def clear_caches(self): # pylint: disable=import-outside-toplevel
from Orange.misc import environ
log.info("Clearing caches")
self._rm_tree(environ.cache_dir())
log.info("Clearing data")
self._rm_tree(environ.data_dir(versioned=True))
self._rm_tree(environ.data_dir(versioned=False))
def data_dir():
"""Return the application data directory. If the directory path
does not yet exists then create it.
"""
from Orange.misc import environ
path = os.path.join(environ.data_dir(), "canvas")
if not os.path.isdir(path):
os.makedirs(path, exist_ok=True)
return path
def data_dir():
"""
Return the Orange application data directory. If the directory path
does not yet exists then create it.
"""
path = os.path.join(environ.data_dir(), "canvas")
try:
os.makedirs(path, exist_ok=True)
except OSError:
pass
return path
def __init__(self, parent=None):
QObject.__init__(self, parent)
assert QThread.currentThread() is QApplication.instance().thread()
netmanager = self._NETMANAGER_REF and self._NETMANAGER_REF()
if netmanager is None:
netmanager = QNetworkAccessManager()
cache = QNetworkDiskCache()
cache.setCacheDirectory(
os.path.join(data_dir(), "geo", __name__ + ".GeoMap.Cache"))
netmanager.setCache(cache)
ImageLoader._NETMANAGER_REF = weakref.ref(netmanager)
self._netmanager = netmanager
def tag_list():
"""List of available tags and their pretty-print with indices"""
server_url = "http://butler.fri.uni-lj.si/datasets/"
PATH = os.path.join(data_dir(), "datasets")
local_files = LocalFiles(PATH, serverfiles=ServerFiles(server=server_url))
local_info = local_files.serverfiles.allinfo()
nested_tags = [i["tags"] for i in local_info.values() if i["tags"]]
all_tags = sorted(list(set(itertools.chain(*nested_tags))))
w = max(len(t) for t in all_tags)
n = int(75 / (w + 5))
s = ["{:>3}-{:<{width}}".format(i, t, width=w) for i, t in enumerate(all_tags)]
c = "\n".join(["".join(s[x:x + n]) for x in range(0, len(s), n)])
return all_tags, c
def tag_list():
"""List of available tags and their pretty-print with indices"""
server_url = "http://butler.fri.uni-lj.si/datasets/"
PATH = os.path.join(data_dir(), "datasets")
local_files = LocalFiles(PATH, serverfiles=ServerFiles(server=server_url))
local_info = local_files.serverfiles.allinfo()
nested_tags = [i["tags"] for i in local_info.values() if i["tags"]]
all_tags = sorted(list(set(itertools.chain(*nested_tags))))
w = max(len(t) for t in all_tags)
n = int(75 / (w + 5))
s = [
"{:>3}-{:<{width}}".format(i, t, width=w)
for i, t in enumerate(all_tags)
]
c = "\n".join(["".join(s[x:x + n]) for x in range(0, len(s), n)])
return all_tags, c
def __init__(self):
self.local_data = os.path.join(data_dir(versioned=False), 'udpipe/')
self.serverfiles = serverfiles.ServerFiles(self.server_url)
self.localfiles = serverfiles.LocalFiles(self.local_data,
serverfiles=self.serverfiles)
self._supported_languages = []
def __init__(self):
super().__init__()
self.allinfo_local = {}
self.allinfo_remote = {}
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
# current_output does not equal selected_id when, for instance, the
# data is still downloading
self.current_output = None
self._header_labels = [
header['label'] for _, header in self.HEADER_SCHEMA]
self._header_index = namedtuple(
'_header_index', [info_tag for info_tag, _ in self.HEADER_SCHEMA])
self.Header = self._header_index(
*[index for index, _ in enumerate(self._header_labels)])
self.__awaiting_state = None # type: Optional[_FetchState]
self.filterLineEdit = QLineEdit(
textChanged=self.filter, placeholderText="Search for data set ..."
