def create_console(self, script):
usage_sections = parse_section('usage:', script.__doc__)
if len(usage_sections) == 0:
raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
if len(usage_sections) > 1:
raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
DocoptExit.usage = usage_sections[0]
pattern = parse_pattern(formal_usage(DocoptExit.usage), parse_defaults(script.__doc__))
paths = []
paths.append({
"flags": [opt for opt in parse_defaults(script.__doc__) if not opt.argcount and opt.name not in ["--help", "--version"]],
"extras": [opt for opt in parse_defaults(script.__doc__) if not opt.argcount and opt.name in ["--help", "--version"]],
"options": [opt for opt in parse_defaults(script.__doc__) if opt.argcount and not opt.value],
"default_options": [opt for opt in parse_defaults(script.__doc__) if opt.value],
"arguments": [arg.name for arg in pattern.flat(Argument)],
})
return {
"name": script.__name__,
"file": script.__file__,
"doc": script.__doc__,
"paths": paths,
}
def docopt(doc, argv=None, help=True, version=None, options_first=False): # @ReservedAssignment help
"""Re-implementation of docopt.docopt() function to parse ANYTHING at
the end (for proxying django options)."""
if argv is None:
argv = sys.argv[1:]
DocoptExit.usage = printable_usage(doc)
options = parse_defaults(doc)
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
argv = parse_argv(TokenStream(argv, DocoptExit), list(options), options_first)
pattern_options = set(pattern.flat(Option))
for ao in pattern.flat(AnyOptions):
doc_options = parse_defaults(doc)
ao.children = list(set(doc_options) - pattern_options)
extras(help, version, argv, doc)
__matched, __left, collected = pattern.fix().match(argv)
# if matched and left == []: # better error message if left?
if collected: # better error message if left?
result = Dict((a.name, a.value) for a in (pattern.flat() + collected))
collected_django_options = len(result.get("DJANGO_OPTIONS", []))
result["DJANGO_OPTIONS"] = (
result.get("DJANGO_OPTIONS", []) + sys.argv[len(collected) + (collected_django_options or 1) :]
)
# If any of the collected arguments are also in the DJANGO_OPTIONS,
# then exit because we don't want users to have put options for kalite
# at the end of the command
if any(map(lambda x: x.name in map(lambda x: x.split("=")[0], result["DJANGO_OPTIONS"]), collected)):
sys.stderr.write(
"Cannot mix django manage command options with kalite options. "
"Always put django management options last.\n\n"
)
raise DocoptExit()
return result
raise DocoptExit()
def __init__(self, docopt_str, base_descriptor):
with open(base_descriptor, "r") as base_desc:
self.descriptor = collections.OrderedDict(json.load(base_desc))
del self.descriptor['groups']
del self.descriptor['inputs']
del self.descriptor['output-files']
self.docopt_str = docopt_str
self.dependencies = collections.OrderedDict()
self.all_desc_and_type = collections.OrderedDict()
self.unique_ids = []
try:
# docopt code snippet to extract args tree (pattern)
# should run if docopt script is valid
options = parse_defaults(docopt_str)
self.pattern = parse_pattern(
formal_usage(self._parse_section('usage:', docopt_str)[0]),
options)
argv = parse_argv(TokenStream(sys.argv[1:], DocoptLanguageError),
list(options), False)
pattern_options = set(self.pattern.flat(Option))
for options_shortcut in self.pattern.flat(AnyOptions):
doc_options = parse_defaults(docopt_str)
options_shortcut.children = list(
set(doc_options) - pattern_options)
matched, left, collected = self.pattern.fix().match(argv)
except Exception:
os.remove(base_descriptor)
raise_error(ImportError, "Invalid docopt script")
def usage(self):
"""Extract usage from a specified command.
This is useful if usage not defined in subclass, but it is recommended
to define them there.
"""
opt = docopt.parse_defaults(self.__doc__)
return dict({a.short or a.long: bool(a.argcount) for a in opt})
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='ontree 0.0.0')
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
verbose = args['--verbose']
sgg._verbose = verbose
sgv._verbose = verbose
sgc._verbose = verbose
sgd._verbose = verbose
if verbose:
log.setLevel('DEBUG')
if args['--test']:
test()
elif args['server']:
api = args['--api']
if api is not None:
scigraph.scigraph_client.BASEPATH = api
sgg._basePath = api
sgv._basePath = api
sgc._basePath = api
# reinit curies state
sgc.__init__(cache=sgc._get == sgc._cache_get,
verbose=sgc._verbose)
sgd._basePath = api
api_key = args['--key']
if api_key:
sgg.api_key = api_key
sgv.api_key = api_key
sgc.api_key = api_key
sgd.api_key = api_key
scs = OntTerm.query.services[0]
scs.api_key = api_key
scs.setup(instrumented=OntTerm)
_data_endpoint = args['--data-api']
data_endpoint = (_data_endpoint if _data_endpoint else
scigraph.scigraph_client.BASEPATH)
app = server(verbose=verbose, data_endpoint=data_endpoint)
# app.debug = False
# app.run(host='localhost', port=args['--port'], threaded=True) # nginxwoo
# app.debug = True
app.run(host='0.0.0.0', port=args['--port'], threaded=True) # nginxwoo
# FIXME pypy3 has some serious issues yielding when threaded=True, gil issues?
os.sys.exit()
else:
direction = both if args[
'--both'] else out if args['--incoming'] else inc
# TODO default direction table to match to expected query behavior based on rdf direction
pred = args['<predicate-curie>']
root = args['<root-curie>']
render(pred, root, direction)
def cli():
options = docopt(__doc__)
defaults = dict(map(lambda x: (x.long, x.value), parse_defaults(__doc__)))
try:
main(options, defaults)
except RuntimeWarning as w:
print(" Warning: %s" % w, file=sys.stderr)
sys.exit(1)
def setup(cls, doc, argv=None, **kwargs):
""" kwargs are passed to docopt """
from docopt import docopt, parse_defaults
args = docopt(doc, argv=argv, **kwargs)
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(doc)
}
options = cls(args, defaults, argv=argv)
return options, args, defaults
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='slimgen 0.0.0')
defaults = {o.name:o.value if o.argcount else None for o in parse_defaults(__doc__)}
options = Options(args, defaults)
main = Main(options)
if main.options.debug:
print(main.options)
main()
def docopt(doc,
argv=None,
help=True,
version=None,
options_first=False): # @ReservedAssignment help
"""Re-implementation of docopt.docopt() function to parse ANYTHING at
the end (for proxying django options)."""
