def on_gene_sets_download(self, result):
# make sure this happens in the main thread.
# Qt insists that widgets be created within the GUI(main) thread.
assert threading.current_thread() == threading.main_thread()
self.progress_bar.finish()
self.setStatusMessage('')
tax_id, sets = result
self.set_hierarchy_model(self.hierarchy_widget,
*hierarchy_tree(tax_id, sets))
self.organism_select_combobox.setEnabled(True) # re-enable combobox
self.update_info_box()
self.mapped_genes = self.gene_matcher.map_input_to_ncbi()
self.workers = defaultdict(list)
self.progress_bar_iterations = dict()
for selected_hierarchy in [*self.get_hierarchies()]:
gene_sets = geneset.load_gene_sets(selected_hierarchy)
worker = Worker(get_collections,
gene_sets,
self.mapped_genes,
progress_callback=True,
partial_result=True)
worker.signals.error.connect(self.handle_error)
worker.signals.finished.connect(self.handle_worker_finished)
worker.signals.progress.connect(self._progress_advance)
worker.signals.partial_result.connect(self.populate_data_model)
worker.setAutoDelete(False)
self.workers[selected_hierarchy] = worker
self.progress_bar_iterations[selected_hierarchy] = len(gene_sets)
def download_gene_sets(self):
tax_id = self._get_selected_organism()
self.Error.clear()
# do not allow user to change organism when download task is running
self.organism_select_combobox.setEnabled(False)
# reset hierarchy widget state
self.hierarchy_widget.clear()
# clear data view
self.init_item_model()
# get all gene sets for selected organism
gene_sets = geneset.list_all(organism=tax_id)
# init progress bar
self.progress_bar = ProgressBar(self, iterations=len(gene_sets) * 100)
# status message
self.setStatusMessage('downloading sets')
worker = Worker(download_gene_sets, gene_sets, progress_callback=True)
worker.signals.progress.connect(self._progress_advance)
worker.signals.result.connect(self.on_gene_sets_download)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def commit(self):
self.Error.clear()
selected_item = self.experimentsWidget.currentItem(
) # get selected TreeItem
self.selected_item = selected_item.gen_data_id
if selected_item:
# init progress bar
self.progress_bar = gui.ProgressBar(self, iterations=1)
# status message
self.setStatusMessage('downloading experiment data')
worker = Worker(
self.res.download_etc_data,
selected_item.gen_data_id,
table_name=selected_item.data_name,
progress_callback=True,
)
worker.signals.progress.connect(self.progress_advance)
worker.signals.result.connect(self.send_to_output)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def load_experiments(self):
if self.res:
# init progress bar
self.progress_bar = gui.ProgressBar(self, iterations=2)
# status message
self.setStatusMessage('downloading experiments')
worker = Worker(self.res.fetch_etc_objects, progress_callback=True)
worker.signals.progress.connect(self.progress_advance)
worker.signals.result.connect(self.load_experiments_result)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def match_genes(self):
if self.gene_matcher:
# init progress bar
self.progress_bar = ProgressBar(self,
iterations=len(
self.gene_matcher.genes))
# status message
self.setStatusMessage('gene matcher running')
worker = Worker(self.gene_matcher.run_matcher,
progress_callback=True)
worker.signals.progress.connect(self._progress_advance)
worker.signals.finished.connect(self.handle_matcher_results)
# move download process to worker thread
self.threadpool.start(worker)
def download_gene_sets(self):
self.Error.clear()
# reset hierarchy widget state
self.hierarchy_widget.clear()
# clear data view
self.init_item_model()
# get all gene sets for selected organism
gene_sets = geneset.list_all(organism=self.tax_id)
# status message
self.setStatusMessage('downloading sets')
worker = Worker(download_gene_sets, self.tax_id, gene_sets)
worker.signals.result.connect(self.on_gene_sets_download)
# move download process to worker thread
self.threadpool.start(worker)
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 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()