/usr/share/pyshared/nipype/utils/config.py is in python-nipype 0.5.3-2wheezy2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# vi: set ft=python sts=4 ts=4 sw=4 et:
'''
Created on 20 Apr 2010
logging options : INFO, DEBUG
hash_method : content, timestamp
@author: Chris Filo Gorgolewski
'''
import ConfigParser
from json import load, dump
import os
import shutil
from StringIO import StringIO
from warnings import warn
from ..external import portalocker
homedir = os.environ['HOME']
default_cfg = """
[logging]
workflow_level = INFO
filemanip_level = INFO
interface_level = INFO
log_to_file = false
log_directory = %s
log_size = 16384000
log_rotate = 4
[execution]
create_report = true
crashdump_dir = %s
hash_method = timestamp
job_finished_timeout = 5
keep_inputs = false
local_hash_check = false
matplotlib_backend = Agg
plugin = Linear
remove_node_directories = false
remove_unnecessary_outputs = true
single_thread_matlab = true
stop_on_first_crash = false
stop_on_first_rerun = false
use_relative_paths = false
[check]
interval = 1209600
""" % (homedir, os.getcwd())
class NipypeConfig(object):
"""Base nipype config class
"""
def __init__(self, *args, **kwargs):
self._config = ConfigParser.ConfigParser()
config_dir = os.path.expanduser('~/.nipype')
if not os.path.exists(config_dir):
os.makedirs(config_dir)
old_config_file = os.path.expanduser('~/.nipype.cfg')
new_config_file = os.path.join(config_dir, 'nipype.cfg')
# To be deprecated in two releases
if os.path.exists(old_config_file):
if os.path.exists(new_config_file):
msg=("Detected presence of both old (%s, used by versions "
"< 0.5.2) and new (%s) config files. This version will "
"proceed with the new one. We advise to merge settings "
"and remove old config file if you are not planning to "
"use previous releases of nipype.") % (old_config_file,
new_config_file)
warn(msg)
else:
warn("Moving old config file from: %s to %s" % (old_config_file,
new_config_file))
shutil.move(old_config_file, new_config_file)
self.data_file = os.path.join(config_dir, 'nipype.json')
self._config.readfp(StringIO(default_cfg))
self._config.read([new_config_file, old_config_file, 'nipype.cfg'])
def set_default_config(self):
self._config.readfp(StringIO(default_cfg))
def enable_debug_mode(self):
"""Enables debug configuration
"""
self._config.set('execution', 'stop_on_first_crash', 'true')
self._config.set('execution', 'remove_unnecessary_outputs', 'false')
self._config.set('execution', 'keep_inputs', 'true')
self._config.set('logging', 'workflow_level', 'DEBUG')
self._config.set('logging', 'interface_level', 'DEBUG')
def set_log_dir(self, log_dir):
"""Sets logging directory
This should be the first thing that is done before any nipype class
with logging is imported.
"""
self._config.set('logging', 'log_directory', log_dir)
def get(self, section, option):
return self._config.get(section, option)
def set(self, section, option, value):
return self._config.set(section, option, value)
def getboolean(self, section, option):
return self._config.getboolean(section, option)
def has_option(self, section, option):
return self._config.has_option(section, option)
@property
def _sections(self):
return self._config._sections
def get_data(self, key):
if not os.path.exists(self.data_file):
return None
with open(self.data_file, 'rt') as file:
portalocker.lock(file, portalocker.LOCK_EX)
datadict = load(file)
if key in datadict:
return datadict[key]
return None
def save_data(self, key, value):
datadict = {}
if os.path.exists(self.data_file):
with open(self.data_file, 'rt') as file:
portalocker.lock(file, portalocker.LOCK_EX)
datadict = load(file)
with open(self.data_file, 'wt') as file:
portalocker.lock(file, portalocker.LOCK_EX)
datadict[key] = value
dump(datadict, file)
def update_config(self, config_dict):
for section in ['execution', 'logging', 'check']:
if section in config_dict:
for key, val in config_dict[section].items():
if not key.startswith('__'):
self._config.set(section, key, str(val))
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