def SubmitDownloadTask(self, domain, filename):
"""
Submit the (domain, filename) to be downloaded/updated.
"""
self.cancelButton.setEnabled(True)
index = self.updateItemIndex(domain, filename)
_, tree_item, opt_widget = self.updateItems[index]
if self.accessCode:
sf = serverfiles.ServerFiles(access_code=self.accessCode)
else:
sf = serverfiles.ServerFiles()
task = DownloadTask(domain, filename, sf)
self.executor.submit(task)
self.progress.adjustRange(0, 100)
pb = ItemProgressBar(self.filesView)
pb.setRange(0, 100)
pb.setTextVisible(False)
task.advanced.connect(pb.advance)
task.advanced.connect(self.progress.advance)
task.finished.connect(pb.hide)
task.finished.connect(self.onDownloadFinished, Qt.QueuedConnection)
task.exception.connect(self.onDownloadError, Qt.QueuedConnection)
self.filesView.setItemWidget(tree_item, 2, pb)
# Clear the text so it does not show behind the progress bar.
tree_item.setData(2, Qt.DisplayRole, "")
pb.show()
# Disable the options widget
opt_widget.setEnabled(False)
self._tasks.append(task)
def RetrieveFilesList(self):
self.progress.setRange(0, 3)
self.serverFiles = serverfiles.ServerFiles(access_code=self.accessCode)
task = Task(function=partial(retrieveFilesList, self.serverFiles,
self.domains,
methodinvoke(self.progress, "advance")))
task.resultReady.connect(self.SetFilesList)
task.exceptionReady.connect(self.HandleError)
self.executor.submit(task)
self.setEnabled(False)
gene_sets = []
for (ef, efv), genes in sets.items():
ef_display = display_string(ef)
gs = GeneSet(genes, "Diff. expressed in %s=%s." % (ef_display, efv), id=ef + ":" + efv,
description="Diff. expressed in %s=%s." % (ef_display, efv),
link="http://www.ebi.ac.uk/gxa/qrs?specie_0={organism}&gprop_0=&gnot_0=&gval_0=&fact_1=&fexp_1=UPDOWN&fmex_1=&fval_1=%22{efv}%22+&view=hm".format( \
organism = "+".join(organism.lower().split()), efv = "+".join(efv.lower().split())), organism=org_code, hierarchy=("Gene Expression Atlas", display_string(condition)))
gene_sets.append(gs)
final_set = GeneSets(gene_sets)
print final_set
exit()
from Orange.bio.obiGeneSets import register
import Orange.utils.serverfiles as serverfiles
import sys
try:
sf_server = serverfiles.ServerFiles(sys.argv[1], sys.argv[2])
except:
print "argv[1] = username, argv[2] = password"
exit()
set_split = final_set.split_by_hierarchy()
for s in set_split:
register(s, sf_server)
print "Gene sets successfully registered..."
def __init__(self, parent=None, signalManager=None,
name="Databases update", wantCloseButton=False,
searchString="", showAll=True, domains=None,
accessCode=""):
OWWidget.__init__(self, parent, signalManager, name, wantMainArea=False)
self.searchString = searchString
self.accessCode = accessCode
self.showAll = showAll
self.domains = domains
self.serverFiles = serverfiles.ServerFiles()
box = OWGUI.widgetBox(self.controlArea, orientation="horizontal")
self.lineEditFilter = \
OWGUIEx.lineEditHint(box, self, "searchString", "Filter",
caseSensitive=False,
delimiters=" ",
matchAnywhere=True,
listUpdateCallback=self.SearchUpdate,
callbackOnType=True,
callback=self.SearchUpdate)
box = OWGUI.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
QObject.connect(self.filesView.model(),
SIGNAL("layoutChanged()"),
self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = OWGUI.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = OWGUI.button(box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = OWGUI.button(box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown")
self.cancelButton = OWGUI.button(box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates.")
OWGUI.rubber(box)
OWGUI.lineEdit(box, self, "accessCode", "Access Code",
orientation="horizontal",
callback=self.RetrieveFilesList)
self.retryButton = OWGUI.button(box, self, "Retry",
callback=self.RetrieveFilesList)
self.retryButton.hide()
box = OWGUI.widgetBox(self.controlArea, orientation="horizontal")
OWGUI.rubber(box)
if wantCloseButton:
OWGUI.button(box, self, "Close",
callback=self.accept,
tooltip="Close")
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
import Orange.utils.serverfiles as serverfiles
import Orange.utils.environ as environ
import os, sys
import optparse
import gzip, shutil
usage = """usage: %prog [options] [update_script ...]"""
parser = optparse.OptionParser(usage=usage)
parser.add_option("-u", "--user", help="User name")
parser.add_option("-p", "--password", help="Password")
parser.add_option("-l",
"--log-dir",
dest="log_dir",
help="Directory to store the logs",
default="./")
parser.add_option("-m",
"--mailto",
help="e-mail the results to EMAIL",
metavar="EMAIL",
default=None)
option, args = parser.parse_args()
if not option.user or not option.password:
print "Pass -u username -p password!"
sys.exit(1)
sf_server = serverfiles.ServerFiles(option.user, option.password)
sf_local = Orange.utils.serverfiles