bio-logger 0.6.1 → 0.9.0

data/Gemfile

@@ -2,6 +2,7 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem 'log4r', '>= 1.1.9'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -10,5 +11,6 @@ group :development do
   gem "bundler", "~> 1.0.0"
   gem "jeweler", "~> 1.5.2"
   gem "rcov", ">= 0"
-  gem "bio", ">= 1.4.1"
+  # gem "bio", ">= 1.4.1"
+  gem "rspec", ">= 2.3.0"
 end

data/Gemfile.lock

@@ -1,22 +1,32 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio (1.4.1)
+    diff-lcs (1.1.2)
     git (1.2.5)
     jeweler (1.5.2)
       bundler (~> 1.0.0)
       git (>= 1.2.5)
       rake
+    log4r (1.1.9)
     rake (0.8.7)
     rcov (0.9.9)
+    rspec (2.3.0)
+      rspec-core (~> 2.3.0)
+      rspec-expectations (~> 2.3.0)
+      rspec-mocks (~> 2.3.0)
+    rspec-core (2.3.1)
+    rspec-expectations (2.3.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.3.0)
     shoulda (2.11.3)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bio (>= 1.4.1)
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
+  log4r (>= 1.1.9)
   rcov
+  rspec (>= 2.3.0)
   shoulda

data/README.rdoc

@@ -1,37 +1,47 @@
 = bio-logger
 
 This is a plugin for nailing down problems with big data parsers,
-common in bioinformatics, and sane handling of errors and exceptions in different
-situations (log-act). A logger can be made to behave differently as
+nowadays so common in bioinformatics, and sane handling of errors and
+exceptions in different situations (log-act). 
+
+For example, using bio-logger, messages can be
+filtered from the program
+
+  log.filter { | level, sub_level, msg | sub_level == 3 or level <= ERROR }
+
+or can be made to behave differently based on roles of the caller as
 
 * NormalUser
 * Developer (or FailOnError)
 * WebServer
 * FaultTolerant systems
 
-One example of the use of having different behaviours, is when a program logs a
-warning to stdout as a user, but raises an exception as a developer.
-In Bioinformatics this is a common scenario when dealing with parsers.
-Large data files sometimes contain errors. As a user you want to
-continue and hope for the best (logging the error). As a developer you
-want to see how you can fix the problem. Waiting for a full run and
-checking the logs is tedious. The logger can be helpful here, and
-avoids sticking 'temporary' solutions in code.
+One example of the use of having different behaviours, is when a
+program logs a warning to stdout when called as a user, but raises an
+exception when called as a developer.  In Bioinformatics this is a
+common scenario when dealing with parsers.  Large data files sometimes
+contain errors. As a user you want to continue and hope for the best
+(logging the error). As a developer you want to see how you can fix
+the problem. Waiting for a full run and checking the logs is tedious.
+The logger can be helpful here, and avoids sticking 'temporary'
+solutions in code.
 
 bio-logger builds up on log4r functionality, which comes with multiple
 handlers, such as a rotating and remote logging, and is thread-safe.
-Next to adding behaviours, bio-logger introduces a more fine-grained
+Next to adding filtering and behaviours, bio-logger introduces a more fine-grained
 approach for logging errors. I.e. within 'debug', 'info', 'warn',
-'error' and 'fatal', an additional value 1..9 can be set to limit
+'error' and 'fatal', an additional value (the sub_level) can be set to limit
 output and logging. This, again, can be helpful when dealing with huge
-log files. Switch a not so important and validated DEBUG, INFO or
-WARN, to a higher sub level will take it out of the logs. This can
-also make sense when deploying applications under different scenarios.
-
-Log4r is useful, compared to the standard Ruby logger,
-because it allows you to set reporting leaves by log type. I.e. if
-everything in BioRuby works, except for the BLAST parser, or some
-plugin, the logger
+log files. One way is to switch a not so important and validated
+DEBUG, INFO or WARN, to a higher sub level will take it out of the
+logs. Another option is to log only the messages of a certain value,
+or to regex on the message - i.e. you get othogonal differentiation of
+values and types (see the filter example below). This can also make
+sense when deploying applications under different scenarios.
+
+Log4r is useful, compared to the standard Ruby logger, because it
+allows you to set reporting leaves by log type. I.e. if everything in
+BioRuby works, except for the BLAST parser, or some plugin, the logger
 can be tuned only to log BLAST debug level, and everything else at
 normal level.
 
