rbbt-util 5.6.14 → 5.6.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4e0c8c6ded43303be8e60d1b3f296c01a7eb71d9
-  data.tar.gz: 16641eeaa05112c42e6d4cbf19225a241f838910
+  metadata.gz: dc353002e2a5fdbaaf0bbfc97b8fa79f5bdc4ffe
+  data.tar.gz: b912bbecb036910d98c35e3a5822f3fe2b9a9e4c
 SHA512:
-  metadata.gz: 8cbac69ebc91242fb6a0343a082a7e90d4bb1746b93b2af1b750e71a14745f77256351f539223da2ffc3918a1270410c8bdd4d5efaa590e83fbcbff60fe19742
-  data.tar.gz: de45c205481873a3d514e160275fa22a6182d2862796d09c1cb6e54009645ee29dc8d132dc739282fb09adc45bfb0f6ce089047f61089876db5d57b34e9565ba
+  metadata.gz: 409f4d6abe74bac82970a076ac9165843813f06524e61d0b6ab60c1c29d643f1f9b374b54d21c9e78b1472048f8c2431be0cc6693559e852c42e4258cff66372
+  data.tar.gz: 9064bdc5ff2a21b3b5844f8a10b963b0856383711dbda184d52238bc5ae591974d4c42a475fdecf954edd63a58802adcd9f798c22e40a0529f08054c9e197cc4

data/bin/rbbt

@@ -3,7 +3,18 @@
 require 'rbbt'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):-cd--command_dir* Directory from where to load commands:--profile Profile execution:--nocolor Disable colored output:--locate_file Locate file been executed")
+options = SOPT.setup <<EOF
+This command controls many aspects of the Rbbt framework, from configuration tasks to running applications. 
+
+$ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'"
+
+
+--log*                  #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}
+-cd--command_dir*       #{Log.color :yellow, "Directory from where to load commands"}
+--profile               #{Log.color :yellow, "Profile execution"}
+--nocolor               #{Log.color :yellow, "Disable colored output"}
+--locate_file           #{Log.color :yellow, "Locate file been executed"}
+EOF
 
 Log.nocolor = true if options[:nocolor]
 locate = options.delete :locate_file
@@ -18,20 +29,17 @@ else
   $rbbt_command_dir = Rbbt.share.rbbt_commands
 end
 
+SOPT.description =<<EOF
+Commands are implemented in separate files under the Rbbt path '#{$rbbt_command_dir}'. 
+Known locations are: #{([$rbbt_command_dir] + $rbbt_command_dir.find_all) * ", " }. 
+You can place your own commads at #{$rbbt_command_dir.find(:user)}.
+EOF
+
 if options[:profile]
   require 'ruby-prof'
   RubyProf.start
 end
 
-SOPT.synopsys = "rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'"
-SOPT.summary = "Ruby bioinformatics toolkit"
-SOPT.description = <<-EOF
-This command controls many aspects of the Rbbt framework, from configuration tasks to running applications. 
-
-Commands are implemented in separate files under the Rbbt path '#{$rbbt_command_dir}'. 
-Known locations are: #{([$rbbt_command_dir] + $rbbt_command_dir.find_all) * ", " }. 
-You can place your own commads at #{$rbbt_command_dir.find(:user)}.
-EOF
 
 def prev_dir(prev)
     rbbt_command_dir = $rbbt_command_dir
@@ -76,6 +84,7 @@ def rbbt_usage(prev = nil)
     end
   end
   puts
+  true
 end
 
 def print_error(error, backtrace = nil)
@@ -102,34 +111,34 @@ def cmd_alias
 end
     
 dir = $rbbt_command_dir
-prev = []
+$previous_commands = []
 
 cmd_alias
 
 begin
   while ARGV.any?
-    command = ARGV.shift
+    $command = ARGV.shift
     case
-    when File.directory?(dir[command].find)
-      prev << command
-      dir = dir[command]
-    when dir[command].exists?
+    when File.directory?(dir[$command].find)
+      $previous_commands << $command
+      dir = dir[$command]
+    when dir[$command].exists?
       if locate
-        puts dir[command].find
+        puts dir[$command].find
         exit 0
       else
-        load dir[command].find
+        load dir[$command].find
         exit 0
       end
     else
-      error = "Command '#{command }' not understood"
-      rbbt_usage(prev)
+      error = "Command '#{$command }' not understood"
+      rbbt_usage($previous_commands)
       print_error(error)
       exit -1
     end
   end
 