if argv is None:
argv = sys.argv[1:]
DocoptExit.usage = printable_usage(doc)
options = parse_defaults(doc)
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
argv = parse_argv(TokenStream(argv, DocoptExit), list(options),
options_first)
pattern_options = set(pattern.flat(Option))
for ao in pattern.flat(AnyOptions):
doc_options = parse_defaults(doc)
ao.children = list(set(doc_options) - pattern_options)
extras(help, version, argv, doc)
__matched, __left, collected = pattern.fix().match(argv)
# if matched and left == []: # better error message if left?
if collected: # better error message if left?
result = Dict((a.name, a.value) for a in (pattern.flat() + collected))
collected_django_options = len(result.get('DJANGO_OPTIONS', []))
result['DJANGO_OPTIONS'] = (result.get('DJANGO_OPTIONS', []) +
sys.argv[len(collected) +
(collected_django_options or 1):])
# If any of the collected arguments are also in the DJANGO_OPTIONS,
# then exit because we don't want users to have put options for kalite
# at the end of the command
if any(
map(
lambda x: x.name in map(lambda x: x.split("=")[0], result[
'DJANGO_OPTIONS']), collected)):
sys.stderr.write(
"Cannot mix django manage command options with kalite options. "
"Always put django management options last.\n\n")
raise DocoptExit()
return result
raise DocoptExit()
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='googapis 0.0.0')
defaults = {o.name:o.value if o.argcount else None for o in parse_defaults(__doc__)}
options = Options(args, defaults)
main = Main(options)
if main.options.debug:
log.setLevel('DEBUG')
print(main.options)
main()
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__)
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
debug = args['--debug']
options = Options(args, defaults)
main = Main(options)
main()
def parse_params(cmd):
# This creates a parameter tree (CommandParams object) for the target docopt tool.
# Also returns a second parameter, a dict of:
# option->option-help-string
from docopt import parse_defaults, parse_pattern, formal_usage, printable_usage
usage = get_usage(cmd)
options = parse_defaults(usage)
pattern = parse_pattern(formal_usage(printable_usage(usage)), options)
param_tree = CommandParams()
build_command_tree(pattern, param_tree)
return param_tree, dict(list(get_options_descriptions(usage)))
def parse_params(cmd):
# this function creates a parameter tree for the target docopt tool.
# a parameter tree is a CommandParams instance, see the documentation of the class
# this function also returns a second parameter, which is a dictionary of option->option help string
from docopt import parse_defaults, parse_pattern, formal_usage, printable_usage
usage = get_usage(cmd)
options = parse_defaults(usage)
pattern = parse_pattern(formal_usage(printable_usage(usage)), options)
param_tree = CommandParams()
build_command_tree(pattern, param_tree)
return param_tree, dict(list(get_options_descriptions(usage)))
def parse_params(cmd, given_usage=None):
# This creates a parameter tree (CommandParams object) for the target docopt tool.
# Also returns a second parameter, a dict of:
# option->option-help-string
from docopt import parse_defaults, parse_pattern, formal_usage, printable_usage
usage = get_usage(cmd) if given_usage is None else given_usage
options = parse_defaults(usage)
pattern = parse_pattern(formal_usage(printable_usage(usage)), options)
param_tree = CommandParams()
build_command_tree(pattern, param_tree)
return param_tree, dict(list(get_options_descriptions(usage)))
def pattern(self):
"""Returns a docopt match pattern."""
try:
from docopt import parse_defaults, formal_usage, parse_pattern
except ImportError:
LOGGER.warning('docopt not installed.')
LOGGER.warning('Command help pattern generation unavailable.')
return None
usage = self.usage
options = parse_defaults(usage)
return parse_pattern(formal_usage(usage), options)
def dochelper(doc):
""" Helper to add defaults from ENV to pydoc. """
doc_ = doc
for default in docopt.parse_defaults(doc):
optname = default.name.strip('-').replace('-', '_').upper()
envname = EnvOption.prefix() + optname
optval = os.getenv(envname)
if optval is not None:
search = r"(^ *(%s|%s|%s %s) .*?$)" \
% (default.short, default.long, default.short, default.long)
for match in re.findall(search, doc, re.MULTILINE):
whole = match[0]
if not re.search(r"\[default: .*?\]", whole):
doc_ = doc_.replace(
whole, "%s [default: %s]" % (whole, optval))
return doc_
def settable_options(doc, argv, ignore, options_first):
"""Determine which options we can set, which ones are boolean, and which ones are repeatable.
All set items are option long names.
:param str doc: Docstring from docoptcfg().
:param iter argv: CLI arguments from docoptcfg().
:param iter ignore: Options to ignore from docoptcfg().
:param bool options_first: docopt argument from docoptcfg().
:return: Settable options, boolean options, repeatable options, and short to long option name mapping.
:rtype: tuple
"""
settable, booleans, repeatable, short_map = set(), set(), set(), dict()
# Determine which options are settable by docoptcfg and which ones are flags/booleans.
options = docopt.parse_defaults(doc)
short_map.update((o.short, o.long) for o in options)
parsed_argv = docopt.parse_argv(
docopt.TokenStream(argv, docopt.DocoptExit), list(options),
options_first)
overridden = [o.long for o in parsed_argv if hasattr(o, 'long')]
for option in options:
if option.long in overridden or (option.long in ignore or option.short
in ignore) or option.long is None:
continue
if option.argcount == 0:
booleans.add(option.long)
settable.add(option.long)
# Determine which options are repeatable.
if settable and '...' in doc:
pattern = docopt.parse_pattern(
docopt.formal_usage(docopt.DocoptExit.usage), options)
for option in pattern.fix().flat():
if not hasattr(option, 'long'):
continue # Positional argument or sub-command.
if getattr(option, 'long') not in settable:
continue # Don't care about this if we can't set it.
