def config_program(
wrapped, *args, # keep for clize
return_: parameters.one_of('<cfg_from_args>', '<gen_names_and_log>', '<end>') = '<end>',
b_interact=False,
log='',
verbose: parameters.one_of('CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET') = 'INFO',
**kwargs # keep for clize
):
"""
----------------------------
Add data from CSV-like files
to Pandas HDF5 store*.h5
----------------------------
"program": program behaviour:
:param return_: choices=[],
<cfg_from_args>: returns cfg based on input args only and exit,
<gen_names_and_log>: execute init_input_cols() and also returns fun_proc_loaded function... - see main()
:param log_,
:param verbose_,
"""
kw_args = locals()
if __debug__:
del kw_args['kw_args'] # exist if debug
return wrapped(*args, cfg_program=kw_args, **kwargs)
def with_prog_config(
wrapped,
config_path='to_pandas_hdf5/csv2h5_ini/csv2h5_vaex.yml',
return_: parameters.one_of('<cfg_from_args>', '<gen_names_and_log>', '<end>')='<end>',
# b_interact=False,
# verbose=:
**kwargs):
"""
overwrite command line arguments with program and in
:param wrapped:
:param return_: parameters.one_of('<cfg_from_args>', '<gen_names_and_log>', '<end>')='<end>',
:param in_:
:return:
"""
global l
@hydra.main(config_path=config_path)
def main_cfg(cfg: DictConfig):
global l
# cfg = cfg_from_args(argparser_files(), **kwargs)
if not cfg or not cfg['program'].get('return'):
print('Can not initialise')
return cfg
elif cfg['program']['return'] == '<cfg_from_args>': # to help testing
return cfg
l = init_logging(logging, None, cfg['program']['log'], cfg['program']['verbose'])
print('\n' + this_prog_basename(__file__), end=' started. ')
try:
cfg['in']['paths'], cfg['in']['nfiles'], cfg['in']['path'] = init_file_names(
**cfg['in'], b_interact=cfg['program']['b_interact'])
except Ex_nothing_done as e:
print(e.message)
return ()
return cfg
def wrap(**kwargs):
return wrapped(**main_cfg(kwargs))
return wrap
def main(flavour: one_of('harmful', 'agonism')):
fieldnames = ('Drug 1', 'Drug 2', 'DDI Type', 'Time', 'Unit')
writer = csv.DictWriter(sys.stdout,
fieldnames=fieldnames,
lineterminator='\n')
writer.writeheader()
for ddi in enrich(dinto.all_ddis()):
ddi['Drug 1'] = ddi['drug_a']
ddi['Drug 2'] = ddi['drug_b']
ddi['Time'] = ddi['spacing']
ddi['Unit'] = ddi['unit']
if flavour == 'harmful':
ddi['DDI Type'] = 'bad' if ddi[flavour] else 'good'
if flavour == 'agonism':
ddi['DDI Type'] = 'agonism' if ddi[flavour] else 'antagonism'
writer.writerow({k: ddi[k] for k in fieldnames})
try:
mod = importlib.import_module('.' + self.value, __name__)
return mod.Writer
except (ImportError, AttributeError):
log.warning("%s format has no writer implementation",
self.value,
exc_info=True)
DEFAULT_FORMAT = Format.TEXT
"""str: the name of the default format."""
@wrappers.decorator
@modifiers.autokwoargs
@modifiers.annotate(fmt=parameters.one_of(*map(attrgetter('value'), Format)))
@modifiers.annotate(kwargs=parser.Parameter.IGNORE)
def with_format(wrapped, fmt=DEFAULT_FORMAT, *args, **kwargs):
"""Provide ``--format`` argument.
Args:
format (str, optional): one of :class:`Format` values. Defaults to
``'text'``.
Raises:
clize.errors.CliValueError: if the format argument is invalid.
