class OWGEODatasets(OWWidget): name = "GEO Data Sets" description = DESCRIPTION icon = "../widgets/icons/GEODataSets.svg" priority = PRIORITY inputs = [] outputs = [("Expression Data", Orange.data.Table)] settingsList = [ "outputRows", "mergeSpots", "gdsSelectionStates", "splitterSettings", "currentGds", "autoCommit", "datasetNames" ] outputRows = Setting(True) mergeSpots = Setting(True) gdsSelectionStates = Setting({}) currentGds = Setting(None) datasetNames = Setting({}) splitterSettings = Setting(( b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02', b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01' )) autoCommit = Setting(False) def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.selectionChanged = False self.filterString = "" self.datasetName = "" ## GUI box = gui.widgetBox(self.controlArea, "Info", addSpace=True) self.infoBox = gui.widgetLabel(box, "Initializing\n\n") box = gui.widgetBox(self.controlArea, "Output", addSpace=True) gui.radioButtonsInBox(box, self, "outputRows", ["Genes in rows", "Samples in rows"], "Rows", callback=self.commitIf) gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) gui.separator(box) self.nameEdit = gui.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited) self.nameEdit.setPlaceholderText("") if sys.version_info < (3, ): box = gui.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = gui.button(box, self, "Commit", callback=self.commit) cb = gui.checkBox(box, self, "autoCommit", "Commit on any change") gui.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) else: gui.auto_commit(self.controlArea, self, "autoCommit", "Commit", box="Commit") self.commitIf = self.commit gui.rubber(self.controlArea) gui.widgetLabel(self.mainArea, "Filter") self.filterLineEdit = QLineEdit(textChanged=self.filter) self.completer = TokenListCompleter(self, caseSensitivity=Qt.CaseInsensitive) self.filterLineEdit.setCompleter(self.completer) self.mainArea.layout().addWidget(self.filterLineEdit) splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QTreeView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = gui.widgetBox(splitterH, "Description") self.infoGDS = gui.widgetLabel(box, "") self.infoGDS.setWordWrap(True) gui.rubber(box) box = gui.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"]) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = [ "dataset_id", "title", "platform_organism", "description" ] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float, ))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None @Slot(float) def _setProgress(self, value): self.progressBarValue = value def _initializemodel(self): assert self.thread() is QThread.currentThread() model, self.gds_info, self.gds = self._inittask.result() model.setParent(self) proxy = self.treeWidget.model() proxy.setFilterKeyColumn(0) proxy.setFilterRole(TextFilterRole) proxy.setFilterCaseSensitivity(False) proxy.setFilterFixedString(self.filterString) proxy.setSourceModel(model) proxy.sort(0, Qt.DescendingOrder) self.progressBarFinished() self.setBlocking(False) self.setEnabled(True) filter_items = " ".join(gds[key] for gds in self.gds for key in self.searchKeys) tr_chars = ",.:;!?(){}[]_-+\\|/%#@$^&*<>~`" tr_table = str.maketrans(tr_chars, " " * len(tr_chars)) filter_items = filter_items.translate(tr_table) filter_items = sorted(set(filter_items.split(" "))) filter_items = [item for item in filter_items if len(item) > 3] self.completer.setTokenList(filter_items) if self.currentGds: current_id = self.currentGds["dataset_id"] gdss = [(i, qunpack(proxy.data(proxy.index(i, 1), Qt.DisplayRole))) for i in range(proxy.rowCount())] current = [i for i, data in gdss if data and data == current_id] if current: current_index = proxy.index(current[0], 0) self.treeWidget.selectionModel().select( current_index, QItemSelectionModel.Select | QItemSelectionModel.Rows) self.treeWidget.scrollTo(current_index, QTreeView.PositionAtCenter) for i in range(8): self.treeWidget.resizeColumnToContents(i) self.treeWidget.setColumnWidth( 1, min(self.treeWidget.columnWidth(1), 