@@ -39,7 +49,8 @@ In other words, bio-logger helps in tracking down problems and
 provide a way of avoiding sprinkling $stderr.print statements through
 the code base.
 
-To support applications, bio-logger can also parse command line switches:
+To support applications, bio-logger can also help parse command line
+switches:
 
 add (multiple) loggers:
 
@@ -51,6 +62,8 @@ specify global log level:
   --trace  debug               Show all messages 
   --trace  warn                Show messages more serious than 'warn'
   --trace  warn:3              Show messaged more serious that 'warn' level 3
+  --trace  "=3"                Show all messages with sub-level==3
+  --trace  "=sub_level == 3 or level <= ERROR" Set filter
 
 overrides:
 
@@ -103,7 +116,7 @@ streams. It is also possible to change behaviours by module.
   log.fatal "This is a message with level FATAL"
   log.warn3 "This is a message with level WARN:3"
 
-  # Restrict output to WARN:3
+  # Restrict output to messages <=WARN:3
   log.level = WARN
   log.sub_level = 3
   log.info("This is a message with level INFO")      # not logged
@@ -111,6 +124,15 @@ streams. It is also possible to change behaviours by module.
   log.warn1("This is a message with level WARN:1")   # logged
   log.warn("This is a message with level WARN")      # logged
 
+  # Restrict output for DEBUG, INFO, WARN to sub_level 3
+  log.filter { | level, sub_level, msg | sub_level == 3 or level <= ERROR }
+  log.warn8("This is a message with level WARN:8")   # not logged
+  log.warn3("This is a message with level WARN:3")   # logged
+  log.warn1("This is a message with level WARN:1")   # not logged
+  log.info3("This is a message with level INFO:3")   # logged
+  log.error("This is a message with level ERROR")    # logged
+  log.reset_filter
+
   # Fetch the BLAST logger (assuming it exists)
   blastlog = LoggerPlus['blast']
   blastlog.warn("This is a message with level WARN") # logged

data/Rakefile

@@ -21,8 +21,8 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Pjotr Prins"]
   # Include your dependencies below. Runtime dependencies are required when using your gem,
   # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
-  gem.add_runtime_dependency 'log4r', '> 1.1.6'
-  gem.add_development_dependency 'rspec', '> 1.2.3'
+  # gem.add_runtime_dependency 'log4r', '> 1.1.6'
+  # gem.add_development_dependency 'rspec', '>= 2.3.0'
 end
 Jeweler::RubygemsDotOrgTasks.new
 
@@ -31,6 +31,7 @@ Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
   test.pattern = 'test/**/test_*.rb'
   test.verbose = true
+  Kernel.system('rspec spec/*.rb')
 end
 
 require 'rcov/rcovtask'

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.9.0

data/bio-logger.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-logger}
-  s.version = "0.6.1"
+  s.version = "0.9.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = %q{2011-01-12}
+  s.date = %q{2011-01-17}
   s.description = %q{Log4r wrapper for BioRuby}
   s.email = %q{pjotr.public01@thebird.nl}
   s.extra_rdoc_files = [
@@ -28,8 +28,10 @@ Gem::Specification.new do |s|
     "lib/bio-logger.rb",
     "lib/bio/log/logger.rb",
     "lib/bio/log/loggercli.rb",
+    "lib/bio/log/loggerfilter.rb",
     "lib/bio/log/loggersublevels.rb",
     "lib/bio/log/loggerusers.rb",
+    "lib/bio/log/patchlog4r.rb",
     "spec/biologger_cli_spec.rb",
     "spec/biologger_spec.rb",
     "test/helper.rb",
@@ -52,30 +54,27 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<log4r>, [">= 1.1.9"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_runtime_dependency(%q<log4r>, ["> 1.1.6"])
-      s.add_development_dependency(%q<rspec>, ["> 1.2.3"])
+      s.add_development_dependency(%q<rspec>, [">= 2.3.0"])
     else
+      s.add_dependency(%q<log4r>, [">= 1.1.9"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<log4r>, ["> 1.1.6"])
-      s.add_dependency(%q<rspec>, ["> 1.2.3"])
+      s.add_dependency(%q<rspec>, [">= 2.3.0"])
     end
   else
+    s.add_dependency(%q<log4r>, [">= 1.1.9"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
     s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<log4r>, ["> 1.1.6"])
-    s.add_dependency(%q<rspec>, ["> 1.2.3"])
+    s.add_dependency(%q<rspec>, [">= 2.3.0"])
   end
 end
 

