button(Method.Model) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = Method.Model self.update_varview() self.commit() def get_method_for_column(self, column_index): # type: (int) -> impute.BaseImputeMethod """ Return the imputation method for column by its index. """ assert 0 <= column_index < len(self.varmodel) idx = self.varmodel.index(column_index, 0) state = idx.data(StateRole) if state is None: state = (Method.AsAboveSoBelow, ()) return self.create_imputer(state[0], *state[1]) def _invalidate(self): self.modified = True if self.__task is not None: self.cancel() self.commit() def commit(self): self.cancel() self.warning() self.Error.imputation_failed.clear() self.Error.model_based_imputer_sparse.clear() summary = len(self.data) if self.data else self.info.NoOutput detail = format_summary_details(self.data) if self.data else "" self.info.set_output_summary(summary, detail) if not self.data or not self.varmodel.rowCount(): self.Outputs.data.send(self.data) self.modified = False return data = self.data impute_state = [(i, var, self.get_method_for_column(i)) for i, var in enumerate(self.varmodel)] # normalize to the effective method bypasing AsDefault impute_state = [(i, var, m.method if isinstance(m, AsDefault) else m) for i, var, m in impute_state] def impute_one(method, var, data): # Readability counts, pylint: disable=no-else-raise # type: (impute.BaseImputeMethod, Variable, Table) -> Any if isinstance(method, impute.Model) and data.is_sparse(): raise SparseNotSupported() elif isinstance(method, impute.DropInstances): return RowMask(method(data, var)) elif not method.supports_variable(var): raise VariableNotSupported(var) else: return method(data, var) futures = [] for _, var, method in impute_state: f = self.executor.submit(impute_one, copy.deepcopy(method), var, data) futures.append(f) w = qconcurrent.FutureSetWatcher(futures) w.doneAll.connect(self.__commit_finish) w.progressChanged.connect(self.__progress_changed) self.__task = Task(futures, w) self.progressBarInit() self.setInvalidated(True) @Slot() def __commit_finish(self): assert QThread.currentThread() is self.thread() assert self.__task is not None futures = self.__task.futures assert len(futures) == len(self.varmodel) assert self.data is not None def get_variable(variable, future, drop_mask) \ -> Optional[List[Orange.data.Variable]]: # Returns a (potentially empty) list of variables, # or None on failure that should interrupt the imputation assert future.done() try: res = future.result() except SparseNotSupported: self.Error.model_based_imputer_sparse() return [] # None? except VariableNotSupported: self.Warning.cant_handle_var(variable.name) return [] except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error for %s", variable.name, exc_info=True) self.Error.imputation_failed(variable.name) return None if isinstance(res, RowMask): drop_mask |= res.mask newvar = variable else: newvar = res if isinstance(newvar, Orange.data.Variable): newvar = [newvar] return newvar def create_data(attributes, class_vars): domain = Orange.data.Domain(attributes, class_vars, self.data.domain.metas) try: return self.data.from_table(domain, self.data[~drop_mask]) except Exception: # pylint: disable=broad-except log = logging.getLogger(__name__) log.info("Error", exc_info=True) self.Error.imputation_failed("Unknown") return None self.__task = None self.setInvalidated(False) self.progressBarFinished() attributes = [] class_vars = [] drop_mask = np.zeros(len(self.data), bool) for i, (var, fut) in enumerate(zip(self.varmodel, futures)): newvar = get_variable(var, fut, drop_mask) if newvar is None: data = None break if i < len(self.data.domain.attributes): attributes.extend(newvar) else: class_vars.extend(newvar) else: data = create_data(attributes, class_vars) self.Outputs.data.send(data) self.modified = False summary = len(data) if data else self.info.NoOutput details = format_summary_details(data) if data else "" self.info.set_output_summary(summary, details) @Slot(int, int) def __progress_changed(self, n, d): assert QThread.currentThread() is self.thread() assert self.__task is not None self.progressBarSet(100. * n / d) def cancel(self): self.__cancel(wait=False) def __cancel(self, wait=False): if self.__task is not None: task, self.__task = self.__task, None task.cancel() task.watcher.doneAll.disconnect(self.__commit_finish) task.watcher.progressChanged.disconnect(self.__progress_changed) if wait: concurrent.futures.wait(task.futures) task.watcher.flush() self.progressBarFinished() self.setInvalidated(False) def onDeleteWidget(self): self.__cancel(wait=True) super().onDeleteWidget() def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.get_method_for_column(i) if not isinstance(method, AsDefault): specific.append("{} ({})".format(var.name, str(method))) default = self.create_imputer(Method.AsAboveSoBelow) if specific: self.report_items((("Default method", default.name), ("Specific imputers", ", ".join(specific)))) else: self.report_items((("Method", default.name), )) def _on_var_selection_changed(self): # Method is well documented, splitting it is not needed for readability, # thus pylint: disable=too-many-branches indexes = self.selection.selectedIndexes() defmethod = (Method.AsAboveSoBelow, ()) methods = [index.data(StateRole) for index in indexes] methods = [m if m is not None else defmethod for m in methods] methods = set(methods) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) fixed_value = None value_stack_enabled = False current_value_widget = None if len(methods) == 1: method_type, parameters = methods.pop() for m in Method: if method_type == m: self.variable_button_group.button(m).setChecked(True) if method_type == Method.Default: (fixed_value, ) = parameters elif self.variable_button_group.checkedButton() is not None: # Uncheck the current button self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) assert self.variable_button_group.checkedButton() is None # Update variable methods GUI enabled state based on selection. for method in Method: # use a default constructed imputer to query support imputer = self.create_imputer(method) enabled = all( imputer.supports_variable(var) for var in selected_vars) button = self.variable_button_group.button(method) button.setEnabled(enabled) # Update the "Value" edit GUI. if not has_discrete: # no discrete variables -> allow mass edit for all (continuous