300)) self.treeWidget.setColumnWidth( 2, min(self.treeWidget.columnWidth(2), 200)) self.updateInfo() def updateInfo(self): gds_info = self.gds_info text = ("%i datasets\n%i datasets cached\n" % (len(gds_info), len(glob.glob(serverfiles.localpath("GEO") + "/GDS*")))) filtered = self.treeWidget.model().rowCount() if len(self.gds) != filtered: text += ("%i after filtering") % filtered self.infoBox.setText(text) def updateSelection(self, *args): current = self.treeWidget.selectedIndexes() mapToSource = self.treeWidget.model().mapToSource current = [mapToSource(index).row() for index in current] if current: self.currentGds = self.gds[current[0]] self.setAnnotations(self.currentGds) self.infoGDS.setText(self.currentGds.get("description", "")) self.nameEdit.setPlaceholderText(self.currentGds["title"]) self.datasetName = \ self.datasetNames.get(self.currentGds["dataset_id"], "") else: self.currentGds = None self.nameEdit.setPlaceholderText("") self.datasetName = "" self.commitIf() def setAnnotations(self, gds): self._annotationsUpdating = True self.annotationsTree.clear() annotations = defaultdict(set) subsetscount = {} for desc in gds["subsets"]: annotations[desc["type"]].add(desc["description"]) subsetscount[desc["description"]] = str(len(desc["sample_id"])) for type, subsets in annotations.items(): key = (gds["dataset_id"], type) subsetItem = QTreeWidgetItem(self.annotationsTree, [type]) subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable | Qt.ItemIsTristate) subsetItem.setCheckState( 0, self.gdsSelectionStates.get(key, Qt.Checked)) subsetItem.key = key for subset in subsets: key = (gds["dataset_id"], type, subset) item = QTreeWidgetItem( subsetItem, [subset, subsetscount.get(subset, "")]) item.setFlags(item.flags() | Qt.ItemIsUserCheckable) item.setCheckState( 0, self.gdsSelectionStates.get(key, Qt.Checked)) item.key = key self._annotationsUpdating = False self.annotationsTree.expandAll() for i in range(self.annotationsTree.columnCount()): self.annotationsTree.resizeColumnToContents(i) def annotationSelectionChanged(self, item, column): if self._annotationsUpdating: return for i in range(self.annotationsTree.topLevelItemCount()): item = self.annotationsTree.topLevelItem(i) self.gdsSelectionStates[item.key] = item.checkState(0) for j in range(item.childCount()): child = item.child(j) self.gdsSelectionStates[child.key] = child.checkState(0) def filter(self): filter_string = unicode(self.filterLineEdit.text()) proxyModel = self.treeWidget.model() if proxyModel: strings = filter_string.lower().strip().split() proxyModel.setFilterFixedStrings(strings) self.updateInfo() def selectedSamples(self): """ Return the currently selected sample annotations. The return value is a list of selected (sample type, sample value) tuples. .. note:: if some Sample annotation type has no selected values. this method will return all values for it. """ samples = [] unused_types = [] used_types = [] for stype in childiter(self.annotationsTree.invisibleRootItem()): selected_values = [] all_values = [] for sval in childiter(stype): value = (str(stype.text(0)), str(sval.text(0))) if self.gdsSelectionStates.get(sval.key, True): selected_values.append(value) all_values.append(value) if selected_values: samples.extend(selected_values) used_types.append(str(stype.text(0))) else: # If no sample of sample type is selected we don't filter # on it. samples.extend(all_values) unused_types.append(str(stype.text(0))) return samples, used_types def commitIf(self): if self.autoCommit: self.commit() else: self.selectionChanged = True @Slot(int, int) def progressCompleted(self, value, total): if total > 0: self.progressBarSet(100. * value / total, processEvents=False) else: pass # TODO: report 'indeterminate progress' def commit(self): if self.currentGds: self.error(0) sample_type = None self.progressBarInit(processEvents=None) _, groups = self.selectedSamples() if len(groups) == 1 and self.outputRows: sample_type = groups[0] self.setEnabled(False) self.setBlocking(True) progress = methodinvoke(self, "progressCompleted", (int, int)) def