def test_locate_sample_datasets(self):
with self.assertRaises(OSError):
FileFormat.locate("iris.tab", search_dirs=[os.path.dirname(__file__)])
iris = FileFormat.locate("iris.tab", search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
# test extension adding
iris = FileFormat.locate("iris", search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
def test_locate_sample_datasets(self):
with self.assertRaises(OSError):
FileFormat.locate("iris.tab",
search_dirs=[os.path.dirname(__file__)])
iris = FileFormat.locate("iris.tab",
search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
# test extension adding
iris = FileFormat.locate("iris",
search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
def _relocate_recent_files(self):
if self.recent_files and not self.recent_paths:
# backward compatibility settings restore
existing = [
path for path in self.recent_files if os.path.exists(path)
]
existing = [RecentPath(path, None, None) for path in existing]
self.recent_paths.extend(existing)
self.recent_files = []
paths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
paths.append(("basedir", basedir))
rec = []
for recent in self.recent_paths:
resolved = recent.resolve(paths)
if resolved is not None:
rec.append(RecentPath.create(resolved.abspath, paths))
elif recent.search(paths) is not None:
rec.append(RecentPath.create(recent.search(paths), paths))
elif recent.prefix == "url-datasets":
valid, _ = self.is_url_valid(recent.abspath)
if valid:
rec.append(recent)
self.recent_paths = rec
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("~/")
readers = [
f for f in FileFormat.formats
if getattr(f, "read", None) and getattr(f, "EXTENSIONS", None)
]
filename, reader, _ = open_filename_dialog(start_file, None, 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()
def browseFile(self, in_demos=0):
if in_demos:
try:
startfile = get_sample_datasets_dir()
except AttributeError:
startfile = ""
if not startfile or not os.path.exists(startfile):
widgetsdir = os.path.dirname(gui.__file__)
orangedir = os.path.dirname(widgetsdir)
startfile = os.path.join(orangedir, "doc", "datasets")
if not startfile or not os.path.exists(startfile):
d = os.getcwd()
if os.path.basename(d) == "canvas":
d = os.path.dirname(d)
startfile = os.path.join(os.path.dirname(d), "doc", "datasets")
if not os.path.exists(startfile):
QtGui.QMessageBox.information(None, "File",
"Cannot find the directory with example data sets")
return
else:
if self.recent_files and self.recent_files[0] != "(none)":
startfile = self.recent_files[0]
else:
startfile = os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(
self, 'Open Orange Data File', startfile, self.dlgFormats)
if not filename:
return
if filename in self.recent_files:
self.recent_files.remove(filename)
self.recent_files.insert(0, filename)
self.set_file_list()
self.open_file(self.recent_files[0])
def browse_file(self, in_demos=False):
if in_demos:
try:
start_file = get_sample_datasets_dir()
except AttributeError:
start_file = ""
if not start_file or not os.path.exists(start_file):
widgets_dir = os.path.dirname(gui.__file__)
orange_dir = os.path.dirname(widgets_dir)
start_file = os.path.join(orange_dir, "doc", "datasets")
if not start_file or not os.path.exists(start_file):
d = os.getcwd()
if os.path.basename(d) == "canvas":
d = os.path.dirname(d)
start_file = os.path.join(os.path.dirname(d), "doc", "datasets")
if not os.path.exists(start_file):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with example data sets")
return
else:
if self.recent_paths:
start_file = self.recent_paths[0].abspath
else:
start_file = os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(
self, 'Open Orange Data File', start_file, self.dlg_formats)
if not filename:
return
self._add_path(filename)
self.set_file_list()
self.source = self.LOCAL_FILE
self.load_data()
def _relocate_recent_files(self):
if self.recent_files and not self.recent_paths:
# backward compatibility settings restore
existing = [path for path in self.recent_files
if os.path.exists(path)]
existing = [RecentPath(path, None, None) for path in existing]
self.recent_paths.extend(existing)
self.recent_files = []
paths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
paths.append(("basedir", basedir))
rec = []
for recent in self.recent_paths:
resolved = recent.resolve(paths)
if resolved is not None:
rec.append(RecentPath.create(resolved.abspath, paths))
elif recent.search(paths) is not None:
rec.append(RecentPath.create(recent.search(paths), paths))
elif recent.prefix == "url-datasets":
valid, _ = self.is_url_valid(recent.abspath)
if valid:
rec.append(recent)
self.recent_paths = rec
def browse_files(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 data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filenames = QFileDialog.getOpenFileNames(self,
'Open Multiple Data Files',
start_file, self.dlg_formats)
if isinstance(filenames, tuple): # has a file description
filenames = filenames[0]
if not filenames:
return
for f in filenames:
self.add_path(f)
self.lb.addItem(f)
self._update_sheet_combo()
self.load_data()
def _add_path(self, filename):
searchpaths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
searchpaths.append(("basedir", basedir))
recent = RecentPath.create(filename, searchpaths)
if recent in self.recent_paths:
self.recent_paths.remove(recent)
self.recent_paths.insert(0, recent)
def _add_path(self, filename):
searchpaths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
searchpaths.append(("basedir", basedir))
recent = RecentPath.create(filename, searchpaths)
