def _load_data(self):
self.available_db_sources = get_available_db_sources()
file_name = self.available_db_sources[
self.selected_db_source]['filename']
try:
serverfiles.update(serverfiles_domain, file_name)
except ConnectionError:
raise ConnectionError('Can not connect to {}. '
'Using only local files.'.format(
serverfiles.server_url))
finally:
file_path = serverfiles.localpath_download(serverfiles_domain,
file_name)
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 setUpClass(cls):
"""Code executed only once for all tests"""
super().setUpClass()
file_name = "panglao_gene_markers.tab"
serverfiles.update(SERVER_FILES_DOMAIN, file_name)
file_path = serverfiles.localpath_download(SERVER_FILES_DOMAIN, file_name)
cls.panglao = Table.from_file(file_path)
file_name = "cellMarker_gene_markers.tab"
serverfiles.update(SERVER_FILES_DOMAIN, file_name)
file_path = serverfiles.localpath_download(SERVER_FILES_DOMAIN, file_name)
cls.cell_markers = Table.from_file(file_path)
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 _source_changed(self) -> None:
"""
Respond on change of the source and download the data.
"""
if self.available_sources:
file_name = self.available_sources[self.selected_source]['filename']
try:
serverfiles.update(SERVER_FILES_DOMAIN, file_name)
except requests.exceptions.ConnectionError:
# try to update file. Ignore network errors.
pass
try:
file_path = serverfiles.localpath_download(SERVER_FILES_DOMAIN, file_name)
except requests.exceptions.ConnectionError as err:
# Unexpected error.
raise err
self.data = Table.from_file(file_path)
def load_matcher_file(self, domain, filename):
# this starts download if files are not on local machine
file_path = serverfiles.localpath_download(domain, filename)
# download new version before using this file for gene name matching
serverfiles.update(domain, filename)
def case_insensitive_keys(matcher_dict):
updated_dict = {MAP_SOURCES: matcher_dict[MAP_SOURCES],
MAP_GENE_ID: matcher_dict[MAP_GENE_ID],
MAP_LOCUS: matcher_dict[MAP_LOCUS],
MAP_SYNONYMS: defaultdict(list),
MAP_SYMBOL: defaultdict(list),
MAP_NOMENCLATURE: defaultdict(list)}
for key, value in matcher_dict[MAP_SYMBOL].items():
# ensure string, we are using string methods (upper, lower)
key = ensure_type(str(key), str)
updated_dict[MAP_SYMBOL][key] = value
updated_dict[MAP_SYMBOL][key.upper()] = value
updated_dict[MAP_SYMBOL][key.lower()] = value
for key, value in matcher_dict[MAP_SYNONYMS].items():
key = ensure_type(str(key), str)
updated_dict[MAP_SYNONYMS][key] = value
updated_dict[MAP_SYNONYMS][key.upper()] = value
updated_dict[MAP_SYNONYMS][key.lower()] = value
for key, value in matcher_dict[MAP_NOMENCLATURE].items():
key = ensure_type(str(key), str)
updated_dict[MAP_NOMENCLATURE][key] = value
updated_dict[MAP_NOMENCLATURE][key.upper()] = value
updated_dict[MAP_NOMENCLATURE][key.lower()] = value
return updated_dict
with open(file_path, 'rb') as pickle_file:
if not self._case_insensitive:
return pickle.load(pickle_file)
else:
return case_insensitive_keys(pickle.load(pickle_file))