def StartDownload(self):
self.updateWidget.removeButton.setEnabled(False)
self.updateWidget.updateButton.setEnabled(False)
self.setData(2, Qt.DisplayRole, QVariant(""))
serverFiles = orngServerFiles.ServerFiles(access_code=self.master.accessCode if self.master.accessCode else None)
pb = ItemProgressBar(self.treeWidget())
pb.setRange(0, 100)
pb.setTextVisible(False)
self.task = AsyncCall(threadPool=QThreadPool.globalInstance())
if not getattr(self.master, "_sum_progressBar", None):
self.master._sum_progressBar = OWGUI.ProgressBar(self.master,0)
self.master._sum_progressBar.in_progress = 0
master_pb = self.master._sum_progressBar
master_pb.iter += 100
master_pb.in_progress += 1
self._progressBarRedirect = ProgressBarRedirect(QThread.currentThread(), master_pb)
# QObject.connect(self.thread, SIGNAL("advance()"), lambda :(pb.setValue(pb.value()+1), master_pb.advance()))
QObject.connect(self.task, SIGNAL("advance()"), pb.advance, Qt.QueuedConnection)
QObject.connect(self.task, SIGNAL("advance()"), self._progressBarRedirect.advance, Qt.QueuedConnection)
QObject.connect(self.task, SIGNAL("finished(QString)"), self.EndDownload, Qt.QueuedConnection)
self.treeWidget().setItemWidget(self, 2, pb)
pb.show()
self.task.apply_async(orngServerFiles.download, args=(self.domain, self.filename, serverFiles), kwargs=dict(callback=self.task.emitAdvance))
def UpdateFilesList(self):
self.retryButton.hide()
# self.progressBarInit()
pb = OWGUI.ProgressBar(self, 3)
self.filesView.clear()
# self.tagsWidget.clear()
self.allTags = set()
allTitles = set()
self.updateItems = []
if self.accessCode:
self.serverFiles = orngServerFiles.ServerFiles(
access_code=self.accessCode)
self.error(0)
try:
domains = self.serverFiles.listdomains(
) if self.domains is None else self.domains
pb.advance()
serverInfo = dict([(dom, self.serverFiles.allinfo(dom))
for dom in domains])
pb.advance()
except IOError, ex:
self.error(
0,
"Could not connect to server! Press the Retry button to try again."
)
self.retryButton.show()
domains = orngServerFiles.listdomains(
) if self.domains is None else self.domains
pb.advance()
serverInfo = {}
pb.advance()
def files_report():
import orngServerFiles as sf
sf = sf.ServerFiles()
html = []
for domain in sf.listdomains():
if domain not in ["demo", "demo2", "test", "gad"]:
allinfo = sf.allinfo(domain)
html += ["<h2>%s</h2>" % domain,
"<table><tr><th>Title</th><th>Date</th><th>Filename</th></tr>"] + \
["<tr><td>%s</td><td>%s</td><td>%s</td></tr>" % (info["title"], info["datetime"], file) \
for file, info in allinfo.items()] + \
["</table>"]
return "\n".join(html)
def __init__(self, parent=None, signalManager=None, name="Databases update", wantCloseButton=False, searchString="", showAll=True, domains=None, accessCode=""):
OWWidget.__init__(self, parent, signalManager, name)
self.searchString = searchString
self.accessCode = accessCode
self.showAll = showAll
self.domains = domains
self.serverFiles = orngServerFiles.ServerFiles()
box = OWGUI.widgetBox(self.mainArea, orientation="horizontal")
import OWGUIEx
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.mainArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(["Options", "Title", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.setItemDelegate(UpdateItemDelegate(self.filesView))
self.connect(self.filesView.model(), SIGNAL("layoutChanged()"), self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = OWGUI.widgetBox(self.mainArea, orientation="horizontal")
OWGUI.button(box, self, "Update all local files", callback=self.UpdateAll, tooltip="Update all updatable files")
OWGUI.button(box, self, "Download filtered", callback=self.DownloadFiltered, tooltip="Download all filtered files shown")
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.mainArea, orientation="horizontal")
OWGUI.rubber(box)
if wantCloseButton:
OWGUI.button(box, self, "Close", callback=self.accept, tooltip="Close")
## statusBar = QStatusBar()
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
## statusBar.addWidget(self.infoLabel)
## self.mainArea.layout().addWidget(statusBar)
self.mainArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.allTags = []
self.resize(800, 600)
# QTimer.singleShot(50, self.UpdateFilesList)
QTimer.singleShot(50, self.RetrieveFilesList)
##!interval=7 ##[email protected] import obiPPI, orngServerFiles import os, sys, shutil, urllib2, tarfile from getopt import getopt opt = dict(getopt(sys.argv[1:], "u:p:", ["user="******"password="******"-u", opt.get("--user", "username")) password = opt.get("-p", opt.get("--password", "password")) serverFiles = orngServerFiles.ServerFiles(username, password) try: os.mkdir(orngServerFiles.localpath("PPI")) except OSError: pass obiPPI.MIPS.download() try: serverFiles.create_domain("PPI") except Exception, ex: print ex filename = orngServerFiles.localpath("PPI", "mppi.gz") serverFiles.upload("PPI", "allppis.xml", filename, "MIPS Protein interactions", tags=[
def RetrieveFilesList(self):
self.serverFiles = orngServerFiles.ServerFiles(access_code=self.accessCode)
self.pb = ProgressBar(self, 3)
self.async_retrieve = createTask(retrieveFilesList, (self.serverFiles, self.domains, self.pb.advance), onResult=self.SetFilesList, onError=self.HandleError)
self.setEnabled(False)
results[-1][2] = parts[1].strip("\t ")
ontology.close()
output = file('mesh-ontology.dat', 'w')
for i in results:
print i[0] + "\t"
output.write(i[0] + "\t")
g = len(i[1])
for k in i[1]:
g -= 1
if (g > 0):
output.write(k + ";")
else:
output.write(k + "\t" + i[2] + "\n")
output.close()
print "Ontology downloaded."
ordinary = orngServerFiles.ServerFiles()
authenticated = orngServerFiles.ServerFiles(username, password)
authenticated.upload('MeSH',
'mesh-ontology.dat',
'mesh-ontology.dat',
title="MeSH ontology",
tags=['MeSH', 'ontology', 'orngMeSH'])
#authenticated.upload('MeSH', 'cid-annotation.dat', 'cid-annotation.dat', title="Annotation for chemicals (CIDs)", tags =['CID','MeSH','orngMeSH','annotation'])
authenticated.unprotect('MeSH', 'mesh-ontology.dat')
os.remove('mesh-ontology.dat')
print "Ontology uploaded to server."
import orngServerFiles
reload(orngServerFiles)
domain = "demo"
# remove the domain from the local repository
if domain in orngServerFiles.listdomains():
orngServerFiles.remove_domain(domain, force=True)
# download all the files for this domain from the server
server = orngServerFiles.ServerFiles()
for filename in server.listfiles(domain):
orngServerFiles.download(domain, filename, verbose=False)
# make sure that both file lists are the same
files_on_server = server.listfiles(domain)
print "Domain: %s" % domain
intersection = set(files_on_server).intersection(set(orngServerFiles.listfiles(domain)))
if len(intersection) == len(files_on_server):
print "Same number of files on server and local repository."
else:
print "Directories on server and local repository are different."
