class OWPIPAx(widget.OWWidget): name = "PIPAx" description = "Access data from PIPA RNA-Seq database." icon = "../widgets/icons/PIPA.svg" priority = 35 inputs = [] outputs = [("Data", Orange.data.Table)] username = settings.Setting("") password = settings.Setting("") log2 = settings.Setting(False) rtypei = settings.Setting(5) # hardcoded rpkm mapability polya excludeconstant = settings.Setting(False) joinreplicates = settings.Setting(False) #: The stored current selection (in experiments view) #: SelectionByKey | None currentSelection = settings.Setting(None) #: Stored selections (presets) #: list of SelectionByKey storedSelections = settings.Setting([]) #: Stored column sort keys (from Sort view) #: list of strings storedSortingOrder = settings.Setting( ["Strain", "Experiment", "Genotype", "Timepoint"]) experimentsHeaderState = settings.Setting( {name: False for _, name in HEADER[:ID_INDEX + 1]} ) def __init__(self, parent=None, signalManager=None, name="PIPAx"): super().__init__(parent) self.selectedExperiments = [] self.buffer = dicty.CacheSQLite(bufferfile) self.searchString = "" self.result_types = [] self.mappings = {} self.controlArea.setMaximumWidth(250) self.controlArea.setMinimumWidth(250) gui.button(self.controlArea, self, "Reload", callback=self.Reload) gui.button(self.controlArea, self, "Clear cache", callback=self.clear_cache) b = gui.widgetBox(self.controlArea, "Experiment Sets") self.selectionSetsWidget = SelectionSetsWidget(self) self.selectionSetsWidget.setSizePolicy( QSizePolicy.Preferred, QSizePolicy.Maximum) def store_selections(modified): if not modified: self.storedSelections = self.selectionSetsWidget.selections self.selectionSetsWidget.selectionModified.connect(store_selections) b.layout().addWidget(self.selectionSetsWidget) gui.separator(self.controlArea) b = gui.widgetBox(self.controlArea, "Sort output columns") self.columnsSortingWidget = SortedListWidget(self) self.columnsSortingWidget.setSizePolicy( QSizePolicy.Preferred, QSizePolicy.Maximum) def store_sort_order(): self.storedSortingOrder = self.columnsSortingWidget.sortingOrder self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order) b.layout().addWidget(self.columnsSortingWidget) sorting_model = QStringListModel(SORTING_MODEL_LIST) self.columnsSortingWidget.setModel(sorting_model) gui.separator(self.controlArea) box = gui.widgetBox(self.controlArea, 'Expression Type') self.expressionTypesCB = gui.comboBox( box, self, "rtypei", items=[], callback=self.UpdateResultsList) gui.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values") gui.checkBox(self.controlArea, self, "joinreplicates", "Average replicates (use median)") gui.checkBox(self.controlArea, self, "log2", "Logarithmic (base 2) transformation") self.commit_button = gui.button(self.controlArea, self, "&Commit", callback=self.Commit) self.commit_button.setDisabled(True) gui.rubber(self.controlArea) box = gui.widgetBox(self.controlArea, "Authentication") gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"searchString", "Search", callbackOnType=True, callback=self.SearchUpdate) self.headerLabels = [t[1] for t in HEADER] self.experimentsWidget = QTreeWidget() self.experimentsWidget.setHeaderLabels(self.headerLabels) self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection) self.experimentsWidget.setRootIsDecorated(False) self.experimentsWidget.setSortingEnabled(True) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.experimentsWidget, self.experimentsWidget ) self.experimentsWidget.header().installEventFilter(contextEventFilter) self.experimentsWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole)) self.experimentsWidget.setAlternatingRowColors(True) self.experimentsWidget.selectionModel().selectionChanged.connect( self.onSelectionChanged) self.selectionSetsWidget.setSelectionModel( self.experimentsWidget.selectionModel() ) self.mainArea.layout().addWidget(self.experimentsWidget) # Restore the selection states from the stored settings self.selectionSetsWidget.selections = self.storedSelections self.columnsSortingWidget.sortingOrder = self.storedSortingOrder self.restoreHeaderState() self.experimentsWidget.header().geometriesChanged.connect( self.saveHeaderState) self.dbc = None self.AuthSet() QTimer.singleShot(100, self.UpdateExperiments) def sizeHint(self): return QSize(800, 600) def AuthSet(self): if len(self.username): self.passf.setDisabled(False) else: self.passf.setDisabled(True) def AuthChanged(self): self.AuthSet() self.ConnectAndUpdate() def ConnectAndUpdate(self): self.Connect() self.UpdateExperiments(reload=True) def Connect(self): self.error(1) self.warning(1) def en(x): return x if len(x) else None self.dbc = dicty.PIPAx(cache=self.buffer, username=en(self.username), password=self.password) # check password if en(self.username) != None: try: self.dbc.mappings(reload=True) except dicty.AuthenticationError: self.error(1, "Wrong username or password") self.dbc = None except Exception as ex: print("Error when contacting the PIPA database", ex) sys.excepthook(*sys.exc_info()) try: # maybe cached? self.dbc.mappings() self.warning(1, "Can not access database - using cached data.") except Exception as ex: self.dbc = None self.error(1, "Can not access database.") def Reload(self): self.UpdateExperiments(reload=True) def clear_cache(self): self.buffer.clear() self.Reload() def rtype(self): """Return selected result template type """ if self.result_types: return self.result_types[self.rtypei][0] else: return "-1" def UpdateExperimentTypes(self): self.expressionTypesCB.clear() items = [desc for _, desc in self.result_types] self.expressionTypesCB.addItems(items) self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1)) def UpdateExperiments(self, reload=False): self.experimentsWidget.clear() self.items = [] self.progressBarInit() if not self.dbc: self.Connect() mappings = {} result_types = [] sucind = False # success indicator for database index try: mappings = self.dbc.mappings(reload=reload) result_types = self.dbc.result_types(reload=reload) sucind = True except Exception as ex: try: mappings = self.dbc.mappings() result_types = self.dbc.result_types() self.warning(0, "Can not access database - using cached data.") sucind = True except Exception as ex: self.error(0, "Can not access database.") if sucind: self.warning(0) self.error(0) self.mappings = mappings self.result_types = result_types self.UpdateExperimentTypes() self.UpdateResultsList(reload=reload) self.progressBarFinished() if