def send_to_output(self, etc_json):
self.progress_bar.finish()
self.setStatusMessage('')
data = etc_to_table(etc_json, self.setTimeVariable)
data_hints.set_hint(data, TAX_ID, self.orgnism)
data_hints.set_hint(data, GENE_NAME, self.setTimeVariable)
self.Outputs.etc_data.send(data)
def Commit(self):
if not self.dbc:
self.Connect()
start = time.time()
pb = gui.ProgressBar(self, iterations=1000)
ids = []
for item in self.experimentsWidget.selectedItems():
ids += str(item.text(5)).split(",")
table = self.dbc.get_single_data(
ids=ids, exclude_constant_labels=self.excludeconstant,
callback=pb.advance)
end = int(time.time() - start)
pb.finish()
data_hints.set_hint(table, "taxid", "352472", 10.0)
data_hints.set_hint(table, "genesinrows", False, 10.0)
self.send("Data", table)
def Commit(self):
if not self.dbc:
self.Connect()
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(10))
annots = self.mappings[unique_id]
ids.append((annots["data_id"], annots["id"]))
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = dict((name, key) for key, name in HEADER)
hview = self.experimentsWidget.header()
shownHeaders = [label for i, label in \
list(enumerate(self.headerLabels))[1:] \
if not hview.isSectionHidden(i)
]
allowed_labels = [reverse_header_dict.get(label, label) \
for label in shownHeaders]
if self.joinreplicates and "id" not in allowed_labels:
# need 'id' labels in join_replicates for attribute names
allowed_labels.append("id")
if len(ids):
table = self.dbc.get_data(ids=ids, result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
# bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=["replicate", "data_id", "mappings_id",
"data_name", "id", "unique_id"],
namefn=None,
avg=dicty.median
)
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name) \
for name in sortOrder])
attributes = sorted(table.domain.attributes,
key=sorting_key)
domain = Orange.data.Domain(
attributes, table.domain.class_var, table.domain.metas)
table = table.from_table(domain, table)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def Commit(self):
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(ID_INDEX))
ids.append(unique_id)
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = {name: name for key, name in HEADER}
reverse_header_dict["ID"] = "id"
allowed_labels = None
def namefn(a):
name = SORTING_MODEL_LIST[self.exnamei]
name = reverse_header_dict.get(name, "id")
return dict(a)[name]
if len(ids):
table = self.dbc.get_data(
ids=ids,
result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels,
namefn=namefn)
if self.joinreplicates:
table = dicty.join_replicates(
table,
ignorenames=self.dbc.IGNORE_REPLICATE,
namefn="name",
avg=dicty.median,
fnshow=lambda x: " | ".join(map(str, x)))
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(
atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except ValueError:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([
optfloat(atts.get(reverse_header_dict[name], ""), name)
for name in sortOrder
])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(attributes, table.domain.class_vars,
table.domain.metas)
table = Orange.data.Table.from_table(domain, table)
table = Orange.data.Table(domain, table)
if self.transpose:
experiments = [at for at in table.domain.variables]
attr = [
compat.ContinuousVariable.make(ex['DDB'].value)
for ex in table
]
metavars = sorted(table.domain.variables[0].attributes.keys())
metavars = [
compat.StringVariable.make(name) for name in metavars
]
domain = compat.create_domain(attr, None, metavars)
metavars = compat.get_metas(domain)
metas = [[exp.attributes[var.name] for var in metavars]
for exp in experiments]
table = compat.create_table(domain, table.X.transpose(), None,
metas)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def Commit(self):
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(ID_INDEX))
ids.append(unique_id)
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = {name: name for key, name in HEADER}
reverse_header_dict["ID"] = "id"
allowed_labels = None
def namefn(a):
name = SORTING_MODEL_LIST[self.exnamei]
name = reverse_header_dict.get(name, "id")
return dict(a)[name]
if len(ids):
table = self.dbc.get_data(
ids=ids, result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels,
namefn=namefn)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=self.dbc.IGNORE_REPLICATE,
namefn="name",
avg=dicty.median,
fnshow=lambda x: " | ".join(map(str, x)))
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except ValueError:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name)
for name in sortOrder])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(
attributes, table.domain.class_vars, table.domain.metas)
table = Orange.data.Table.from_table(domain, table)
table = Orange.data.Table(domain, table)
if self.transpose:
experiments = [at for at in table.domain.variables]
attr = [compat.ContinuousVariable.make(ex['DDB'].value) for ex in table]
metavars = sorted(table.domain.variables[0].attributes.keys())
metavars = [compat.StringVariable.make(name) for name in metavars]
domain = compat.create_domain(attr, None, metavars)
metas = [[exp.attributes[var.name] for var in metavars] for exp in experiments]
table = compat.create_table(domain, table.X.transpose(), None, metas)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
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 = 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 = Table(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, TAX_ID, self.currentGds.get("taxid", ""))
data_hints.set_hint(data, GENE_NAME, bool(self.outputRows))
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 Commit(self):
if not self.dbc:
self.Connect()
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(10))
annots = self.mappings[unique_id]
ids.append((annots["data_id"], annots["id"]))
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = dict((name, key) for key, name in HEADER)
hview = self.experimentsWidget.header()
shownHeaders = [label for i, label in \
list(enumerate(self.headerLabels))[1:] \
if not hview.isSectionHidden(i)
]
allowed_labels = [reverse_header_dict.get(label, label) \
for label in shownHeaders]
if self.joinreplicates and "id" not in allowed_labels:
# need 'id' labels in join_replicates for attribute names
allowed_labels.append("id")
if len(ids):
table = self.dbc.get_data(
ids=ids,
result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
# bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=[
"replicate", "data_id",
"mappings_id", "data_name",
"id", "unique_id"
],
namefn=None,
avg=dicty.median)
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(
atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name) \
for name in sortOrder])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(attributes, table.domain.class_var,
table.domain.metas)
table = table.from_table(domain, table)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def Commit(self):
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(ID_INDEX))
ids.append(unique_id)
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = {name: key for key, name in HEADER}
allowed_labels = None
if len(ids):
table = self.dbc.get_data(
ids=ids, result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=self.dbc.IGNORE_REPLICATE,
namefn=None,
avg=dicty.median)
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except ValueError:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name)
for name in sortOrder])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(
attributes, table.domain.class_vars, table.domain.metas)
table = Orange.data.Table.from_table(domain, table)
table = Orange.data.Table(domain, table)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()