def process_signals_for_widget(self, node, widget, signals):
"""
Process new signals for the OWBaseWidget.
"""
# This replaces the old OWBaseWidget.processSignals method
if sip.isdeleted(widget):
log.critical("Widget %r was deleted. Cannot process signals",
widget)
return
app = QCoreApplication.instance()
for signal in signals:
link = signal.link
value = signal.value
# Check and update the dynamic link state
if link.is_dynamic():
link.dynamic_enabled = can_enable_dynamic(link, value)
if not link.dynamic_enabled:
# Send None instead
value = None
handler = link.sink_channel.handler
if handler.startswith("self."):
handler = handler.split(".", 1)[1]
handler = getattr(widget, handler)
if link.sink_channel.single:
args = (value,)
else:
args = (value, signal.id)
log.debug("Process signals: calling %s.%s (from %s with id:%s)",
type(widget).__name__, handler.__name__, link, signal.id)
app.setOverrideCursor(Qt.WaitCursor)
try:
handler(*args)
except Exception:
sys.excepthook(*sys.exc_info())
log.exception("Error calling '%s' of '%s'",
handler.__name__, node.title)
finally:
app.restoreOverrideCursor()
app.setOverrideCursor(Qt.WaitCursor)
try:
widget.handleNewSignals()
except Exception:
sys.excepthook(*sys.exc_info())
log.exception("Error calling 'handleNewSignals()' of '%s'",
node.title)
finally:
app.restoreOverrideCursor()
def process_signals_for_widget(self, node, widget, signals):
"""
Process new signals for the OWBaseWidget.
"""
# This replaces the old OWBaseWidget.processSignals method
if sip.isdeleted(widget):
log.critical("Widget %r was deleted. Cannot process signals",
widget)
return
app = QCoreApplication.instance()
for signal in signals:
link = signal.link
value = signal.value
# Check and update the dynamic link state
if link.is_dynamic():
link.dynamic_enabled = can_enable_dynamic(link, value)
if not link.dynamic_enabled:
# Send None instead
value = None
handler = link.sink_channel.handler
if handler.startswith("self."):
handler = handler.split(".", 1)[1]
handler = getattr(widget, handler)
if link.sink_channel.single:
args = (value, )
else:
args = (value, signal.id)
log.debug("Process signals: calling %s.%s (from %s with id:%s)",
type(widget).__name__, handler.__name__, link, signal.id)
app.setOverrideCursor(Qt.WaitCursor)
try:
handler(*args)
except Exception:
sys.excepthook(*sys.exc_info())
log.exception("Error calling '%s' of '%s'", handler.__name__,
node.title)
finally:
app.restoreOverrideCursor()
app.setOverrideCursor(Qt.WaitCursor)
try:
widget.handleNewSignals()
except Exception:
sys.excepthook(*sys.exc_info())
log.exception("Error calling 'handleNewSignals()' of '%s'",
node.title)
finally:
app.restoreOverrideCursor()
def __call__(self, exc_type, exc_value, tb):
if self._stream:
header = exc_type.__name__ + ' Exception'
if QThread.currentThread() != QCoreApplication.instance().thread():
header += " (in non-GUI thread)"
text = traceback.format_exception(exc_type, exc_value, tb)
text.insert(0, '{:-^79}\n'.format(' ' + header + ' '))
text.append('-' * 79 + '\n')
self._stream.writelines(text)
self.handledException.emit((exc_type, exc_value, tb))
def __call__(self, exc_type, exc_value, tb):
if self._stream:
header = exc_type.__name__ + ' Exception'
if QThread.currentThread() != QCoreApplication.instance().thread():
header += " (in non-GUI thread)"
text = traceback.format_exception(exc_type, exc_value, tb)
text.insert(0, '{:-^79}\n'.format(' ' + header + ' '))
text.append('-' * 79 + '\n')
self._stream.writelines(text)
self.handledException.emit((exc_type, exc_value, tb))
def __call__(self, exc_type, exc_value, tb):
if self._stream:
header = exc_type.__name__ + " Exception"
if QThread.currentThread() != QCoreApplication.instance().thread():
header += " (in non-GUI thread)"
text = traceback.format_exception(exc_type, exc_value, tb)
text.insert(0, "{:-^79}\n".format(" " + header + " "))
text.append("-" * 79 + "\n")
self._stream.writelines(text)
self.handledException.emit(((exc_type, exc_value, tb), self._canvas))
def init(self):
"""
Initialize the QCoreApplication.organizationDomain, applicationName,
applicationVersion and the default settings format.