self.currentSelection: self.currentSelection.select( self.experimentsWidget.selectionModel()) self.handle_commit_button() def UpdateResultsList(self, reload=False): results_list = {} try: results_list = self.dbc.results_list(self.rtype(), reload=reload) except Exception as ex: try: results_list = self.dbc.results_list(self.rtype()) except Exception as ex: self.error(0, "Can not access database.") self.results_list = results_list mappings_key_dict = dict(((m["data_id"], m["id"]), key) \ for key, m in self.mappings.items()) def mapping_unique_id(annot): """Map annotations dict from results_list to unique `mappings` ids. """ data_id, mappings_id = annot["data_id"], annot["mappings_id"] return mappings_key_dict[data_id, mappings_id] elements = [] # softly change the view so that the selection stays the same items_shown = {} for i, item in enumerate(self.items): c = str(item.text(10)) items_shown[c] = i items_to_show = dict((mapping_unique_id(annot), annot) for annot in self.results_list.values()) add_items = set(items_to_show) - set(items_shown) delete_items = set(items_shown) - set(items_to_show) i = 0 while i < self.experimentsWidget.topLevelItemCount(): it = self.experimentsWidget.topLevelItem(i) if str(it.text(10)) in delete_items: self.experimentsWidget.takeTopLevelItem(i) else: i += 1 delete_ind = set([items_shown[i] for i in delete_items]) self.items = [it for i, it in enumerate(self.items) if i not in delete_ind] for r_annot in [items_to_show[i] for i in add_items]: d = defaultdict(lambda: "?", r_annot) row_items = [""] + [d.get(key, "?") for key, _ in HEADER[1:]] try: time_dict = literal_eval(row_items[DATE_INDEX]) date_rna = date(time_dict["fullYearUTC"], time_dict["monthUTC"] + 1, # Why is month 0 based? time_dict["dateUTC"]) row_items[DATE_INDEX] = date_rna.strftime("%x") except Exception: row_items[DATE_INDEX] = '' row_items[ID_INDEX] = mapping_unique_id(r_annot) elements.append(row_items) ci = MyTreeWidgetItem(self.experimentsWidget, row_items) self.items.append(ci) for i in range(len(self.headerLabels)): self.experimentsWidget.resizeColumnToContents(i) # which is the ok buffer version # FIXME: what attribute to use for version? self.wantbufver = \ lambda x, ad=self.results_list: \ defaultdict(lambda: "?", ad[x])["date"] self.wantbufver = lambda x: "0" self.UpdateCached() def UpdateCached(self): if self.wantbufver and self.dbc: fn = self.dbc.download_key_function() result_id_key = dict(((m["data_id"], m["mappings_id"]), key) \ for key, m in self.results_list.items()) for item in self.items: c = str(item.text(10)) mapping = self.mappings[c] data_id, mappings_id = mapping["data_id"], mapping["id"] r_id = result_id_key[data_id, mappings_id] # Get the buffered version buffered = self.dbc.inBuffer(fn(r_id)) value = " " if buffered == self.wantbufver(r_id) else "" item.setData(0, Qt.DisplayRole, value) def SearchUpdate(self, string=""): for item in self.items: item.setHidden(not all(s in item \ for s in self.searchString.split()) ) 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 onSelectionChanged(self, selected, deselected): self.handle_commit_button() def handle_commit_button(self): self.currentSelection = \ SelectionByKey(self.experimentsWidget.selectionModel().selection(), key=(1, 2, 3, 10)) self.commit_button.setDisabled(not len(self.currentSelection)) def saveHeaderState(self): hview = self.experimentsWidget.header() for i, label in enumerate(self.headerLabels): self.experimentsHeaderState[label] = hview.isSectionHidden(i) def restoreHeaderState(self): hview = self.experimentsWidget.header() state = self.experimentsHeaderState for i, label in enumerate(self.headerLabels): hview.setSectionHidden(i, state.get(label, True)) self.experimentsWidget.resizeColumnToContents(i)
class OWDatabasesUpdate(OWWidget): name = "Databases Update" description = "Update local systems biology databases." icon = "../widgets/icons/OWDatabasesUpdate.svg" priority = 1 inputs = [] outputs = [] want_main_area = False def __init__(self, parent=None, signalManager=None, name="Databases update"): OWWidget.__init__(self, parent, signalManager, name, wantMainArea=False) self.searchString = "" fbox = gui.widgetBox(self.controlArea, "Filter") self.completer = TokenListCompleter(self, caseSensitivity=Qt.CaseInsensitive) self.lineEditFilter = QLineEdit(textChanged=self.search_update) self.lineEditFilter.setCompleter(self.completer) fbox.layout().addWidget(self.lineEditFilter) box = gui.widgetBox(self.controlArea, "Files") self.filesView = QTreeWidget(self) self.filesView.setHeaderLabels(header_labels) self.filesView.setRootIsDecorated(False) self.filesView.setUniformRowHeights(True) self.filesView.setSelectionMode(QAbstractItemView.NoSelection) self.filesView.setSortingEnabled(True) self.filesView.sortItems(header.Title, Qt.AscendingOrder) self.filesView.setItemDelegateForColumn( 0, UpdateOptionsItemDelegate(self.filesView)) self.filesView.model().layoutChanged.connect(self.search_update) box.layout().addWidget(self.filesView) layout = QHBoxLayout() gui.widgetBox(self.controlArea, margin=0, orientation=layout) self.updateButton = gui.button( box, self, "Update all", callback=self.update_all, tooltip="Update all updatable files", ) self.downloadButton = gui.button( box, self, "Download all", callback=self.download_filtered, tooltip="Download all filtered files shown") self.cancelButton = gui.button( box, self, "Cancel", callback=self.cancel_active_threads, tooltip="Cancel scheduled downloads/updates.") self.addButton = gui.button(box, self, "Add ...", callback=self.__handle_dialog, tooltip="Add files for personal use.") layout.addWidget(self.updateButton) layout.addWidget(self.downloadButton) layout.addWidget(self.cancelButton) layout.addStretch() layout.addWidget(self.addButton) # Enable retryButton once connection is established # self.retryButton = gui.button( # box, self, "Reconnect", callback=self.initialize_files_view # ) # self.retryButton.hide() self.resize(800, 600) self.update_items = [] self._dialog = None self.progress_bar = None # threads self.threadpool = QThreadPool(self) #self.threadpool.setMaxThreadCount(1) self.workers = list() self.initialize_files_view() def __handle_dialog(self): if not self._dialog: self._dialog = FileUploadHelper(self) self._dialog.show() def __progress_advance(self): # GUI should be updated in main thread. That's why we are calling advance method here if self.progress_bar: self.progress_bar.advance() def handle_worker_exception(self, ex): self.progress_bar.finish() self.setStatusMessage('') if isinstance(ex, ConnectionError): # TODO: set warning messages pass print(ex) def initialize_files_view(self): # self.retryButton.hide() # clear view self.filesView.clear() # init progress bar self.progress_bar = gui.ProgressBar(self, iterations=3) # status message self.setStatusMessage('initializing') worker = Worker(evaluate_files_state, progress_callback=True) worker.signals.progress.connect(self.