vars) value_stack_enabled = True current_value_widget = self.value_double elif len(selected_vars) == 1: # single discrete var -> enable and fill the values combo value_stack_enabled = True current_value_widget = self.value_combo self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) else: # mixed type selection -> disable value_stack_enabled = False current_value_widget = None self.variable_button_group.button(Method.Default).setEnabled(False) self.value_stack.setEnabled(value_stack_enabled) if current_value_widget is not None: self.value_stack.setCurrentWidget(current_value_widget) if fixed_value is not None: # set current value if current_value_widget is self.value_combo: self.value_combo.setCurrentIndex(fixed_value) elif current_value_widget is self.value_double: self.value_double.setValue(fixed_value) else: assert False def set_method_for_current_selection(self, method_index): # type: (Method) -> None indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): # type: (List[QModelIndex], Method) -> None if method_index == Method.AsAboveSoBelow: for index in indexes: self.varmodel.setData(index, None, StateRole) elif method_index == Method.Default: current = self.value_stack.currentWidget() if current is self.value_combo: value = self.value_combo.currentIndex() else: value = self.value_double.value() for index in indexes: state = (int(Method.Default), (value, )) self.varmodel.setData(index, state, StateRole) else: state = (int(method_index), ()) for index in indexes: self.varmodel.setData(index, state, StateRole) self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData(index, self.get_method_for_column(index.row()), DisplayMethodRole) def _on_value_selected(self): # The fixed 'Value' in the widget has been changed by the user. self.variable_button_group.button(Method.Default).setChecked(True) self.set_method_for_current_selection(Method.Default) def reset_variable_state(self): indexes = list(map(self.varmodel.index, range(len(self.varmodel)))) self.set_method_for_indexes(indexes, Method.AsAboveSoBelow) self.variable_button_group.button( Method.AsAboveSoBelow).setChecked(True) def _store_state(self): # type: () -> VariableState """ Save the current variable imputation state """ state = {} # type: VariableState for i, var in enumerate(self.varmodel): index = self.varmodel.index(i) m = index.data(StateRole) if m is not None: state[var_key(var)] = m return state def _restore_state(self, state): # type: (VariableState) -> None """ Restore the variable imputation state from the saved state """ def check(state): # check if state is a proper State if isinstance(state, tuple) and len(state) == 2: m, p = state if isinstance(m, int) and isinstance(p, tuple) and \ 0 <= m < len(Method): return True return False for i, var in enumerate(self.varmodel): m = state.get(var_key(var), None) if check(m): self.varmodel.setData(self.varmodel.index(i), m, StateRole) def storeSpecificSettings(self): self._variable_imputation_state = self._store_state() super().storeSpecificSettings()
class OWFile(widget.OWWidget, RecentPathsWComboMixin): name = "File" id = "orange.widgets.data.file" description = "Read data from an input file or network " \ "and send a data table to the output." icon = "icons/File.svg" priority = 10 category = "Data" keywords = ["file", "load", "read", "open"] class Outputs: data = Output("Data", Table, doc="Attribute-valued dataset read from the input file.") want_main_area = False buttons_area_orientation = None SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())] SIZE_LIMIT = 1e7 LOCAL_FILE, URL = range(2) settingsHandler = PerfectDomainContextHandler( match_values=PerfectDomainContextHandler.MATCH_VALUES_ALL) # pylint seems to want declarations separated from definitions recent_paths: List[RecentPath] recent_urls: List[str] variables: list # Overload RecentPathsWidgetMixin.recent_paths to set defaults recent_paths = Setting([ RecentPath("", "sample-datasets", "iris.tab"), RecentPath("", "sample-datasets", "titanic.tab"), RecentPath("", "sample-datasets", "housing.tab"), RecentPath("", "sample-datasets", "heart_disease.tab"), RecentPath("", "sample-datasets", "brown-selected.tab"), RecentPath("", "sample-datasets", "zoo.tab"), ]) recent_urls = Setting([]) source = Setting(LOCAL_FILE) sheet_names = Setting({}) url = Setting("") variables = ContextSetting([]) domain_editor = SettingProvider(DomainEditor) class Information(widget.OWWidget.Information): no_file_selected = Msg("No file selected.") class Warning(widget.OWWidget.Warning): file_too_big = Msg("The file is too large to load automatically." " Press Reload to load.") load_warning = Msg("Read warning:\n{}") performance_warning = Msg( "Categorical variables with >100 values may decrease performance.") renamed_vars = Msg("Some variables have been renamed " "to avoid duplicates.\n{}") multiple_targets = Msg("Most widgets do not support multiple targets") class Error(widget.OWWidget.Error): file_not_found = Msg("File not found.") missing_reader = Msg("Missing reader.") sheet_error = Msg("Error listing available sheets.") unknown = Msg("Read error:\n{}") UserAdviceMessages = [ widget.Message( "Use CSV File Import widget for advanced options " "for comma-separated files", "use-csv-file-import"), widget.Message( "This widget loads only tabular data. Use other widgets to load " "other data types like models, distance matrices and networks.", "other-data-types") ] def __init__(self): super().__init__() RecentPathsWComboMixin.__init__(self) self.domain = None self.data = None self.loaded_file = "" self.reader = None readers = [ f for f in FileFormat.formats if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None) ] def group_readers_per_addon_key(w): # readers from Orange.data.io should go first def package(w): package = w.qualified_name().split(".")