data/lib/bio-logger.rb

@@ -1,12 +1,12 @@
-
 require "rubygems"
 begin
-  gem "log4r" , "> 1.1.8"
+  gem "log4r" 
 rescue
 	$stderr.print "log4r not installed, bailing out...\n"
   exit 1
 end
 
 require 'log4r'
+require 'bio/log/patchlog4r'
 require 'bio/log/logger'
 require 'bio/log/loggercli'

data/lib/bio/log/logger.rb

@@ -1,5 +1,6 @@
 
 require 'bio/log/loggersublevels'
+require 'bio/log/loggerfilter'
 require 'bio/log/loggerusers'
 require 'bio/log/loggercli'
 
@@ -12,6 +13,14 @@ module Bio
     # Derived from the Log4r Logger class
     class LoggerPlus < Logger
       include LoggerSubLevels
+      include LoggerFilter
+
+      def default_level
+        # Log4r::Logger::DEBUG
+        6
+      end
+      def default_sub_level
+      end
 
       def debug_ msg, options = {}
         if options[:act]
@@ -53,6 +62,10 @@ module Bio
         end
       end
 
+      def [] name
+        super
+      end
+
     end
 
   end

data/lib/bio/log/loggercli.rb

@@ -24,27 +24,50 @@ module Bio
 
       # Parse and store trace options
       def CLI::trace s
+        level = nil
         sub_level = nil
+        filter = nil
 
         opts = {}
+        # ---- split fields
         a = s.split(':')
-        if a.last =~ /^\d+$/
+        if a.last =~ /^=(\d+)$/
+          # ---- set exact filter
+          filter = "sub_level==#{$1}"
+          a.pop
+        elsif a.last =~ /^=/
+          # ---- set filter
+          filter = $'
+          a.pop
+        elsif a.last =~ /^\d+$/
+          # ---- the last field is the sub level
           sub_level = a.pop.to_i
+          # ---- The fore-last field is the level
+          level = a.pop.downcase
+        else
+          level = a.pop.downcase
         end
-        level = a.pop.downcase
+        # ---- If there is another field it contains logger name(s)
+        #      otherwise it is a global
         outputter = 
           if a.size == 2 
             a.shift
           end
         if a.size == 0
-          a = [:default] 
+          a = [:default]  # global
         else
-          a = a[0].split(',')
+          a = a[0].split(',') # one or more logger name(s)
         end
+        # ---- update every logger
         a.each do | type |
-          opts[type] = { :level => level, :sub_level => sub_level }
+          opts[type] = {}
+          opts[type][:level] = level if level
+          opts[type][:sub_level] = sub_level if sub_level
+          opts[type][:filter] = filter if filter
           opts[type][:outputter_name] = outputter if outputter
+          # p [type,opts[type]]
         end
+        # ---- Set the globals
         LoggerPlusGlobal.instance.trace ||= {}
         LoggerPlusGlobal.instance.trace = LoggerPlusGlobal.instance.trace.merge(opts)
       end
@@ -59,6 +82,7 @@ module Bio
         default = trace[:default] if trace[:default]
         trace[logname] ||= {} if logname
         trace.each do | name, opts |
+          # p [name, opts]
           next if name == :default
           logger_type = type
           logger_type = default[:outputter_name] if default[:outputter_name]
@@ -75,6 +99,14 @@ module Bio
             end
           set_levels(logger, default) if default
           set_levels(logger, opts)
+          filter = default[:filter]
+          filter = opts[:filter] if opts[:filter]
+          if filter
+            # p filter
+            filter2 = "logger.filter { |level,sub_level,msg| #{filter} }" 
+            # p filter2
+            eval(filter2)
+          end
         end
       end
 

