def __init__(self, parent=None, signalManager=None,
title="Databases Pack"):
super(OWDatabasesPack, self).__init__(
parent, signalManager, title, wantMainArea=False)
self.fileslist = [("Taxonomy", "ncbi_taxonomy.tar.gz")]
self.downloadurl = "https://dl.dropboxusercontent.com/u/100248799/sf_pack.tar.gz"
self.downloadmessage = (
"Downloading a subset of available databases for a smoother " +
"ride through the workshop"
)
self.loadSettings()
self._tmpfile = None
self.reply = None
# Locks held on server files
self.locks = []
self.net_manager = QNetworkAccessManager()
# Lock all files in files list so any other (in process) atempt to
# download the files waits)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, self.downloadmessage)
self.info.setWordWrap(True)
box = OWGUI.widgetBox(self.controlArea, "Status")
self.statusinfo = OWGUI.widgetLabel(box, "Please wait")
self.statusinfo.setWordWrap(True)
self.progressbar = QProgressBar()
box.layout().addWidget(self.progressbar)
self.setMinimumWidth(250)
already_available = [(domain, filename)
for domain in serverfiles.listdomains()
for filename in serverfiles.listfiles(domain)]
if set(self.fileslist) <= set(already_available):
# All files are already downloaded
self.statusinfo.setText("All files already available")
self.setStatusMessage("Done")
else:
for domain, filename in self.fileslist + [("_tmp_cache_", "pack")]:
manager = serverfiles._lock_file(domain, filename)
try:
manager.__enter__()
except Exception:
warnings.warn("Could not acquire lock for {0} {0}"
.format(domain, filename))
self.warning(0, "...")
else:
self.locks.append(manager)
QTimer.singleShot(0, self.show)
QTimer.singleShot(0, self.run)
def initialize(self):
if self.__initialized:
# Already initialized
return
self.progressBarFinished()
self.organisms = sorted(
set([
name.split(".")[-2]
for name in serverfiles.listfiles("NCBI_geneinfo")
] + gene.NCBIGeneInfo.essential_taxids()))
self.organismComboBox.addItems(
[taxonomy.name(tax_id) for tax_id in self.organisms])
if self.taxid in self.organisms:
self.organismIndex = self.organisms.index(self.taxid)
self.infoLabel.setText("No data on input\n")
self.__initialized = True
self.initfuture = None
self.setBlocking(False)
def initialize(self):
if self.__initialized:
# Already initialized
return
self.progressBarFinished()
self.organisms = sorted(
set([name.split(".")[-2] for name in
serverfiles.listfiles("NCBI_geneinfo")] +
gene.NCBIGeneInfo.essential_taxids())
)
self.organismComboBox.addItems(
[taxonomy.name(tax_id) for tax_id in self.organisms]
)
if self.taxid in self.organisms:
self.organismIndex = self.organisms.index(self.taxid)
self.infoLabel.setText("No data on input\n")
self.__initialized = True
self.initfuture = None
self.setBlocking(False)
def __init__(self, parent=None, signalManager=None, title="Databases Pack"):
super(OWDatabasesPack, self).__init__(parent, signalManager, title, wantMainArea=False)
self.fileslist = [("Taxonomy", "ncbi_taxonomy.tar.gz")]
self.downloadurl = "https://dl.dropboxusercontent.com/u/100248799/sf_pack.tar.gz"
self.downloadmessage = (
"Downloading a subset of available databases for a smoother " + "ride through the workshop"
)
self.loadSettings()
self._tmpfile = None
self.reply = None
# Locks held on server files
self.locks = []
self.net_manager = QNetworkAccessManager()
# Lock all files in files list so any other (in process) atempt to
# download the files waits)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, self.downloadmessage)
self.info.setWordWrap(True)
box = OWGUI.widgetBox(self.controlArea, "Status")
self.statusinfo = OWGUI.widgetLabel(box, "Please wait")
self.statusinfo.setWordWrap(True)
self.progressbar = QProgressBar()
box.layout().addWidget(self.progressbar)
self.setMinimumWidth(250)
already_available = [
(domain, filename) for domain in serverfiles.listdomains() for filename in serverfiles.listfiles(domain)
]
if set(self.fileslist) <= set(already_available):
# All files are already downloaded
self.statusinfo.setText("All files already available")
self.setStatusMessage("Done")
else:
for domain, filename in self.fileslist + [("_tmp_cache_", "pack")]:
manager = serverfiles._lock_file(domain, filename)
try:
manager.__enter__()
except Exception:
warnings.warn("Could not acquire lock for {0} {0}".format(domain, filename))
self.warning(0, "...")
else:
self.locks.append(manager)
QTimer.singleShot(0, self.show)
QTimer.singleShot(0, self.run)
