change in the obi programme according to the new obitools3.apps module
creation
This commit is contained in:
193
python/obi.py
193
python/obi.py
@ -16,25 +16,16 @@ It defines classes_and_methods
|
||||
@deffield updated: Updated
|
||||
'''
|
||||
|
||||
import sys
|
||||
import pkgutil
|
||||
import argparse
|
||||
import logging
|
||||
import json
|
||||
|
||||
default_config = {
|
||||
|
||||
'obi' : { 'log' : True,
|
||||
default_config = { 'software' : "The OBITools",
|
||||
'log' : False,
|
||||
'loglevel' : 'INFO',
|
||||
'version' : False,
|
||||
'progress' : True
|
||||
}
|
||||
|
||||
}
|
||||
root_config_name='obi'
|
||||
|
||||
|
||||
|
||||
from obitools3 import command
|
||||
from obitools3.apps.config import getConfiguration # @UnresolvedImport
|
||||
from obitools3.version import version
|
||||
|
||||
__all__ = []
|
||||
@ -47,182 +38,12 @@ TESTRUN = 0
|
||||
PROFILE = 0
|
||||
|
||||
|
||||
|
||||
def loadCommand(name,loader):
|
||||
'''
|
||||
Load a command module from its name and an ImpLoader
|
||||
|
||||
This function is for internal use
|
||||
|
||||
@param name: name of the module
|
||||
@type name: str
|
||||
@param loader: the module loader
|
||||
@type loader: ImpLoader
|
||||
|
||||
@return the loaded module
|
||||
@rtype: module
|
||||
'''
|
||||
|
||||
module = loader.find_module(name).load_module(name)
|
||||
return module
|
||||
|
||||
def getCommandsList():
|
||||
'''
|
||||
Returns the list of sub-commands available to the main `obi` command
|
||||
|
||||
@return: a dict instance with key corresponding to each command and
|
||||
value corresponding to the module
|
||||
|
||||
@rtype: dict
|
||||
'''
|
||||
cmds = dict((x[1],loadCommand(x[1],x[0]))
|
||||
for x in pkgutil.iter_modules(command.__path__)
|
||||
if not x[2])
|
||||
return cmds
|
||||
|
||||
def getLogger(config):
|
||||
'''
|
||||
Returns the logger as defined by the command line option
|
||||
or by the config file
|
||||
:param config:
|
||||
'''
|
||||
|
||||
output = config['obi']['outputfilename']
|
||||
level = config['obi']['loglevel']
|
||||
logfile= config['obi']['log']
|
||||
|
||||
rootlogger = logging.getLogger()
|
||||
logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s] %(message)s")
|
||||
|
||||
stderrHandler = logging.StreamHandler(sys.stderr)
|
||||
stderrHandler.setFormatter(logFormatter)
|
||||
|
||||
rootlogger.addHandler(stderrHandler)
|
||||
|
||||
if logfile:
|
||||
fileHandler = logging.FileHandler("%s.log" % output)
|
||||
fileHandler.setFormatter(logFormatter)
|
||||
rootlogger.addHandler(fileHandler)
|
||||
|
||||
try:
|
||||
loglevel = getattr(logging, level)
|
||||
except:
|
||||
loglevel = logging.INFO
|
||||
|
||||
rootlogger.setLevel(loglevel)
|
||||
|
||||
config['obi']['logger']=rootlogger
|
||||
|
||||
return rootlogger
|
||||
|
||||
|
||||
class ObiParser(argparse.ArgumentParser):
|
||||
def error(self, message):
|
||||
sys.stderr.write('error: %s\n' % message)
|
||||
self.print_help()
|
||||
sys.exit(2)
|
||||
|
||||
def buildArgumentParser():
|
||||
parser = ObiParser()
|
||||
|
||||
parser.add_argument('--version', dest='obi:version',
|
||||
action='store_true',
|
||||
default=False,
|
||||
help='Print the version of the OBITools')
|
||||
|
||||
parser.add_argument('--no-log', dest='obi:log',
|
||||
action='store_false',
|
||||
default=None,
|
||||
help='Do not create a logfile for the data analyze')
|
||||
|
||||
parser.add_argument('--no-progress', dest='obi:progress',
|
||||
action='store_false',
|
||||
default=None,
|
||||
help='Do not print the progress bar during analyzes')
|
||||
|
||||
subparsers = parser.add_subparsers(title='subcommands',
|
||||
description='valid subcommands',
|
||||
help='additional help')
|
||||
|
||||
commands = getCommandsList()
|
||||
|
||||
for c in commands:
|
||||
module = commands[c]
|
||||
|
||||
if hasattr(module, "run"):
|
||||
if hasattr(module, "__title__"):
|
||||
sub = subparsers.add_parser(c,help=module.__title__)
|
||||
else:
|
||||
sub = subparsers.add_parser(c)
|
||||
|
||||
if hasattr(module, "addOptions"):
|
||||
module.addOptions(sub)
|
||||
|
||||
sub.set_defaults(**{'obi:module' : module})
|
||||
|
||||
return parser
|
||||
|
||||
def buildDefaultConfiguration():
|
||||
global default_config
|
||||
|
||||
commands = getCommandsList()
|
||||
|
||||
for c in commands:
|
||||
module = commands[c]
|
||||
|
||||
assert hasattr(module, "run")
|
||||
|
||||
if hasattr(module, 'default_config'):
|
||||
default_config[c]=module.default_config
|
||||
else:
|
||||
default_config[c]={}
|
||||
|
||||
return default_config
|
||||
|
||||
|
||||
def getConfiguration():
|
||||
global default_config
|
||||
|
||||
if '__done__' in default_config:
|
||||
return default_config
|
||||
|
||||
parser = buildArgumentParser()
|
||||
options = vars(parser.parse_args())
|
||||
|
||||
config = buildDefaultConfiguration()
|
||||
|
||||
|
||||
for k in options:
|
||||
section,key = k.split(':')
|
||||
s = config[section]
|
||||
if options[k] is not None:
|
||||
s[key]=options[k]
|
||||
|
||||
if config['obi']['version']:
|
||||
print("The OBITools - Version %s" % __version__)
|
||||
sys.exit(0)
|
||||
|
||||
if not 'module' in config['obi']:
|
||||
print('\nError: No obi command specified',file=sys.stderr)
|
||||
parser.print_help()
|
||||
sys.exit(2)
|
||||
|
||||
|
||||
if config['obi']['outputfilename'] is None:
|
||||
config['obi']['outputfilename']=config['obi']['indexfilename']
|
||||
|
||||
getLogger(config)
|
||||
|
||||
config['__done__']=True
|
||||
|
||||
return config
|
||||
|
||||
|
||||
if __name__ =="__main__":
|
||||
|
||||
config = getConfiguration()
|
||||
config = getConfiguration(root_config_name,
|
||||
default_config)
|
||||
|
||||
config['obi']['module'].run(config)
|
||||
config[root_config_name]['module'].run(config)
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user