__progress_advance) worker.signals.result.connect(self.set_files_list) worker.signals.error.connect(self.handle_worker_exception) # move download process to worker thread self.threadpool.start(worker) self.setEnabled(False) def __create_action_button(self, fs, retry=None): if not fs.state not in [OUTDATED, USER_FILE] or not retry: self.filesView.setItemWidget(fs.tree_item, header.Update, None) button = QToolButton(None) if not retry: if fs.state == OUTDATED: button.setText('Update') button.clicked.connect( partial(self.submit_download_task, fs.domain, fs.filename, True)) elif fs.state == USER_FILE: if not fs.info_server: button.setText('Remove') button.clicked.connect( partial(self.submit_remove_task, fs.domain, fs.filename)) else: button.setText('Use server version') button.clicked.connect( partial(self.submit_download_task, fs.domain, fs.filename, True)) else: button.setText('Retry') button.clicked.connect( partial(self.submit_download_task, fs.domain, fs.filename, True)) button.setMaximumWidth(120) button.setMaximumHeight(20) button.setMinimumHeight(20) if sys.platform == "darwin": button.setAttribute(Qt.WA_MacSmallSize) self.filesView.setItemWidget(fs.tree_item, header.Update, button) def set_files_list(self, result): """ Set the files to show. """ assert threading.current_thread() == threading.main_thread() self.progress_bar.finish() self.setStatusMessage('') self.setEnabled(True) self.update_items = result all_tags = set() for fs in self.update_items: fs.tree_item = FileStateItem(fs) fs.download_option = DownloadOption(state=fs.state) fs.download_option.download_clicked.connect( partial(self.submit_download_task, fs.domain, fs.filename)) fs.download_option.remove_clicked.connect( partial(self.submit_remove_task, fs.domain, fs.filename)) # add widget items to the QTreeWidget self.filesView.addTopLevelItems( [fs.tree_item for fs in self.update_items]) # add action widgets to tree items for fs in self.update_items: self.filesView.setItemWidget(fs.tree_item, header.Download, fs.download_option) if fs.state in [USER_FILE, OUTDATED]: self.__create_action_button(fs) all_tags.update(fs.tags) self.filesView.setColumnWidth( header.Download, self.filesView.sizeHintForColumn(header.Download)) for column in range(1, len(header_labels)): self.filesView.resizeColumnToContents(column) hints = [hint for hint in sorted(all_tags) if not hint.startswith("#")] self.completer.setTokenList(hints) self.search_update() self.toggle_action_buttons() self.cancelButton.setEnabled(False) def toggle_action_buttons(self): selected_items = [ fs for fs in self.update_items if not fs.tree_item.isHidden() ] def button_check(sel_items, state, button): for item in sel_items: if item.state != state: button.setEnabled(False) else: button.setEnabled(True) break button_check(selected_items, OUTDATED, self.updateButton) button_check(selected_items, AVAILABLE, self.downloadButton) def search_update(self, searchString=None): strings = str(self.lineEditFilter.text()).split() for fs in self.update_items: hide = not all(UpdateItem_match(fs, string) for string in strings) fs.tree_item.setHidden(hide) self.toggle_action_buttons() def update_all(self): for fs in self.update_items: if fs.state == OUTDATED and not fs.tree_item.isHidden(): self.submit_download_task(fs.domain, fs.filename) def download_filtered(self): for fs in self.update_items: if not fs.tree_item.isHidden() and fs.state in [ AVAILABLE, OUTDATED ]: self.submit_download_task(fs.domain, fs.filename, start=False) self.run_download_tasks() def submit_download_task(self, domain, filename, start=True): """ Submit the (domain, filename) to be downloaded/updated. """ # get selected tree item index = self.tree_item_index(domain, filename) fs = self.update_items[index] worker = Worker(download_server_file, fs, index, progress_callback=True) worker.signals.progress.connect(self.__progress_advance) worker.signals.result.connect(self.on_download_finished) worker.signals.error.connect(self.on_download_exception) self.workers.append(worker) if start: self.run_download_tasks() def run_download_tasks(self): self.cancelButton.setEnabled(True) # init progress bar self.progress_bar = gui.ProgressBar(self, iterations=len(self.workers) * 100) # status message self.setStatusMessage('downloading') # move workers to threadpool [self.threadpool.start(worker) for worker in self.workers] self.filesView.setDisabled(True) # reset list of workers self.workers = list() def on_download_exception(self, ex): assert threading.current_thread() == threading.main_thread() self.progress_bar.finish() self.setStatusMessage('') print(ex) if isinstance(ex, ValueError): fs, index = ex.args # restore state and retry fs.refresh_state() fs.tree_item.update_data(fs) fs.download_option.state = fs.state self.__create_action_button(fs, retry=True) def on_download_finished(self, result): assert threading.current_thread() == threading.main_thread() # We check if all workers have completed. If not, continue if self.progress_bar.count == 100 or self.threadpool.activeThreadCount( ) == 0: self.filesView.setDisabled(False) self.progress_bar.finish() self.setStatusMessage('') fs, index = result # re-evaluate File State info = serverfiles.info(fs.domain, fs.filename) fs.refresh_state(info_local=info, info_server=info) # reinitialize treeWidgetItem fs.tree_item.update_data(fs) # reinitialize OptionWidget fs.download_option.state = fs.state self.filesView.setItemWidget(fs.tree_item, header.Update, None) self.toggle_action_buttons() for column in range(1, len(header_labels)): self.filesView.resizeColumnToContents(column) def submit_remove_task(self, domain, filename): serverfiles.LOCALFILES.remove(domain, filename) index = self.tree_item_index(domain, filename) fs = self.update_items[index] if fs.state == USER_FILE: self.filesView.takeTopLevelItem( self.filesView.indexOfTopLevelItem(fs.tree_item)) self.update_items.remove(fs) # self.filesView.removeItemWidget(index) else: # refresh item state fs.info_local = None fs.refresh_state() # reinitialize treeWidgetItem fs.tree_item.update_data(fs) # reinitialize OptionWidget fs.download_option.state = fs.state self.toggle_action_buttons() def cancel_active_threads(self): """ Cancel all pending update/download tasks (that have not yet started). """ if self.threadpool: self.threadpool.clear() def tree_item_index(self, domain, filename): for i, fs in enumerate(self.update_items): if fs.domain == domain and fs.filename == filename: return i raise ValueError("%r, %r not in update list" % (domain, filename)) def onDeleteWidget(self): self.cancel_active_threads() OWWidget.onDeleteWidget(self)
