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