if getattr(option, 'long') in booleans and getattr(
option, 'value') == 0:
repeatable.add(getattr(option, 'long'))
elif hasattr(getattr(option, 'value'), '__iter__'):
repeatable.add(getattr(option, 'long'))
return settable, booleans, repeatable, short_map
def dochelper(doc):
""" Helper to add defaults from ENV to pydoc. """
doc_ = doc
for default in docopt.parse_defaults(doc):
optname = default.name.strip('-').replace('-', '_').upper()
envname = EnvOption.prefix() + optname
optval = os.getenv(envname)
if optval is not None:
search = r"(^ *({}|{}|{} {}) .*?$)".format(default.short,
default.long,
default.short,
default.long)
for match in re.findall(search, doc, re.MULTILINE):
whole = match[0]
if not re.search(r"\[default: .*?\]", whole):
doc_ = doc_.replace(
whole, "{} [default: {}]".format(whole, optval))
return doc_
def main():
from docopt import docopt
from docopt import parse_defaults
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
args = docopt(__doc__, version='scigraph-codegen 1.0.0')
ssd = 'https://scicrunch.org/swagger-docs'
if args['--api'] == defaults['--basepath']:
args['--api'] = ssd
if args['--api'] == 'https://scicrunch.org/api/1/scigraph':
args['--api'] = ssd
if args['--api'] == ssd:
State2.path_prefix = '/scigraph'
output_file, api, version, basepath = (args['--' + k]
for k in ('output-file', 'api',
'scigraph-version',
'basepath'))
version = int(version)
basepath = None if basepath == 'default' else basepath
if version < 2:
state = State
docs_path = 'api-docs'
else:
state = State2
docs_path = 'swagger.json'
api_url = f'{api}/{docs_path}'
print(api_url)
dynamics = [f'{d}/swagger.json' for d in args['--dynamic']]
if dynamics:
print('dynamics:', dynamics)
s = state(api_url, basepath, dynamics=dynamics)
code = s.code()
with open(output_file, 'wt') as f:
f.write(code)
import os
os.system(f'python {output_file}')
def settable_options(doc, argv, ignore, options_first):
"""Determine which options we can set, which ones are boolean, and which ones are repeatable.
All set items are option long names.
:param str doc: Docstring from docoptcfg().
:param iter argv: CLI arguments from docoptcfg().
:param iter ignore: Options to ignore from docoptcfg().
:param bool options_first: docopt argument from docoptcfg().
:return: Settable options, boolean options, repeatable options, and short to long option name mapping.
:rtype: tuple
"""
settable, booleans, repeatable, short_map = set(), set(), set(), dict()
# Determine which options are settable by docoptcfg and which ones are flags/booleans.
options = docopt.parse_defaults(doc)
short_map.update((o.short, o.long) for o in options)
parsed_argv = docopt.parse_argv(docopt.TokenStream(argv, docopt.DocoptExit), list(options), options_first)
overridden = [o.long for o in parsed_argv if hasattr(o, 'long')]
for option in options:
if option.long in overridden or (option.long in ignore or option.short in ignore):
continue
if option.argcount == 0:
booleans.add(option.long)
settable.add(option.long)
# Determine which options are repeatable.
if settable and '...' in doc:
pattern = docopt.parse_pattern(docopt.formal_usage(docopt.DocoptExit.usage), options)
for option in pattern.fix().flat():
if not hasattr(option, 'long'):
continue # Positional argument or sub-command.
if getattr(option, 'long') not in settable:
continue # Don't care about this if we can't set it.
if getattr(option, 'long') in booleans and getattr(option, 'value') == 0:
repeatable.add(getattr(option, 'long'))
elif hasattr(getattr(option, 'value'), '__iter__'):
repeatable.add(getattr(option, 'long'))
return settable, booleans, repeatable, short_map
def main(args={o.name: o.value for o in parse_defaults(__doc__)}):
#print(args)
if not args['--refresh'] and args['--input'] and Path(
args['--input']).exists():
with open(args['--input'], 'rt') as f:
input = json.load(f)
else:
response = requests.get(
'http://api.brain-map.org/api/v2/data/query.json?criteria='
'model::Specimen,rma::criteria,[is_cell_specimen$eq%27true%27],'
'products[name$eq%27Mouse%20Cell%20Types%27],'
'rma::include,structure,donor(transgenic_lines),'
'specimen_tags,cell_soma_locations,rma::options[num_rows$eqall]')
input = response.json()['msg']
with open(args['--input'], 'wt') as f:
json.dump(input, f, indent=4)
act = AllenCellTypes(input, args['--output'])
act.build_transgenic_lines()
act.build_neurons()
return act.config
def docopt_cmd_completion(func, **kwargs):
options = parse_defaults(func.__doc__)
pattern = parse_pattern(formal_usage(printable_usage(func.__doc__)),
options).children[0]
def get_state(it, pattern):
try:
value = next(it)
except StopIteration:
return pattern
res = []
for x in pattern:
if ((type(x[0]) == list and value in flatten(x[0])) or
value == x[0]):
res.append(x[1:])
if res:
return get_state(it, res)
return []
def wrapper(self, text, line, begidx, endidx):
argv = shlex.split(line[:endidx])[1:]
if not line[endidx - 1].isspace():
target = argv[-1]
argv = argv[:-1]
else:
target = ''
state = get_state(iter(argv), pattern.noflat())
res = []
for x in state:
if type(x[0]) == list:
res.extend(flatten(x[0]))
else:
res.append(x[0])
return list(set(x for x in res if x.startswith(target)))
wrapper.__name__ = str('complete_' + func.__name__[3:])
wrapper.__module__ = func.__module__
wrapper.__doc__ = func.__doc__
return wrapper
def docopt_cmd_completion(func, **kwargs):
options = parse_defaults(func.__doc__)
pattern = parse_pattern(formal_usage(printable_usage(func.__doc__)),
options).children[0]
def get_state(it, pattern):
try:
value = next(it)
except StopIteration:
return pattern
res = []
for x in pattern:
if ((type(x[0]) == list and value in flatten(x[0]))
or value == x[0]):
res.append(x[1:])
if res:
return get_state(it, res)
return []
def wrapper(self, text, line, begidx, endidx):
argv = shlex.split(line[:endidx])[1:]
if not line[endidx - 1].isspace():
target = argv[-1]
argv = argv[:-1]
else:
target = ''
state = get_state(iter(argv), pattern.noflat())
res = []
for x in state:
if type(x[0]) == list:
res.extend(flatten(x[0]))
else:
res.append(x[0])
return list(set(x for x in res if x.startswith(target)))
wrapper.__name__ = str('complete_' + func.__name__[3:])
wrapper.__module__ = func.__module__
wrapper.__doc__ = func.__doc__
return wrapper
def main():
args = docopt.docopt(__doc__)
try:
if args['<docopt>'] is not None:
with open(args['<docopt>'], 'r') as f:
args['<docopt>'] = f.read()
elif args['<docopt>'] is None and sys.stdin.isatty():
print(__doc__.strip("\n"))
sys.exit("")
else:
args['<docopt>'] = sys.stdin.read()
except IOError as e:
sys.exit(e)
doc = args['<docopt>']
usage = parse_section('usage:', doc)
s = ['More than one ', '"usage:" (case-insensitive)', ' not found.']
