rbbt-util 5.44.1 → 6.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 488a57247f23d41f8c94aa64cb38cf666c99ee43c4fa14399ed77b8bb1854519
+  metadata.gz: b6312e564dc119b942bb279017a12bd3571f27b1caa57db746c62996e8c73407
+  data.tar.gz: f08802c255d5967bf211bf801fbeb7f91e9d2a82804f51393061ce422e7fc26e
 SHA512:
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-  data.tar.gz: 91e775b843358c29df1d87e1d9d5db8a92c37d842fd05757cc810a5f4c77a38cfe154a0a368429abb921cf43014333361426546a43aac09eabe81f07ca4315a5
+  metadata.gz: 2f74e126c73d121853002d2918ef5cb8c9b181c7c2264d7eb7c9f4a4d78441fc6b026f1b27eca445613717fff6a8f0169f9aeb86d33afeafe2eebed696685cc3
+  data.tar.gz: 93ddc50c5c0f5b45e79449f81788405fada4ad9aabaeac1f6fd908765184a79220e2960472a460a973afedd31ae2ad389c60d67a80e4b82ae63ac70748bf8a25

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2022 Miguel Vázquez García
+Copyright (c) 2010-2024 Miguel Vázquez García
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/bin/rbbt

@@ -1,4 +1,9 @@
 #!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(__dir__, '../lib')
+
+ENV["SCOUT_NOCOLOR"] = "true" if ARGV.include? "--nocolor"
+
+ENV["SCOUT_NO_PROGRESS"] = "true" if ARGV.include? "--nobar"
 
 class CmdStop < Exception
   attr_accessor :exit_status
@@ -6,6 +11,8 @@ class CmdStop < Exception
     @exit_status = exit_status
   end
 end
+
+# Add paths to scout repos under --dev to LOAD_PATHS
 dev_dir = nil
 if _i = ARGV.index("--dev")
   dev_dir = ARGV[_i+1]
@@ -25,117 +32,84 @@ if dev_dir.nil?
   ARGV.delete _s if _s
 end
 
+if dev_dir.nil? && ENV["SCOUT_DEV"]
+  dev_dir = ENV["SCOUT_DEV"]
+  ARGV.delete "--dev"
+  ARGV.delete dev_dir
+end
+
 if dev_dir
-  Dir.glob(File.join(File.expand_path(dev_dir),'rbbt-*/lib')).each do |f|
-    $LOAD_PATH.unshift f
+  ['scout-*/lib'].each do |pattern|
+    Dir.glob(File.join(File.expand_path(dev_dir), pattern)).each do |f|
+      $LOAD_PATH.unshift f
+    end
+  end
+  ['rbbt-*/lib'].each do |pattern|
+    Dir.glob(File.join(File.expand_path(dev_dir), pattern)).each do |f|
+      next if f.include? 'rbbt-util'
+      $LOAD_PATH.unshift f
+    end
   end
 end
 
-require 'rbbt'
-require 'rbbt/util/simpleopt'
-require 'rbbt/util/config'
+require_relative '../lib/rbbt'
 
-Log.nocolor = true if ARGV.include? "--nocolor"
+require 'scout'
+
+require 'scout/simple_opt'
 
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit
 
-$ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'
+$ #{$0} <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'
 