if recent in self.recent_paths:
self.recent_paths.remove(recent)
self.recent_paths.insert(0, recent)
def browse_file(self, in_demos=0):
if in_demos:
try:
start_file = get_sample_datasets_dir()
except AttributeError:
start_file = ""
if not start_file or not os.path.exists(start_file):
widgets_dir = os.path.dirname(gui.__file__)
orange_dir = os.path.dirname(widgets_dir)
start_file = os.path.join(orange_dir, "doc", "datasets")
if not start_file or not os.path.exists(start_file):
d = os.getcwd()
if os.path.basename(d) == "canvas":
d = os.path.dirname(d)
start_file = os.path.join(os.path.dirname(d), "doc", "datasets")
if not os.path.exists(start_file):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with example data sets")
return
else:
if self.recent_paths:
start_file = self.recent_paths[0].abspath
else:
start_file = os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(
self, 'Open Orange Data File', start_file, self.dlgFormats)
if not filename:
return
searchpaths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
searchpaths.append(("basedir", basedir))
recent = RecentPath.create(filename, searchpaths)
if recent in self.recent_paths:
self.recent_paths.remove(recent)
self.recent_paths.insert(0, recent)
self.set_file_list()
self.open_file(self.recent_paths[0].abspath)
def _relocate_recent_files(self):
paths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
paths.append(("basedir", basedir))
rec = []
for recent in self.recent_paths:
resolved = recent.resolve(paths)
if resolved is not None:
rec.append(RecentPath.create(resolved.abspath, paths))
elif recent.search(paths) is not None:
rec.append(RecentPath.create(recent.search(paths), paths))
self.recent_paths = rec
def _relocate_recent_files(self):
paths = [("sample-datasets", get_sample_datasets_dir())]
basedir = self.workflowEnv().get("basedir", None)
if basedir is not None:
paths.append(("basedir", basedir))
rec = []
for recent in self.recent_paths:
resolved = recent.resolve(paths)
if resolved is not None:
rec.append(RecentPath.create(resolved.abspath, paths))
elif recent.search(paths) is not None:
rec.append(RecentPath.create(recent.search(paths), paths))
self.recent_paths = rec
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 data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename, _ = QFileDialog.getOpenFileName(
self, 'Open Orange Data File', start_file, dialog_formats())
if not filename:
return
self.add_path(filename)
self.source = self.LOCAL_FILE
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, "文件", "无法找到文件")
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()
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 data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename, _ = QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file, self.dlg_formats)
if not filename:
return
self.add_path(filename)
self.source = self.LOCAL_FILE
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("~/")
readers = [f for f in FileFormat.formats
if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None)]
filename, reader, _ = open_filename_dialog(start_file, None, 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()
def browse_file(self, in_demos=False):
if in_demos:
try:
start_file = get_sample_datasets_dir()
except AttributeError:
start_file = ""
if not start_file or not os.path.exists(start_file):
widgets_dir = os.path.dirname(gui.__file__)
orange_dir = os.path.dirname(widgets_dir)
start_file = os.path.join(orange_dir, "doc", "datasets")
if not start_file or not os.path.exists(start_file):
d = os.getcwd()
if os.path.basename(d) == "canvas":
d = os.path.dirname(d)
start_file = os.path.join(os.path.dirname(d), "doc",
"datasets")
if not os.path.exists(start_file):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with example data sets")
return
else:
if self.recent_paths:
start_file = self.recent_paths[0].abspath
else:
start_file = os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file,
self.dlg_formats)
if not filename:
return
self._add_path(filename)
self.set_file_list()
self.source = self.LOCAL_FILE
self.load_data()
def browse_file(self, in_demos=0):
if in_demos:
try:
start_file = get_sample_datasets_dir()
except AttributeError:
start_file = ""
if not start_file or not os.path.exists(start_file):
widgets_dir = os.path.dirname(gui.__file__)
orange_dir = os.path.dirname(widgets_dir)
start_file = os.path.join(orange_dir, "doc", "datasets")
if not start_file or not os.path.exists(start_file):
d = os.getcwd()
if os.path.basename(d) == "canvas":
d = os.path.dirname(d)
start_file = os.path.join(os.path.dirname(d), "doc",
"datasets")
if not os.path.exists(start_file):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with example data sets")
return
else:
if self.recent_files and self.recent_files[0] != "(none)":
start_file = self.recent_files[0]
else:
start_file = os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file,
self.dlgFormats)
if not filename:
return
if filename in self.recent_files:
self.recent_files.remove(filename)
self.recent_files.insert(0, filename)
self.set_file_list()
self.open_file(self.recent_files[0])
class OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "File"
id = "orange.widgets.data.file"
description = "Read a data from an input file or network" \
"and send the data table to the output."
icon = "icons/File.svg"
priority = 10
category = "Data"
keywords = ["data", "file", "load", "read"]
outputs = [
widget.OutputSignal(
"Data",
Table,
doc="Attribute-valued data set read from the input file.")