[:-1] package = package[:2] if ".".join(package) == "Orange.data": return ["0"] # force "Orange" to come first return package return package(w), w.DESCRIPTION self.available_readers = sorted(set(readers), key=group_readers_per_addon_key) layout = QGridLayout() layout.setSpacing(4) gui.widgetBox(self.controlArea, orientation=layout, box='Source') vbox = gui.radioButtons(None, self, "source", box=True, callback=self.load_data, addToLayout=False) rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False) layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter) box = gui.hBox(None, addToLayout=False, margin=0) box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.file_combo.activated[int].connect(self.select_file) box.layout().addWidget(self.file_combo) layout.addWidget(box, 0, 1) file_button = gui.button(None, self, '...', callback=self.browse_file, autoDefault=False) file_button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon)) file_button.setSizePolicy(Policy.Maximum, Policy.Fixed) layout.addWidget(file_button, 0, 2) reload_button = gui.button(None, self, "Reload", callback=self.load_data, autoDefault=False) reload_button.setIcon(self.style().standardIcon( QStyle.SP_BrowserReload)) reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed) layout.addWidget(reload_button, 0, 3) self.sheet_box = gui.hBox(None, addToLayout=False, margin=0) self.sheet_combo = QComboBox() self.sheet_combo.activated[str].connect(self.select_sheet) self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.sheet_label = QLabel() self.sheet_label.setText('Sheet') self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.sheet_box.layout().addWidget(self.sheet_label, Qt.AlignLeft) self.sheet_box.layout().addWidget(self.sheet_combo, Qt.AlignVCenter) layout.addWidget(self.sheet_box, 2, 1) self.sheet_box.hide() rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False) layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter) self.url_combo = url_combo = QComboBox() url_model = NamedURLModel(self.sheet_names) url_model.wrap(self.recent_urls) url_combo.setLineEdit(LineEditSelectOnFocus()) url_combo.setModel(url_model) url_combo.setSizePolicy(Policy.Ignored, Policy.Fixed) url_combo.setEditable(True) url_combo.setInsertPolicy(url_combo.InsertAtTop) url_edit = url_combo.lineEdit() l, t, r, b = url_edit.getTextMargins() url_edit.setTextMargins(l + 5, t, r, b) layout.addWidget(url_combo, 3, 1, 1, 3) url_combo.activated.connect(self._url_set) # whit completer we set that combo box is case sensitive when # matching the history completer = QCompleter() completer.setCaseSensitivity(Qt.CaseSensitive) url_combo.setCompleter(completer) layout = QGridLayout() layout.setSpacing(4) gui.widgetBox(self.controlArea, orientation=layout, box='File Type') box = gui.hBox(None, addToLayout=False, margin=0) box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.reader_combo = QComboBox(self) self.reader_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) self.reader_combo.activated[int].connect(self.select_reader) box.layout().addWidget(self.reader_combo) layout.addWidget(box, 0, 1) box = gui.vBox(self.controlArea, "Info") self.infolabel = gui.widgetLabel(box, 'No data loaded.') box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)") self.domain_editor = DomainEditor(self) self.editor_model = self.domain_editor.model() box.layout().addWidget(self.domain_editor) box = gui.hBox(box) gui.button(box, self, "Reset", callback=self.reset_domain_edit, autoDefault=False) gui.rubber(box) self.apply_button = gui.button(box, self, "Apply", callback=self.apply_domain_edit) self.apply_button.setEnabled(False) self.apply_button.setFixedWidth(170) self.editor_model.dataChanged.connect( lambda: self.apply_button.setEnabled(True)) hBox = gui.hBox(self.controlArea) gui.rubber(hBox) gui.button(hBox, self, "Browse documentation datasets", callback=lambda: self.browse_file(True), autoDefault=False) gui.rubber(hBox) self.set_file_list() # Must not call open_file from within __init__. open_file # explicitly re-enters the event loop (by a progress bar) self.setAcceptDrops(True) if self.source == self.LOCAL_FILE: last_path = self.last_path() if last_path and os.path.exists(last_path) and \ os.path.getsize(last_path) > self.SIZE_LIMIT: self.Warning.file_too_big() return QTimer.singleShot(0, self.load_data) @staticmethod def sizeHint(): return QSize(600, 550) def select_file(self, n): assert n < len(self.recent_paths) super().select_file(n) if self.recent_paths: self.source = self.LOCAL_FILE self.load_data() self.set_file_list() def select_sheet(self): self.recent_paths[0].sheet = self.sheet_combo.currentText() self.load_data() def select_reader(self, n): if self.source != self.LOCAL_FILE: return # ignore for URL's if self.recent_paths: path = self.recent_paths[0] if n == 0: # default path.file_format = None self.load_data() elif n <= len(self.available_readers): reader = self.available_readers[n - 1] path.file_format = reader.qualified_name() self.load_data() else: # the rest include just qualified names path.file_format = self.reader_combo.itemText(n) self.load_data() def _url_set(self): url = self.url_combo.currentText() pos = self.recent_urls.index(url) url = url.strip() if not urlparse(url).scheme: url = 'http://' + url self.url_combo.setItemText(pos, url) self.recent_urls[pos] = url self.source = self.URL self.load_data() def browse_file(self, in_demos=False): if in_demos: start_file = get_sample_datasets_dir() if not os.path.exists(start_file): QMessageBox.information( None, "File", "Cannot find the directory with documentation datasets") return else: start_file = self.last_path() or os.path.expanduser("~/") filename, reader, _ = open_filename_dialog(start_file, None, self.available_readers) if not filename: return self.add_path(filename) if reader is not None: self.recent_paths[0].file_format = reader.qualified_name() self.source = self.LOCAL_FILE self.load_data() # Open a file, create data from it and send it over the data channel def load_data(self): # We need to catch any exception type since anything can happen in # file readers self.closeContext() self.domain_editor.set_domain(None) self.apply_button.setEnabled(False) self.clear_messages() self.set_file_list() error = self._try_load() if error: error() self.data = None self.sheet_box.hide() self.Outputs.data.send(None) self.infolabel.setText("No data.") def _try_load(self): self._initialize_reader_combo() # pylint: disable=broad-except if self.source == self.LOCAL_FILE: if self.last_path() is None: return self.Information.no_file_selected elif not os.path.exists(self.last_path()): return self.Error.file_not_found else: url = self.url_combo.currentText().strip() if not url: return self.Information.no_file_selected def mark_problematic_reader(): self.reader_combo.setItemData(self.reader_combo.currentIndex(), QBrush(Qt.red), Qt.ForegroundRole) try: self.reader = self._get_reader() # also sets current reader