Should only be run once at application startup.
"""
QCoreApplication.setOrganizationDomain(self.OrganizationDomain)
QCoreApplication.setApplicationName(self.ApplicationName)
QCoreApplication.setApplicationVersion(self.ApplicationVersion)
QSettings.setDefaultFormat(QSettings.IniFormat)
app = QCoreApplication.instance()
if app is not None:
QCoreApplication.sendEvent(app, QEvent(QEvent.PolishRequest))
def _fetch_indicators(self, progress=lambda val: None):
"""Background task for fetching indicators."""
progress(0)
def row_item(display_value, item_values=None):
"""Generate a cell item for a given row."""
if not item_values:
item_values = {}
item = QtGui.QStandardItem()
item.setData(display_value, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
progress(10)
filter_ = self._main_widget.basic_indicator_filter()
data = self._api.get_indicators(filter_=filter_)
self._indicator_data = {ind["id"]: ind for ind in data}
progress(70)
indicators = [[""] + row
for row in self._api.get_indicator_list(filter_=filter_)]
model = QtGui.QStandardItemModel()
model.setHorizontalHeaderLabels(indicators[0])
for row in indicators[1:]:
search_string = " | ".join(row).lower()
row_data = [row_item(item) for item in row]
row_data[0].setData(search_string, TEXTFILTERROLE)
row_data[1].setData(self._get_link(row[1]), gui.LinkRole)
model.appendRow(row_data)
progress(100)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model
def wrapper(*args):
app = QCoreApplication.instance()
self = args[0]
def execWithArgs():
self.qpart.show()
QTest.qWaitForWindowExposed(self.qpart)
_processPendingEvents(app)
try:
func(*args)
finally:
_processPendingEvents(app)
app.quit()
QTimer.singleShot(0, execWithArgs)
app.exec_()
def __call__(self, exc_type, exc_value, tb):
if self.stream is None:
stream = sys.stderr
else:
stream = self.stream
if stream is not None:
header = exc_type.__name__ + ' Exception'
if QThread.currentThread() != QCoreApplication.instance().thread():
header += " (in non-GUI thread)"
text = traceback.format_exception(exc_type, exc_value, tb)
text.insert(0, '{:-^79}\n'.format(' ' + header + ' '))
text.append('-' * 79 + '\n')
stream.writelines(text)
try:
stream.flush()
except Exception:
pass
self.handledException.emit((exc_type, exc_value, tb))
def process_signals_for_widget(self, node, widget, signals):
# type: (SchemeNode, OWBaseWidget, List[Signal]) -> None
"""
Process new signals for the OWBaseWidget.
"""
app = QCoreApplication.instance()
try:
app.setOverrideCursor(Qt.WaitCursor)
for signal in signals:
link = signal.link
value = signal.value
handler = link.sink_channel.handler
if handler.startswith("self."):
handler = handler.split(".", 1)[1]
handler = getattr(widget, handler)
if link.sink_channel.single:
args = (value, )
else:
args = (value, signal.id)
log.debug(
"Process signals: calling %s.%s (from %s with id:%s)",
type(widget).__name__, handler.__name__, link, signal.id)
try:
handler(*args)
except Exception:
log.exception("Error calling '%s' of '%s'",
handler.__name__, node.title)
raise
try:
widget.handleNewSignals()
except Exception:
log.exception("Error calling 'handleNewSignals()' of '%s'",
node.title)
raise
finally:
app.restoreOverrideCursor()
def get_event_loop() -> asyncio.AbstractEventLoop:
"""
Get the asyncio.AbstractEventLoop for the main Qt application thread.
The QCoreApplication instance must already have been created.
Must only be called from the main Qt application thread.
"""
try:
# Python >= 3.7
get_running_loop = asyncio.get_running_loop # type: ignore
except AttributeError:
get_running_loop = asyncio._get_running_loop # type: ignore
app = QCoreApplication.instance()
if app is None:
raise RuntimeError("QCoreApplication is not running")
if app.thread() is not QThread.currentThread():
raise RuntimeError("Called from non-main thread")
loop: Optional[asyncio.AbstractEventLoop]
try:
loop = get_running_loop()
except RuntimeError:
loop = None
else:
if loop is not None:
return loop
qt_api = os.environ.get("QT_API", "").lower()
if qt_api == "pyqt5":
os.environ["QT_API"] = "PyQt5"
elif qt_api == "pyside2":
os.environ["QT_API"] = "PySide2"
import qasync
if loop is None:
loop = qasync.QEventLoop(app)
# Do not use qasync.QEventLoop's default executor which uses QThread
# based pool and exhibits https://github.com/numpy/numpy/issues/11551
loop.set_default_executor(futures.ThreadPoolExecutor())
return loop
def setUp(self) -> None:
self.app = QCoreApplication.instance()
if self.app is None:
self.app = QCoreApplication([])
super().setUp()
def setUp(self):
self.app = QCoreApplication.instance()
if self.app is None:
self.app = QCoreApplication([])
def get_gds_model(progress=lambda val: None):
"""
Initialize and return a GDS datasets model.