get_data(gds_id, report_genes, transpose, sample_type, title): gds_ensure_downloaded(gds_id, progress) gds = geo.GDS(gds_id) data = gds.getdata(report_genes=report_genes, transpose=transpose, sample_type=sample_type) data.name = title return data get_data = partial(get_data, self.currentGds["dataset_id"], report_genes=self.mergeSpots, transpose=self.outputRows, sample_type=sample_type, title=self.datasetName or self.currentGds["title"]) self._datatask = Task(function=get_data) self._datatask.finished.connect(self._on_dataready) self._executor.submit(self._datatask) 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 splitterMoved(self, *args): self.splitterSettings = [ bytes(sp.saveState()) for sp in self.splitters ] def send_report(self): self.report_items("GEO Dataset", [("ID", self.currentGds['dataset_id']), ("Title", self.currentGds['title']), ("Organism", self.currentGds['sample_organism'])]) self.report_items("Data", [("Samples", self.currentGds['sample_count']), ("Features", self.currentGds['feature_count']), ("Genes", self.currentGds['gene_count'])]) self.report_name("Sample annotations") subsets = defaultdict(list) for subset in self.currentGds['subsets']: subsets[subset['type']].append( (subset['description'], len(subset['sample_id']))) self.report_html += "<ul>" for type in subsets: self.report_html += "<b>" + type + ":</b></br>" for desc, count in subsets[type]: self.report_html += 9 * " " + "<b>{}:</b> {}</br>".format( desc, count) self.report_html += "</ul>" def onDeleteWidget(self): if self._inittask: self._inittask.future().cancel() self._inittask.finished.disconnect(self._initializemodel) if self._datatask: self._datatask.future().cancel() self._datatask.finished.disconnect(self._on_dataready) self._executor.shutdown(wait=False) super(OWGEODatasets, self).onDeleteWidget() def onNameEdited(self): if self.currentGds: gds_id = self.currentGds["dataset_id"] self.datasetNames[gds_id] = unicode(self.nameEdit.text()) self.commitIf()
class OWGEODatasets(OWWidget): name = "GEO Data Sets" description = DESCRIPTION icon = "../widgets/icons/GEODataSets.svg" priority = PRIORITY inputs = [] outputs = [("Expression Data", Orange.data.Table)] settingsList = ["outputRows", "mergeSpots", "gdsSelectionStates", "splitterSettings", "currentGds", "autoCommit", "datasetNames"] outputRows = Setting(True) mergeSpots = Setting(True) gdsSelectionStates = Setting({}) currentGds = Setting(None) datasetNames = Setting({}) splitterSettings = Setting( (b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02', b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01') ) autoCommit = Setting(False) def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.selectionChanged = False self.filterString = "" self.datasetName = "" ## GUI box = gui.widgetBox(self.controlArea, "Info", addSpace=True) self.infoBox = gui.widgetLabel(box, "Initializing\n\n") box = gui.widgetBox(self.controlArea, "Output", addSpace=True) gui.radioButtonsInBox(box, self, "outputRows", ["Genes in rows", "Samples in rows"], "Rows", callback=self.commitIf) gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) gui.separator(box) self.nameEdit = gui.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited ) self.nameEdit.setPlaceholderText("") if sys.version_info < (3, ): box = gui.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = gui.button( box, self, "Commit", callback=self.commit) cb = gui.checkBox(box, self, "autoCommit", "Commit on any change") gui.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) else: gui.auto_commit(self.controlArea, self, "autoCommit", "Commit", box="Commit") self.commitIf = self.commit gui.rubber(self.controlArea) gui.widgetLabel(self.mainArea, "Filter") self.filterLineEdit = QLineEdit( textChanged=self.filter ) self.completer = TokenListCompleter( self, caseSensitivity=Qt.CaseInsensitive ) self.filterLineEdit.setCompleter(self.completer) self.mainArea.layout().addWidget(self.filterLineEdit) splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QTreeView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection ) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = gui.widgetBox(splitterH, "Description") self.infoGDS = gui.widgetLabel(box, "") self.infoGDS.setWordWrap(True) gui.rubber(box) box = gui.