]
want_main_area = False
resizing_enabled = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
LOCAL_FILE, URL = range(2)
settingsHandler = XlsContextHandler()
# 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"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
dlg_formats = ("All readable files ({});;".format(
'*' + ' *'.join(FileFormat.readers.keys())) + ";;".join(
"{} (*{})".format(f.DESCRIPTION, ' *'.join(f.EXTENSIONS))
for f in sorted(set(FileFormat.readers.values()),
key=list(FileFormat.readers.values()).index)))
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
layout = QtGui.QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File", addToLayout=False)
layout.addWidget(rb_button, 0, 0, QtCore.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(
QtGui.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.reload,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QtGui.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 = gui.comboBox(None,
self,
"xls_sheet",
callback=self.load_data,
sendSelectedValue=True)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QtGui.QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label,
QtCore.Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo,
QtCore.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, QtCore.Qt.AlignVCenter)
self.url_combo = url_combo = QtGui.QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
url_combo.setMaximumWidth(500)
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, 3, 3)
url_combo.activated.connect(self._url_set)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.hBox(self.controlArea)
gui.button(box,
self,
"Browse documentation data sets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
# Set word wrap, so long warnings won't expand the widget
self.warnings.setWordWrap(True)
self.warnings.setSizePolicy(Policy.Ignored, Policy.MinimumExpanding)
self.set_file_list()
if self.last_path() is not None:
self.fill_sheet_combo(self.last_path())
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
QtCore.QTimer.singleShot(0, self.load_data)
def reload(self):
if self.recent_paths:
basename = self.file_combo.currentText()
path = self.recent_paths[0]
if basename in [path.relpath, path.basename]:
self.source = self.LOCAL_FILE
if self.is_multisheet_excel(path.abspath):
self.fill_sheet_combo(path.abspath)
return self.load_data()
self.select_file(len(self.recent_paths) + 1)
def select_file(self, n):
if n < len(self.recent_paths):
super().select_file(n)
self.fill_sheet_combo(self.last_path())
# TODO: This is weird. Has it remained here from "Browse data sets"
# or from when this combo was editable? A `n` this large can come from
# `reload`, but ... how?!
elif n:
path = self.file_combo.currentText()
if os.path.exists(path):
self.add_path(path)
else:
self.info.setText('Data was not loaded:')
self.warnings.setText("File {} does not exist".format(path))
self.file_combo.removeItem(n)
self.file_combo.lineEdit().setText(path)
return
if self.recent_paths:
self.source = self.LOCAL_FILE
self.load_data()
self.set_file_list()
def _url_set(self):
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):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with documentation data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file,
self.dlg_formats)
if not filename:
return
self.add_path(filename)
self.source = self.LOCAL_FILE
self.fill_sheet_combo(filename)
self.load_data()
def fill_sheet_combo(self, path):
if os.path.exists(path) and self.is_multisheet_excel(path):
self.closeContext()
self.sheet_combo.clear()
self.sheet_box.show()
book = open_workbook(path)
sheet_names = [
str(book.sheet_by_index(i).name) for i in range(book.nsheets)
]
self.sheet_combo.addItems(sheet_names)
self.openContext(path, sheet_names)
else:
self.sheet_box.hide()
@staticmethod
def is_multisheet_excel(fn):
try:
return open_workbook(fn).nsheets > 1
except XLRDError:
return False
# Open a file, create data from it and send it over the data channel
def load_data(self):
def load(method, fn):
with catch_warnings(record=True) as warnings:
data = method(fn)
self.warning(33,
warnings[-1].message.args[0] if warnings else '')
return data, fn
def load_from_file():
fn = self.last_path()
if not fn:
return None, ""
if not os.path.exists(fn):
dir_name, basename = os.path.split(fn)
if os.path.exists(os.path.join(".", basename)):
fn = os.path.join(".", basename)
self.information(
"Loading '{}' from the current directory.".format(
basename))
if self.is_multisheet_excel(fn):
data = ExcelFormat.read_file(fn + ':' + self.xls_sheet)
if data:
return data, fn
try:
return load(Table.from_file, fn)
except Exception as exc:
self.warnings.setText(str(exc))
# Let us not remove from recent files: user may fix them
raise
def load_from_network():
combo = self.url_combo
model = combo.model()
# combo.currentText does not work when the widget is initialized
url = model.data(model.index(combo.currentIndex()),
QtCore.Qt.EditRole)
if not url:
return None, ""
elif "://" not in url:
url = "http://" + url
try:
data, url = load(Table.from_url, url)
except:
self.warnings.setText(
"URL '{}' does not contain valid data".format(url))
# Don't remove from recent_urls:
# resource may reappear, or the user mistyped it
# and would like to retrieve it from history and fix it.
raise
combo.clearFocus()
if "://docs.google.com/spreadsheets" in url:
model.add_name(url, data.name)
self.url = \
"{} from {}".format(data.name.replace("- Sheet1", ""), url)
combo.lineEdit().setPlaceholderText(self.url)
return data, data.name
else:
self.url = url
return data, url
self.warning()
self.information()
try:
loader = [load_from_file, load_from_network][self.source]
self.data, self.loaded_file = loader()
except:
self.info.setText("Data was not loaded:")
self.data = None
self.loaded_file = ""
return
else:
self.warnings.setText("")
data = self.data
if data is None:
self.send("Data", None)
self.info.setText("No data loaded")
return
domain = data.domain
text = "{} instance(s), {} feature(s), {} meta attribute(s)".format(
len(data), len(domain.attributes), len(domain.metas))
if domain.has_continuous_class:
text += "\nRegression; numerical class."
elif domain.has_discrete_class:
text += "\nClassification; discrete class with {} values.".format(
len(domain.class_var.values))
elif data.domain.class_vars:
text += "\nMulti-target; {} target variables.".format(
len(data.domain.class_vars))
else:
text += "\nData has no target variable."