:param progress: A progress callback.
:rval tuple:
A tuple of (QStandardItemModel, geo.GDSInfo, [geo.GDS])
.. note::
The returned QStandardItemModel's thread affinity is set to
the GUI thread.
"""
progress(1)
info = geo.GDSInfo()
search_keys = ["dataset_id", "title", "platform_organism", "description"]
cache_dir = serverfiles.localpath(geo.DOMAIN)
gds_link = "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc={0}"
pm_link = "http://www.ncbi.nlm.nih.gov/pubmed/{0}"
gds_list = []
def is_cached(gds):
return os.path.exists(
os.path.join(cache_dir, gds["dataset_id"]) + ".soft.gz")
def item(displayvalue, item_values={}):
item = QStandardItem()
item.setData(displayvalue, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
def gds_to_row(gds):
#: Text for easier full search.
search_text = " | ".join(
[gds.get(key, "").lower() for key in search_keys])
row = [
item(" " if is_cached(gds) else "", {TextFilterRole: search_text}),
item(gds["dataset_id"],
{LinkRole: gds_link.format(gds["dataset_id"])}),
item(gds["title"]),
item(gds["platform_organism"]),
item(len(gds["samples"])),
item(gds["feature_count"]),
item(gds["gene_count"]),
item(len(gds["subsets"])),
item(
gds.get("pubmed_id", ""), {
LinkRole:
pm_link.format(gds["pubmed_id"])
if gds.get("pubmed_id") else None
})
]
return row
model = QStandardItemModel()
model.setHorizontalHeaderLabels([
"", "ID", "Title", "Organism", "Samples", "Features", "Genes",
"Subsets", "PubMedID"
])
progress(20)
for gds in info.values():
model.appendRow(gds_to_row(gds))
gds_list.append(gds)
progress(50)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model, info, gds_list
def do_work(self):
self.function()
self.moveToThread(QCoreApplication.instance().thread())
self.done.emit()
def get_gds_model(progress=lambda val: None):
"""
Initialize and return a GDS datasets model.
:param progress: A progress callback.
:rval tuple:
A tuple of (QStandardItemModel, geo.GDSInfo, [geo.GDS])
.. note::
The returned QStandardItemModel's thread affinity is set to
the GUI thread.
"""
progress(1)
info = geo.GDSInfo()
search_keys = ["dataset_id", "title", "platform_organism", "description"]
cache_dir = serverfiles.localpath(geo.DOMAIN)
gds_link = "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc={0}"
pm_link = "http://www.ncbi.nlm.nih.gov/pubmed/{0}"
gds_list = []
def is_cached(gds):
return os.path.exists(os.path.join(cache_dir, gds["dataset_id"]) +
".soft.gz")
def item(displayvalue, item_values={}):
item = QStandardItem()
item.setData(displayvalue, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
def gds_to_row(gds):
#: Text for easier full search.
search_text = " | ".join([gds.get(key, "").lower()
for key in search_keys])
row = [
item(" " if is_cached(gds) else "",
{TextFilterRole: search_text}),
item(gds["dataset_id"],
{LinkRole: gds_link.format(gds["dataset_id"])}),
item(gds["title"]),
item(gds["platform_organism"]),
item(len(gds["samples"])),
item(gds["feature_count"]),
item(gds["gene_count"]),
item(len(gds["subsets"])),
item(gds.get("pubmed_id", ""),
{LinkRole: pm_link.format(gds["pubmed_id"])
if gds.get("pubmed_id")
else None})
]
return row
model = QStandardItemModel()
model.setHorizontalHeaderLabels(
["", "ID", "Title", "Organism", "Samples", "Features",
"Genes", "Subsets", "PubMedID"]
)
progress(20)
for gds in info.values():
model.appendRow(gds_to_row(gds))
gds_list.append(gds)
progress(50)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model, info, gds_list
def setUp(self):
self.app = QCoreApplication.instance()
if self.app is None:
self.app = QCoreApplication([])