data/lib/bio/log/loggerfilter.rb

@@ -0,0 +1,36 @@
+
+module Bio
+  module Log
+
+    # The filter logger changes behaviour
+    module LoggerFilter
+
+      def filter &filter_func
+        @use_filter = filter_func
+        @outputters.each do | out | 
+          # p [:adding_filter_to,out]
+          out.class.send(:define_method, :filtered?) do |l,s,m|
+            # p [:called,l,s,m]
+            filter_func.call(l,s,m)
+          end
+          raise 'hell' if !out.class.method_defined?(:filtered?)
+        end
+        @level = default_level  # will recreate logger methods
+        @sub_level = default_sub_level
+      end
+
+      def reset_filter
+        @use_filter = nil
+        @outputters.each do | out | 
+          if out.class.method_defined?(:filtered?)
+            out.class.send(:remove_method, :filtered?)
+          end
+        end
+        @level = default_level  # will recreate logger methods
+        @sub_level = default_sub_level
+      end
+
+    end
+
+  end
+end

data/lib/bio/log/loggersublevels.rb

@@ -9,142 +9,187 @@ module Bio
       attr_accessor :sub_level
 
       def debug1(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,1,s)
         debug(s) if !sub_level or sub_level >= 1
       end
       def debug2(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,2,s)
         debug(s) if !sub_level or sub_level >= 2
       end
       def debug3(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,3,s)
         debug(s) if !sub_level or sub_level >= 3
       end
       def debug4(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,4,s)
         debug(s) if !sub_level or sub_level >= 4
       end
       def debug5(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,5,s)
         debug(s) if !sub_level or sub_level >= 5
       end
       def debug6(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,6,s)
         debug(s) if !sub_level or sub_level >= 6
       end
       def debug7(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,7,s)
         debug(s) if !sub_level or sub_level >= 7
       end
       def debug8(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,8,s)
         debug(s) if !sub_level or sub_level >= 8
       end
       def debug9(s)
+        return nil if @use_filter and !@use_filter.call(DEBUG,9,s)
         debug(s) if !sub_level or sub_level >= 9
       end
 
       def info1(s)
+        return nil if @use_filter and !@use_filter.call(INFO,1,s)
         info(s) if !sub_level or sub_level >= 1
       end
       def info2(s)
+        return nil if @use_filter and !@use_filter.call(INFO,2,s)
         info(s) if !sub_level or sub_level >= 2
       end
       def info3(s)
+        return nil if @use_filter and !@use_filter.call(INFO,3,s)
         info(s) if !sub_level or sub_level >= 3
       end
       def info4(s)
+        return nil if @use_filter and !@use_filter.call(INFO,4,s)
         info(s) if !sub_level or sub_level >= 4
       end
       def info5(s)
+        return nil if @use_filter and !@use_filter.call(INFO,5,s)
         info(s) if !sub_level or sub_level >= 5
       end
       def info6(s)
+        return nil if @use_filter and !@use_filter.call(INFO,6,s)
         info(s) if !sub_level or sub_level >= 6
       end
       def info7(s)
+        return nil if @use_filter and !@use_filter.call(INFO,7,s)
         info(s) if !sub_level or sub_level >= 7
       end
       def info8(s)
+        return nil if @use_filter and !@use_filter.call(INFO,8,s)
         info(s) if !sub_level or sub_level >= 8
       end
       def info9(s)
+        return nil if @use_filter and !@use_filter.call(INFO,9,s)
         info(s) if !sub_level or sub_level >= 9
       end
 