if 'Timestamp' in data.domain:
# Google Forms uses this header to timestamp responses
text += '\n\nFirst entry: {}\nLast entry: {}'.format(
data[0, 'Timestamp'], data[-1, 'Timestamp'])
self.info.setText(text)
add_origin(data, self.loaded_file)
self.send("Data", data)
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 = "~/" + \
self.loaded_file[len(home):].lstrip("/").lstrip("\\")
else:
name = self.loaded_file
if self.sheet_combo.isVisible():
name += " ({})".format(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)
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
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)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
domain_editor = SettingProvider(DomainEditor)
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
load_warning = widget.Msg("Read warning:\n{}")
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
missing_reader = widget.Msg("Missing reader.")
sheet_error = widget.Msg("Error listing available sheets.")
unknown = widget.Msg("Read error:\n{}")
class NoFileSelected:
pass
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
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=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 = gui.comboBox(
None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True,
)
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, 3, 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)
box = gui.vBox(self.controlArea, "Info")
self.infolabel = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
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(self.controlArea)
gui.button(box,
self,
"Browse documentation datasets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
gui.button(box, self, "Reset", callback=self.reset_domain_edit)
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))
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 _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("~/")
readers = [
f for f in FileFormat.formats
if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None)
]
filename, reader, _ = open_filename_dialog(start_file, None, 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):
# pylint: disable=broad-except
if self.last_path() and not os.path.exists(self.last_path()):
return self.Error.file_not_found
try:
self.reader = self._get_reader()
assert self.reader is not None
except Exception:
return self.Error.missing_reader
if self.reader is self.NoFileSelected:
self.Outputs.data.send(None)
return None
try:
self._update_sheet_combo()
except Exception:
return self.Error.sheet_error
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read()
except Exception as ex:
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()
if path is None:
return self.NoFileSelected
if self.recent_paths and self.recent_paths[0].file_format:
qname = self.recent_paths[0].file_format
reader_class = class_from_qualified_name(qname)
reader = reader_class(path)
else:
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()
if url:
return UrlReader(url)
else:
return self.NoFileSelected
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):
if self.reader.sheet:
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)
else:
self.sheet_combo.setCurrentIndex(0)
@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 apply_domain_edit(self):
if self.data is None:
table = None
else:
domain, cols = self.domain_editor.get_domain(
self.data.domain, self.data)
if not (domain.variables or domain.metas):
table = None
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.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 IOError:
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 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 = ["data", "file", "load", "read"]
outputs = [
widget.OutputSignal(
"Data",
Table,
doc="Attribute-valued data set read from the input file.")
]
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
SIZE_LIMIT = 1e7
LOCAL_FILE, URL = range(2)
settingsHandler = PerfectDomainContextHandler()
# 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"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
dlg_formats = ("All readable files ({});;".format(
'*' + ' *'.join(FileFormat.readers.keys())) + ";;".join(
"{} (*{})".format(f.DESCRIPTION, ' *'.join(f.EXTENSIONS))
for f in sorted(set(FileFormat.readers.values()),
key=list(FileFormat.readers.values()).index)))
domain_editor = SettingProvider(DomainEditor)
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=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 = gui.comboBox(
None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True,
)
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.MinimumExpanding, 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, 3, 3)
url_combo.activated.connect(self._url_set)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
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(self.controlArea)
gui.button(box,
self,
"Browse documentation data sets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
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))
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)
def sizeHint(self):
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 _url_set(self):
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 data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename, _ = QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file, self.dlg_formats)
if not filename:
return
self.add_path(filename)
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
# pylint: disable=broad-except
self.closeContext()
self.domain_editor.set_domain(None)
self.apply_button.setEnabled(False)
self.clear_messages()
self.set_file_list()
if self.last_path() and not os.path.exists(self.last_path()):
self.Error.file_not_found()
self.send("Data", None)
self.info.setText("No data.")
return
error = None
try:
self.reader = self._get_reader()
if self.reader is None:
self.data = None
self.send("Data", None)
self.info.setText("No data.")
self.sheet_box.hide()
return
except Exception as ex:
error = ex
if not error:
self._update_sheet_combo()
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read()
except Exception as ex:
log.exception(ex)
error = ex
self.warning(warnings[-1].message.args[0] if warnings else '')
if error:
self.data = None
self.send("Data", None)
self.info.setText("An error occurred:\n{}".format(error))
self.sheet_box.hide()
return
self.info.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
def _get_reader(self):
"""
Returns
-------
FileFormat
"""
if self.source == self.LOCAL_FILE:
reader = FileFormat.get_reader(self.last_path())
if self.recent_paths and self.recent_paths[0].sheet:
reader.select_sheet(self.recent_paths[0].sheet)
return reader
elif self.source == self.URL:
url = self.url_combo.currentText().strip()
if url:
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):
if self.reader.sheet:
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)
else:
self.sheet_combo.setCurrentIndex(0)
def _describe(self, table):
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] = "<b>{}</b>".format(descs[0])
if descs:
text += "<p>{}</p>".format("<br/>".join(descs))
text += "<p>{} instance(s), {} feature(s), {} meta attribute(s)".\
format(len(table), len(domain.attributes), len(domain.metas))
if domain.has_continuous_class:
text += "<br/>Regression; numerical class."
elif domain.has_discrete_class:
text += "<br/>Classification; discrete class with {} values.".\
format(len(domain.class_var.values))
elif table.domain.class_vars:
text += "<br/>Multi-target; {} target variables.".format(
len(table.domain.class_vars))
else:
text += "<br/>Data has no target variable."