index assert self.reader is not None except MissingReaderException: mark_problematic_reader() return self.Error.missing_reader except Exception as ex: mark_problematic_reader() log.exception(ex) return lambda x=ex: self.Error.unknown(str(x)) try: self._update_sheet_combo() except Exception: return self.Error.sheet_error with log_warnings() as warnings: try: data = self.reader.read() except Exception as ex: mark_problematic_reader() log.exception(ex) return lambda x=ex: self.Error.unknown(str(x)) if warnings: self.Warning.load_warning(warnings[-1].message.args[0]) self.infolabel.setText(self._describe(data)) self.loaded_file = self.last_path() add_origin(data, self.loaded_file) self.data = data self.openContext(data.domain) self.apply_domain_edit() # sends data return None def _get_reader(self) -> FileFormat: if self.source == self.LOCAL_FILE: path = self.last_path() self.reader_combo.setEnabled(True) if self.recent_paths and self.recent_paths[0].file_format: qname = self.recent_paths[0].file_format qname_index = { r.qualified_name(): i for i, r in enumerate(self.available_readers) } if qname in qname_index: self.reader_combo.setCurrentIndex(qname_index[qname] + 1) else: # reader may be accessible, but not in self.available_readers # (perhaps its code was moved) self.reader_combo.addItem(qname) self.reader_combo.setCurrentIndex( len(self.reader_combo) - 1) try: reader_class = class_from_qualified_name(qname) except Exception as ex: raise MissingReaderException( f'Can not find reader "{qname}"') from ex reader = reader_class(path) else: self.reader_combo.setCurrentIndex(0) reader = FileFormat.get_reader(path) if self.recent_paths and self.recent_paths[0].sheet: reader.select_sheet(self.recent_paths[0].sheet) return reader else: url = self.url_combo.currentText().strip() return UrlReader(url) def _update_sheet_combo(self): if len(self.reader.sheets) < 2: self.sheet_box.hide() self.reader.select_sheet(None) return self.sheet_combo.clear() self.sheet_combo.addItems(self.reader.sheets) self._select_active_sheet() self.sheet_box.show() def _select_active_sheet(self): try: idx = self.reader.sheets.index(self.reader.sheet) self.sheet_combo.setCurrentIndex(idx) except ValueError: # Requested sheet does not exist in this file self.reader.select_sheet(None) self.sheet_combo.setCurrentIndex(0) def _initialize_reader_combo(self): self.reader_combo.clear() filters = [format_filter(f) for f in self.available_readers] self.reader_combo.addItems([DEFAULT_READER_TEXT] + filters) self.reader_combo.setCurrentIndex(0) self.reader_combo.setDisabled(True) # additional readers may be added in self._get_reader() @staticmethod def _describe(table): def missing_prop(prop): if prop: return f"({prop * 100:.1f}% missing values)" else: return "(no missing values)" domain = table.domain text = "" attrs = getattr(table, "attributes", {}) descs = [ attrs[desc] for desc in ("Name", "Description") if desc in attrs ] if len(descs) == 2: descs[0] = f"<b>{descs[0]}</b>" if descs: text += f"<p>{'<br/>'.join(descs)}</p>" text += f"<p>{len(table)} instance(s)" missing_in_attr = missing_prop(table.has_missing_attribute() and table.get_nan_frequency_attribute()) missing_in_class = missing_prop(table.has_missing_class() and table.get_nan_frequency_class()) text += f"<br/>{len(domain.attributes)} feature(s) {missing_in_attr}" if domain.has_continuous_class: text += f"<br/>Regression; numerical class {missing_in_class}" elif domain.has_discrete_class: text += "<br/>Classification; categorical class " \ f"with {len(domain.class_var.values)} values {missing_in_class}" elif table.domain.class_vars: text += "<br/>Multi-target; " \ f"{len(table.domain.class_vars)} target variables " \ f"{missing_in_class}" else: text += "<br/>Data has no target variable." text += f"<br/>{len(domain.metas)} meta attribute(s)" text += "</p>" if 'Timestamp' in table.domain: # Google Forms uses this header to timestamp responses text += f"<p>First entry: {table[0, 'Timestamp']}<br/>" \ f"Last entry: {table[-1, 'Timestamp']}</p>" return text def storeSpecificSettings(self): self.current_context.modified_variables = self.variables[:] def retrieveSpecificSettings(self): if hasattr(self.current_context, "modified_variables"): self.variables[:] = self.current_context.modified_variables def reset_domain_edit(self): self.domain_editor.reset_domain() self.apply_domain_edit() def _inspect_discrete_variables(self, domain): for var in chain(domain.variables, domain.metas): if var.is_discrete and len(var.values) > 100: self.Warning.performance_warning() def apply_domain_edit(self): self.Warning.performance_warning.clear() self.Warning.renamed_vars.clear() if self.data is None: table = None else: domain, cols, renamed = \ self.domain_editor.get_domain(self.data.domain, self.data, deduplicate=True) if not (domain.variables or domain.metas): table = None elif domain is self.data.domain: table = self.data else: X, y, m = cols table = Table.from_numpy(domain, X, y, m, self.data.W) table.name = self.data.name table.ids = np.array(self.data.ids) table.attributes = getattr(self.data, 'attributes', {}) self._inspect_discrete_variables(domain) if renamed: self.Warning.renamed_vars(f"Renamed: {', '.join(renamed)}") self.Warning.multiple_targets( shown=table is not None and len(table.domain.class_vars) > 1) self.Outputs.data.send(table) self.apply_button.setEnabled(False) def get_widget_name_extension(self): _, name = os.path.split(self.loaded_file) return os.path.splitext(name)[0] def send_report(self): def get_ext_name(filename): try: return FileFormat.names[os.path.splitext(filename)[1]] except KeyError: return "unknown" if self.data is None: self.report_paragraph("File", "No file.") return if self.source == self.LOCAL_FILE: home = os.path.expanduser("~") if self.loaded_file.startswith(home): # os.path.join does not like ~ name = "~" + os.path.sep + \ self.loaded_file[len(home):].lstrip("/").lstrip("\\") else: name = self.loaded_file if self.sheet_combo.isVisible(): name += f" ({self.sheet_combo.currentText()})" self.report_items("File", [("File name", name), ("Format", get_ext_name(name))]) else: self.report_items("Data", [("Resource", self.url), ("Format", get_ext_name(self.url))]) self.report_data("Data", self.data) @staticmethod def dragEnterEvent(event): """Accept drops of valid file urls""" urls = event.mimeData().urls() if urls: try: FileFormat.get_reader(urls[0].toLocalFile()) event.acceptProposedAction() except MissingReaderException: pass def dropEvent(self, event): """Handle file drops""" urls = event.mimeData().urls() if urls: self.add_path(urls[0].toLocalFile()) # add first file self.source = self.LOCAL_FILE self.load_data() def workflowEnvChanged(self, key, value, oldvalue): """ Function called when environment changes (e.g. while saving the scheme) It make sure that all environment connected values are modified (e.g. relative file paths are changed) """ self.update_file_list(key, value, oldvalue)
