def main():
memoryCheck(7300000000)
ncbigene_make()
build(Chebi, n_jobs=1)
chebi_dead().write()
if False:
from pyontutils.qnamefix import cull_prefixes
with open('/tmp/chebi-debug.xml', 'wb') as f:
ChebiOntSrc.raw.write(f)
#with open('/tmp/chebi-debug.ttl', 'wb') as f: f.write(ChebiOntSrc._data[2].serialize(format='nifttl'))
g = cull_prefixes(ChebiOntSrc._data[2])
g.filename = '/tmp/chebi-debug.ttl'
g.write()
embed()
def main():
olr = auth.get_path('ontology-local-repo')
resources = auth.get_path('resources')
if not olr.exists():
raise FileNotFoundError(f'{olr} does not exist cannot continue')
if not resources.exists():
raise FileNotFoundError(f'{resources} does not exist cannot continue')
from docopt import docopt
args = docopt(__doc__, version='parcellation 0.0.1')
# import all ye submodules we have it sorted! LabelBase will find everything for us. :D
if not args['--local']:
from nifstd_tools.parcellation.aba import Artifacts as abaArts
from nifstd_tools.parcellation.fsl import FSL # Artifacts is attached to the class
from nifstd_tools.parcellation.whs import Artifacts as whsArts
from nifstd_tools.parcellation.berman import Artifacts as bermArts
from nifstd_tools.parcellation.paxinos import Artifacts as paxArts
from nifstd_tools.parcellation.swanson import Artifacts as swArts
from nifstd_tools.parcellation.freesurfer import Artifacts as fsArts
onts = getOnts()
_ = *(print(ont) for ont in onts),
out = build(*onts,
parcBridge,
fail=args['--fail'],
n_jobs=int(args['--jobs']))
if args['--stats']:
breakpoint()
def main():
from docopt import docopt
# import from this file to avoid __main__ vs module issues
# when trying to debug inspect in an ipython instance
# who doesn't love completely inconsistent behavior within
# purely interpreted code? can you imagine what is going to
# happen if python ever gets a real compiler !?
try:
from scr_sync import Registry, RegistrySource
except:
try:
from nifstd_tools.scr_sync import Registry, RegistrySource
except:
pass
args = docopt(__doc__, version='registry-sync 1.0.0')
(user, host, port, database, git_remote, git_local, org,
repo) = (args['--' + k]
for k in ('user', 'host', 'port', 'database', 'git-remote',
'git-local', 'org', 'repo'))
remote = os.path.join(git_remote, org, repo)
local = Path(git_local, repo)
if not local.exists():
local.parent
else:
Registry.local_base = local
RegistrySource.source = f'{host}:{port}/{database}'
Registry.config(user=user, host=host, port=port, database=database)
if not args['--test']:
graph, = build(Registry, n_jobs=1)
def main():
getOnts()
return
out = build(
DHBALabels,
DMBALabels,
HBALabels,
MBALabels,
)
def main():
from docopt import docopt
args = docopt(__doc__, version='registry-sync 1.0.0')
(user, host, port, database, git_remote, git_local, org,
repo) = (args['--' + k]
for k in ('user', 'host', 'port', 'database', 'git-remote',
'git-local', 'org', 'repo'))
remote = os.path.join(git_remote, org, repo)
local = Path(git_local, repo)
if not local.exists():
local.parent
RegistrySource.source = f'{host}:{port}/{database}'
Registry.config(user=user, host=host, port=port, database=database)
if not args['--test']:
graph, = build(Registry, n_jobs=1)
def main():
build(ksDefs, n_jobs=1)
def main():
build(DKTLabels, FreeSurferLabels)
def main():
from pyontutils.core import build
build(WHSSDLabels)
