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()