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"] ) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged ) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = ["dataset_id", "title", "platform_organism", "description"] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float,))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None @Slot(float) def _setProgress(self, value): self.progressBarValue = value def _initializemodel(self): assert self.thread() is QThread.currentThread() model, self.gds_info, self.gds = self._inittask.result() model.setParent(self) proxy = self.treeWidget.model() proxy.setFilterKeyColumn(0) proxy.setFilterRole(TextFilterRole) proxy.setFilterCaseSensitivity(False) proxy.setFilterFixedString(self.filterString) proxy.setSourceModel(model) proxy.sort(0, Qt.DescendingOrder) self.progressBarFinished() self.setBlocking(False) self.setEnabled(True) filter_items = " ".join( gds[key] for gds in self.gds for key in self.searchKeys ) tr_chars = ",.:;!?(){}[]_-+\\|/%#@$^&*<>~`" tr_table = str.maketrans(tr_chars, " " * len(tr_chars)) filter_items = filter_items.translate(tr_table) filter_items = sorted(set(filter_items.split(" "))) filter_items = [item for item in filter_items if len(item) > 3] self.completer.setTokenList(filter_items) if self.currentGds: current_id = self.currentGds["dataset_id"] gdss = [(i, qunpack(proxy.data(proxy.index(i, 1), Qt.DisplayRole))) for i in range(proxy.rowCount())] current = [i for i, data in gdss if data and data == current_id] if current: current_index = proxy.index(current[0], 0) self.treeWidget.selectionModel().select( current_index, QItemSelectionModel.Select | QItemSelectionModel.Rows ) self.treeWidget.scrollTo( current_index, QTreeView.PositionAtCenter) for i in range(8): self.treeWidget.resizeColumnToContents(i) self.treeWidget.setColumnWidth( 1, min(self.treeWidget.columnWidth(1), 300)) self.treeWidget.setColumnWidth( 2, min(self.treeWidget.columnWidth(2), 200)) self.updateInfo() def updateInfo(self): gds_info = self.gds_info text = ("%i datasets\n%i datasets cached\n" % (len(gds_info), len(glob.glob(serverfiles.localpath("GEO") + "/GDS*")))) filtered = self.treeWidget.model().rowCount() if len(self.gds) != filtered: text += ("%i after filtering") % filtered self.infoBox.setText(text) def updateSelection(self, *args): current = self.treeWidget.selectedIndexes() mapToSource = self.treeWidget.model().mapToSource current = [mapToSource(index).row() for index in current] if current: self.currentGds = self.gds[current[0]] self.setAnnotations(self.currentGds) self.infoGDS.setText(self.currentGds.get("description", "")) self.nameEdit.setPlaceholderText(self.currentGds["title"]) self.datasetName = \ self.datasetNames.get(self.currentGds["dataset_id"], "") else: self.currentGds = None self.nameEdit.setPlaceholderText("") self.datasetName = "" self.commitIf() def setAnnotations(self, gds): self._annotationsUpdating = True self.annotationsTree.clear() annotations = defaultdict(set) subsetscount = {} for desc in gds["subsets"]: annotations[desc["type"]].add(desc["description"]) subsetscount[desc["description"]] = str(len(desc["sample_id"])) for type, subsets in annotations.items(): key = (gds["dataset_id"], type) subsetItem = QTreeWidgetItem(self.annotationsTree, [type]) subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable | Qt.ItemIsTristate) subsetItem.setCheckState( 0, self.gdsSelectionStates.get(key, Qt.Checked) ) subsetItem.key = key for subset in subsets: key = (gds["dataset_id"], type, subset) item = QTreeWidgetItem( subsetItem, [subset, subsetscount.get(subset, "")] ) item.setFlags(item.flags() | Qt.ItemIsUserCheckable) item.setCheckState( 0, self.gdsSelectionStates.get(key, Qt.Checked) ) item.key = key self._annotationsUpdating = False self.annotationsTree.expandAll() for i in range(self.annotationsTree.columnCount()): self.annotationsTree.resizeColumnToContents(i) def