Mercurial > repos > urgi-team > teiso
view TEisotools-1.0/commons/core/LoggerFactory.py @ 6:20ec0d14798e draft
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author | urgi-team |
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date | Wed, 20 Jul 2016 05:00:24 -0400 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. ## @mainpage Documentation of the REPET API # # Welcome to the API documentation! # This API is a set of packages and classes for pipeline(s) development. # # @par The "logger" package # # Logging is managed via LoggerFactory. This class creates instances of logging.logging python class. It's strongly encouraged to use this factory each time you need to log something. # # @par The "checker" package # # This package is a set of classes designed to facilitate development of different kind of checks: filesystem checks, environment checks, configuration file checks ... # # Classes should subclass checker::IChecker or if a logger is needed: checker::AbstractChecker. # # Methods should raise checker::CheckerException. # # Use checker::ConfigChecker and checker::ConfigException for configuration files checks. # # checker::CheckerUtils is a set of small static methods shared by other classes of checker package. # # @par The "coord" package # # This package is a set of classes dedicated to coordinates manipulations. # # A coord::Range instance records a region on a given sequence (start, end and sequence name). # # A coord::Map instance is a coord::Range instance and record a named region on a given sequence (start, end, sequence name and name). # # A coord::Set instance is a coord::Map instance and record a named region on a given sequence with an identifier (start, end, sequence name, name and id). # # A coord::Align instance handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity). # # A coord::Path instance is a coord::Align instance and handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier. # # A coord::Match instance is a coord::Path instance and handle a chain of match(es) between two sequences, query and subject, with an identifier and the length of the input sequences. # # coord::Align, coord::Map, coord::Path and coord::Set come with utils classes: coord::AlignUtils, coord::MapUtils, coord::PathUtils and coord::SetUtils. # # @par The "seq" package # # This package a set of classes dedicated to sequences manipulations. # # A seq::Bioseq instance records a sequence with its header. seq::Bioseq comes with an utils class: seq::BioseqUtils. # # A seq::BioseqDB instance handle a collection of a Bioseq (header-sequence). # # A seq::AlignedBioseqDB instance is a multiple sequence alignment representation. # # A seq::FastaUtils is a set of static methods for fasta file manipulation. # # @par The "sql" package # # This package is dedicated to persistance of coord package objects. # All classes come with dedicated interfaces. Use these interfaces for class manipulation. # Class names patterns are ITable*Adaptator and Table*Adaptator. # # sql::ITablePathAdaptator, sql::TablePathAdaptator / # sql::ITableSetAdaptator, sql::TableSetAdaptator / # sql::ITableSeqAdaptator, sql::TableSeqAdaptator / # sql::ITableMapAdaptator, sql::TableMapAdaptator / # sql::ITableMatchAdaptator, sql::TableMatchAdaptator. # import logging import sys DEFAULT_LEVEL = 1 DEFAULT_FORMAT = "%(asctime)s - %(module)s - %(levelname)s - %(message)s" DATE_FORMAT = "%Y-%m-%d %H:%M:%S" ## Use this class to create a instance of logging class. # class LoggerFactory(object): def createLogger(name, verbosity = DEFAULT_LEVEL, format = DEFAULT_FORMAT, out = sys.stdout): log = logging.getLogger(name) hasStreamHandler = False for handler in log.handlers: if handler.__class__ == logging.StreamHandler: hasStreamHandler = True break if not hasStreamHandler: formatter = logging.Formatter(format, DATE_FORMAT) handler = logging.StreamHandler(out) handler.setFormatter(formatter) log.addHandler(handler) LoggerFactory.setLevel(log, verbosity) return log createLogger = staticmethod(createLogger) def setLevel(log, verbosity): log.disabled = False if verbosity >= 4: log.setLevel(logging.DEBUG) elif verbosity == 3: log.setLevel(logging.INFO) elif verbosity == 2: log.setLevel(logging.WARNING) elif verbosity == 1: log.setLevel(logging.ERROR) elif verbosity == 0: log.disabled = True setLevel = staticmethod(setLevel)