class OWGenExpress(widget.OWWidget): name = "GenExpress" description = "Expression data from GenExpress." icon = "../widgets/icons/GenCloud.svg" priority = 36 inputs = [] outputs = [("Data", Orange.data.Table)] username = settings.Setting("anonymous") password = settings.Setting("") log2 = settings.Setting(False) transpose = settings.Setting(False) rtypei = settings.Setting(0) projecti = settings.Setting(0) serveri = settings.Setting(0) exnamei = settings.Setting(6) excludeconstant = settings.Setting(False) joinreplicates = settings.Setting(False) currentSelection = settings.Setting(None) experimentsHeaderState = settings.Setting({ name: False for _, name in HEADER[:ID_INDEX + 1]} ) storedSortOrder = settings.Setting([]) storedSelections = settings.Setting([]) def __init__(self, parent=None): super().__init__(parent) self.servers = [ ('https://dictyexpress.research.bcm.edu/', 'dictyExpress'), ('https://cloud.genialis.com/', 'Genialis'), ] self.selectedExperiments = [] self.buffer = dicty.CacheSQLite(bufferfile) self.searchString = "" self.items = [] self.result_types = [] self.controlArea.setMaximumWidth(250) self.controlArea.setMinimumWidth(250) box = gui.widgetBox(self.controlArea, 'Project') self.projectCB = gui.comboBox( box, self, "projecti", items=[], callback=self.ProjectChosen) self.projects = [] b = gui.widgetBox(self.controlArea, "Selection bookmarks") self.selectionSetsWidget = SelectionSetsWidget(self) self.selectionSetsWidget.setSizePolicy( QSizePolicy.Preferred, QSizePolicy.Maximum) def store_selections(modified): if not modified: self.storedSelections = self.selectionSetsWidget.selections self.selectionSetsWidget.selectionModified.connect(store_selections) b.layout().addWidget(self.selectionSetsWidget) gui.separator(self.controlArea) b = gui.widgetBox(self.controlArea, "Sort output columns") self.columnsSortingWidget = SortedListWidget(self) self.columnsSortingWidget.setSizePolicy( QSizePolicy.Preferred, QSizePolicy.Maximum) box = gui.widgetBox(self.controlArea, 'Experiment name') self.experimentNameCB = gui.comboBox( box, self, "exnamei", items=SORTING_MODEL_LIST) b.layout().addWidget(self.columnsSortingWidget) sorting_model = QStringListModel(SORTING_MODEL_LIST) self.columnsSortingWidget.setModel(sorting_model) self.columnsSortingWidget.sortingOrder = self.storedSortOrder def store_sort_order(): self.storedSortOrder = self.columnsSortingWidget.sortingOrder self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order) gui.separator(self.controlArea) box = gui.widgetBox(self.controlArea, 'Expression Type') self.expressionTypesCB = gui.comboBox( box, self, "rtypei", items=[], callback=self.UpdateResultsList) gui.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values") gui.checkBox(self.controlArea, self, "joinreplicates", "Average replicates (use median)") gui.checkBox(self.controlArea, self, "log2", "Logarithmic (base 2) transformation") gui.checkBox(self.controlArea, self, "transpose", "Genes as columns") self.commit_button = gui.button(self.controlArea, self, "&Commit", callback=self.Commit) self.commit_button.setDisabled(True) gui.rubber(self.controlArea) box = gui.widgetBox(self.controlArea, 'Server') gui.comboBox(box, self, "serveri", items=[title for url, title in self.servers], callback=self.ServerChosen) gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"Clear cache", callback=self.clear_cache) gui.lineEdit(self.mainArea, self, "searchString", "Search", callbackOnType=True, callback=self.SearchUpdate) self.headerLabels = [t[1] for t in HEADER] self.experimentsWidget = QTreeWidget() self.experimentsWidget.setHeaderLabels(self.headerLabels) self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection) self.experimentsWidget.setRootIsDecorated(False) self.experimentsWidget.setSortingEnabled(True) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.experimentsWidget, self.experimentsWidget) self.experimentsWidget.header().installEventFilter(contextEventFilter) self.experimentsWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole)) self.experimentsWidget.setAlternatingRowColors(True) self.experimentsWidget.selectionModel().selectionChanged.connect( self.onSelectionChanged) self.selectionSetsWidget.setSelectionModel( self.experimentsWidget.selectionModel()) self.selectionSetsWidget.setSelections(self.storedSelections) self.mainArea.layout().addWidget(self.experimentsWidget) self.restoreHeaderState() self.experimentsWidget.header().geometriesChanged.connect( self.saveHeaderState) self.dbc = None self.AuthSet() QTimer.singleShot(100, self.ConnectAndUpdate) def sizeHint(self): return QSize(800, 600) def AuthSet(self): if len(self.username): self.passf.setDisabled(False) else: self.passf.setDisabled(True) def AuthChanged(self): self.AuthSet() self.ConnectAndUpdate() def ConnectAndUpdate(self): self.Connect() if self.dbc: def get_data_count(project_id): # XXX: is there a better way? # Note: limit 0 would return all objects return self.dbc.gen.api.data.get(case_ids__contains=project_id, type__startswith='data:expression:', limit=1)['meta']['total_count'] self.projects = sorted([p for p in self.dbc.projects().items() if get_data_count(p[0]) > 0], key=lambda x: x[1]) self.UpdateProjects() self.ProjectChosen() self.UpdateExperimentTypes() def Connect(self): self.error(1) self.warning(1) username = '******' password = '******' url = self.servers[self.serveri][0] if self.username: username = self.username password = self.password if username.lower() in ['*****@*****.