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 inputs = [("Data", Orange.data.Table, "set_data"), ("Learner", Learner, "set_learner")] outputs = [("Data", Orange.data.Table)] DEFAULT_LEARNER = SimpleTreeLearner() METHODS = [AsDefault(), impute.DoNotImpute(), impute.Average(), impute.AsValue(), impute.Model(DEFAULT_LEARNER), impute.Random(), impute.DropInstances(), impute.Default()] DEFAULT, DO_NOT_IMPUTE, MODEL_BASED_IMPUTER, AS_INPUT = 0, 1, 4, 7 settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(DO_NOT_IMPUTE) variable_methods = settings.ContextSetting({}) autocommit = settings.Setting(False) default_value = settings.Setting(0.) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, method in enumerate(self.METHODS): if not method.columns_only: button = QRadioButton(method.name) button.setChecked(i == self.default_method_index) button_group.addButton(button, i) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView( selectionMode=QListView.ExtendedSelection ) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed ) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for i, method in enumerate(self.METHODS): button = QRadioButton(text=method.name) button_group.addButton(button, i) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected ) self.value_combo.currentIndexChanged.connect(self._on_value_changed) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, value=self.default_value ) self.value_stack = value_stack = QStackedLayout() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addLayout(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection ) method_layout.addStretch(2) reset_button = QPushButton( "Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_methods, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit( self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.layout().insertSpacing(0, 80) box.layout().insertWidget(0, self.report_button) self.data = None self.modified = False self.default_method = self.METHODS[self.default_method_index] self.update_varview() @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: self._default_method_index = index self.default_button_group.button(index).setChecked(True) self.default_method = self.METHODS[self.default_method_index] self.METHODS[self.DEFAULT].method = self.default_method # update variable view for index in map(self.varmodel.index, range(len(self.varmodel))): self.varmodel.setData(index, self.variable_methods.get(index.row(), self.METHODS[self.DEFAULT]), Qt.UserRole) self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @check_sql_input def set_data(self, data): self.closeContext() self.varmodel[:] = [] self.variable_methods = {} self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) self.update_varview() self.unconditional_commit() def set_learner(self, learner): self.learner = learner or self.DEFAULT_LEARNER imputer = self.METHODS[self.MODEL_BASED_IMPUTER] imputer.learner = self.learner button = self.default_button_group.button(self.MODEL_BASED_IMPUTER) button.setText(imputer.name) variable_button = self.variable_button_group.button(self.MODEL_BASED_IMPUTER) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = self.MODEL_BASED_IMPUTER self.commit() def get_method_for_column(self, column_index): """Returns the imputation method for column by its index. """ if not isinstance(column_index, int): column_index = column_index.row() return self.variable_methods.get(column_index, self.METHODS[self.DEFAULT]) def _invalidate(self): self.modified = True self.commit() def commit(self): data = self.data if self.data is not None: if not len(self.data): self.send("Data", self.data) self.modified = False return drop_mask = np.zeros(len(self.data), bool) attributes = [] class_vars = [] self.warning() with self.progressBar(len(self.varmodel)) as progress: for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, self.default_method) if not method.supports_variable(var): self.warning("Default method can not handle '{}'". format(var.name)) elif isinstance(method, impute.DropInstances): drop_mask |= method(self.data, var) else: var = method(self.data, var) if isinstance(var, Orange.data.Variable): var = [var] if i < len(self.data.domain.attributes): attributes.extend(var) else: class_vars.extend(var) progress.advance() domain = Orange.data.Domain(attributes, class_vars, self.data.domain.metas) data = self.data.from_table(domain, self.data[~drop_mask]) self.send("Data", data) self.modified = False def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, None) if method is not None: specific.append("{} ({})".format(var.name, str(method))) default = self.default_method.name if specific: self.report_items(( ("Default method", default), ("Specific imputers", ", ".join(specific)) )) else: self.report_items((("Method", default),)) def _on_var_selection_changed(self): indexes = self.selection.selectedIndexes() methods = set(self.get_method_for_column(i.row()).name for i in indexes) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) if len(methods) == 1: method = methods.pop() for i, m in enumerate(self.METHODS): if method == m.name: self.variable_button_group.button(i).setChecked(True) elif self.variable_button_group.checkedButton() is not None: self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) for method, button in zip(self.METHODS, self.variable_button_group.buttons()): enabled = all(method.supports_variable(var) for var in selected_vars) button.setEnabled(enabled) if not has_discrete: self.value_stack.setEnabled(True) self.value_stack.setCurrentWidget(self.value_double) self._on_value_changed() elif len(selected_vars) == 1: self.value_stack.setEnabled(True) self.value_stack.setCurrentWidget(self.value_combo) self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) self._on_value_changed() else: