def scigraph_stress(rate,
timeout=5,
verbose=False,
debug=False,
scigraph=auth.get('scigraph-api')):
# TODO use the api classes
with open((auth.get_path('resources') / 'chebi-subset-ids.txt').as_posix(),
'rt') as f:
urls = [
os.path.join(scigraph, f'vocabulary/id/{curie.strip()}')
for curie in f.readlines()
]
print(urls)
url_blaster(urls, rate, timeout, verbose, debug)
def gencode(self):
""" Run this to generate the code """
resp = requests.get(self.api_url)
if not resp.ok:
if resp.status_code == 401 and 'scicrunch.org' in self.api_url:
resp = requests.get(
self.api_url,
params={'key': auth.get('scigraph-api-key')})
else:
resp.raise_for_status()
ledict = resp.json()
for durl in self._dynamics:
dj = requests.get(durl).json()
for p in dj['paths']:
if p.startswith('/dynamic') and p not in ledict['paths']:
ledict['paths'][p] = dj['paths'][p]
ledict = self.dotopdict(ledict)
out = self.dodict(ledict)
self._code = out
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)