text += "</p>"
if 'Timestamp' in table.domain:
# Google Forms uses this header to timestamp responses
text += '<p>First entry: {}<br/>Last entry: {}</p>'.format(
table[0, 'Timestamp'], table[-1, 'Timestamp'])
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 apply_domain_edit(self):
if self.data is not None:
domain, cols = self.domain_editor.get_domain(
self.data.domain, self.data)
X, y, m = cols
X = np.array(X).T if len(X) else np.empty((len(self.data), 0))
y = np.array(y).T if len(y) else None
dtpe = object if any(
isinstance(m, StringVariable) for m in domain.metas) else float
m = np.array(m, dtype=dtpe).T if len(m) else None
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', {})
else:
table = self.data
self.send("Data", 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 += " ({})".format(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)
def dragEnterEvent(self, event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(
OSX_NSURL_toLocalFile(urls[0]) or urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(
OSX_NSURL_toLocalFile(urls[0])
or urls[0].toLocalFile()) # add first file
self.source = self.LOCAL_FILE
self.load_data()
class OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "File"
id = "orange.widgets.data.file"
description = "Read a data from an input file or network " \
"and send the data table to the output."
icon = "icons/File.svg"
priority = 10
category = "Data"
keywords = ["data", "file", "load", "read"]
outputs = [widget.OutputSignal(
"Data", Table,
doc="Attribute-valued data set read from the input file.")]
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
LOCAL_FILE, URL = range(2)
settingsHandler = PerfectDomainContextHandler()
# 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"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
dlg_formats = (
"All readable files ({});;".format(
'*' + ' *'.join(FileFormat.readers.keys())) +
";;".join("{} (*{})".format(f.DESCRIPTION, ' *'.join(f.EXTENSIONS))
for f in sorted(set(FileFormat.readers.values()),
key=list(FileFormat.readers.values()).index)))
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QtGui.QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None, self, "source", box=True, addSpace=True,
callback=self.load_data, addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, QtCore.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(
QtGui.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(
QtGui.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 = gui.comboBox(None, self, "xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True)
self.sheet_combo.setSizePolicy(
Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QtGui.QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(
Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(
self.sheet_label, QtCore.Qt.AlignLeft)
self.sheet_box.layout().addWidget(
self.sheet_combo, QtCore.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, QtCore.Qt.AlignVCenter)
self.url_combo = url_combo = QtGui.QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.MinimumExpanding, 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, 3, 3)
url_combo.activated.connect(self._url_set)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
domain_editor = DomainEditor(self.variables)
self.editor_model = domain_editor.model()
box.layout().addWidget(domain_editor)
box = gui.hBox(self.controlArea)
gui.button(
box, self, "Browse documentation data sets",
callback=lambda: self.browse_file(True), autoDefault=False)
gui.rubber(box)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
self.apply_button = gui.button(
box, self, "Apply", callback=self.apply_domain_edit)
self.apply_button.hide()
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(self.apply_button.show)
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
QtCore.QTimer.singleShot(0, self.load_data)
self.setAcceptDrops(True)
def sizeHint(self):
return QtCore.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 _url_set(self):
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):
QtGui.QMessageBox.information(
None, "File",
"Cannot find the directory with documentation data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename = QtGui.QFileDialog.getOpenFileName(
self, 'Open Orange Data File', start_file, self.dlg_formats)
if not filename:
return
self.loaded_file = filename
self.add_path(filename)
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):
self.reader = self._get_reader()
self._update_sheet_combo()
errors = []
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read()
except Exception as ex:
errors.append("An error occurred:")
errors.append(str(ex))
data = None
self.editor_model.reset()
self.warning(warnings[-1].message.args[0] if warnings else '')
if data is None:
self.send("Data", None)
self.info.setText("\n".join(errors))
return
self.info.setText(self._describe(data))
add_origin(data, self.loaded_file or self.last_path())
self.send("Data", data)
self.editor_model.set_domain(data.domain)
self.data = data
def _get_reader(self):
"""
Returns
-------
FileFormat
"""
if self.source == self.LOCAL_FILE:
reader = FileFormat.get_reader(self.last_path())
if self.recent_paths and self.recent_paths[0].sheet:
reader.select_sheet(self.recent_paths[0].sheet)
return reader
elif self.source == self.URL:
return UrlReader(self.url_combo.currentText())
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):
if self.reader.sheet:
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)
else:
self.sheet_combo.setCurrentIndex(0)
def _describe(self, table):
domain = table.domain
text = "{} instance(s), {} feature(s), {} meta attribute(s)".format(
len(table), len(domain.attributes), len(domain.metas))
if domain.has_continuous_class:
text += "\nRegression; numerical class."
elif domain.has_discrete_class:
text += "\nClassification; discrete class with {} values.".format(
len(domain.class_var.values))
elif table.domain.class_vars:
text += "\nMulti-target; {} target variables.".format(
len(table.domain.class_vars))
else:
text += "\nData has no target variable."
