def Commit(self):
if not self.dbc:
self.Connect()
allTables = []
import time
start = time.time()
pb = OWGUI.ProgressBar(self, iterations=1000)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
ids += str(item.text(5)).split(",")
table = self.dbc.get_single_data(
ids=ids,
callback=pb.advance,
exclude_constant_labels=self.excludeconstant)
end = int(time.time() - start)
pb.finish()
#self.send("Example table", None)
# table.taxid = "352472"
# table.genesinrows = False
from Orange.orng.orngDataCaching import data_hints
data_hints.set_hint(table, "taxid", "352472", 10.0)
data_hints.set_hint(table, "genesinrows", False, 10.0)
self.send("Example table", table)
def Commit(self):
if not self.dbc:
self.Connect()
allTables = []
import time
start = time.time()
pb = OWGUI.ProgressBar(self, iterations=1000)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
ids += str(item.text(5)).split(",")
table = self.dbc.get_single_data(ids=ids, callback=pb.advance, exclude_constant_labels=self.excludeconstant)
end = int(time.time()-start)
pb.finish()
#self.send("Example table", None)
# table.taxid = "352472"
# table.genesinrows = False
from Orange.orng.orngDataCaching import data_hints
data_hints.set_hint(table, "taxid", "352472", 10.0)
data_hints.set_hint(table, "genesinrows", False, 10.0)
self.send("Example table", table)
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarFinished(processEvents=False)
try:
data = self._datatask.result()
except urlrequest.URLError as error:
self.error(0, ("Error while connecting to the NCBI ftp server! "
"'%s'" % error))
sys.excepthook(type(error), error, getattr(error, "__traceback__"))
return
finally:
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for meta in data.domain.metas:
out.append((meta.name, ex[meta].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name,
ex[data.domain.class_var].value))
return out
samples = set(samples)
mask = [samples.issuperset(samplesinst(ex)) for ex in data]
data = data[numpy.array(mask, dtype=bool)]
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = Orange.data.Domain([
attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())
], data.domain.class_var, data.domain.metas)
# domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes)
data = Orange.data.Table(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), " ", Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarSet(50)
try:
data = self._datatask.result()
except urllib2.URLError as error:
self.error(0, "Error while connecting to the NCBI ftp server! %r" %
error)
self._datatask = None
self.progressBarFinished()
return
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for i, a in data.domain.get_metas().items():
out.append((a.name, ex[i].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name, ex[-1].value))
return out
samples = set(samples)
select = [1 if samples.issuperset(samplesinst(ex)) else 0
for ex in data]
data = data.select(select)
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = orange.Domain(
[attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())],
data.domain.classVar
)
domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes
)
data = orange.ExampleTable(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
self.progressBarFinished()
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), QVariant(" "), Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarFinished(processEvents=False)
try:
data = self._datatask.result()
except urlrequest.URLError as error:
self.error(0, ("Error while connecting to the NCBI ftp server! "
"'%s'" % error))
sys.excepthook(type(error), error, getattr(error, "__traceback__"))
return
finally:
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for meta in data.domain.metas:
out.append((meta.name, ex[meta].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name,
ex[data.domain.class_var].value))
return out
samples = set(samples)
mask = [samples.issuperset(samplesinst(ex)) for ex in data]
data = data[numpy.array(mask, dtype=bool)]
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = Orange.data.Domain(
[attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())],
data.domain.class_var,
data.domain.metas
)
# domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes
)
data = Orange.data.Table(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), " ", Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarSet(50)
try:
data = self._datatask.result()
except urllib2.URLError as error:
self.error(0, "Error while connecting to the NCBI ftp server! %r" %
error)
self._datatask = None
self.progressBarFinished()
return
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for i, a in data.domain.get_metas().items():
out.append((a.name, ex[i].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name, ex[-1].value))
return out
samples = set(samples)
select = [1 if samples.issuperset(samplesinst(ex)) else 0
for ex in data]
data = data.select(select)
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = orange.Domain(
[attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())],
data.domain.classVar
)
domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes
)
data = orange.ExampleTable(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
self.progressBarFinished()
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), QVariant(" "), Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