self.variable_button_group.button(self.AS_INPUT).setEnabled(False) self.value_stack.setEnabled(False) def set_method_for_current_selection(self, method_index): indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): if method_index == self.DEFAULT: for index in indexes: self.variable_methods.pop(index, None) else: method = self.METHODS[method_index].copy() for index in indexes: self.variable_methods[index.row()] = method self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData(index, self.get_method_for_column(index.row()), Qt.UserRole) def _on_value_selected(self): self.variable_button_group.button(self.AS_INPUT).setChecked(True) self._on_value_changed() def _on_value_changed(self): widget = self.value_stack.currentWidget() if widget is self.value_combo: value = self.value_combo.currentText() else: value = self.value_double.value() self.default_value = value self.METHODS[self.AS_INPUT].default = value index = self.variable_button_group.checkedId() if index == self.AS_INPUT: self.set_method_for_current_selection(index) def reset_variable_methods(self): indexes = map(self.varmodel.index, range(len(self.varmodel))) self.set_method_for_indexes(indexes, self.DEFAULT) self.variable_button_group.button(self.DEFAULT).setChecked(True)
class OWSql(OWBaseSql): name = "SQL Table" id = "orange.widgets.data.sql" description = "Load dataset from SQL." icon = "icons/SQLTable.svg" priority = 30 category = "Data" keywords = ["load"] class Outputs: data = Output("Data", Table, doc="Attribute-valued dataset read from the input file.") settings_version = 2 table = Setting(None) sql = Setting("") guess_values = Setting(True) download = Setting(False) materialize = Setting(False) materialize_table_name = Setting("") class Information(OWBaseSql.Information): data_sampled = Msg("Data description was generated from a sample.") class Warning(OWBaseSql.Warning): missing_extension = Msg("Database is missing extensions: {}") class Error(OWBaseSql.Error): no_backends = Msg("Please install a backend to use this widget.") def __init__(self): # Lint self.backends = None self.backendcombo = None self.tables = None self.tablecombo = None self.sqltext = None self.custom_sql = None self.downloadcb = None super().__init__() def _setup_gui(self): super()._setup_gui() self._add_backend_controls() self._add_tables_controls() def _add_backend_controls(self): box = self.serverbox self.backends = BackendModel(Backend.available_backends()) self.backendcombo = QComboBox(box) if self.backends: self.backendcombo.setModel(self.backends) else: self.Error.no_backends() box.setEnabled(False) box.layout().insertWidget(0, self.backendcombo) def _add_tables_controls(self): vbox = gui.vBox(self.controlArea, "Tables", addSpace=True) box = gui.vBox(vbox) self.tables = TableModel() self.tablecombo = QComboBox( minimumContentsLength=35, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength) self.tablecombo.setModel(self.tables) self.tablecombo.setToolTip('table') self.tablecombo.activated[int].connect(self.select_table) box.layout().addWidget(self.tablecombo) self.custom_sql = gui.vBox(box) self.custom_sql.setVisible(False) self.sqltext = QTextEdit(self.custom_sql) self.sqltext.setPlainText(self.sql) self.custom_sql.layout().addWidget(self.sqltext) mt = gui.hBox(self.custom_sql) cb = gui.checkBox(mt, self, 'materialize', 'Materialize to table ') cb.setToolTip('Save results of the query in a table') le = gui.lineEdit(mt, self, 'materialize_table_name') le.setToolTip('Save results of the query in a table') gui.button(self.custom_sql, self, 'Execute', callback=self.open_table) box.layout().addWidget(self.custom_sql) gui.checkBox(box, self, "guess_values", "Auto-discover categorical variables", callback=self.open_table) self.downloadcb = gui.checkBox(box, self, "download", "Download data to local memory", callback=self.open_table) def highlight_error(self, text=""): err = ['', 'QLineEdit {border: 2px solid red;}'] self.servertext.setStyleSheet(err['server' in text or 'host' in text]) self.usernametext.setStyleSheet(err['role' in text]) self.databasetext.setStyleSheet(err['database' in text]) def get_backend(self): if self.backendcombo.currentIndex() < 0: return None return self.backends[self.backendcombo.currentIndex()] def on_connection_success(self): if getattr(self.backend, 'missing_extension', False): self.Warning.missing_extension(", ".join( self.backend.missing_extension)) self.download = True self.downloadcb.setEnabled(False) if not is_postgres(self.backend): self.download = True self.downloadcb.setEnabled(False) super().on_connection_success() self.refresh_tables() self.select_table() def on_connection_error(self, err): super().on_connection_error(err) self.highlight_error(str(err).split("\n")[0]) def clear(self): super().clear() self.Warning.missing_extension.clear() self.downloadcb.setEnabled(True) self.highlight_error() self.tablecombo.clear() self.tablecombo.repaint() def refresh_tables(self): self.tables.clear() if self.backend is None: self.data_desc_table = None return self.tables.append("Select a table") self.tables.append("Custom SQL") self.tables.extend(self.backend.list_tables(self.schema)) index = self.tablecombo.findText(str(self.table)) self.tablecombo.setCurrentIndex(index if index != -1 else 0) self.tablecombo.repaint() # Called on tablecombo selection change: def select_table(self): curIdx = self.tablecombo.currentIndex() if self.tablecombo.itemText(curIdx) != "Custom SQL": self.custom_sql.setVisible(False) return self.open_table() else: self.custom_sql.setVisible(True) self.data_desc_table = None self.database_desc["Table"] = "(None)" self.table = None if len(str(self.sql)) > 14: return self.open_table() return None def get_table(self): curIdx = self.tablecombo.currentIndex() if curIdx <= 0: if self.database_desc: self.database_desc["Table"] = "(None)" self.data_desc_table = None return None if self.tablecombo.itemText(curIdx) != "Custom SQL": self.table = self.tables[self.tablecombo.currentIndex()] self.database_desc["Table"] = self.table if "Query" in self.database_desc: del self.database_desc["Query"] what = self.table else: what = self.sql = self.sqltext.toPlainText() self.table = "Custom SQL" if self.materialize: if not self.materialize_table_name: self.Error.connection( "Specify a table name to materialize the query") return None try: with self.backend.execute_sql_query( "DROP TABLE IF EXISTS " + self.materialize_table_name): pass with self.backend.execute_sql_query( "CREATE TABLE " + self.materialize_table_name + " AS " + self.sql): pass with self.backend.execute_sql_query( "ANALYZE " + self.materialize_table_name): pass except BackendError as ex: self.Error.connection(str(ex)) return None try: table = SqlTable(dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password), what, backend=type(self.backend), inspect_values=False) except BackendError as ex: self.Error.connection(str(ex)) return None self.Error.connection.clear() sample = False if table.approx_len() > LARGE_TABLE and self.guess_values: confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Attribute discovery might take " "a long time on large tables.