change in the obi programme according to the new obitools3.apps module
creation
This commit is contained in:
203
python/obi.py
203
python/obi.py
@ -16,30 +16,21 @@ It defines classes_and_methods
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@deffield updated: Updated
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'''
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import sys
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import pkgutil
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import argparse
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import logging
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import json
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default_config = {
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default_config = { 'software' : "The OBITools",
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'log' : False,
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'loglevel' : 'INFO',
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'progress' : True
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}
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'obi' : { 'log' : True,
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'loglevel' : 'INFO',
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'version' : False,
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'progress' : True
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}
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}
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root_config_name='obi'
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from obitools3 import command
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from obitools3.apps.config import getConfiguration # @UnresolvedImport
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from obitools3.version import version
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__all__ = []
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__all__ = []
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__version__ = version
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__date__ = '2014-09-28'
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__date__ = '2014-09-28'
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__updated__ = '2014-09-28'
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DEBUG = 1
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@ -47,182 +38,12 @@ TESTRUN = 0
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PROFILE = 0
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def loadCommand(name,loader):
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'''
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Load a command module from its name and an ImpLoader
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This function is for internal use
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@param name: name of the module
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@type name: str
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@param loader: the module loader
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@type loader: ImpLoader
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@return the loaded module
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@rtype: module
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'''
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module = loader.find_module(name).load_module(name)
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return module
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def getCommandsList():
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'''
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Returns the list of sub-commands available to the main `obi` command
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@return: a dict instance with key corresponding to each command and
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value corresponding to the module
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@rtype: dict
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'''
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cmds = dict((x[1],loadCommand(x[1],x[0]))
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for x in pkgutil.iter_modules(command.__path__)
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if not x[2])
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return cmds
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def getLogger(config):
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'''
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Returns the logger as defined by the command line option
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or by the config file
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:param config:
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'''
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output = config['obi']['outputfilename']
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level = config['obi']['loglevel']
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logfile= config['obi']['log']
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rootlogger = logging.getLogger()
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logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s] %(message)s")
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stderrHandler = logging.StreamHandler(sys.stderr)
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stderrHandler.setFormatter(logFormatter)
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rootlogger.addHandler(stderrHandler)
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if logfile:
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fileHandler = logging.FileHandler("%s.log" % output)
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fileHandler.setFormatter(logFormatter)
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rootlogger.addHandler(fileHandler)
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try:
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loglevel = getattr(logging, level)
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except:
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loglevel = logging.INFO
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rootlogger.setLevel(loglevel)
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config['obi']['logger']=rootlogger
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return rootlogger
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class ObiParser(argparse.ArgumentParser):
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def error(self, message):
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sys.stderr.write('error: %s\n' % message)
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self.print_help()
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sys.exit(2)
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def buildArgumentParser():
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parser = ObiParser()
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parser.add_argument('--version', dest='obi:version',
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action='store_true',
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default=False,
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help='Print the version of the OBITools')
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parser.add_argument('--no-log', dest='obi:log',
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action='store_false',
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default=None,
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help='Do not create a logfile for the data analyze')
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parser.add_argument('--no-progress', dest='obi:progress',
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action='store_false',
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default=None,
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help='Do not print the progress bar during analyzes')
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subparsers = parser.add_subparsers(title='subcommands',
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description='valid subcommands',
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help='additional help')
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commands = getCommandsList()
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for c in commands:
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module = commands[c]
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if hasattr(module, "run"):
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if hasattr(module, "__title__"):
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sub = subparsers.add_parser(c,help=module.__title__)
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else:
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sub = subparsers.add_parser(c)
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if hasattr(module, "addOptions"):
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module.addOptions(sub)
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sub.set_defaults(**{'obi:module' : module})
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return parser
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def buildDefaultConfiguration():
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global default_config
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commands = getCommandsList()
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for c in commands:
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module = commands[c]
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assert hasattr(module, "run")
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if hasattr(module, 'default_config'):
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default_config[c]=module.default_config
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else:
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default_config[c]={}
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return default_config
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def getConfiguration():
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global default_config
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if '__done__' in default_config:
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return default_config
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parser = buildArgumentParser()
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options = vars(parser.parse_args())
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config = buildDefaultConfiguration()
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for k in options:
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section,key = k.split(':')
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s = config[section]
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if options[k] is not None:
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s[key]=options[k]
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if config['obi']['version']:
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print("The OBITools - Version %s" % __version__)
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sys.exit(0)
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if not 'module' in config['obi']:
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print('\nError: No obi command specified',file=sys.stderr)
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parser.print_help()
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sys.exit(2)
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if config['obi']['outputfilename'] is None:
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config['obi']['outputfilename']=config['obi']['indexfilename']
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getLogger(config)
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config['__done__']=True
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return config
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if __name__ =="__main__":
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config = getConfiguration()
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config = getConfiguration(root_config_name,
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default_config)
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config['obi']['module'].run(config)
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config[root_config_name]['module'].run(config)
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