if 'Timestamp' in table.domain:
# Google Forms uses this header to timestamp responses
text += '\n\nFirst entry: {}\nLast entry: {}'.format(
table[0, 'Timestamp'], table[-1, 'Timestamp'])
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 apply_domain_edit(self):
attributes = []
class_vars = []
metas = []
places = [attributes, class_vars, metas]
X, y, m = [], [], []
cols = [X, y, m] # Xcols, Ycols, Mcols
def is_missing(x):
return str(x) in ("nan", "")
for column, (name, tpe, place, vals, is_con), (orig_var, orig_plc) in \
zip(count(), self.editor_model.variables,
chain([(at, 0) for at in self.data.domain.attributes],
[(cl, 1) for cl in self.data.domain.class_vars],
[(mt, 2) for mt in self.data.domain.metas])):
if place == 3:
continue
if orig_plc == 2:
col_data = list(chain(*self.data[:, orig_var].metas))
else:
col_data = list(chain(*self.data[:, orig_var]))
if name == orig_var.name and tpe == type(orig_var):
var = orig_var
elif tpe == DiscreteVariable:
values = list(str(i) for i in set(col_data) if not is_missing(i))
var = tpe(name, values)
col_data = [np.nan if is_missing(x) else values.index(str(x))
for x in col_data]
elif tpe == StringVariable and type(orig_var) == DiscreteVariable:
var = tpe(name)
col_data = [orig_var.repr_val(x) if not np.isnan(x) else ""
for x in col_data]
else:
var = tpe(name)
places[place].append(var)
cols[place].append(col_data)
domain = Domain(attributes, class_vars, metas)
X = np.array(X).T if len(X) else np.empty((len(self.data), 0))
y = np.array(y).T if len(y) else None
dtpe = object if any(isinstance(m, StringVariable)
for m in domain.metas) else float
m = np.array(m, dtype=dtpe).T if len(m) else None
table = Table.from_numpy(domain, X, y, m, self.data.W)
self.send("Data", table)
self.apply_button.hide()
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 = "~/" + \
self.loaded_file[len(home):].lstrip("/").lstrip("\\")
else:
name = self.loaded_file
if self.sheet_combo.isVisible():
name += " ({})".format(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)
def dragEnterEvent(self, event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(OSX_NSURL_toLocalFile(urls[0]) or
urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(OSX_NSURL_toLocalFile(urls[0]) or
urls[0].toLocalFile()) # add first file
self.source = self.LOCAL_FILE
self.load_data()
class OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "文件(File)"
id = "orange.widgets.data.file"
description = "从输入文件或网络读取数据并将数据表发送到输出。"
icon = "icons/File.svg"
priority = 10
category = "数据(Data)"
keywords = ["file", "load", "read", "open", "wenjian"]
class Outputs:
data = Output("数据(Data)",
Table,
doc="Attribute-valued dataset read from the input file.",
replaces=['Data'])
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='数据源')
vbox = gui.radioButtons(None,
self,
"source",
box=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "文件:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.Expanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.Expanding, Policy.Fixed)
self.file_combo.setMinimumSize(QSize(100, 1))
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,
"重新加载",
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.Expanding, Policy.Fixed)
self.sheet_combo.setMinimumSize(QSize(50, 1))
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='文件类型')
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.Expanding, Policy.Fixed)
self.reader_combo = QComboBox(self)
self.reader_combo.setSizePolicy(Policy.Expanding, Policy.Fixed)
self.reader_combo.setMinimumSize(QSize(100, 1))
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, "信息")
self.infolabel = gui.widgetLabel(box, '未加载数据.')
box = gui.widgetBox(self.controlArea, "列(双击编辑)")
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,
"重置",
callback=self.reset_domain_edit,
autoDefault=False)
gui.rubber(box)
self.apply_button = gui.button(box,
self,
"应用",
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,
"浏览文档数据集",
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, "文件", "无法找到文件")
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("无数据")
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}% 个缺失值)"
else:
return "(无缺失值)"
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)} 条数据"
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/>特征数目: {len(domain.attributes)} {missing_in_attr}"
if domain.has_continuous_class:
text += f"<br/>回归; 数值类 {missing_in_class}"
elif domain.has_discrete_class:
text += "<br/>分类: 分类种类共 " \
f"{len(domain.class_var.values)} 个 {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/>元属性: { len(domain.metas)}"
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 OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "领域编辑器2"
icon = "icons/gear.svg"
id = "orange.widgets.data.file"
description = "Read data from an input file or network " \
"and send a data table to the output."
priority = 10
category = "Data"
keywords = ["file", "load", "read", "open"]
class Outputs:
data = Output("领域背景", Table, doc="专业领域背景的介绍")
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
SIZE_LIMIT = 1e7
LOCAL_FILE, URL = range(2)
settingsHandler = PerfectDomainContextHandler(
match_values=PerfectDomainContextHandler.MATCH_VALUES_ALL)
# 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"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
domain_editor = SettingProvider(DomainEditor)
##用于警告代码可以无视
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
load_warning = widget.Msg("Read warning:\n{}")
##用于报错代码可以无视
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
missing_reader = widget.Msg("Missing reader.")
sheet_error = widget.Msg("Error listing available sheets.")
