def setup_environment(argv):
print("Configuring environment...")
import os
import os.path
from utilities.configFileParser import resolveDataSinkOption, parseFile
from utilities.pathHandling import validatePath
from utilities import misc
environment, experiment, pipeline, cluster = parseFile(
argv["--ExperimentConfig"], argv["--pe"], argv["--workphase"])
pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)
if cluster is None:
print("Running on local")
#raise NotImplementedError("Running local has old code and has not been tested!")
#assert argv["--wfrun"] in argvWFRUN, \
# "wfrun options for clusters can only be given when the configuration file's CLUSTER option == True"
#os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wf_template_runner"]))
else:
load_modules(cluster['modules']) # Load modules if not already done ## MODS PATH
# print os.environ['LOADEDMODULES']
#if environment['virtualenv_dir'] is not None: # MODS PATH
#activate_this = validatePath(
# os.path.join(environment['virtualenv_dir'], 'bin', 'activate_this.py'), False, False)
#if os.path.exists( activate_this ) :
# exec(open(activate_this).read(), dict(__file__=activate_this))
utilities_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'utilities')
configure_env = validatePath(os.path.join(utilities_path, 'configure_env.py'), False, False)
# Add the AutoWorkup directory to the PYTHONPATH every time - REQUIRED FOR CLUSTER DISPATCHING
environment['env']['PYTHONPATH'] = environment['env']['PYTHONPATH'] + ":" + os.path.dirname(__file__)
exec(open(configure_env).read() , dict(__file__=__file__,
append_os_path=environment['env']['PATH'],
append_sys_path=environment['env']['PYTHONPATH'])
) # MODS PATH
print("@"*80)
print(environment['env']['PYTHONPATH'])
print("@"*80)
print(environment['env']['PATH'])
print("@"*80)
from nipype import config
config.enable_debug_mode()
#config.enable_provenance()
from utilities.package_check import verify_packages
verify_packages()
if 'FREESURFER' in experiment['components']: # FREESURFER MODS
configure_FS = validatePath(os.path.join(utilities_path, 'utilities', 'configure_FS.py'), False, False)
exec(open(configure_FS).read(), dict(FS_VARS=misc.FS_VARS, env=environment['env']))
print("FREESURFER needs to check for sane environment here!") # TODO: raise warning, write method, what???
for key, value in list(environment['env'].items()):
if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
pass
else:
os.environ[key] = value # Do not use os.putenv (see Python documentation)
return environment, experiment, pipeline, cluster
def setup(argv):
print "Configuring environment..."
import os, os.path
from utilities.configFileParser import resolveDataSinkOption, parseFile
from utilities.pathHandling import validatePath
from utilities import misc
environment, experiment, pipeline, cluster = parseFile(
argv["--ExperimentConfig"], argv["--pe"])
pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)
if cluster is None:
assert argv["--wfrun"] in misc.WFRUN, \
"wfrun options for clusters can only be given when the configuration file's CLUSTER option == True"
os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wfrun"]))
else:
load_modules(cluster['modules']
) # Load modules if not already done ## MODS PATH
# print os.environ['LOADEDMODULES']
if environment['virtualenv_dir']: ## MODS PATH
activate_this = validatePath(
os.path.join(environment['virtualenv_dir'], 'bin',
'activate_this.py'), False, False)
execfile(activate_this, dict(__file__=activate_this))
utilities_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'utilities')
configure_env = validatePath(
os.path.join(utilities_path, 'configure_env.py'), False, False)
# Add the AutoWorkup directory to the PYTHONPATH every time - REQUIRED FOR CLUSTER DISPATCHING
environment['env']['PYTHONPATH'] = environment['env'][
'PYTHONPATH'] + ":" + os.path.dirname(__file__)
execfile(
configure_env,
dict(__file__=__file__,
append_os_path=environment['env']['PATH'],
append_sys_path=environment['env']['PYTHONPATH'])) ## MODS PATH
from nipype import config
config.enable_debug_mode()
from utilities.package_check import verify_packages
verify_packages()
if 'FREESURFER' in experiment['components']: ## FREESURFER MODS
configure_FS = validatePath(
os.path.join(utilities_path, 'utilities', 'configure_FS.py'),
False, False)
execfile(configure_FS,
dict(FS_VARS=misc.FS_VARS, env=environment['env']))
print "FREESURFER needs to check for sane environment here!" # TODO: raise warning, write method, what???
for key, value in environment['env'].items():
if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
pass
else:
os.environ[
key] = value # Do not use os.putenv (see Python documentation)
return environment, experiment, pipeline, cluster
def setup(argv):
print "Configuring environment..."
import os, os.path
from utilities.configFileParser import resolveDataSinkOption, parseFile
from utilities.pathHandling import validatePath
from utilities import misc
environment, experiment, pipeline, cluster = parseFile(argv["--ExperimentConfig"], argv["--pe"], argv['--wfrun'])
pipeline['ds_overwrite'] = resolveDataSinkOption(argv, pipeline)
if cluster is None:
assert argv["--wfrun"] in misc.WFRUN, \
"wfrun options for clusters can only be given when the configuration file's CLUSTER option == True"
os.environ['NSLOTS'] = str(misc.get_cpus(argv["--wfrun"]))
else:
load_modules(cluster['modules']) # Load modules if not already done ## MODS PATH
# print os.environ['LOADEDMODULES']
if environment['virtualenv']: ## MODS PATH
activate_this = validatePath(os.path.join(environment['virtualenv'], 'bin', 'activate_this.py'))
execfile(activate_this, dict(__file__=activate_this))
utilities_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'utilities')
configure_env = validatePath(os.path.join(utilities_path, 'configure_env.py'))
execfile(configure_env, dict(__file__=__file__,
append_os_path=environment['env']['PATH'],
append_sys_path=environment['env']['PYTHONPATH'])
) ## MODS PATH
from nipype import config
config.enable_debug_mode()
from utilities.package_check import verify_packages
verify_packages()
if 'FREESURFER' in experiment['components']: ## FREESURFER MODS
configure_FS = validatePath(os.path.join(utilities_path, 'utilities', 'configure_FS.py'))
execfile(configure_FS, dict(FS_VARS=misc.FS_VARS, env=environment['env']))
print "FREESURFER needs to check for sane environment here!" # TODO: raise warning, write method, what???
for key, value in environment['env'].items():
if key in ['PATH', 'PYTHONPATH'] + misc.FS_VARS:
pass
else:
os.environ[key] = value # Do not use os.putenv (see Python documentation)
return environment, experiment, pipeline, cluster