       def warn1(s)
+        return nil if @use_filter and !@use_filter.call(WARN,1,s)
         warn(s) if !sub_level or sub_level >= 1
       end
       def warn2(s)
+        return nil if @use_filter and !@use_filter.call(WARN,2,s)
         warn(s) if !sub_level or sub_level >= 2
       end
       def warn3(s)
+        return nil if @use_filter and !@use_filter.call(WARN,3,s)
         warn(s) if !sub_level or sub_level >= 3
       end
       def warn4(s)
+        return nil if @use_filter and !@use_filter.call(WARN,4,s)
         warn(s) if !sub_level or sub_level >= 4
       end
       def warn5(s)
+        return nil if @use_filter and !@use_filter.call(WARN,5,s)
         warn(s) if !sub_level or sub_level >= 5
       end
       def warn6(s)
+        return nil if @use_filter and !@use_filter.call(WARN,6,s)
         warn(s) if !sub_level or sub_level >= 6
       end
       def warn7(s)
+        return nil if @use_filter and !@use_filter.call(WARN,7,s)
         warn(s) if !sub_level or sub_level >= 7
       end
       def warn8(s)
+        return nil if @use_filter and !@use_filter.call(WARN,8,s)
         warn(s) if !sub_level or sub_level >= 8
       end
       def warn9(s)
+        return nil if @use_filter and !@use_filter.call(WARN,9,s)
         warn(s) if !sub_level or sub_level >= 9
       end
 
       def error1(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,1,s)
         error(s) if !sub_level or sub_level >= 1
       end
       def error2(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,2,s)
         error(s) if !sub_level or sub_level >= 2
       end
       def error3(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,3,s)
         error(s) if !sub_level or sub_level >= 3
       end
       def error4(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,4,s)
         error(s) if !sub_level or sub_level >= 4
       end
       def error5(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,5,s)
         error(s) if !sub_level or sub_level >= 5
       end
       def error6(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,6,s)
         error(s) if !sub_level or sub_level >= 6
       end
       def error7(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,7,s)
         error(s) if !sub_level or sub_level >= 7
       end
       def error8(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,8,s)
         error(s) if !sub_level or sub_level >= 8
       end
       def error9(s)
+        return nil if @use_filter and !@use_filter.call(ERROR,9,s)
         error(s) if !sub_level or sub_level >= 9
       end
 
       def fatal1(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,1,s)
         fatal(s) if !sub_level or sub_level >= 1
       end
       def fatal2(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,2,s)
         fatal(s) if !sub_level or sub_level >= 2
       end
       def fatal3(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,3,s)
         fatal(s) if !sub_level or sub_level >= 3
       end
       def fatal4(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,4,s)
         fatal(s) if !sub_level or sub_level >= 4
       end
       def fatal5(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,5,s)
         fatal(s) if !sub_level or sub_level >= 5
       end
       def fatal6(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,6,s)
         fatal(s) if !sub_level or sub_level >= 6
       end
       def fatal7(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,7,s)
         fatal(s) if !sub_level or sub_level >= 7
       end
       def fatal8(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,8,s)
         fatal(s) if !sub_level or sub_level >= 8
       end
       def fatal9(s)
+        return nil if @use_filter and !@use_filter.call(FATAL,9,s)
         fatal(s) if !sub_level or sub_level >= 9
       end
 

data/lib/bio/log/loggerusers.rb

@@ -30,7 +30,7 @@ module Bio
     class FailOnError < NormalUser
       def error logger, msg
         logger.error msg
-        raise FailOnErrorException
+        raise FailOnErrorException,msg
       end
 
       def fatal logger, msg

data/lib/bio/log/patchlog4r.rb

@@ -0,0 +1,40 @@
+module Log4r
+  class Outputter < Monitor
+
+    # Log4r creates the logging methods dynamically - quite cleverly creating
+    # only those methods that are required, but not that transparent. 
+    #
+    # To add filter support we 'monkey patch' the original implementation of
+    # +define_log+ in 'outputterfactory.rb' by adding in the filter call.
+    # This slows down the run time, but that is not so important.
+    #
+    class OutputterFactory 
+      # original comment: we need to synch the actual write/format for thread saftyness
+      def self.define_log(mname, level, out)
+        return if mname == 'off' || mname == 'all'
+        # p [mname,level,out]
+        # 
+        # At runtime, self and logevent are available to the method:
+        # [:self, #<Log4r::StderrOutputter:0x9f8975c @mon_owner=nil, @mon_count=0, @mon_mutex=#<Mutex:0x9f89694>, @name="stderr", @level=0, @formatter=#<Log4r::DefaultFormatter:0x9f7c174 @depth=7>, @out=#<IO:<STDERR>>>]
+        # [:logevent, #<Log4r::LogEvent:0xa198de0 @data="As Developer ERROR should fail", @tracer=nil, @level=4, @name="mylog", @fullname="mylog">]
+
+        mstr = 
+            %-
+            def out.#{mname}(logevent)
+              if self.class.method_defined?(:filtered?) 
+                # p logevent
+                if !filtered?(logevent.level,nil,logevent.data)
+                  # p "**** returning nil for "+logevent.data
+                  return nil
+                end
+              end
+              canonical_log(logevent)
+            end
+            -
+        module_eval mstr
+      end
+
+    end
+  end
+end
+