unknown = widget.Msg("Read error:\n{}")
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QGridLayout() ##画布的布局，使用网格划分的方式
gui.widgetBox(self.controlArea, margin=20, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter) #确定位置0,0
box = gui.hBox(None, addToLayout=False, margin=0) #水平box
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed) #设置size
self.file_combo.setSizePolicy(Policy.MinimumExpanding,
Policy.Fixed) # 按钮和下拉菜单的联合体
self.file_combo.activated[int].connect(
self.select_file) ##使用.connect（功能函数）来实现与功能函数的连接
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1) #确定位置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)
## 含Information的box设置
box = gui.widgetBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, '请设置领域特征')
# self.warnings = gui.widgetLabel(box, '')
##下面几句控制含有table的box
box = gui.widgetBox(self.controlArea, "双击进行编辑")
self.domain_editor = DomainEditor(self) ##对table操作的事情在DomainEditor内部定义
self.editor_model = self.domain_editor.model() ##设置与Apply激活状态有关
box.layout().addWidget(self.domain_editor)
## Apply 按钮
box = gui.hBox(self.controlArea)
# gui.button(
# box, self, "Browse documentation datasets",
# callback=lambda: self.browse_file(True), autoDefault=False)
# gui.rubber(box)
self.apply_button = gui.button(box,
self,
"应用",
callback=self.apply_domain_edit)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
# print('editor_model',self.editor_model)
## 如果数据改变就激活apply按钮.dataChange表示是否改变数据
self.editor_model.dataChanged.connect(
lambda: self.apply_button.setEnabled(True))
self.set_file_list() ##设置文件列表中的项
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
self.setAcceptDrops(True) ##表示接受响应释放操作
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()表示在s秒后调用一个槽函数（self.load_data）
QTimer.singleShot(0, self.load_data)
def sizeHint(self):
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()
## 读取文件
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("~/")
readers = [
f for f in FileFormat.formats
if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None)
]
filename, reader, _ = open_filename_dialog(start_file, None, 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()
## 获取数据self.data,方式是调用了_try_load函数，并且将数据send到Output的channel中
# 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() ##重新设置widget 的context
self.domain_editor.set_domain(None) #把domain设置为None
self.apply_button.setEnabled(False) #把apply button设置为不可见
self.clear_messages()
self.set_file_list()
##这句话判断数据导入是否有错误
error = self._try_load()
if error:
error()
self.data = None
# self.sheet_box.hide()
self.Outputs.data.send(None)
self.info.setText("无数据.")
## 导入数据的核心方法：获取self.data数据，同时判断这个出错可能性
def _try_load(self):
# pylint: disable=broad-except
if self.last_path() and not os.path.exists(self.last_path()):
return self.Error.file_not_found
try:
self.reader = self._get_reader() ##这里获取reader
assert self.reader is not None
except Exception:
return self.Error.missing_reader
try:
self._update_sheet_combo()
except Exception:
return self.Error.sheet_error
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read() ##通过这句话读取数据,这是的data已经是table型数据了
print('jia', type(data))
except Exception as ex:
log.exception(ex)
return lambda x=ex: self.Error.unknown(str(x))
if warnings:
self.Warning.load_warning(warnings[-1].message.args[0])
self.info.setText(self._describe(data)) #描述info的text
self.loaded_file = self.last_path() ##描述文档地址
add_origin(data, self.loaded_file)
self.data = data
# print('liangyue',dir(self.data))
self.openContext(data.domain)
# print('data',data)
self.apply_domain_edit() # sends data
## 获取导入文件的格式
def _get_reader(self):
"""
Returns
-------
FileFormat
"""
if self.source == self.LOCAL_FILE:
path = self.last_path()
if self.recent_paths and self.recent_paths[0].file_format:
qname = self.recent_paths[0].file_format
reader_class = class_from_qualified_name(qname)
reader = reader_class(path)
print('reader_class', reader_class)
else:
reader = FileFormat.get_reader(path)
# Return reader instance that can be used to read the file
if self.recent_paths and self.recent_paths[0].sheet:
reader.select_sheet(self.recent_paths[0].sheet)
return reader
elif self.source == self.URL:
url = self.url_combo.currentText().strip()
if url:
return UrlReader(url)
## 更新file的下拉列表中的内容
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):
if self.reader.sheet:
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)
else:
self.sheet_combo.setCurrentIndex(0)
## 下面是info的描述语句
def _describe(self, table):
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] = "<b>{}</b>".format(descs[0])
if descs:
text += "<p>{}</p>".format("<br/>".join(descs))
text += "<p>{} 个实例数据(s), {} 个输入特征(s), {} 个元特征(s)".\
format(len(table), len(domain.attributes), len(domain.metas))
if domain.has_continuous_class:
text += "<br/>回归模型 ."
elif domain.has_discrete_class:
text += "<br/>分类模型; 共分为 {} 类.".\
format(len(domain.class_var.values))
elif table.domain.class_vars:
text += "<br/>多目标模型; {} 个目标".format(len(table.domain.class_vars))
else:
text += "<br/>无目标值."