"""
if fmt.writer is None:
raise errors.CliValueError(
'{} is unavailable (missing requirements?)'.format(fmt.value))
return wrapped(fmt=Format(fmt), *args, **kwargs)
fh = open(filepath, mode='r')
line = fh.readline()
log.info('Determing Taxa file source...')
if 'k__' in line:
return taxa_import_gg(filepath)
else:
return taxa_import_rdp(filepath)
except Exception as e:
log.error(f'Whoops while importing {filepath}.')
raise e
types_of_imports = parameters.one_of(
('sample', "sample metadata"),
('analysis', "analysis sets with names, descriptions"),
('count', "otu count table, pct abundance per sample"),
('fasta', "otu seq fasta"),
('taxa', "otu annotations (taxonomy)"),
)
def parse_import(
*,
filepath: ['p', str] = None,
filetype: ['t', types_of_imports] = None,
):
"""Perform imports of files into OTUdb, as indicated.
:param filepath: path to file to be imported (REQUIRED)
:param filetype: which type of file are you importing?
class RepTests(object):
mapped_basic = ('par:a',
parameters.mapped([
('greeting', ['hello'], 'h1'),
('parting', ['goodbye'], 'h2'),
]), 'par')
mapped_default = ('par:a="greeting"',
parameters.mapped([
('greeting', ['hello'], 'h1'),
('parting', ['goodbye'], 'h2'),
]), '[par]')
mapped_alternate_list = ('par:a',
parameters.mapped([
('greeting', ['hello'], 'h1'),
('parting', ['goodbye'], 'h2'),
],
list_name="options"), 'par')
mapped_no_list = ('par:a',
parameters.mapped([
('greeting', ['hello'], 'h1'),
('parting', ['goodbye'], 'h2'),
],
list_name=None), 'par')
mapped_kw = ('*, par:a',
parameters.mapped([
('greeting', ['hello'], 'h1'),
('parting', ['goodbye'], 'h2'),
],
list_name=None), '--par=STR')
mapped_force_icase = ('par:a',
parameters.mapped([(1, ['thing'], 'h')],
case_sensitive=False), 'par')
mapped_force_scase = ('par:a',
parameters.mapped([
(1, ['Thing'], 'h'),
],
case_sensitive=True), 'par')
mapped_imply_scase = ('par:a',
parameters.mapped([
(1, ['thing'], 'h'),
(2, ['Thing'], 'h'),
]), 'par')
mapped_bad_icase = ('par:a',
parameters.mapped([
(1, ['thing'], 'h'),
(2, ['Thing'], 'h'),
],
case_sensitive=False), 'par')
oneof_basic = 'par:a', parameters.one_of('hello', 'goodbye', 'bye'), 'par'
oneof_help = ('par:a', parameters.one_of(('hello', 'h1'),
('bye', 'h2')), 'par')
multi_basic = '*, par:a', parameters.multi(), '[--par=STR...]'
multi_req = '*, par:a', parameters.multi(1), '--par=STR...'
multi_min = '*, par:a', parameters.multi(2), '--par=STR...'
multi_max = '*, par:a', parameters.multi(max=2), '[--par=STR...]'
multi_bound = '*, par:a', parameters.multi(min=2, max=3), '--par=STR...'
multi_conv = '*, par:a', (parameters.multi(), int), '[--par=INT...]'
multi_last_opt = ('*args, par:a', (parameters.multi(), Parameter.L),
'[--par=STR...] [args...]')
margs_basic = '*args:a', parameters.multi(), '[args...]'
margs_req = '*args:a', parameters.multi(1), 'args...'
margs_min = '*args:a', parameters.multi(2), 'args...'
margs_max = '*args:a', parameters.multi(max=2), '[args...]'
margs_bound = '*args:a', parameters.multi(min=2, max=3), 'args...'
margs_conv = '*args:a', (parameters.multi(), int), '[args...]'
margs_last_opt = ('*args:a, par=""', (parameters.multi(), Parameter.L),
'[--par=STR] [args...]')
@parameters.argument_decorator
def _blank(arg):
return arg + 'x'
deco_blank_pos = 'par:a', _blank, 'par'
deco_blank_posd = 'par:a="d"', _blank, '[par]'
deco_blank_kw = '*, par:a', _blank, '--par=STR'
deco_blank_kwd = '*, par:a="d"', _blank, '[--par=STR]'
deco_blank_args = '*par:a', _blank, '[par...]'