usage = {0: s[1:], 1: usage[0] if usage else None}.get(len(usage), s[:2])
if isinstance(usage, list):
raise docopt.DocoptLanguageError(''.join(usage))
options = docopt.parse_defaults(doc)
pattern = docopt.parse_pattern(docopt.formal_usage(usage), options)
fsm = ragel_ast(pattern)
leafs, commands, arguments, flags, options = parse_leafs(pattern)
command_fields = '\n '.join(
map(lambda c: 'int {0};'.format(clean_name(c)), commands))
flag_fields = '\n '.join(
map(lambda c: 'int {0};'.format(clean_name(c)), flags))
option_fields = '\n '.join(
map(lambda c: 'char* {0};'.format(clean_name(c)), options))
argument_fields = '\n '.join(
map(lambda c: 'char* {0};'.format(clean_name(c)), arguments))
command_actions = '\n '.join(
map(
lambda c: 'action command_{0}{{ fsm->opt->{0} = 1; }}'.format(
clean_name(c)), commands))
flag_actions = '\n '.join(
map(
lambda c: 'action option_{0}{{ fsm->opt->{0} = 1; }}'.format(
clean_name(c)), flags))
option_actions = '\n '.join(
map(
lambda c:
'action option_{0}{{ fsm->opt->{0} = strdup(fsm->buffer); }}'.
format(clean_name(c)), options))
argument_actions = '\n '.join(
map(
lambda c:
'action argument_{0}{{ fsm->opt->{0} = strdup(fsm->buffer); }}'.
format(clean_name(c)), arguments))
options_with_defaults = filter(lambda x: x.value is not None, options)
option_defaults = '\n '.join(
map(
lambda c: 'fsm->opt->{0} = strdup("{1}");'.format(
clean_name(c), c.value), options_with_defaults))
usage = '\n '.join(
map(lambda l: 'fprintf(stdout, "{0}\\n");'.format(l), doc.split('\n')))
file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"template.rl")
print(
Template(open(file).read()).safe_substitute(
fsm=fsm,
usage=usage,
command_fields=command_fields,
flag_fields=flag_fields,
option_fields=option_fields,
argument_fields=argument_fields,
command_actions=command_actions,
flag_actions=flag_actions,
option_actions=option_actions,
argument_actions=argument_actions,
option_defaults=option_defaults,
))
def _parse_docopt(doc):
options = docopt.parse_defaults(doc)
pure_doc = docopt.formal_usage(docopt.printable_usage(doc))
pattern = docopt.parse_pattern(pure_doc, options)
return pattern
def counterfactual():
arguments = docopt.docopt(__doc__)
dataset = arguments['--dataset']
thought_vector_size = int(arguments['--thought-vector'])
encoder_model = arguments['--encoder']
decoder_model = arguments['--decoder']
classifier_model = arguments['--classifier']
epochs = int(arguments['--epochs'])
decay = float(arguments['--decay'])
learning_rate = float(arguments['--learning-rate'])
gan_type = arguments['--gan-type']
perceptual_layers = int(arguments['--perceptual-layers'])
img_width = int(arguments['--img-width'])
try:
experiment_timestamp = int(arguments['--timestamp'])
except ValueError:
experiment_timestamp = int(time.time())
experiment_name = '-'.join(
str(x) for x in [
dataset,
thought_vector_size,
encoder_model,
decoder_model,
classifier_model,
experiment_timestamp,
])
timestamp = int(time.time())
#Download the dataset if it doesn't already exist
# TODO: security lol
os.system('scripts/download_{}.py'.format(dataset))
train_dataset = os.path.expanduser(
'~/data/{}_train.dataset'.format(dataset))
test_dataset = os.path.expanduser('~/data/{}_test.dataset'.format(dataset))
# Fill params with defaults
import main
defaults = {
opt.long: opt.value
for opt in docopt.parse_defaults(main.__doc__)
}
params = {main.argname(k): main.argval(defaults[k]) for k in defaults}
# TODO: Merge main.py params with these params in some nice elegant way
# Like, imagine if each experiment could inherit all the main.py params
# But it would also have its own params which override the inherited ones
# This is beginning to sound dangerously object-oriented
params['experiment_name'] = experiment_name
params['encoder_input_filename'] = test_dataset
params['decoder_input_filename'] = test_dataset
params['classifier_input_filename'] = test_dataset
params['vocabulary_filename'] = train_dataset
params['encoder_datatype'] = 'img'
params['decoder_datatype'] = 'img'
params['classifier_datatype'] = 'lab'
params['encoder_model'] = encoder_model
params['decoder_model'] = decoder_model
params['discriminator_model'] = encoder_model
params['classifier_model'] = classifier_model
params['thought_vector_size'] = thought_vector_size
params['img_width_encoder'] = img_width
params['img_width_decoder'] = img_width
params['epochs'] = epochs
params['learning_rate'] = learning_rate
params['decay'] = decay
params['perceptual_loss_layers'] = perceptual_layers
params['batches_per_epoch'] = 50
params['enable_classifier'] = True
params['enable_discriminator'] = True
params['enable_perceptual_loss'] = True
params['encoder_weights'] = 'encoder_{}.h5'.format(encoder_model)
params['decoder_weights'] = 'decoder_{}.h5'.format(decoder_model)
params['classifier_weights'] = 'classifier_{}.h5'.format(classifier_model)
params['discriminator_weights'] = 'discriminator_{}.h5'.format(
encoder_model)
params['gan_type'] = gan_type
params['learning_rate_disc'] = learning_rate * .1
params['learning_rate_generator'] = learning_rate * .1
# TODO: security lol
os.system('mkdir ~/results/{}'.format(experiment_name))
save_params(experiment_name, params)
import transcoder
# First train a manifold
train_params = params.copy()
train_params['stdout_filename'] = 'stdout_train_{}.txt'.format(timestamp)