annotationSelectionChanged(self, item, column): if self._annotationsUpdating: return for i in range(self.annotationsTree.topLevelItemCount()): item = self.annotationsTree.topLevelItem(i) self.gdsSelectionStates[item.key] = item.checkState(0) for j in range(item.childCount()): child = item.child(j) self.gdsSelectionStates[child.key] = child.checkState(0) def filter(self): filter_string = unicode(self.filterLineEdit.text()) proxyModel = self.treeWidget.model() if proxyModel: strings = filter_string.lower().strip().split() proxyModel.setFilterFixedStrings(strings) self.updateInfo() def selectedSamples(self): """ Return the currently selected sample annotations. The return value is a list of selected (sample type, sample value) tuples. .. note:: if some Sample annotation type has no selected values. this method will return all values for it. """ samples = [] unused_types = [] used_types = [] for stype in childiter(self.annotationsTree.invisibleRootItem()): selected_values = [] all_values = [] for sval in childiter(stype): value = (str(stype.text(0)), str(sval.text(0))) if self.gdsSelectionStates.get(sval.key, True): selected_values.append(value) all_values.append(value) if selected_values: samples.extend(selected_values) used_types.append(str(stype.text(0))) else: # If no sample of sample type is selected we don't filter # on it. samples.extend(all_values) unused_types.append(str(stype.text(0))) return samples, used_types def commitIf(self): if self.autoCommit: self.commit() else: self.selectionChanged = True @Slot(int, int) def progressCompleted(self, value, total): if total > 0: self.progressBarSet(100. * value / total, processEvents=False) else: pass # TODO: report 'indeterminate progress' def commit(self): if self.currentGds: self.error(0) sample_type = None self.progressBarInit(processEvents=None) _, groups = self.selectedSamples() if len(groups) == 1 and self.outputRows: sample_type = groups[0] self.setEnabled(False) self.setBlocking(True) progress = methodinvoke(self, "progressCompleted", (int, int)) def get_data(gds_id, report_genes, transpose, sample_type, title): gds_ensure_downloaded(gds_id, progress) gds = geo.GDS(gds_id) data = gds.getdata( report_genes=report_genes, transpose=transpose, sample_type=sample_type ) data.name = title return data get_data = partial( get_data, self.currentGds["dataset_id"], report_genes=self.mergeSpots, transpose=self.outputRows, sample_type=sample_type, title=self.datasetName or self.currentGds["title"] ) self._datatask = Task(function=get_data) self._datatask.finished.connect(self._on_dataready) self._executor.submit(self._datatask) 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 splitterMoved(self, *args): self.splitterSettings = [bytes(sp.saveState()) for sp in self.splitters] def send_report(self): self.report_items("GEO Dataset", [("ID", self.currentGds['dataset_id']), ("Title", self.currentGds['title']), ("Organism", self.currentGds['sample_organism'])]) self.report_items("Data", [("Samples", self.currentGds['sample_count']), ("Features", self.currentGds['feature_count']), ("Genes", self.currentGds['gene_count'])]) self.report_name("Sample annotations") subsets = defaultdict(list) for subset in self.currentGds['subsets']: subsets[subset['type']].append((subset['description'], len(subset['sample_id']))) self.report_html += "<ul>" for type in subsets: self.report_html += "<b>" + type + ":</b></br>" for desc, count in subsets[type]: self.report_html += 9 * " " + "<b>{}:</b> {}</br>".format(desc, count) self.report_html += "</ul>" def onDeleteWidget(self): if self._inittask: self._inittask.future().cancel() self._inittask.finished.disconnect(self._initializemodel) if self._datatask: self._datatask.future().cancel() self._datatask.finished.disconnect(self._on_dataready) self._executor.shutdown(wait=False) super(OWGEODatasets, self).onDeleteWidget() def onNameEdited(self): if self.currentGds: gds_id = self.currentGds["dataset_id"] self.datasetNames[gds_id] = unicode(self.nameEdit.text()) self.commitIf()