**', 'anonymous']: username = '******' password = '******' self.dbc = None self.projects = [] self.result_types = [] try: self.dbc = Genesis( address=url, username=username, password=password, cache=self.buffer) except requests.exceptions.ConnectionError: self.dbc = Genesis( address=url, username=username, password=password, connect=False, cache=self.buffer) self.warning(1, "Could not connect to server, working from cache.") except Exception: self.error(1, "Wrong username or password.") self.UpdateProjects() self.UpdateExperimentTypes() # clear lists def Reload(self): self.UpdateExperiments(reload=True) def clear_cache(self): self.buffer.clear() self.Reload() def rtype(self): """Return selected result template type """ if self.result_types: return self.result_types[self.rtypei] else: return None def UpdateExperimentTypes(self): self.expressionTypesCB.clear() items = [self.result_types_labels[desc] for desc in self.result_types] self.expressionTypesCB.addItems(items) #do not update anything if the list is empty if len(self.result_types): self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1)) def UpdateProjects(self): self.projectCB.clear() items = [desc for pid, desc in self.projects] self.projectCB.addItems(items) #do not update anything if the list if empty if len(self.projects) > 0: self.projecti = max(0, min(self.projecti, len(self.projects) - 1)) def UpdateExperiments(self, reload=False): self.experimentsWidget.clear() if not self.dbc or not self.dbc.projectid: # the connection did not succeed return self.items = [] self.progressBarInit() result_types = [] result_types_labels = [] sucind = False # success indicator for database index try: result_types, result_types_labels = self.dbc.result_types(reload=reload) sucind = True except Exception: try: result_types, result_types_labels = self.dbc.result_types() self.warning(0, "Can not access database - using cached data.") sucind = True except Exception: self.error(0, "Can not access database.") if sucind: self.warning(0) self.error(0) self.result_types = result_types self.result_types_labels = result_types_labels self.UpdateExperimentTypes() self.UpdateResultsList(reload=reload) self.progressBarFinished() if self.currentSelection: self.currentSelection.select(self.experimentsWidget.selectionModel()) self.handle_commit_button() def ProjectChosen(self, reload=False): if self.projects: self.dbc.projectid = self.projects[self.projecti][0] else: self.dbc.projectid = None self.UpdateExperiments(reload=reload) def ServerChosen(self): self.ConnectAndUpdate() def UpdateResultsList(self, reload=False): results_list = self.dbc.results_list(self.rtype(), reload=reload) try: results_list = self.dbc.results_list(self.rtype(), reload=reload) except Exception: try: results_list = self.dbc.results_list(self.rtype()) except Exception: self.error(0, "Can not access database.") self.results_list = results_list #softly change the view so that the selection stays the same items_shown = {} for i, item in enumerate(self.items): c = str(item.text(ID_INDEX)) items_shown[c] = i items_to_show = set(id_ for id_ in self.results_list) add_items = set(items_to_show) - set(items_shown) delete_items = set(items_shown) - set(items_to_show) i = 0 while i < self.experimentsWidget.topLevelItemCount(): it = self.experimentsWidget.topLevelItem(i) if str(it.text(ID_INDEX)) in delete_items: self.experimentsWidget.takeTopLevelItem(i) else: i += 1 delete_ind = set([items_shown[i] for i in delete_items]) self.items = [it for i, it in enumerate(self.items) if i not in delete_ind] for r_annot in add_items: d = defaultdict(lambda: "?", self.results_list[r_annot]) row_items = [""] + [to_text(d.get(key, "?")) for key, _ in HEADER[1:]] row_items[ID_INDEX] = r_annot ci = MyTreeWidgetItem(self.experimentsWidget, row_items) self.items.append(ci) for i in range(len(self.headerLabels)): self.experimentsWidget.resizeColumnToContents(i) self.wantbufver = lambda x: self.results_list[x]["date_modified"] self.UpdateCached() def UpdateCached(self): if self.wantbufver and self.dbc: for item in self.items: id = str(item.text(ID_INDEX)) version = self.dbc._in_buffer(id + "|||" + self.rtype()) value = " " if version == self.wantbufver(id) else "" item.setData(0, Qt.DisplayRole, value) def SearchUpdate(self, string=""): for item in self.items: item.setHidden( not all(s in item for s in self.searchString.split())) 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 onSelectionChanged(self, selected, deselected): self.handle_commit_button() def handle_commit_button(self): self.currentSelection = \ SelectionByKey(self.experimentsWidget.selectionModel().selection(), key=(ID_INDEX,)) self.commit_button.setDisabled(not len(self.currentSelection)) def saveHeaderState(self): hview = self.experimentsWidget.header() for i, label in enumerate(self.headerLabels): self.experimentsHeaderState[label] = hview.isSectionHidden(i) def restoreHeaderState(self): hview = self.experimentsWidget.header() state = self.experimentsHeaderState for i, label in enumerate(self.headerLabels): hview.setSectionHidden(i, state.get(label, True)) self.experimentsWidget.resizeColumnToContents(i)
class OWGenExpress(widget.OWWidget): name = "GenExpress" description = "Expression data from GenExpress." icon = "../widgets/icons/GenCloud.svg" priority = 36 inputs = [] outputs = [("Data", Orange.data.Table)] username = settings.Setting("anonymous") password = settings.Setting("") log2 = settings.Setting(False) transpose = settings.Setting(False) rtypei = settings.Setting(0) projecti = settings.Setting(0) serveri = settings.Setting(0) exnamei = settings.Setting(6) excludeconstant = settings.Setting(False) joinreplicates = settings.Setting(False) currentSelection = settings.Setting(None) experimentsHeaderState = settings.Setting( {name: False for _, name in HEADER[:ID_INDEX + 1]}) storedSortOrder = settings.Setting([]) storedSelections = settings.Setting([]) def __init__(self, parent=None): super().__init__(parent) self.servers = [ ('https://dictyexpress.research.bcm.edu/', 'dictyExpress'), ('https://cloud.genialis.com/', 'Genialis'), ] self.selectedExperiments = [] self.buffer = dicty.CacheSQLite(bufferfile) self.searchString = "" self.items = [] self.result_types = [] self.controlArea.setMaximumWidth(250) self.controlArea.setMinimumWidth(250) box = gui.widgetBox(self.controlArea, 'Project') self.projectCB = gui.comboBox(box, self, "projecti", items=[], callback=self.ProjectChosen) self.projects = [] b = gui.widgetBox(self.controlArea, "Selection bookmarks") self.selectionSetsWidget = SelectionSetsWidget(self) self.selectionSetsWidget.