text += "</p>"
if 'Timestamp' in table.domain:
# Google Forms uses this header to timestamp responses
text += '<p>First entry: {}<br/>Last entry: {}</p>'.format(
table[0, 'Timestamp'], table[-1, 'Timestamp'])
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
## 对Ourputs的data赋值为table
def apply_domain_edit(self):
if self.data is None:
table = None
else:
domain, cols = self.domain_editor.get_domain(
self.data.domain, self.data)
printData = self.data
printDomain = self.data.domain
if not (domain.variables or domain.metas):
table = None
else:
X, y, m = cols
#X是输入，domain.attributes;y是输出class_var;m是元特征
## 下面解决将self.data的数据付给了table。
# 1data's name; 2数据编号ids；3数据属性attributes
table = Table.from_numpy(domain, X, y, m, self.data.W)
table.name = self.data.name
index = self.data.ids
table.ids = np.array(self.data.ids)
# print('ids',table.ids)
data = self.data
table.attributes = getattr(self.data, 'attributes', {})
## 将table的属性定义为{}
''' 对Ourputs的data赋值为table'''
# print('table is :',table)
# print('table domain',table.domain)
# print('table name',table.name)
# print('table class_var name',table.domain.class_vars[0].name)
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 += " ({})".format(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)
def dragEnterEvent(self, event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(
OSX_NSURL_toLocalFile(urls[0]) or urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(
OSX_NSURL_toLocalFile(urls[0])
or 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 OWVcfFile(widget.OWWidget, RecentPathsWComboMixin):
name = "VCF File"
id = "orangecontrib.variants.widgets.vcf"
description = "Read data from a VCF file."
icon = "icons/VCFFile.svg"
priority = 10
category = "Variants"
keywords = ["data", "vcf", "file", "load", "read"]
class Outputs:
data = Output(
"Data",
Table,
doc="Attribute-valued data set read from the input file.")
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
SIZE_LIMIT = 1e7
settingsHandler = PerfectDomainContextHandler(
match_values=PerfectDomainContextHandler.MATCH_VALUES_ALL)
# Overload RecentPathsWidgetMixin.recent_paths to set defaults
recent_paths = Setting([
RecentPath("", "sample-datasets", "small.vcf"),
])
quality = Setting(1)
cb_qual = Setting(True)
frequency = Setting(1)
cb_freq = Setting(True)
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.variants = None
self.table = None
self.loaded_file = ""
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
label = gui.widgetLabel(self, " File: ")
layout.addWidget(label, 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)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
def enable_apply():
self.apply_button.setEnabled(True)
box = gui.vBox(self.controlArea, "Filtering")
_, qspin = gui.spin(box,
self,
'quality',
0,
999,
step=1,
label='Quality threshold (QT)',
callback=enable_apply,
checked='cb_qual',
checkCallback=enable_apply)
qspin.setToolTip("Minimum quality to use reads.")
_, fspin = gui.spin(box,
self,
'frequency',
0,
999,
step=1,
label='Frequency threshold (FT)',
callback=enable_apply,
checked='cb_freq',
checkCallback=enable_apply)
fspin.setToolTip("Keep only variants with at least this many "
"occurrences of alternative alleles.")
gui.rubber(self.controlArea)
box = gui.hBox(self.controlArea)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
gui.rubber(box)
self.apply_button = gui.button(box, self, "Apply", callback=self.apply)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
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)
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)
def sizeHint(self):
return QSize(500, 200)
def select_file(self, n):
assert n < len(self.recent_paths)
super().select_file(n)
if self.recent_paths:
self.load_data()
self.set_file_list()
def browse_file(self):
start_file = self.last_path() or os.path.expanduser("~/")
dialog_formats = "VCF files (*.vcf);;All files (*)"
filename, _ = QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file, dialog_formats)
if not filename:
return
self.add_path(filename)
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
# pylint: disable=broad-except
self.apply_button.setEnabled(False)
self.clear_messages()
self.set_file_list()
if not self.last_path() or not os.path.exists(self.last_path()):
if self.last_path():
self.Error.file_not_found()
self.Outputs.data.send(None)
self.info.setText("No data.")
return
error = None
if not error:
with catch_warnings(record=True) as warnings:
try:
variants = VariantData(self.last_path())
except Exception as ex:
log.exception(ex)
error = ex
self.warning(warnings[-1].message.args[0] if warnings else '')
if error:
self.variants = self.table = None
self.Outputs.data.send(None)
self.info.setText("An error occurred:\n{}".format(error))
return
self.loaded_file = self.last_path()
self.variants = variants
self.apply() # sends data
def update_info(self):
pl = lambda x: '' if x == 1 else 's'
text = ""
if self.variants is not None:
nsamples, nvariants = self.variants.gt.T.shape
text += ("<p>Before filtering:<br/>" +
" {} sample{}, {} variant{}</p>").\
format(nsamples, pl(nsamples), nvariants, pl(nvariants), )
if self.table is not None:
nsamples, nvariants = self.table.X.shape
below = np.isnan(self.table.X).sum() / self.table.X.size * 100
text += ("<p>After filtering:<br/>" +
" {} sample{}, {} variant{}<br/>" +
" {:.2f}% reads below QT</p>").\
format(nsamples, pl(nsamples), nvariants, pl(nvariants), below)
self.info.setText(text)
def apply(self):
if self.variants is None:
self.table = None
else:
q = self.quality if self.cb_qual else None
f = self.frequency if self.cb_freq else None
self.table = self.variants.get_data(q, f)
self.update_info()
self.Outputs.data.send(self.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):
if self.table is None:
self.report_paragraph("VCF File", "No file.")
return
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
self.report_items("VCF File", [
("File name", name),
])
parameters = [("Quality", self.quality, self.cb_qual),
("Frequency", self.frequency, self.cb_freq)]
self.report_items("Filtering parameters",
[(name, value)
for name, value, enabled in parameters if enabled])
self.report_data("Data", self.table)
def dragEnterEvent(self, event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(
OSX_NSURL_toLocalFile(urls[0]) or urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(
OSX_NSURL_toLocalFile(urls[0])
or urls[0].toLocalFile()) # add first file
self.load_data()
