diff TEisotools-1.0/commons/core/LoggerFactory.py @ 6:20ec0d14798e draft

Uploaded

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+++ b/TEisotools-1.0/commons/core/LoggerFactory.py	Wed Jul 20 05:00:24 2016 -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)