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Maximum) def store_selections(modified): if not modified: self.storedSelections = self.selectionSetsWidget.selections self.selectionSetsWidget.selectionModified.connect(store_selections) b.layout().addWidget(self.selectionSetsWidget) gui.separator(self.controlArea) b = gui.widgetBox(self.controlArea, "Sort output columns") self.columnsSortingWidget = SortedListWidget(self) self.columnsSortingWidget.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Maximum) box = gui.widgetBox(self.controlArea, 'Experiment name') self.experimentNameCB = gui.comboBox(box, self, "exnamei", items=SORTING_MODEL_LIST) b.layout().addWidget(self.columnsSortingWidget) sorting_model = QStringListModel(SORTING_MODEL_LIST) self.columnsSortingWidget.setModel(sorting_model) self.columnsSortingWidget.sortingOrder = self.storedSortOrder def store_sort_order(): self.storedSortOrder = self.columnsSortingWidget.sortingOrder self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order) gui.separator(self.controlArea) box = gui.widgetBox(self.controlArea, 'Expression Type') self.expressionTypesCB = gui.comboBox(box, self, "rtypei", items=[], callback=self.UpdateResultsList) gui.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values") gui.checkBox(self.controlArea, self, "joinreplicates", "Average replicates (use median)") gui.checkBox(self.controlArea, self, "log2", "Logarithmic (base 2) transformation") gui.checkBox(self.controlArea, self, "transpose", "Genes as columns") self.commit_button = gui.button(self.controlArea, self, "&Commit", callback=self.Commit) self.commit_button.setDisabled(True) gui.rubber(self.controlArea) box = gui.widgetBox(self.controlArea, 'Server') gui.comboBox(box, self, "serveri", items=[title for url, title in self.servers], callback=self.ServerChosen) gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"Clear cache", callback=self.clear_cache) gui.lineEdit(self.mainArea, self, "searchString", "Search", callbackOnType=True, callback=self.SearchUpdate) self.headerLabels = [t[1] for t in HEADER] self.experimentsWidget = QTreeWidget() self.experimentsWidget.setHeaderLabels(self.headerLabels) self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection) self.experimentsWidget.setRootIsDecorated(False) self.experimentsWidget.setSortingEnabled(True) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.experimentsWidget, self.experimentsWidget) self.experimentsWidget.header().installEventFilter(contextEventFilter) self.experimentsWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole)) self.experimentsWidget.setAlternatingRowColors(True) self.experimentsWidget.selectionModel().selectionChanged.connect( self.onSelectionChanged) self.selectionSetsWidget.setSelectionModel( self.experimentsWidget.selectionModel()) self.selectionSetsWidget.setSelections(self.storedSelections) self.mainArea.layout().addWidget(self.experimentsWidget) self.restoreHeaderState() self.experimentsWidget.header().geometriesChanged.connect( self.saveHeaderState) self.dbc = None self.AuthSet() QTimer.singleShot(100, self.ConnectAndUpdate) def sizeHint(self): return QSize(800, 600) def AuthSet(self): if len(self.username): self.passf.setDisabled(False) else: self.passf.setDisabled(True) def AuthChanged(self): self.AuthSet() self.ConnectAndUpdate() def ConnectAndUpdate(self): self.Connect() if self.dbc: def get_data_count(project_id): # XXX: is there a better way? # Note: limit 0 would return all objects return self.dbc.gen.api.data.get( case_ids__contains=project_id, type__startswith='data:expression:', limit=1)['meta']['total_count'] self.projects = sorted([ p for p in self.dbc.projects().items() if get_data_count(p[0]) > 0 ], key=lambda x: x[1]) self.UpdateProjects() self.ProjectChosen() self.UpdateExperimentTypes() def Connect(self): self.error(1) self.warning(1) username = '******' password = '******' url = self.servers[self.serveri][0] if self.username: username = self.username password = self.password if username.lower() in ['*****@*****.**', 'anonymous']: username = '******' password = '******' self.dbc = None self.projects = [] self.result_types = [] try: self.dbc = Genesis(address=url, username=username, password=password, cache=self.buffer) except requests.exceptions.ConnectionError: self.dbc = Genesis(address=url, username=username, password=password, connect=False, cache=self.buffer) self.warning(1, "Could not connect to server, working from cache.") except Exception: self.error(1, "Wrong username or password.") self.UpdateProjects() self.UpdateExperimentTypes() # clear lists def Reload(self): self.UpdateExperiments(reload=True) def clear_cache(self): self.buffer.clear() self.Reload() def rtype(self): """Return selected result template type """ if self.result_types: return self.result_types[self.rtypei] else: return None def UpdateExperimentTypes(self): self.expressionTypesCB.clear() items = [self.result_types_labels[desc] for desc in self.result_types] self.expressionTypesCB.addItems(items) #do not update anything if the list is empty if len(self.result_types): self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1)) def UpdateProjects(self): self.projectCB.clear() items = [desc for pid, desc in self.projects] self.projectCB.addItems(items) #do not update anything if the list if empty if len(self.projects) > 0: self.projecti = max(0, min(self.projecti, len(self.projects) - 1)) def UpdateExperiments(self, reload=False): self.experimentsWidget.clear() if not self.dbc or not self.dbc.projectid: # the connection did not succeed return self.items = [] self.progressBarInit() result_types = [] result_types_labels = [] sucind = False # success indicator for database index try: result_types, result_types_labels = self.dbc.result_types( reload=reload) sucind = True except Exception: try: result_types, result_types_labels = self.dbc.result_types() self.warning(0, "Can not access database - using cached data.") sucind = True except Exception: self.error(0, "Can not access database.") if sucind: self.warning(0) self.error(0) self.result_types = result_types self.result_types_labels = result_types_labels self.UpdateExperimentTypes() self.UpdateResultsList(reload=reload) self.progressBarFinished() if self.currentSelection: self.currentSelection.select( self.experimentsWidget.selectionModel()) self.handle_commit_button() def ProjectChosen(self, reload=False): if self.projects: self.dbc.projectid = self.projects[self.projecti][0] else: self.dbc.projectid = None self.UpdateExperiments(reload=reload) def