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = TreeViewWithReturn(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
uniformRowHeights=True,
toolTip="Press Return or double-click to send"
)
# the method doesn't exists yet, pylint: disable=unnecessary-lambda
self.view.doubleClicked.connect(self.commit)
self.view.returnPressed.connect(self.commit)
box = gui.widgetBox(self.splitter, "说明", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
proxy = QSortFilterProxyModel()
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.assign_delegates()
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def __init__(self):
self.local_data = os.path.join(data_dir(versioned=False), 'sentiment/')
self.serverfiles = serverfiles.ServerFiles(self.server_url)
self.localfiles = serverfiles.LocalFiles(self.local_data,
serverfiles=self.serverfiles)
self._supported_languages = []
def __init__(self):
self.local_data = os.path.join(data_dir(versioned=False), 'udpipe/')
self.serverfiles = serverfiles.ServerFiles(self.server_url)
self.localfiles = serverfiles.LocalFiles(self.local_data,
serverfiles=self.serverfiles)
def local_cache_path():
return os.path.join(data_dir(), "datasets")
import os
import serverfiles
from Orange.misc.environ import data_dir
import orangecontrib.infrared # loads file readers
server = serverfiles.ServerFiles("http://193.2.72.57/infrared-data/")
localfiles = serverfiles.LocalFiles(
os.path.join(data_dir(), "orange-infrared"), serverfiles=server)
def spectra20nea():
return localfiles.localpath_download("spectra20.nea")
def dust():
localfiles.localpath_download("20160831_06_Paris_25x_highmag.dat")
return localfiles.localpath_download("20160831_06_Paris_25x_highmag.hdr")
import os
import serverfiles
from Orange.misc.environ import data_dir
import orangecontrib.spectroscopy # loads file readers
server = serverfiles.ServerFiles("http://193.2.72.57/infrared-data/")
localfiles = serverfiles.LocalFiles(os.path.join(data_dir(),
"orange-infrared"),
serverfiles=server)
def spectra20nea():
return localfiles.localpath_download("spectra20.nea")
def dust():
localfiles.localpath_download("20160831_06_Paris_25x_highmag.dat")
return localfiles.localpath_download("20160831_06_Paris_25x_highmag.hdr")
import os
from Orange.misc.environ import data_dir
def progress_bar_milestones(count, iterations=100):
return set([int(i * count / float(iterations)) for i in range(iterations)])
local_cache = os.path.join(data_dir(), 'bioinformatics/')
def ensure_type(value, types):
if isinstance(value, types):
return value
else:
raise TypeError(
'Wrong variable type. {value} is {value_type}, but should be {types}'
.format(value=value, value_type=type(value), types=types))
def __init__(self):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(HEADER)
proxy = QSortFilterProxyModel()
proxy.setSourceModel(model)
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.view.setItemDelegateForColumn(
Header.Size, SizeDelegate(self))
self.view.setItemDelegateForColumn(
Header.Local, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.view.setItemDelegateForColumn(
Header.Instances, NumericalDelegate(self))
self.view.setItemDelegateForColumn(
Header.Variables, NumericalDelegate(self))
self.view.resizeColumnToContents(Header.Local)
if self.header_state:
self.view.header().restoreState(self.header_state)
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def local_cache_path(path):
return os.path.join(data_dir(), path)
import os
import serverfiles
from Orange.misc.environ import data_dir
import orangecontrib.spectroscopy # loads file readers
server = serverfiles.ServerFiles("http://193.2.72.57/infrared-data/")
localfiles = serverfiles.LocalFiles(
os.path.join(data_dir(), "orange-infrared"), serverfiles=server)
def spectra20nea():
return localfiles.localpath_download("spectra20.nea")
def dust():
localfiles.localpath_download("20160831_06_Paris_25x_highmag.dat")
return localfiles.localpath_download("20160831_06_Paris_25x_highmag.hdr")
"""
import os
import json
import numpy as np
from serverfiles import LocalFiles, ServerFiles
from Orange.data import Table, Domain, StringVariable, DiscreteVariable
from Orange.data import filter as table_filter
from Orange.misc.environ import data_dir
from orangecontrib.bioinformatics.widgets.utils.data import TableAnnotation
domain = 'geo'
_local_cache_path = os.path.join(data_dir(), domain)
_all_info_file = os.path.join(_local_cache_path, '__INFO__')
_server_url = 'http://download.biolab.si/datasets/geo/'
pubmed_url = 'http://www.ncbi.nlm.nih.gov/pubmed/{}'
server_files = ServerFiles(server=_server_url)
local_files = LocalFiles(_local_cache_path, serverfiles=server_files)
def is_cached(gds_id):
return os.path.exists(os.path.join(_local_cache_path, gds_id + '.tab'))
def info_cache(f):
"""Store content of __INFO__ file locally."""
def __init__(self):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self._header_labels = [header['label'] for _, header in self.HEADER_SCHEMA]
self._header_index = namedtuple('_header_index', [info_tag for info_tag, _ in self.HEADER_SCHEMA])
self.Header = self._header_index(*[index for index, _ in enumerate(self._header_labels)])
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
uniformRowHeights=True,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
proxy = QSortFilterProxyModel()
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.assign_delegates()
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