train_params['encoder_input_filename'] = train_dataset
train_params['decoder_input_filename'] = train_dataset
train_params['classifier_input_filename'] = train_dataset
train_params['mode'] = 'train'
if train_params['epochs'] > 0:
transcoder.main(**train_params)
# Evaluate the classifier
"""
eval_params = params.copy()
eval_params['decoder_model'] = params['classifier_model']
eval_params['decoder_datatype'] = params['classifier_datatype']
eval_params['decoder_weights'] = params['classifier_weights']
eval_params['enable_classifier'] = False
eval_params['enable_discriminator'] = False
eval_params['stdout_filename'] = 'stdout_eval_{}.txt'.format(timestamp)
eval_params['mode'] = 'evaluate'
transcoder.main(**eval_params)
"""
# Generate a "dream" video
dream_params = params.copy()
dream_params['video_filename'] = 'dream_output_{}.mjpeg'.format(timestamp)
dream_params['stdout_filename'] = 'stdout_dream_{}.txt'.format(timestamp)
dream_params['enable_discriminator'] = False
dream_params['mode'] = 'dream'
transcoder.main(**dream_params)
# Re-encode the video to mp4 for storage
encode_video(experiment_name, dream_params['video_filename'])
# Add counterfactuals
counter_params = params.copy()
counter_params['video_filename'] = 'counterfactual_output_{}.mjpeg'.format(
timestamp)
counter_params['stdout_filename'] = 'stdout_counterfactual_{}.txt'.format(
timestamp)
counter_params['enable_discriminator'] = False
counter_params['mode'] = 'counterfactual'
for _ in range(3):
transcoder.main(**counter_params)
# Re-encode the video to mp4 for storage
encode_video(experiment_name, counter_params['video_filename'])
# Touch a file to mark the experiment as finished
filename = os.path.expanduser(
'~/results/{}/finished'.format(experiment_name))
open(filename, 'w').write('OK')
from docopt import parse_defaults
from joblib import Parallel, delayed
from ttlser import CustomTurtleSerializer
from pyontutils.core import OntGraph
from pyontutils.utils import noneMembers, TODAY, setPS1, refile, TermColors as tc, log
from pyontutils.namespaces import getCuries, OntCuries
from pyontutils.hierarchies import creatTree
from pyontutils.closed_namespaces import rdf, rdfs, owl, skos, oboInOwl, dc
try:
breakpoint
except NameError:
from IPython import embed as breakpoint
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
COMMIT_HASH_HEAD_LEN = 8
CONFIG_HASH_HEAD_LEN = 8
bigleaves = 'go.owl', 'uberon.owl', 'pr.owl', 'doid.owl', 'taxslim.owl', 'chebislim.ttl', 'ero.owl'
Query = namedtuple('Query', ['root', 'relationshipType', 'direction', 'depth'])
class NotBuiltError(FileNotFoundError):
pass
def identity_json(blob,
args["<docopt>"] = sys.stdin.read()
if args["--template"] is None:
args["--template"] = os.path.join(os.path.dirname(os.path.realpath(__file__)), "template.c")
with open(args["--template"], "r") as f:
args["--template"] = f.read()
except IOError as e:
sys.exit(e)
doc = args["<docopt>"]
usage = docopt.parse_section("usage:", doc)
s = ["More than one ", '"usage:" (case-insensitive)', " not found."]
usage = {0: s[1:], 1: usage[0] if usage else None}.get(len(usage), s[:2])
if isinstance(usage, list):
raise docopt.DocoptLanguageError("".join(usage))
all_options = docopt.parse_defaults(doc)
pattern = docopt.parse_pattern(docopt.formal_usage(usage), all_options)
leafs, commands, arguments, flags, options = parse_leafs(pattern, all_options)
t_commands = ";\n ".join("int %s" % c_name(cmd.name) for cmd in commands)
t_commands = ("\n /* commands */\n " + t_commands + ";") if t_commands != "" else ""
t_arguments = ";\n ".join("char *%s" % c_name(arg.name) for arg in arguments)
t_arguments = ("\n /* arguments */\n " + t_arguments + ";") if t_arguments != "" else ""
t_flags = ";\n ".join("int %s" % c_name(flag.long or flag.short) for flag in flags)
t_flags = ("\n /* options without arguments */\n " + t_flags + ";") if t_flags != "" else ""
t_options = ";\n ".join("char *%s" % c_name(opt.long or opt.short) for opt in options)
t_options = ("\n /* options with arguments */\n " + t_options + ";") if t_options != "" else ""
t_defaults = ", ".join(to_c(leaf.value) for leaf in leafs)
t_defaults = re.sub(r'"(.*?)"', r'(char*) "\1"', t_defaults)
t_defaults = "\n ".join(textwrap.wrap(t_defaults, 72))
t_defaults = ("\n " + t_defaults + ",") if t_defaults != "" else ""
def main(local=False):
from scibot.config import api_token, username, group, group2
print(username, group, group2) # sanity check
from scibot.sync import __doc__ as sync__doc__, Locker, client
from scibot.config import syncword
if syncword is None:
raise KeyError('Please set the SCIBOT_SYNC environment variable')
from docopt import docopt, parse_defaults
_sdefaults = {o.name:o.value if o.argcount else None for o in parse_defaults(sync__doc__)}
_backup_sync_port = int(_sdefaults['--port'])
app = Flask('scibot bookmarklet server')
if __name__ == '__main__':
args = docopt(__doc__)
_sync_port = args['--sync-port']
if _sync_port:
sync_port = int(_sync_port)
else:
sync_port = _backup_sync_port
else:
sync_port = _backup_sync_port
chan = 'localhost', sync_port
# TODO
#try:
#except AuthenticationError as e:
#raise e
send = run(client, chan, syncword)
URL_LOCK = Locker(send)
app.URL_LOCK = URL_LOCK
#@app.route('/synctest', methods=['GET'])
def synctest():
URL_LOCK.start_uri('a-test-uri')
URL_LOCK.stop_uri('a-test-uri')
return 'test-passed?'