data/spec/biologger_cli_spec.rb

@@ -33,19 +33,27 @@ describe Bio::Log::CLI, "bio-logger command line parsing" do
   end
   it "should parse --trace  debug to show all messages" do
     CLI.trace("debug")
-    @global.trace[:default].should == { :level => 'debug', :sub_level => nil } 
+    @global.trace[:default].should == { :level => 'debug' } 
   end
   it "should parse --trace  warn to show how messages more serious than 'warn'" do
     CLI.trace("warn")
-    @global.trace[:default].should == { :level => 'warn', :sub_level => nil } 
+    @global.trace[:default].should == { :level => 'warn' } 
   end
   it "should parse --trace  warn:3 to show messaged more serious that 'warn' level 3" do
     CLI.trace("warn:3")
     @global.trace[:default].should == { :level => 'warn', :sub_level => 3 } 
   end
+  it "should parse --trace =3 to show level 3 only" do
+    CLI.trace("=3")
+    @global.trace[:default].should == { :filter => "sub_level==3" } 
+  end
+  it "should parse --trace \"=sub_level == 3 or level <= ERROR\"" do
+    CLI.trace("=sub_level == 3 or level <= ERROR")
+    @global.trace[:default].should == { :filter => "sub_level == 3 or level <= ERROR" } 
+  end
   it "should parse --trace  blast:debug to override level for 'blast'" do
     CLI.trace("blast:debug")
-    @global.trace.should == {"blast"=>{:level=>"debug", :sub_level=>nil}}
+    @global.trace.should == {"blast"=>{:level=>"debug"}}
   end
   it "should parse --trace  gff3:info:5 to override level for 'gff3' to info level 5" do
     CLI.trace("gff3:info:5")
@@ -55,10 +63,14 @@ describe Bio::Log::CLI, "bio-logger command line parsing" do
     CLI.trace("blast,gff3:debug:5")
     @global.trace.should == {"blast"=>{:level=>"debug", :sub_level=>5}, "gff3"=>{:level=>"debug", :sub_level=>5}} 
   end
+  it "should parse --trace \"blast:=sub_level == 3 or level <= ERROR\"" do
+    CLI.trace("blast:=sub_level == 3 or level <= ERROR")
+    @global.trace['blast'].should == { :filter => "sub_level == 3 or level <= ERROR" } 
+  end
   it "should parse --trace  stderr:blast:debug to override level for 'blast' on stderr" do
     CLI.trace("stderr:blast:debug")
     @global.trace.should ==
-      {"blast"=>{:level=>"debug", :sub_level=>nil, :outputter_name=>"stderr"}}
+      {"blast"=>{:level=>"debug", :outputter_name=>"stderr"}}
   end
   it "should parse --trace  stderr:blast,gff3:debug:1 to override level for 'blast' on stderr" do
     CLI.trace("stderr:blast,gff3:debug:1")

data/spec/biologger_spec.rb

@@ -33,6 +33,7 @@ describe Bio::Log, "logs" do
   after(:all) do
     File.unlink("file.log")
     File.unlink("TestSize000001.log")
+    @mylog.reset_filter
   end
 