@parameters.argument_decorator
@modifiers.kwoargs(start='kw')
def _kw(arg, kw):
return arg + kw
deco_kw_pos = 'par:a', _kw, '--kw=STR par'
deco_kw_posd = 'par:a="d"', _kw, '[--kw=STR par]'
deco_kw_kw = '*, par:a', _kw, '--kw=STR --par=STR'
deco_kw_kwd = '*, par:a="d"', _kw, '[--kw=STR --par=STR]'
deco_kw_args = '*par:a', _kw, '[--kw=STR par...]'
@parameters.argument_decorator
@modifiers.autokwoargs
def _kwdef(arg, kw='D'):
return arg + kw
deco_def_pos = 'par:a', _kwdef, '[--kw=STR] par'
deco_def_posd = 'par:a="d"', _kwdef, '[[--kw=STR] par]'
deco_def_kw = '*, par:a', _kwdef, '[--kw=STR] --par=STR'
deco_def_kwd = '*, par:a="d"', _kwdef, '[[--kw=STR] --par=STR]'
deco_def_args = '*par:a', _kwdef, '[[--kw=STR] par...]'
@parameters.argument_decorator
@modifiers.autokwoargs
def _flag(arg, f=False):
return arg + ('y' if f else 'n')
deco_flag_pos = 'par:a', _flag, '[-f] par'
deco_flag_posd = 'par:a="d"', _flag, '[[-f] par]'
deco_flag_kw = '*, par:a', _flag, '[-f] --par=STR'
deco_flag_kwd = '*, par:a="d"', _flag, '[[-f] --par=STR]'
deco_flag_args = '*par:a', _flag, '[[-f] par...]'
deco_flag_other = 'par:a, *, x=False', _flag, '[-x] [-f] par'
@parameters.argument_decorator
@modifiers.autokwoargs
def _int(arg, i=0):
return arg + str(i)
deco_int_pos = 'par:a', _int, '[-i INT] par'
deco_int_posd = 'par:a="d"', _int, '[[-i INT] par]'
deco_int_kw = '*, par:a', _int, '[-i INT] --par=STR'
deco_int_kwd = '*, par:a="d"', _int, '[[-i INT] --par=STR]'
deco_int_args = '*par:a', _int, '[[-i INT] par...]'
deco_int_other = 'par:a, *, x=False', _int, '[-x] [-i INT] par'
@parameters.argument_decorator
@modifiers.kwoargs(start='kw')
def _all(arg, kw, flag=False, kwd='D', i=0):
return arg, kw, flag, kwd, i
_all_rep = '--kw=STR [--flag] [--kwd=STR] [-i INT] '
deco_all_pos = 'par:a', _all, _all_rep + 'par'
deco_all_posd = 'par:a="d"', _all, '[' + _all_rep + 'par]'
deco_all_kw = '*, par:a', _all, _all_rep + '--par=STR'
deco_all_kwd = '*, par:a="d"', _all, '[' + _all_rep + '--par=STR]'
deco_all_args = '*par:a', _all, '[' + _all_rep + 'par...]'
@parameters.argument_decorator
@modifiers.kwoargs(start='why')
def _inner(arg, why, zed='zed'):
return '(' + arg + why + zed + ')'
@parameters.argument_decorator
@modifiers.kwoargs(start='ab')
@modifiers.annotate(cd=_inner)
def _nest(arg, ab, cd='cd'):
return '(' + arg + ab + cd + ')'
_nest_rep = '--ab=STR [--why=STR [--zed=STR] --cd=STR] '
deco_nest_pos = 'par:a', _nest, _nest_rep + 'par'
deco_nest_posd = 'par:a="d"', _nest, '[' + _nest_rep + 'par]'
deco_nest_kw = '*, par:a', _nest, _nest_rep + '--par=STR'
deco_nest_kwd = '*, par:a="d"', _nest, '[' + _nest_rep + '--par=STR]'
deco_nest_args = '*par:a', _nest, '[' + _nest_rep + 'par...]'
pn_pos = 'par:a', parameters.pass_name, ''
pn_pos_first = 'par:a, other', parameters.pass_name, 'other'
pn_pos_nextpicky = 'par:a, other:int', parameters.pass_name, 'other'
pn_kw = '*, par:a', parameters.pass_name, ''