synctest()
@app.route('/controlled-tags', methods=['GET'])
def route_controlled_tags():
curator_tags = curatorTags() # TODO need client support for workflow:RRID -> * here
return '\n'.join(curator_tags), 200, {'Content-Type':'text/plain; charset=utf-8'}
@app.route('/rrid', methods=['POST', 'OPTIONS'])
def rrid():
return rrid_wrapper(request, username, api_token, group, 'logs/rrid/', URL_LOCK)
@app.route('/validaterrid', methods=['POST', 'OPTIONS'])
def validaterrid(request):
return rrid_wrapper(request, username, api_token, group2, 'logs/validaterrid/', URL_LOCK)
@app.route('/bookmarklet', methods=['GET'])
def bookmarklet():
return bookmarklet_wrapper(request, 'rrid')
@app.route('/validatebookmarklet', methods=['GET'])
def validatebookmarklet():
return bookmarklet_wrapper(request, 'validaterrid')
@app.route('/export', methods=['GET'])
def export():
print('starting csv export')
output_rows, DATE = export_impl()
data = StringIO()
writer = csv.writer(data)
writer.writerows(sorted(output_rows))
return gzip.compress(data.getvalue().encode()), 200, {
'Content-Type': 'text/csv',
'Content-Disposition': 'attachment;filename = RRID-data-%s.csv' % DATE,
'Content-Encoding': 'gzip'}
@app.route('/export.json', methods=['GET'])
def export_json():
print('starting json export')
output_json, DATE = export_json_impl()
data = json.dumps(output_json, sort_keys=True, indent=4)
return gzip.compress(data.encode()), 200, {
'Content-Type': 'application/json',
'Content-Encoding': 'gzip'}
if not local:
return app
else:
from os.path import expanduser
from wsgiref.simple_server import make_server
from scibot.config import test_host, port_bookmarklet
print('no login detected, running on localhost only')
host = test_host
port = port_bookmarklet
print('host: %s, port %s' % ( host, port ))
server = make_server(host, port, app)
# openssl req -new -x509 -keyout scibot-self-sign-temp.pem -out scibot-self-sign-temp.pem -days 365 -nodes
#server.socket = ssl.wrap_socket(server.socket,
#keyfile='/etc/letsencrypt/live/scibot.scicrunch.io/privkey.pem',
#certfile='/etc/letsencrypt/live/scibot.scicrunch.io/fullchain.pem',
#server_side=True)
server.socket = ssl.wrap_socket(server.socket,
keyfile=expanduser('~/files/certs/scibot_test/tmp-nginx.key'),
certfile=expanduser('~/files/certs/scibot_test/tmp-nginx.crt'),
server_side=True)
server.serve_forever()
def main():
args = docopt.docopt(__doc__, version='none')
with open(args['<docopt_file>'], 'r') as f:
args['<docopt_file>'] = f.read()
template_h_name = args['--template_h']
template_c_name = args['--template_c']
args['template_h_obj'] = read_template_file_contents(args['--template_h'])
args['template_c_obj'] = read_template_file_contents(args['--template_c'])
doc = args['<docopt_file>']
usage = docopt.printable_usage(doc)
all_options = docopt.parse_defaults(doc)
pattern = docopt.parse_pattern(docopt.formal_usage(usage), all_options)
prompt = usage.split()[1].strip()
usage_lines = [x.replace(prompt, "") for x in usage.split('\n')[1:]]
tokens = []
commands = []
# I'm not sure why we have to reach in here, but it "works"
required_commands = pattern.children[0].children
for idx, required in enumerate(required_commands):
parts = [
o.name for o in required.children if isinstance(o, docopt.Command)
]
if not parts:
continue
# "help" is a special case? So exclude?
if "help" in parts:
continue
tokens.extend(parts)
docopt_text = usage_lines[idx].strip(
) if idx < len(usage_lines) else None
commands.append(Command(parts, docopt_text))
if args['--short'] is not None:
doc = doc.replace(prompt + " ", args['--short'] + " ")
rendering = Rendering(args['<module_name>'], commands, prompt, doc,
args['--multithreaded'])
if len(rendering.tokens) > 64:
raise docopt.DocoptExit(
'Too many unique tokens ({}) for Docopt μC (max:64)'.format(
len(rendering.tokens)))
too_long_commands = []
for cmd in rendering.commands:
if len(cmd.parts) > 6:
too_long_commands.append(cmd)
if too_long_commands:
summaries = [
' > {}'.format(" ".join(p for p in c.parts))
for c in too_long_commands
]
raise docopt.DocoptExit('\n'.join([
'The following commands are too long for Docopt μC (max: 6 long):'
] + summaries))
output_h_filename = args['--template_h'].replace(args['--template_prefix'],
rendering.include_name)
output_c_filename = args['--template_c'].replace(args['--template_prefix'],
rendering.include_name)
output_h_filename = os.path.join(args['--output_dir'], output_h_filename)
output_c_filename = os.path.join(args['--output_dir'], output_c_filename)
with open(output_h_filename, 'w') as f:
f.write(args['template_h_obj'].render(rendering=rendering))
with open(output_c_filename, 'w') as f:
f.write(args['template_c_obj'].render(rendering=rendering))
if args["--no-docopt-args-h"] is False:
# copy the docopt header file to the output directory
docopt_args = pkg_resources.resource_filename(
__name__, 'templates/docopt_args.h')
shutil.copy2(docopt_args, args['--output_dir'])
def test_issue_126_defaults_not_parsed_correctly_when_tabs():
section = 'Options:\n\t--foo=<arg> [default: bar]'
assert parse_defaults(section) == [Option(None, '--foo', 1, 'bar')]
-p --profile enable profiling on parsing and serialization
-d --debug launch debugger after parsing and before serialization
"""
import os
import sys
from io import StringIO, TextIOWrapper
from json.decoder import JSONDecodeError
from concurrent.futures import ProcessPoolExecutor
from docopt import docopt, parse_defaults
import rdflib
from rdflib.plugins.parsers.notation3 import BadSyntax
from ttlser.utils import regjsonld
defaults = {o.name:o.value if o.argcount else None for o in parse_defaults(__doc__)}
#GRAPHCLASS = rdflib.Graph
GRAPHCLASS = rdflib.ConjunctiveGraph
def getVersion():
ttlser = rdflib.plugin.get('nifttl', rdflib.serializer.Serializer)
ttlser_version = ttlser._CustomTurtleSerializer__version # FIXME
version = "ttlfmt v0.0.2\nttlser {}".format(ttlser_version)
return version
def prepare(filepath_or_stream, outpath=None, stream=False):
if stream:
infmt_guess = 'turtle'
if outpath is None:
def test_issue_126_defaults_not_parsed_correctly_when_tabs():
section = 'Options:\n\t--foo=<arg> [default: bar]'
assert parse_defaults(section) == [Option(None, '--foo', 1, 'bar')]
from docopt import parse_defaults
from sparcur import exceptions as exc
from sparcur.cli import Report, Options, __doc__ as clidoc
from sparcur.paths import Path, BlackfynnCache
from sparcur.config import auth
from sparcur.server import make_app
from sparcur.backends import BlackfynnRemote
from sparcur.curation import Summary
project_path = Path.cwd()
if not (project_path / Path._cache_class._local_data_dir).exists():
raise exc.NotInProjectError(f'{project_path}')
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(clidoc)
}
args = {
'server': True,
'--raw': False,
'--latest': True,
'--sort-count-desc': True,
'--project-path': project_path,
'--tab-table': False,
'<path>': [],
'--verbose': False,
'--export-path': auth.get_path('export-path'),
'--partial': False,
'--open': False,
}
with open(args['--template'], 'r') as f:
args['--template'] = f.read()
if args['--header']:
with open(template_h_path, 'r') as f:
template_h = f.read()
except IOError as e:
sys.exit(e)
doc = args['<docopt>']
usage = docopt.parse_section('usage:', doc)
s = ['More than one ', '"usage:" (case-insensitive)', ' not found.']