-  rbbt_usage(prev)
+  rbbt_usage($previous_commands)
   exit 0
 
 rescue ParameterException
@@ -145,4 +154,3 @@ ensure
     printer.print(STDOUT, :min_percent => 10)
   end
 end
-

data/lib/rbbt/persist.rb

@@ -260,7 +260,7 @@ module Persist
 
         if is_persisted?(path, persist_options)
           Log.low "Persist up-to-date: #{ path } - #{Misc.fingerprint persist_options}"
-          return nil if persist_options[:no_load]
+          return path if persist_options[:no_load]
           return load_file(path, type) 
         end
 
@@ -269,7 +269,7 @@ module Persist
           Misc.lock lock_filename  do
             if is_persisted?(path, persist_options)
               Log.low "Persist up-to-date (suddenly): #{ path } - #{Misc.fingerprint persist_options}"
-              return nil if persist_options[:no_load]
+              return path if persist_options[:no_load]
               return load_file(path, type) 
             end
 

data/lib/rbbt/tsv.rb

@@ -17,7 +17,7 @@ require 'rbbt/tsv/field_index'
 
 module TSV
   class << self
-    attr_accessor :lock_dir
+    attr_accessor :lock_dir, :unnamed
     
     def lock_dir
       @lock_dir ||= Rbbt.tmp.tsv_open_locks.find
@@ -25,7 +25,7 @@ module TSV
   end
 
   def self.setup(hash, options = {})
-    options = Misc.add_defaults options, :default_value => []
+    options = Misc.add_defaults options, :default_value => [], :unnamed => TSV.unnamed
     default_value = Misc.process_options options, :default_value
     hash = Misc.array2hash(hash, default_value) if Array === hash
     hash.extend TSV
@@ -49,6 +49,8 @@ module TSV
 
     persist_options = Misc.pull_keys options, :persist
 
+    raise "TSV source is nil" if source.nil?
+
     filename = get_filename source
     serializer = Misc.process_options options, :serializer
     unnamed = Misc.process_options options, :unnamed

data/lib/rbbt/tsv/change_id.rb

@@ -12,7 +12,11 @@ module TSV
       orig_type = tsv.type 
       tsv = tsv.to_double if orig_type != :double
 
-      tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
+      if Array === identifiers
+        tsv = tsv.attach identifiers.first, :fields => [format], :persist_input => true, :identifiers => identifiers.last
+      else
+        tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
+      end
       tsv = tsv.reorder(format, tsv.fields - [format])
 
       tsv = tsv.to_flat  if orig_type == :flat
@@ -23,8 +27,9 @@ module TSV
     end
   end
 
-  def change_key(*args)
-    TSV.change_key(self, *args)
+  def change_key(format, options = {})
+    options = Misc.add_defaults options, :identifiers => self.identifiers
+    TSV.change_key(self, format, options)
   end
 
   def self.swap_id(tsv, field, format, options = {})

data/lib/rbbt/util/log.rb

@@ -38,6 +38,10 @@ module Log
     end
   end
 
+  def self.return_line
+    "\033[1A"
+  end
+
   def self.highlight(str = nil)
     if str.nil?
       return "" if nocolor

data/lib/rbbt/util/misc.rb

@@ -322,9 +322,9 @@ module Misc
     end
   end
 
-  def self.remove_long_items(obj)
-    return fingerprint(obj)
-  end
+  #def self.remove_long_items(obj)
+  #  return fingerprint(obj)
+  #end
 
   def self.ensembl_server(organism)
     date = organism.split("/")[1]

data/lib/rbbt/util/simpleopt.rb

@@ -2,6 +2,7 @@ require 'rbbt/util/simpleopt/accessor'
 require 'rbbt/util/simpleopt/doc'
 require 'rbbt/util/simpleopt/parse'
 require 'rbbt/util/simpleopt/get'
+require 'rbbt/util/simpleopt/setup'
 
