def insert_or_update_data(series_df, samples_df):
gse_name = series_df['series_geo_accession'][0]
# Create series and its attributes
attrs = {
cut_prefix(name, 'series_'): uni_cat(series_df[name])
for name in series_df.columns
}
assert attrs['sample_taxid'] == attrs['platform_taxid']
series, created = Series.objects.update_or_create(
gse_name=gse_name, defaults={'attrs': attrs})
# Create platform
gpls = samples_df['sample_platform_id'].unique()
assert len(gpls) == 1
gpl_name = gpls[0]
print(" %s" % gpl_name)
platform, _ = Platform.objects.get_or_create(
gpl_name=gpl_name,
defaults={'specie': SPECIES[attrs['platform_taxid']]})
# If updating check if some samples no longer present,
# mark disappeared samples as deleted.
if not created:
old_samples = Sample.objects.filter(series=series, platform=platform) \
.filter(Q(deleted=None) | Q(deleted='F')) \
.values_list('gsm_name', flat=True)
dead_samples = set(old_samples) - set(samples_df.index)
if dead_samples:
# Use lame boolean-like 'T' cause sharing db with web2py
Sample.objects.filter(series=series, platform=platform, gsm_name__in=dead_samples) \
.update(deleted='T')
print(
colored(' marked %d samples as deleted' % len(dead_samples),
'red'))
# Create/update samples and their attributes
for gsm_name in samples_df.index:
attrs = {
cut_prefix(name, 'sample_'): value.strip()
for name, value in list(samples_df.ix[gsm_name].to_dict().items())
}
Sample.objects.update_or_create(gsm_name=gsm_name,
series=series,
platform=platform,
deleted=None,
defaults={'attrs': attrs})
action = 'inserted' if created else 'updated'
print(
colored(' %s %s, %d samples' % (action, gse_name, len(samples_df)),
'green',
attrs=['bold']))
def remote_ip() -> IPAddress:
"""Return request's IP address (i.e. address of the client)."""
addr = request.environ.get('HTTP_X_FORWARDED_FOR') or request.environ.get(
'REMOTE_ADDR')
# nginx uses ::ffff: as a prefix for IPv4 addresses in ipv6only=off mode.
return ip_address(cut_prefix(addr, '::ffff:'))
def configurable_middleware(call):
prefix = call._func.__name__ + '__'
overwrites = {
cut_prefix(name, prefix): value
for name, value in SETTINGS.get().items() if name.startswith(prefix)
}
return call(**overwrites)
def parse_single_event(event):
REGEX = re.compile(r'EVENT type [0-9]+ [(]([^)]+)[)]')
event_name = re.match(REGEX, event).group(1)
key_code = -1
for line in event.splitlines():
if 'detail:' in line:
key_code = cut_prefix(line.strip(), 'detail: ')
key_code = int(key_code)
return event_name, key_code
def get_keycode_map():
output = subprocess.run(['xmodmap', '-pke'],
check=True,
stdout=subprocess.PIPE).stdout.decode('utf-8')
mappings = output.splitlines()
map_dic = {}
for mapping in mappings:
code, maps = re.split(' = ?', mapping)
code = cut_prefix(code, 'keycode ')
code = int(code)
maps = tuple(maps.split(' '))
map_dic[code] = maps
return map_dic
def lookup(func):
if isinstance(func, str):
ref = func
module, func = _resolve_ref(ref)
# Try to find class method
full_name = _full_name(func)
if full_name != ref:
attr = cut_prefix(ref, full_name).split('.')[0]
try:
func = getattr(func, attr)
except AttributeError:
pass
source_lines, lineno = inspect.getsourcelines(func)
source = ''.join(source_lines)
return '# %s:%d\n%s' % (inspect.getfile(func), lineno, source)
def remote_ip() -> IPAddress:
"""Return request's IP address (i.e. address of the client)."""
addr = request.environ.get('HTTP_X_FORWARDED_FOR') or request.environ.get('REMOTE_ADDR')
# nginx uses ::ffff: as a prefix for IPv4 addresses in ipv6only=off mode.
return ip_address(cut_prefix(addr, '::ffff:'))