usage = {0: s[1:], 1: usage[0] if usage else None}.get(len(usage), s[:2])
if isinstance(usage, list):
raise docopt.DocoptLanguageError(''.join(usage))
all_options = docopt.parse_defaults(doc)
pattern = docopt.parse_pattern(docopt.formal_usage(usage), all_options)
leafs, commands, arguments, flags, options = parse_leafs(
pattern, all_options)
t_commands = ';\n '.join('int %s' % c_name(cmd.name)
for cmd in commands)
t_commands = (('\n /* commands */\n ' + t_commands +
';') if t_commands != '' else '')
t_arguments = ';\n '.join('char *%s' % c_name(arg.name)
for arg in arguments)
t_arguments = (('\n /* arguments */\n ' + t_arguments +
';') if t_arguments != '' else '')
t_flags = ';\n '.join('int %s' % c_name(flag.long or flag.short)
for flag in flags)
t_flags = (('\n /* options without arguments */\n ' + t_flags +
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='ontutils 0.0.1')
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
verbose = args['--verbose']
debug = args['--debug']
repo_name = args['<repo>']
git_local = os.path.expanduser(args['--git-local'])
epoch = args['--epoch']
curies_location = args['--curies']
curies = getCuries(curies_location)
curie_prefixes = set(curies.values())
filenames = args['<file>']
filenames.sort(key=lambda f: os.path.getsize(f),
reverse=True) # make sure the big boys go first
refactor_skip = ('nif.ttl', 'resources.ttl', 'generated/chebislim.ttl',
'unused/ro_bfo_bridge.ttl', 'generated/ncbigeneslim.ttl',
'generated/NIF-NIFSTD-mapping.ttl')
rfilenames = [f for f in filenames if f not in refactor_skip]
if args['devconfig']:
if args['--write']:
file = devconfig.write(args['--output-file'])
print(f'config written to {file}')
elif args['<field>']:
for f in args['<field>']:
print(getattr(devconfig, f, ''))
else:
print(devconfig)
elif args['catalog-extras']:
catalog_extras(args['--fetch'])
elif args['version-iri']:
version_iris(*filenames, epoch=epoch)
elif args['scigraph-stress']:
scigraph_stress(int(args['--rate']), int(args['--timeout']), verbose,
debug)
elif args['deadlinks']:
deadlinks(filenames, int(args['--rate']), int(args['--timeout']),
verbose, debug)
elif args['spell']:
spell(filenames, debug)
elif args['iri-commit']:
make_git_commit_command(git_local, repo_name)
elif args['uri-switch']:
uri_switch(rfilenames, uri_switch_values)
elif args['backend-refactor']:
backend_refactor(rfilenames, backend_refactor_values)
elif args['todo']:
graph = loadall(git_local, repo_name, local=True)
graph_todo(graph, curie_prefixes, uri_switch_values)
embed()
elif args['expand']:
curies['NLXWIKI'] = 'http://legacy.neurolex.org/wiki/'
for curie in args['<curie>']:
prefix, suffix = curie.split(':')
print(curies[prefix] + suffix)
from subprocess import check_output
from collections import OrderedDict
from docopt import docopt, printable_usage, parse_defaults, formal_usage
if __name__ == '__main__':
args = docopt(__doc__, help=True, version=1.0)
base_command = args.get('<tool_help_call>').split(' ')
doc = check_output(base_command)
# Load options and arguments
doc_options, doc_args = optdoc.parse_defaults(doc)
# Load list
usage = printable_usage(doc)
options = parse_defaults(doc)
pattern, arg_list, cmd_list, ids = optdoc.parse_pattern(formal_usage(usage), options)
# print pattern
# Print args, options, cmds, and lists
# print 'ARGS \n' + str(args) + '\n'
# print 'OPTIONS \n' + str(doc_options) + '\n'
# print 'ARGUMENTS \n' + str(doc_args) + '\n'
# print 'LIST OPT/ARGS \n' + str(arg_list)
# print 'CMD \n' + str(cmd_list)
# remove -h/--help from base_command
if '-h' in base_command:
base_command.remove('-h')
elif '--help' in base_command:
base_command.remove('--help')
def main():
import sys
from pyontutils.clifun import Dispatcher, Options as BaseOptions
class Options(BaseOptions):
drive_scopes = (
'appdata',
'file',
'metadata',
'metadata.readonly',
'photos.readonly',
'readonly',
'scripts',)
def __new__(cls, args, defaults):
bads = []
for scope in args['--drive-scope']:
if scope not in cls.drive_scopes:
bads.append(scope)
if bads:
log.error(f'Invalid scopes! {bads}')
sys.exit(1)
return super().__new__(cls, args, defaults)
class Main(Dispatcher):
@property
def _scopes(self):
base = 'https://www.googleapis.com/auth/'
suffix = '.readonly' if self.options.readonly else ''
if self.options.sheets:
yield base + 'spreadsheets' + suffix
if self.options.docs:
yield base + 'doccuments' + suffix
if self.options.drive:
suffixes = []
if suffix:
suffixes.append(suffix)
suffixes += ['.' + s for s in self.options.drive_scope]
if not suffixes:
suffixes = '',
for suffix in suffixes:
yield base + 'drive' + suffix
def auth(self):
newline = '\n'
scopes = list(self._scopes)
if self.options.debug:
log.debug(f'requesting for scopes:\n{newline.join(scopes)}')
service = get_oauth_service(readonly=self.options.readonly, SCOPES=scopes)