\n" "Do you want to auto discover attributes?") confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) if is_postgres(self.backend): sample_button = confirm.addButton("Yes, on a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: self.guess_values = False elif is_postgres(self.backend) and \ confirm.clickedButton() == sample_button: sample = True self.Information.clear() if self.guess_values: QApplication.setOverrideCursor(QCursor(Qt.WaitCursor)) if sample: s = table.sample_time(1) domain = s.get_domain(inspect_values=True) self.Information.data_sampled() else: domain = table.get_domain(inspect_values=True) QApplication.restoreOverrideCursor() table.domain = domain if self.download: if table.approx_len() > AUTO_DL_LIMIT: if is_postgres(self.backend): confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Data appears to be big. Do you really " "want to download it to local memory?") if table.approx_len() <= MAX_DL_LIMIT: confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) sample_button = confirm.addButton("Yes, a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: return None elif confirm.clickedButton() == sample_button: table = table.sample_percentage( AUTO_DL_LIMIT / table.approx_len() * 100) else: if table.approx_len() > MAX_DL_LIMIT: QMessageBox.warning(self, 'Warning', "Data is too big to download.\n") return None else: confirm = QMessageBox.question( self, 'Question', "Data appears to be big. Do you really " "want to download it to local memory?", QMessageBox.Yes | QMessageBox.No, QMessageBox.No) if confirm == QMessageBox.No: return None table.download_data(MAX_DL_LIMIT) table = Table(table) return table @classmethod def migrate_settings(cls, settings, version): if version < 2: # Until Orange version 3.4.4 username and password had been stored # in Settings. cm = cls._credential_manager(settings["host"], settings["port"]) cm.username = settings["username"] cm.password = settings["password"]
class FileLoader(QWidget): activated = pyqtSignal() file_loaded = pyqtSignal() def __init__(self): super().__init__() self.recent_paths = [] self.file_combo = QComboBox() self.file_combo.setMinimumWidth(80) self.file_combo.activated.connect(self._activate) self.browse_btn = QPushButton("...") icon = self.style().standardIcon(QStyle.SP_DirOpenIcon) self.browse_btn.setIcon(icon) self.browse_btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed) self.browse_btn.clicked.connect(self.browse) self.load_btn = QPushButton("") icon = self.style().standardIcon(QStyle.SP_BrowserReload) self.load_btn.setIcon(icon) self.load_btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed) self.load_btn.setAutoDefault(True) self.load_btn.clicked.connect(self.file_loaded) def browse(self): start_file = self.last_path() or os.path.expanduser("~/") formats = ["Text files (*.txt)", "All files (*)"] file_name, _ = QFileDialog.getOpenFileName(None, "Open...", start_file, ";;".join(formats), formats[0]) if not file_name: return self.add_path(file_name) self._activate() def _activate(self): self.activated.emit() self.file_loaded.emit() def set_current_file(self, path: str): if path: self.add_path(path) self.file_combo.setCurrentText(path) else: self.file_combo.setCurrentText("(none)") def get_current_file(self) -> Optional[RecentPath]: index = self.file_combo.currentIndex() if index >= len(self.recent_paths) or index < 0: return None path = self.recent_paths[index] return path if isinstance(path, RecentPath) else None def add_path(self, filename: str): recent = RecentPath.create(filename, []) if recent in self.recent_paths: self.recent_paths.remove(recent) self.recent_paths.insert(0, recent) self.set_file_list() def set_file_list(self): self.file_combo.clear() for i, recent in enumerate(self.recent_paths): self.file_combo.addItem(recent.basename) self.file_combo.model().item(i).setToolTip(recent.abspath) if not os.path.exists(recent.abspath): self.file_combo.setItemData(i, QBrush(Qt.red), Qt.TextColorRole) self.file_combo.addItem(_DEFAULT_NONE) def last_path(self) -> Optional[str]: return self.recent_paths[0].abspath if self.recent_paths else None
class OWImpute(OWWidget): name = "Impute" description = "Impute missing values in the data table." icon = "icons/Impute.svg" priority = 2130 inputs = [("Data", Orange.data.Table, "set_data"), ("Learner", Learner, "set_learner")] outputs = [("Data", Orange.data.Table)] DEFAULT_LEARNER = SimpleTreeLearner() METHODS = [ AsDefault(), impute.DoNotImpute(), impute.Average(), impute.AsValue(), impute.Model(DEFAULT_LEARNER), impute.Random(), impute.DropInstances(), impute.Default() ] DEFAULT, DO_NOT_IMPUTE, MODEL_BASED_IMPUTER, AS_INPUT = 0, 1, 4, 7 settingsHandler = settings.DomainContextHandler() _default_method_index = settings.Setting(DO_NOT_IMPUTE) variable_methods = settings.ContextSetting({}) autocommit = settings.Setting(False) default_value = settings.Setting(0.) want_main_area = False resizing_enabled = False def __init__(self): super().