 module SOPT
 end

data/lib/rbbt/util/simpleopt/get.rb

@@ -38,4 +38,10 @@ module SOPT
     SOPT.parse(opt_str)
     SOPT.consume(ARGV)
   end
+
+  def self.require(options, *parameters)
+    parameters.flatten.each do |parameter|
+      raise ParameterException, "Parameter '#{ parameter }' not given" if options[parameter].nil?
+    end
+  end
 end

data/lib/rbbt/util/simpleopt/parse.rb

@@ -1,4 +1,5 @@
 require 'rbbt/util/simpleopt/accessor'
+
 module SOPT
   def self.fix_shortcut(short, long)
     return short unless short and shortcuts.include?(short)

data/lib/rbbt/util/simpleopt/setup.rb

@@ -0,0 +1,30 @@
+require 'rbbt/util/simpleopt/parse'
+require 'rbbt/util/simpleopt/get'
+require 'rbbt/util/simpleopt/doc'
+module SOPT
+  def self.setup(str)
+    summary, synopsys, description, options = str.split(/\n\n+/)
+
+    if summary[0]=="-"
+      summary, synopsys, description, options = nil, nil, nil, summary
+    end
+
+    if synopsys and synopsys[0] != "$"
+      description, options = synopsys, description
+      synopsys = nil
+    end
+
+    if description and description[0] == "-"
+      description, options = nil, description
+    end
+
+    synopsys.sub!(/^\$\s+/,'') if synopsys
+
+    SOPT.summary = summary.strip if summary
+    SOPT.synopsys = synopsys.strip if synopsys
+    SOPT.description = description.strip if description
+    SOPT.parse options  if options
+
+    SOPT.consume
+  end
+end

data/share/rbbt_commands/tsv/change_id

@@ -2,13 +2,29 @@
 
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
-require 'rbbt/sources/organism'
 
-options = SOPT.get("-f--file* File to process:-f--field* Field to change:-t--target* Target format:-i--identifiers* Identifier file to use")
+options = SOPT.setup <<EOF
+
+Change the ID format of a column in a tsv file
+
+$ rbbt command command [options] -f file
+
+Use - to read from STDIN. The `field` is the tsv column to change.
+the `target` is the target format, as appearing in the `identifiers`
+file or in `Organism.identifiers("Hsa")`.
 
-raise ParameterException, "No file given" unless file = options[:file]
-raise ParameterException, "No field given" unless field = options[:field]
-raise ParameterException, "No target given" unless target = options[:target]
+-f--file* File to process
+-f--field* Field to change
+-t--target* Target format
+-i--identifiers* Identifier file to use
+-h--help Help
+
+EOF
+rbbt_usage and exit 0 if options[:help]
+
+SOPT.require options, :file, :field, :target
+
+require 'rbbt/sources/organism'
 
 identifiers = options[:identifiers] || Organism.identifiers("Hsa").find
 
@@ -32,20 +48,3 @@ tsv.fields = tsv.fields.collect{|f| f == field ? target : f}
 
 puts tsv
 
-exit
-
-#stream = Open.open file
-#header = TSV.parse_header stream
-#field_pos = header.all_fields.index field
-#raise ParameterException, "Unknown field: #{ field }" unless field_pos
-#
-#out = STDOUT
-#out.puts TSV.header_lines :fields => header.fields, :key_field =
-#while line = stream.gets do
-#  if line =~ /^#/
-#    out.puts line
-#    next
-#  else
-#  end
-#end
-#

data/share/rbbt_commands/tsv/values

@@ -3,7 +3,22 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd")
+options = SOPT.setup <<EOF
+
+Pulls the values from a tsv colum
+
+$ rbbt tsv values [options] <filename.tsv|->
+
+Use - to read from STDIN
+
+-tch--tokyocabinet File is a tokyocabinet hash database
+-tcb--tokyocabinet_bd File is a tokyocabinet B database
+-f--field* Limit to a particular field
+-h--help Print this help
+
+EOF
+rbbt_usage and exit 0 if options[:help]
+
 
 file = ARGV.shift
 
@@ -22,4 +37,6 @@ else
   tsv = TSV.open(file)
 end
 
+tsv = tsv.slice(field) if field
+
 tsv.each{|k,v| puts (Array === v ? v.flatten*"\t" : v.to_s ) }

data/share/rbbt_commands/workflow/task

@@ -65,7 +65,7 @@ def SOPT_options(workflow, task)
     short = name.to_s.chars.first
     boolean = workflow.rec_input_types(task.name)[name].to_sym == :boolean
     