   it "should have a stderr logger" do
@@ -77,6 +78,28 @@ describe Bio::Log, "logs" do
     @mylog.info("This is a message with level INFO").should_not == nil
     @mylog.warn8("This is a message with level WARN:8").should_not == nil
   end
+  it "should allow for a filter" do
+    @mylog.filter { |l,s,m| l==INFO }
+    @mylog.info("This is a level filtered message with level INFO")
+    @mylog.warn("NO DISPLAY: This is a level filtered message with level WARN")
+    @mylog.error("NO DISPLAY: This is a level filtered message with level ERROR")
+
+    @mylog.filter { |l,s,m| m =~ /filtered/ }
+    @mylog.info("NO DISPLAY: This is a Filtered message with level XXX")
+    @mylog.info3("DISPLAY This is a filtered message with level XXX")
+
+    @mylog.filter { |l,s,m| s==3 }
+    @mylog.info("NO DISPLAY: This is a filtered message with level INFO")
+    @mylog.info3("DISPLAY This is a filtered message with level INFO:3")
+    @mylog.warn8("NO DISPLAY: This is a filtered message with level WARN:8")
+    @mylog.warn3("DISPLAY This is a filtered message with level WARN:3")
+    @mylog.warn1("NO DISPLAY: This is a filtered message with level WARN:1")
+    @mylog.warn("NO DISPLAY: This is a filtered message with level WARN")
+    @mylog.error("NO DISPLAY: This is a filtered message with level ERROR")
+    @mylog.reset_filter
+    @mylog.info("DISPLAY: This is an unfiltered message with level INFO").should_not == nil
+    @mylog.warn8("DISPLAY: This is an unfiltered message with level WARN:8").should_not == nil
+  end
   it "should override level for 'blast' to info level 5" do
     log = LoggerPlus['blast']
     log.should_not == nil

data/test/test_bio-logger.rb

@@ -1,7 +1,9 @@
 require 'helper'
 
-class TestBioLogger < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
-  end
-end
+# See the ./spec dir
+#
+# class TestBioLogger < Test::Unit::TestCase
+#   should "probably rename this file and start testing for real" do
+#     flunk "hey buddy, you should probably rename this file and start testing for real"
+#   end
+# end

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 6
-  - 1
-  version: 0.6.1
+  - 9
+  - 0
+  version: 0.9.0
 platform: ruby
 authors: 
 - Pjotr Prins
@@ -14,39 +14,39 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-12 00:00:00 +01:00
+date: 2011-01-17 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: shoulda
+  name: log4r
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
-        - 0
-        version: "0"
-  type: :development
+        - 1
+        - 1
+        - 9
+        version: 1.1.9
+  type: :runtime
   prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: bundler
+  name: shoulda
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version 
         segments: 
-        - 1
-        - 0
         - 0
-        version: 1.0.0
+        version: "0"
   type: :development
   prerelease: false
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: jeweler
+  name: bundler
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -54,70 +54,55 @@ dependencies:
       - !ruby/object:Gem::Version 
         segments: 
         - 1
-        - 5
-        - 2
-        version: 1.5.2
+        - 0
+        - 0
+        version: 1.0.0
   type: :development
   prerelease: false
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
-  name: rcov
+  name: jeweler
   requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         segments: 
-        - 0
-        version: "0"
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
   type: :development
   prerelease: false
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  name: bio
+  name: rcov
   requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
-        - 1
-        - 4
-        - 1
-        version: 1.4.1
+        - 0
+        version: "0"
   type: :development
   prerelease: false
   version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: log4r
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">"
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 1
-        - 6
-        version: 1.1.6
-  type: :runtime
-  prerelease: false
-  version_requirements: *id006
 - !ruby/object:Gem::Dependency 
   name: rspec
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">"
+    - - ">="
       - !ruby/object:Gem::Version 
         segments: 
-        - 1
         - 2
         - 3
-        version: 1.2.3
+        - 0
+        version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *id007
+  version_requirements: *id006
 description: Log4r wrapper for BioRuby
 email: pjotr.public01@thebird.nl
 executables: []
@@ -139,8 +124,10 @@ files:
 - lib/bio-logger.rb
 - lib/bio/log/logger.rb
 - lib/bio/log/loggercli.rb
+- lib/bio/log/loggerfilter.rb
 - lib/bio/log/loggersublevels.rb
 - lib/bio/log/loggerusers.rb
+- lib/bio/log/patchlog4r.rb
 - spec/biologger_cli_spec.rb
 - spec/biologger_spec.rb
 - test/helper.rb
@@ -159,7 +146,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 142425075
+      hash: -277148543
       segments: 
       - 0
       version: "0"