__init__() main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, method in enumerate(self.METHODS): if not method.columns_only: button = QRadioButton(method.name) button.setChecked(i == self.default_method_index) button_group.addButton(button, i) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView(selectionMode=QListView.ExtendedSelection) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for i, method in enumerate(self.METHODS): button = QRadioButton(text=method.name) button_group.addButton(button, i) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected) self.value_combo.currentIndexChanged.connect(self._on_value_changed) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, value=self.default_value) self.value_stack = value_stack = QStackedLayout() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addLayout(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection) method_layout.addStretch(2) reset_button = QPushButton("Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_methods, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit(self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.layout().insertSpacing(0, 80) box.layout().insertWidget(0, self.report_button) self.data = None self.modified = False self.default_method = self.METHODS[self.default_method_index] self.update_varview() @property def default_method_index(self): return self._default_method_index @default_method_index.setter def default_method_index(self, index): if self._default_method_index != index: self._default_method_index = index self.default_button_group.button(index).setChecked(True) self.default_method = self.METHODS[self.default_method_index] self.METHODS[self.DEFAULT].method = self.default_method # update variable view for index in map(self.varmodel.index, range(len(self.varmodel))): self.varmodel.setData( index, self.variable_methods.get(index.row(), self.METHODS[self.DEFAULT]), Qt.UserRole) self._invalidate() def set_default_method(self, index): """Set the current selected default imputation method. """ self.default_method_index = index @check_sql_input def set_data(self, data): self.closeContext() self.varmodel[:] = [] self.variable_methods = {} self.modified = False self.data = data if data is not None: self.varmodel[:] = data.domain.variables self.openContext(data.domain) self.update_varview() self.unconditional_commit() def set_learner(self, learner): self.learner = learner or self.DEFAULT_LEARNER imputer = self.METHODS[self.MODEL_BASED_IMPUTER] imputer.learner = self.learner button = self.default_button_group.button(self.MODEL_BASED_IMPUTER) button.setText(imputer.name) variable_button = self.variable_button_group.button( self.MODEL_BASED_IMPUTER) variable_button.setText(imputer.name) if learner is not None: self.default_method_index = self.MODEL_BASED_IMPUTER self.commit() def get_method_for_column(self, column_index): """Returns the imputation method for column by its index. """ if not isinstance(column_index, int): column_index = column_index.row() return self.variable_methods.get(column_index, self.METHODS[self.DEFAULT]) def _invalidate(self): self.modified = True self.commit() def commit(self): data = self.data if self.data is not None: drop_mask = np.zeros(len(self.data), bool) attributes = [] class_vars = [] self.warning() with self.progressBar(len(self.varmodel)) as progress: for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, self.default_method) if not method.supports_variable(var): self.warning( "Default method can not handle '{}'".format( var.name)) elif isinstance(method, impute.DropInstances): drop_mask |= method(self.data, var) else: var = method(self.data, var) if isinstance(var, Orange.data.Variable): var = [var] if i < len(self.data.domain.attributes): attributes.extend(var) else: class_vars.extend(var) progress.advance() domain = Orange.data.Domain(attributes, class_vars, self.data.domain.metas) data = self.data.from_table(domain, self.data[~drop_mask]) self.send("Data", data) self.modified = False def send_report(self): specific = [] for i, var in enumerate(self.varmodel): method = self.variable_methods.get(i, None) if method is not None: specific.append("{} ({})".format(var.name, str(method))) default = self.default_method.name if specific: self.report_items((("Default method", default), ("Specific imputers", ", ".join(specific)))) else: self.report_items((("Method", default), )) def _on_var_selection_changed(self): indexes = self.selection.selectedIndexes() methods = set( self.get_method_for_column(i.row()).name for i in indexes) selected_vars = [self.varmodel[index.row()] for index in indexes] has_discrete = any(var.is_discrete for var in selected_vars) if len(methods) == 1: method = methods.pop() for i, m in enumerate(self.METHODS): if method == m.name: self.variable_button_group.button(i).setChecked(True) elif self.variable_button_group.checkedButton() is not None: self.variable_button_group.setExclusive(False) self.variable_button_group.checkedButton().setChecked(False) self.variable_button_group.setExclusive(True) for method, button in zip(self.METHODS, self.variable_button_group.buttons()): enabled = all( method.supports_variable(var) for var in selected_vars) button.setEnabled(enabled) if not has_discrete: self.value_stack.setEnabled(True) self.value_stack.setCurrentWidget(self.value_double) self._on_value_changed() elif len(selected_vars) == 1: self.value_stack.setEnabled(True) self.value_stack.setCurrentWidget(self.value_combo) self.value_combo.clear() self.value_combo.addItems(selected_vars[0].values) self._on_value_changed() else: self.variable_button_group.button(self.AS_INPUT).setEnabled(False) self.value_stack.setEnabled(False) def set_method_for_current_selection(self, method_index): indexes = self.selection.selectedIndexes() self.set_method_for_indexes(indexes, method_index) def set_method_for_indexes(self, indexes, method_index): if method_index == self.DEFAULT: for index in indexes: self.variable_methods.pop(index, None) else: method = self.METHODS[method_index].copy() for index in indexes: self.variable_methods[index.row()] = method self.update_varview(indexes) self._invalidate() def update_varview(self, indexes=None): if indexes is None: indexes = map(self.varmodel.index, range(len(self.varmodel))) for index in indexes: self.varmodel.setData(index, self.get_method_for_column(index.row()), Qt.UserRole) def _on_value_selected(self): self.variable_button_group.button(self.AS_INPUT).setChecked(True) self._on_value_changed() def _on_value_changed(self): widget = self.value_stack.currentWidget() if widget is self.value_combo: value = self.value_combo.currentText() else: value = self.value_double.value() self.default_value = value self.METHODS[self.AS_INPUT].default = value index = self.variable_button_group.checkedId() if index == self.AS_INPUT: self.set_method_for_current_selection(index) def reset_variable_methods(self): indexes = map(self.varmodel.index, range(len(self.varmodel))) self.set_method_for_indexes(indexes, self.DEFAULT) self.variable_button_group.button(self.DEFAULT).setChecked(True)