-    sopt_options << "-#{short}--#{name}*"
+    sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
   end
 
   sopt_options * ":"
@@ -79,7 +79,7 @@ def fix_options(workflow, task, job_options)
   job_options.each do |name, value|
     value = case option_types[name].to_sym
             when :boolean
-              %w(true TRUE T yes).include? value
+              TrueClass === true or %w(true TRUE T yes).include? value
             when :float
               value.to_f
             when :integer
@@ -255,11 +255,15 @@ begin
 
   if do_fork
     job.fork
+    puts 
     while not job.done?
       message = job.messages ? job.messages.last : "no message"
-      Log.debug "#{job.status}: #{message}"
+      status = job.status
+      puts("No status yet") and next if status.nil?
+      puts Log.return_line + "Waiting on #{job.pid} " + [Log.color(:magenta, status.to_s),message]*" " + " " * 100
       sleep 2
     end
+    Signal.trap(:INT){ job.abort }
     raise job.messages.last if job.error?
     res = job.load
   else

data/test/rbbt/util/simpleopt/test_setup.rb

@@ -0,0 +1,76 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/simpleopt/setup'
+
+class TestSOPTSetup < Test::Unit::TestCase
+  def setup
+    SOPT.inputs = nil
+    SOPT.input_types = nil
+    SOPT.input_descriptions = nil
+    SOPT.input_shortcuts = nil
+  end
+
+  def test_setup
+    SOPT.setup <<-EOF
+Test application
+
+$ test cmd -arg 1
+
+It does some imaginary stuff
+
+-a--arg* Argument
+-a2--arg2* Argument
+
+    EOF
+
+    assert_equal "test cmd -arg 1", SOPT.synopsys
+    assert SOPT.inputs.include? "arg"
+    assert SOPT.inputs.include? "arg2"
+  end
+
+  def test_setup_alt
+    SOPT.setup <<-EOF
+Test application
+
+It does some imaginary stuff
+
+-a--arg* Argument
+-a2--arg2* Argument
+
+    EOF
+
+    assert SOPT.inputs.include? "arg"
+    assert SOPT.inputs.include? "arg2"
+  end
+
+  def test_setup_alt2
+    SOPT.setup <<-EOF
+Test application
+
+-a--arg* Argument
+-a2--arg2* Argument
+
+    EOF
+
+    assert SOPT.inputs.include? "arg"
+    assert SOPT.inputs.include? "arg2"
+  end
+
+  def test_setup_alt3
+    SOPT.setup <<-EOF
+Pulls the values from a tsv colum
+
+$ rbbt tsv values [options] <filename.tsv|->
+
+Use - to read from STDIN
+
+-tch--tokyocabinet File is a tokyocabinet hash database
+-tcb--tokyocabinet_bd File is a tokyocabinet B database
+-h--help Print this help
+    EOF
+
+    assert SOPT.inputs.include? "tokyocabinet"
+  end
+
+end
+
+

data/test/rbbt/util/test_log.rb

@@ -5,5 +5,9 @@ class TestLog < Test::Unit::TestCase
   def test_color
     assert Log.color(:green, "green")
   end
+
+  def test_return_line
+    puts Log.return_line  + "ccc"*3
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.14
+  version: 5.6.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-28 00:00:00.000000000 Z
+date: 2014-03-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -187,6 +187,7 @@ files:
 - lib/rbbt/util/simpleopt/doc.rb
 - lib/rbbt/util/simpleopt/get.rb
 - lib/rbbt/util/simpleopt/parse.rb
+- lib/rbbt/util/simpleopt/setup.rb
 - lib/rbbt/util/tar.rb
 - lib/rbbt/util/task/job.rb
 - lib/rbbt/util/tmpfile.rb
@@ -266,6 +267,7 @@ files:
 - test/rbbt/tsv/test_util.rb
 - test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_cmd.rb
@@ -302,7 +304,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
@@ -310,6 +312,7 @@ test_files:
 - test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.rb
 - test/rbbt/util/test_cmd.rb
+- test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/util/test_chain_methods.rb