ServerChosen(self): self.ConnectAndUpdate() def UpdateResultsList(self, reload=False): results_list = self.dbc.results_list(self.rtype(), reload=reload) try: results_list = self.dbc.results_list(self.rtype(), reload=reload) except Exception: try: results_list = self.dbc.results_list(self.rtype()) except Exception: self.error(0, "Can not access database.") self.results_list = results_list #softly change the view so that the selection stays the same items_shown = {} for i, item in enumerate(self.items): c = str(item.text(ID_INDEX)) items_shown[c] = i items_to_show = set(id_ for id_ in self.results_list) add_items = set(items_to_show) - set(items_shown) delete_items = set(items_shown) - set(items_to_show) i = 0 while i < self.experimentsWidget.topLevelItemCount(): it = self.experimentsWidget.topLevelItem(i) if str(it.text(ID_INDEX)) in delete_items: self.experimentsWidget.takeTopLevelItem(i) else: i += 1 delete_ind = set([items_shown[i] for i in delete_items]) self.items = [ it for i, it in enumerate(self.items) if i not in delete_ind ] for r_annot in add_items: d = defaultdict(lambda: "?", self.results_list[r_annot]) row_items = [""] + [ to_text(d.get(key, "?")) for key, _ in HEADER[1:] ] row_items[ID_INDEX] = r_annot ci = MyTreeWidgetItem(self.experimentsWidget, row_items) self.items.append(ci) for i in range(len(self.headerLabels)): self.experimentsWidget.resizeColumnToContents(i) self.wantbufver = lambda x: self.results_list[x]["date_modified"] self.UpdateCached() def UpdateCached(self): if self.wantbufver and self.dbc: for item in self.items: id = str(item.text(ID_INDEX)) version = self.dbc._in_buffer(id + "|||" + self.rtype()) value = " " if version == self.wantbufver(id) else "" item.setData(0, Qt.DisplayRole, value) def SearchUpdate(self, string=""): for item in self.items: item.setHidden(not all(s in item for s in self.searchString.split())) 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 onSelectionChanged(self, selected, deselected): self.handle_commit_button() def handle_commit_button(self): self.currentSelection = \ SelectionByKey(self.experimentsWidget.selectionModel().selection(), key=(ID_INDEX,)) self.commit_button.setDisabled(not len(self.currentSelection)) def saveHeaderState(self): hview = self.experimentsWidget.header() for i, label in enumerate(self.headerLabels): self.experimentsHeaderState[label] = hview.isSectionHidden(i) def restoreHeaderState(self): hview = self.experimentsWidget.header() state = self.experimentsHeaderState for i, label in enumerate(self.headerLabels): hview.setSectionHidden(i, state.get(label, True)) self.experimentsWidget.resizeColumnToContents(i)
class OWPIPAx(widget.OWWidget): name = "PIPAx" description = "Access data from PIPA RNA-Seq database." icon = "../widgets/icons/PIPA.svg" priority = 35 inputs = [] outputs = [("Data", Orange.data.Table)] username = settings.Setting("") password = settings.Setting("") log2 = settings.Setting(False) rtypei = settings.Setting(5) # hardcoded rpkm mapability polya excludeconstant = settings.Setting(False) joinreplicates = settings.Setting(False) #: The stored current selection (in experiments view) #: SelectionByKey | None currentSelection = settings.Setting(None) #: Stored selections (presets) #: list of SelectionByKey storedSelections = settings.Setting([]) #: Stored column sort keys (from Sort view) #: list of strings storedSortingOrder = settings.Setting( ["Strain", "Experiment", "Genotype", "Timepoint"]) experimentsHeaderState = settings.Setting( {name: False for _, name in HEADER[:ID_INDEX + 1]}) def __init__(self, parent=None, signalManager=None, name="PIPAx"): super().__init__(parent) self.selectedExperiments = [] self.buffer = dicty.CacheSQLite(bufferfile) self.searchString = "" self.result_types = [] self.mappings = {} self.controlArea.setMaximumWidth(250) self.controlArea.setMinimumWidth(250) gui.button(self.controlArea, self, "Reload", callback=self.Reload) gui.button(self.controlArea, self, "Clear cache", callback=self.clear_cache) b = gui.widgetBox(self.controlArea, "Experiment Sets") self.selectionSetsWidget = SelectionSetsWidget(self) self.selectionSetsWidget.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Maximum) def store_selections(modified): if not modified: self.storedSelections = self.selectionSetsWidget.selections self.selectionSetsWidget.selectionModified.connect(store_selections) b.layout().addWidget(self.selectionSetsWidget) gui.separator(self.controlArea) b = gui.widgetBox(self.controlArea, "Sort output columns") self.columnsSortingWidget = SortedListWidget(self) self.columnsSortingWidget.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Maximum) def store_sort_order(): self.storedSortingOrder = self.columnsSortingWidget.sortingOrder self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order) b.layout().addWidget(self.columnsSortingWidget) sorting_model = QStringListModel(SORTING_MODEL_LIST) self.columnsSortingWidget.setModel(sorting_model) gui.separator(self.controlArea) box = gui.widgetBox(self.controlArea, 'Expression Type') self.expressionTypesCB = gui.comboBox(box, self, "rtypei", items=[], callback=self.UpdateResultsList) gui.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values") gui.checkBox(self.controlArea, self, "joinreplicates", "Average replicates (use median)") gui.checkBox(self.controlArea, self, "log2", "Logarithmic (base 2) transformation") self.commit_button = gui.button(self.controlArea, self, "&Commit", callback=self.Commit) self.commit_button.setDisabled(True) gui.rubber(self.controlArea) box = gui.widgetBox(self.controlArea, "Authentication") gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"searchString", "Search", callbackOnType=True, callback=self.SearchUpdate) self.headerLabels = [t[1] for t in HEADER] self.experimentsWidget = QTreeWidget() self.experimentsWidget.setHeaderLabels(self.headerLabels) self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection) self.experimentsWidget.setRootIsDecorated(False) self.experimentsWidget.setSortingEnabled(True) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.experimentsWidget, self.experimentsWidget) self.experimentsWidget.header().installEventFilter(contextEventFilter) self.experimentsWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole)) self.experimentsWidget.setAlternatingRowColors(True) self.experimentsWidget.selectionModel().selectionChanged.connect( self.onSelectionChanged) self.selectionSetsWidget.setSelectionModel( self.experimentsWidget.selectionModel()) self.mainArea.layout().addWidget(self.experimentsWidget) # Restore