# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
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# 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". 
#
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# modify and redistribute granted by the license, users are provided only
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# economic rights,  and the successive licensors  have only  limited
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# same conditions as regards security. 
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## @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)