def config(show, show_source, init_source, db_dir, set, get):
'''CLI for managing configurations.
There are many configurations kept in "template-config.yaml" in source
code directory or "~/.virsorter" (when source code directory is not
writable for user). This file can located with
`virsorter config --show-source`. You can set the configurations with
`virsorter config --set KEY=VAL`. Alternative, you can edit in the
configuration file ("template-config.yaml") directly.
'''
from virsorter.config import (TEMPLATE, SRC_CONFIG_DIR, USER_CONFIG_DIR,
init_config_template)
if init_source:
if db_dir == None:
mes = '--db-dir is required for --init-source'
logging.critical(mes)
sys.exit(1)
else:
if not os.path.isdir(db_dir):
mes = (f'--db-dir {db_dir} does NOT exist yet; Make sure it '
'is created later\n')
logging.warning(mes)
db_dir = os.path.abspath(db_dir)
init_config_template(SRC_CONFIG_DIR, USER_CONFIG_DIR, db_dir)
sys.exit(0)
if not os.path.isfile(TEMPLATE):
mes = ('config file "template-config.yaml" has not been '
'initialized yet; Please use '
'`virsorter config --init-source --db-dir PATH` to initialize')
logging.critical(mes)
sys.exit(1)
config = get_default_config()
if show:
YAML().dump(config, sys.stdout)
sys.exit(0)
if show_source:
mes = f'config file path: {TEMPLATE}\n'
sys.stdout.write(mes)
sys.exit(0)
if get != None:
s = get
lis = [var.strip() for var in s.split(',')]
for var in lis:
temp = config
for i in var.split('.'):
i = i.strip()
try:
temp = temp[i]
except KeyError as e:
mes = f'{i} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
mes = f'{var}: {temp}\n'
sys.stdout.write(mes)
sys.exit(0)
if set != None:
s = set
lis = [item.strip() for item in s.split(',')]
for item in lis:
temp = config
var, val = item.split('=')
var = var.strip()
val = val.strip()
keys = [key.strip() for key in var.split('.')]
for i in range(len(keys)):
if i == (len(keys) - 1):
# stop at 2nd last key
break
key = keys[i]
try:
temp = temp[key]
except KeyError as e:
mes = f'{key} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
last_key = keys[-1]
try:
old_val = temp[last_key]
if isinstance(old_val, int):
try:
val = int(val)
except ValueError as e:
mes = f'{var} is supposed to be an integer'
logging.critical(mes)
sys.exit(1)
elif isinstance(old_val, float):
val = float(val)
try:
val = float(val)
except ValueError as e:
mes = f'{var} is supposed to be a float'
logging.critical(mes)
sys.exit(1)
# only convert to abspath when the old one exists
# since sometimes just want to set relative path
elif os.path.exists(old_val):
val = os.path.abspath(val)
temp[last_key] = val
except KeyError as e:
mes = f'{last_key} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
mes = f'{var}: {old_val} ==> {val}\n'
sys.stdout.write(mes)
with open(TEMPLATE, 'w') as fw:
YAML().dump(config, fw)
sys.exit(0)
def config(show, show_source, init_source, db_dir, set, get):
'''CLI for managing configurations.
There are many configurations kept in "template-config.yaml" in source
code directory or "~/.virsorter" (when source code directory is not
writable for user). This file can located with
`virsorter config --show-source`. You can set the configurations with
`virsorter config --set KEY=VAL`. Alternative, you can edit in the
configuration file ("template-config.yaml") directly.
'''
from virsorter.config import (TEMPLATE, SRC_CONFIG_DIR, USER_CONFIG_DIR,
init_config_template)
if init_source:
if db_dir == None:
mes = '--db-dir is required for --init-source'
logging.critical(mes)
sys.exit(1)
else:
init_config_template(SRC_CONFIG_DIR, USER_CONFIG_DIR, db_dir)
sys.exit(0)
if not os.path.isfile(TEMPLATE):
mes = ('config file "template-config.yaml" has not been '
'initialized yet; Please use '
'`virsorter config --init-source --db-dir PATH` to initialize')
logging.critical(mes)
sys.exit(1)
config = get_default_config()
if show:
YAML().dump(config, sys.stdout)
sys.exit(0)
if show_source:
mes = f'config file path: {TEMPLATE}\n'
sys.stdout.write(mes)
sys.exit(0)
if get != None:
s = get
lis = [var.strip() for var in s.split(',')]
for var in lis:
temp = config
for i in var.split('.'):
i = i.strip()
try:
temp = temp[i]
except KeyError as e:
mes = f'{i} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
mes = f'{var}: {temp}\n'
sys.stdout.write(mes)
sys.exit(0)
if set != None:
s = set
lis = [item.strip() for item in s.split(',')]
for item in lis:
temp = config
var, val = item.split('=')
var = var.strip()
val = val.strip()
keys = [key.strip() for key in var.split('.')]
for i in range(len(keys)):
if i == (len(keys) - 1):
# stop at 2nd last key
break
key = keys[i]
try:
temp = temp[key]
except KeyError as e:
mes = f'{key} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
last_key = keys[-1]
try:
old_val = temp[last_key]
temp[last_key] = val
except KeyError as e:
mes = f'{last_key} is not a key in config file ({TEMPLATE})'
logging.critical(mes)
sys.exit(1)
mes = f'{var}: {old_val} ==> {val}\n'
sys.stdout.write(mes)
with open(TEMPLATE, 'w') as fw:
YAML().dump(config, fw)
sys.exit(0)