the selection states from the stored settings self.selectionSetsWidget.selections = self.storedSelections self.columnsSortingWidget.sortingOrder = self.storedSortingOrder self.restoreHeaderState() self.experimentsWidget.header().geometriesChanged.connect( self.saveHeaderState) self.dbc = None self.AuthSet() QTimer.singleShot(100, self.UpdateExperiments) def sizeHint(self): return QSize(800, 600) def AuthSet(self): if len(self.username): self.passf.setDisabled(False) else: self.passf.setDisabled(True) def AuthChanged(self): self.AuthSet() self.ConnectAndUpdate() def ConnectAndUpdate(self): self.Connect() self.UpdateExperiments(reload=True) def Connect(self): self.error(1) self.warning(1) def en(x): return x if len(x) else None self.dbc = dicty.PIPAx(cache=self.buffer, username=en(self.username), password=self.password) # check password if en(self.username) != None: try: self.dbc.mappings(reload=True) except dicty.AuthenticationError: self.error(1, "Wrong username or password") self.dbc = None except Exception as ex: print("Error when contacting the PIPA database", ex) sys.excepthook(*sys.exc_info()) try: # maybe cached? self.dbc.mappings() self.warning( 1, "Can not access database - using cached data.") except Exception as ex: self.dbc = None self.error(1, "Can not access database.") def Reload(self): self.UpdateExperiments(reload=True) def clear_cache(self): self.buffer.clear() self.Reload() def rtype(self): """Return selected result template type """ if self.result_types: return self.result_types[self.rtypei][0] else: return "-1" def UpdateExperimentTypes(self): self.expressionTypesCB.clear() items = [desc for _, desc in self.result_types] self.expressionTypesCB.addItems(items) self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1)) def UpdateExperiments(self, reload=False): self.experimentsWidget.clear() self.items = [] self.progressBarInit() if not self.dbc: self.Connect() mappings = {} result_types = [] sucind = False # success indicator for database index try: mappings = self.dbc.mappings(reload=reload) result_types = self.dbc.result_types(reload=reload) sucind = True except Exception as ex: try: mappings = self.dbc.mappings() result_types = self.dbc.result_types() self.warning(0, "Can not access database - using cached data.") sucind = True except Exception as ex: self.error(0, "Can not access database.") if sucind: self.warning(0) self.error(0) self.mappings = mappings self.result_types = result_types self.UpdateExperimentTypes() self.UpdateResultsList(reload=reload) self.progressBarFinished() if self.currentSelection: self.currentSelection.select( self.experimentsWidget.selectionModel()) self.handle_commit_button() def UpdateResultsList(self, reload=False): results_list = {} try: results_list = self.dbc.results_list(self.rtype(), reload=reload) except Exception as ex: try: results_list = self.dbc.results_list(self.rtype()) except Exception as ex: self.error(0, "Can not access database.") self.results_list = results_list mappings_key_dict = dict(((m["data_id"], m["id"]), key) \ for key, m in self.mappings.items()) def mapping_unique_id(annot): """Map annotations dict from results_list to unique `mappings` ids. """ data_id, mappings_id = annot["data_id"], annot["mappings_id"] return mappings_key_dict[data_id, mappings_id] elements = [] # softly change the view so that the selection stays the same items_shown = {} for i, item in enumerate(self.items): c = str(item.text(10)) items_shown[c] = i items_to_show = dict((mapping_unique_id(annot), annot) for annot in self.results_list.values()) add_items = set(items_to_show) - set(items_shown) delete_items = set(items_shown) - set(items_to_show) i = 0 while i < self.experimentsWidget.topLevelItemCount(): it = self.experimentsWidget.topLevelItem(i) if str(it.text(10)) in delete_items: self.experimentsWidget.takeTopLevelItem(i) else: i += 1 delete_ind = set([items_shown[i] for i in delete_items]) self.items = [ it for i, it in enumerate(self.items) if i not in delete_ind ] for r_annot in [items_to_show[i] for i in add_items]: d = defaultdict(lambda: "?", r_annot) row_items = [""] + [d.get(key, "?") for key, _ in HEADER[1:]] try: time_dict = literal_eval(row_items[DATE_INDEX]) date_rna = date( time_dict["fullYearUTC"], time_dict["monthUTC"] + 1, # Why is month 0 based? time_dict["dateUTC"]) row_items[DATE_INDEX] = date_rna.strftime("%x") except Exception: row_items[DATE_INDEX] = '' row_items[ID_INDEX] = mapping_unique_id(r_annot) elements.append(row_items) ci = MyTreeWidgetItem(self.experimentsWidget, row_items) self.items.append(ci) for i in range(len(self.headerLabels)): self.experimentsWidget.resizeColumnToContents(i) # which is the ok buffer version # FIXME: what attribute to use for version? self.wantbufver = \ lambda x, ad=self.results_list: \ defaultdict(lambda: "?", ad[x])["date"] self.wantbufver = lambda x: "0" self.UpdateCached() def UpdateCached(self): if self.wantbufver and self.dbc: fn = self.dbc.download_key_function() result_id_key = dict(((m["data_id"], m["mappings_id"]), key) \ for key, m in self.results_list.items()) for item in self.items: c = str(item.text(10)) mapping = self.mappings[c] data_id, mappings_id = mapping["data_id"], mapping["id"] r_id = result_id_key[data_id, mappings_id] # Get the buffered version buffered = self.dbc.inBuffer(fn(r_id)) value = " " if buffered == self.wantbufver(r_id) else "" item.setData(0, Qt.DisplayRole, value) def SearchUpdate(self, string=""): for item in self.items: item.setHidden(not all(s in item \ for s in self.searchString.split()) ) 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 onSelectionChanged(self, selected, deselected): self.handle_commit_button() def handle_commit_button(self): self.currentSelection = \ SelectionByKey(self.experimentsWidget.selectionModel().selection(), key=(1, 2, 3, 10)) self.commit_button.setDisabled(not len(self.currentSelection)) def saveHeaderState(self): hview = self.experimentsWidget.header() for i, label in enumerate(self.headerLabels): self.experimentsHeaderState[label] = hview.isSectionHidden(i) def restoreHeaderState(self): hview = self.experimentsWidget.header() state = self.experimentsHeaderState for i, label in enumerate(self.headerLabels): hview.setSectionHidden(i, state.get(label, True)) self.experimentsWidget.resizeColumnToContents(i)