tweaks logger class to always show in stdout

config/default.yml

@@ -30,7 +30,7 @@ output:
 
 debug:
   level: "info"
-  file:
+  file: output/log.txt
 
 config:
   user: config/user.yml

src/blast.rb

@@ -1,4 +1,4 @@
-require 'logger'
+require_relative 'my_logger'
 require 'yaml'
 #
 require_relative 'blast_interface'
@@ -23,17 +23,22 @@ def initialize(config_path = nil)
     super(config_path)
     # create logger object
     if @store.debug.file.nil?
-      @logger = Logger.new(STDOUT)
+      @logger = MyLogger.new(STDOUT)
     else
-      @logger = Logger.new(@store.debug.file)
+      @logger = MyLogger.new(@store.debug.file)
     end
+    #
     if @store.debug.level == 'info'
       logger.level = Logger::INFO
     elsif @store.debug.level == 'debug'
       logger.level = Logger::DEBUG
     else
       logger.level = Logger::INFO
     end
+    #
+    logger.progname = 'Blast'
+    #
+    logger.info "Log level: #{@store.debug.level}"
     # load config file
     reload_config(config_path)
     #

src/download.rb

@@ -1,4 +1,4 @@
-require 'logger'
+require_relative 'my_logger'
 require 'net/ftp'
 require 'net/http'
 
@@ -72,7 +72,8 @@ def self.download_fvesca(parent_path, logger)
   end
 
   def self.download(parent_path = 'db_and_queries/db')
-    logger = Logger.new(STDOUT)
+    logger = MyLogger.new(STDOUT)
+    logger.progname = 'Download'
     #
     run = proc do |files, parent, fun|
       #

src/my_logger.rb

@@ -0,0 +1,14 @@
+require 'logger'
+
+#
+class MyLogger < Logger
+
+  def add(*args)
+    super
+    puts format_message(format_severity(args[0]),
+                        Time.now,
+                        progname,
+                        args[2]) if @logdev.dev != STDOUT &&
+                                    level <= args[0]
+  end
+end

src/orf_common.rb

@@ -1,13 +1,14 @@
-require 'logger'
+require_relative 'my_logger'
 #
 #
 #
 module ORFCommon
   #
   def initialize(sequence, options)
     # logger for instance
-    @logger      = Logger.new(STDOUT)
-    logger.level = (options[:debug] ? Logger::INFO : Logger::UNKNOWN)
+    @logger         = MyLogger.new(STDOUT)
+    logger.progname = 'ORFCommon'
+    logger.level    = (options[:debug] ? Logger::INFO : Logger::UNKNOWN)
   end
 
   def range_to_s(range, str = '')