def _load_data(self):
self.Warning.using_local_files.clear()
found_sources = {}
try:
found_sources.update(
serverfiles.ServerFiles().allinfo(serverfiles_domain))
except requests.exceptions.ConnectionError:
found_sources.update(serverfiles.allinfo(serverfiles_domain))
self.Warning.using_local_files()
self.available_db_sources = {
item.get('title').split(': ')[-1]: item
for item in found_sources.values()
}
if self.available_db_sources:
file_name = self.available_db_sources[
self.selected_db_source]['filename']
try:
serverfiles.update(serverfiles_domain, file_name)
except requests.exceptions.ConnectionError:
# try to update file. Ignore network errors.
pass
try:
file_path = serverfiles.localpath_download(
serverfiles_domain, file_name)
except requests.exceptions.ConnectionError as err:
# Unexpected error.
raise err
data = Table(file_path)
# enforce order
old_domain = data.domain
new_domain = Domain(
[],
metas=[
old_domain['Organism'],
old_domain['Name'],
old_domain['Entrez ID'],
old_domain['Cell Type'],
old_domain['Function'],
old_domain['Reference'],
old_domain['URL'],
],
)
data = data.transform(new_domain)
self.data = data
def _load_data(self) -> None:
"""
Collect available data sources (marker genes data sets).
"""
self.Warning.using_local_files.clear()
found_sources = {}
try:
found_sources.update(serverfiles.ServerFiles().allinfo(SERVER_FILES_DOMAIN))
except requests.exceptions.ConnectionError:
found_sources.update(serverfiles.allinfo(SERVER_FILES_DOMAIN))
self.Warning.using_local_files()
self.available_sources = {item.get('title').split(': ')[-1]: item for item in found_sources.values()}
def get_available_db_sources():
found_sources = {}
try:
found_sources.update(
serverfiles.ServerFiles().allinfo(serverfiles_domain))
except ConnectionError:
raise ConnectionError(
'Can not connect to {}. Using only local files.'.format(
serverfiles.server_url))
finally:
found_sources.update(serverfiles.allinfo(serverfiles_domain))
return {
item.get('title').split(': ')[-1]: item
for item in found_sources.values()
}
def evaluate_files_state(progress_callback):
progress_callback.emit()
files = []
# fetch remote info
try:
server_info = serverfiles.ServerFiles().allinfo()
except (Timeout, ConnectionError) as e:
raise e
progress_callback.emit()
# fetch local info
local_info = serverfiles.allinfo()
all_info = set(local_info.keys()).union(server_info.keys())
for domain, file_name in sorted(all_info):
files.append(
FileState(domain, file_name,
server_info.get((domain, file_name), None),
local_info.get((domain, file_name), None)))
progress_callback.emit()
return files
def SetFilesList(self, serverInfo):
"""
Set the files to show.
"""
self.setEnabled(True)
localInfo = serverfiles.allinfo()
all_tags = set()
self.filesView.clear()
self.updateItems = []
for item in join_info_dict(localInfo, serverInfo):
tree_item = UpdateTreeWidgetItem(item)
options_widget = UpdateOptionsWidget(item.state)
options_widget.item = item
options_widget.installClicked.connect(
partial(self.SubmitDownloadTask, item.domain, item.filename)
)
options_widget.removeClicked.connect(
partial(self.SubmitRemoveTask, item.domain, item.filename)
)
self.updateItems.append((item, tree_item, options_widget))
all_tags.update(item.tags)
self.filesView.addTopLevelItems(
[tree_item for _, tree_item, _ in self.updateItems]
)
for item, tree_item, options_widget in self.updateItems:
self.filesView.setItemWidget(tree_item, 0, options_widget)
# Add an update button if the file is updateable
if item.state == OUTDATED:
button = QToolButton(
None, text="Update",
maximumWidth=120,
minimumHeight=20,
maximumHeight=20
)
if sys.platform == "darwin":
button.setAttribute(Qt.WA_MacSmallSize)
button.clicked.connect(
partial(self.SubmitDownloadTask, item.domain,
item.filename)
)
self.filesView.setItemWidget(tree_item, 2, button)
self.progress.advance()
self.filesView.setColumnWidth(0, self.filesView.sizeHintForColumn(0))
for column in range(1, 4):
contents_hint = self.filesView.sizeHintForColumn(column)
header_hint = self.filesView.header().sectionSizeHint(column)
width = max(min(contents_hint, 400), header_hint)
self.filesView.setColumnWidth(column, width)
hints = [hint for hint in sorted(all_tags) if not hint.startswith("#")]
self.completer.setTokenList(hints)
self.SearchUpdate()
self.UpdateInfoLabel()
self.toggleButtons()
self.cancelButton.setEnabled(False)
self.progress.setRange(0, 0)