# FIXME decouple this ...
log.info(f'Auth finished successfully for scopes:\n{newline.join(scopes)}')
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='clifun-demo 0.0.0')
passthrough = ('--noauth_local_webserver',
'--auth_host_name',
'--auth_host_port',
'--logging_level')
to_pop = [arg for i, arg in enumerate(sys.argv)
if i and not [None for pt in passthrough if pt in arg]]
for arg in to_pop:
sys.argv.pop(sys.argv.index(arg))
defaults = {o.name:o.value if o.argcount else None for o in parse_defaults(__doc__)}
options = Options(args, defaults)
main = Main(options)
if main.options.debug:
log.setLevel('DEBUG')
print(main.options)
main()
def test_issue_126_defaults_not_parsed_correctly_when_tabs():
section = "Options:\n\t--foo=<arg> [default: bar]"
assert parse_defaults(section) == [
Option(None, "--foo", 1, "bar", "<arg>")
]
def main():
from docopt import docopt, parse_defaults
args = docopt(__doc__, version='ontutils 0.0.1')
defaults = {
o.name: o.value if o.argcount else None
for o in parse_defaults(__doc__)
}
verbose = args['--verbose']
debug = args['--debug']
repo_name = args['<repo>']
git_local = os.path.expanduser(args['--git-local'])
epoch = args['--epoch']
curies_location = args['--curies']
curies = getCuries(curies_location)
curie_prefixes = set(curies.values())
filenames = args['<file>']
filenames.sort(key=lambda f: os.path.getsize(f),
reverse=True) # make sure the big boys go first
refactor_skip = ('nif.ttl', 'resources.ttl', 'generated/chebislim.ttl',
'unused/ro_bfo_bridge.ttl', 'generated/ncbigeneslim.ttl',
'generated/NIF-NIFSTD-mapping.ttl')
rfilenames = [f for f in filenames if f not in refactor_skip]
if args['set']:
from pyontutils.config import auth
uc = auth.user_config
def set_uc(var, value):
with open(uc._path, 'rt') as f:
text = f.read()
if '#' in text:
msg = f'Comments detected! Not writing config! {uc._path}'
raise ValueError(msg)
blob = uc.load()
# XXX NEVER DUMP A CONFIG THIS YOU _WILL_ KLOBBER IT
# BY ACCIDENT AT SOME POINT AND WILL ERASE ANY/ALL COMMENTS
# THERE IS NO SAFETY WITH THIS IMPLEMENTATION
# USERS SHOULD EDIT THEIR CONFIGS DIRECTLY
# except that it makes giving instructions for
# setting values a bit more complicated
blob['auth-variables'][var] = value
uc.dump(blob)
if args['ontology-local-repo']:
var = 'ontology-local-repo'
olr = Path(args['<path>']).expanduser().resolve()
olr_string = olr.as_posix()
set_uc(var, olr_string)
value2 = auth.get_path(var)
if not value2.exists():
msg = f'{var} path does not exist! {value2}'
print(tc.red('WARNING'), msg)
msg = f'{var} path {value2} written to {uc._path}'
print(msg)
assert olr == value2
elif args['scigraph-api-key']:
# FIXME this is a hack on top of orthauth, which will not
#
# check the secrets path first to make sure it is ok
# be implementing programmtic modification of user config
# files any time soon, though it might make sense to have a
# "machine config path" in addition to auth and user config
path = ['scigraph', 'api', 'key']
spath = auth._pathit(uc.get_blob('auth-stores', 'secrets')['path'])
if not spath.parent.exists():
spath.parent.mkdir(parents=True)
spath.parent.chmod(0o0700)
if spath.suffix != '.yaml':
msg = f"Can't write secrets file of type {spath.suffix}"
args = None
raise NotImplementedError(msg)
v = None
try:
s = uc.secrets
v = s(*path)
except:
pass
if v is not None:
v = None
raise ValueError(f'Path already in secrets! {path} in {spath}')
# safely append to the secrets file
key = args['<key>']
path_key = f'\nscigraph:\n api:\n key: {key}'
if not spath.exists():
spath.touch()
spath.chmod(0o0600)
with open(spath, 'a+') as f:
f.write(path_key)
# set the config var
var = 'scigraph-api-key'
value = {'path': ' '.join(path)}
set_uc(var, value) # set the path
# XXX NOTE yes, it is correct to do this only after secrets succeeds
# otherwise it is possible to get into a state where secrets does
# not exist but there is a path pointing to it, so load this
# ontutils file will fail during import time
# test that we got the value we expected
value2 = auth.get(var)
msg = (f'Key written to secrets. {spath} and path to '
f'key was written to config {uc._path}')
print(msg)
assert key == value2, 'Key retrieved does not match key set!'
elif args['devconfig']:
if args['--write']:
file = devconfig.write(args['--output-file'])
print(f'config written to {file}')
elif args['<field>']:
for f in args['<field>']:
print(getattr(devconfig, f, ''))
else:
print(devconfig)
elif args['catalog-extras']:
catalog_extras(args['--fetch'])
elif args['version-iri']:
version_iris(*filenames, epoch=epoch)
elif args['scigraph-stress']:
scigraph_stress(int(args['--rate']), int(args['--timeout']), verbose,
debug)
elif args['deadlinks']:
deadlinks(filenames, int(args['--rate']), int(args['--timeout']),
verbose, debug)
elif args['spell']:
spell(filenames, debug)
elif args['iri-commit']:
make_git_commit_command(git_local, repo_name)
elif args['uri-switch']:
uri_switch(rfilenames, uri_switch_values)
elif args['backend-refactor']:
backend_refactor(rfilenames, backend_refactor_values)
elif args['todo']:
graph = loadall(git_local, repo_name, local=True)
graph_todo(graph, curie_prefixes, uri_switch_values)
breakpoint()
elif args['expand']:
curies['NLXWIKI'] = 'http://legacy.neurolex.org/wiki/'
for curie in args['<curie>']:
prefix, suffix = curie.split(':')
print(curies[prefix] + suffix)