 
 --log*                  #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}
---log_file*             #{Log.color :yellow, "Divert all Rbbt logs from STDERR to the file"}
 --dev*                  #{Log.color :yellow, "Find development libraries in the directory specified"}
--cd--command_dir*       #{Log.color :yellow, "Directory from where to load command scripts"}
---profile               #{Log.color :yellow, "Profile execution"}
 --nocolor               #{Log.color :yellow, "Disable colored output"}
 --nobar                 #{Log.color :yellow, "Disable progress report"}
---nostream              #{Log.color :yellow, "Disable persistance/job streaming"}
---update                #{Log.color :yellow, "Update persisted files when dependencies update"}
---update_tsv            #{Log.color :yellow, "Update persisted TSV files also if source has been updated"}
 --locate_file           #{Log.color :yellow, "Report the location of the script instead of executing it"}
---dump_mem*             #{Log.color :yellow, "Dump strings in memory each second into file"}
--nolock--no_lock_id     #{Log.color :yellow, "Do not track lockfiles with ids (prevent stale file handlers for high-througput and high-concurrency)"}
--ji--jobname_show_inputs  #{Log.color :yellow, "Show inputs as part of the jobname in workflows instead of digesting them"}
 -ck--config_keys*       #{Log.color :yellow, "Override some config keys"}
--srand--random_seed*    #{Log.color :yellow, "Set the random seed"}
 EOF
 
-srand(options[:random_seed].to_i) if options[:random_seed]
-if options[:jobname_show_inputs]
-  ENV["RBBT_INPUT_JOBNAME"] = "true"
-end
+Log.nocolor = true if options[:nocolor]
 
 locate = options.delete :locate_file
 
 if options[:log_file]
-  Log.logfile(options[:log_file])
-end
-
-Log.ignore_stderr do
-  begin
-    require "nokogiri"
-  rescue Exception
-  end
+  Log.logfile(options.delete(:log_file))
 end
 
 if options[:log]
-  Log.severity = options[:log].to_i
+  Log.severity = options.delete(:log).to_i
 else
-  global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
-  if ENV["RBBT_LOG"]
-    Log.severity = ENV["RBBT_LOG"].to_i 
+  global_severity = Log.get_level(Scout.etc.log_severity.read.strip) if Scout.etc.log_severity.exists?
+  if ENV["SCOUT_LOG"]
+    Log.severity = ENV["SCOUT_LOG"].to_i 
   else
-    global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
+    global_severity = Log.get_level(Scout.etc.log_severity.read.strip) if Scout.etc.log_severity.exists?
     Log.severity = global_severity.to_i if global_severity
   end
 end
 
-if options.delete(:no_lock_id)
-  Misc.use_lock_id = false
-end
-
-if mem_dump = options.delete(:dump_mem)
-  require 'rbbt/monitor'
-  Rbbt.dump_memory(mem_dump, String)
-end
-
-if options[:config_keys]
-  options[:config_keys].split(",").each do |config|
+if config_keys = options.delete(:config_keys)
+  config_keys.split(",").each do |config|
     config = config.strip
-    Rbbt::Config.process_config config
+    Scout::Config.process_config config
   end
 end
 
-if options.delete(:update)
-  ENV["RBBT_UPDATE"] = "true"
-end
-
-if options.delete(:update_tsv)
-  ENV["RBBT_UPDATE"] = "true"
-  ENV["RBBT_UPDATE_TSV_PERSIST"] = "true"
-end
-
-if options.delete :nostream
-  ENV["RBBT_NO_STREAM"] = "true"
-end
-
-if options.delete :nobar
-  ENV["RBBT_NO_PROGRESS"] = "true"
-end
-
-if options[:command_dir]
-  $rbbt_command_dir = Path.setup(options[:command_dir].dup)
-else
-  $rbbt_command_dir = Rbbt.share.rbbt_commands
-end
+$scout_command_dir = Scout.bin.scout
+$scout_command_dir.path_maps[:rbbt_bin] = File.join(File.dirname(__dir__), "{PATH/bin\\/scout/bin\\/rbbt}")
+$scout_command_dir.path_maps[:rbbt_commands] = File.join(File.dirname(__dir__), "{PATH/bin\\/scout/share\\/rbbt_commands}")
+$scout_command_dir.path_maps[:scout_commands] = File.join(Scout.root.find(:scout_gear), "{PATH/bin\\/scout/scout_commands}")
 
 SOPT.description =<<EOF
-This command controls many aspects of the Rbbt framework, from configuration tasks to running applications. 
+This command controls many aspects of the Scout 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)}.
+Commands are implemented in separate files under the Scout path '#{$scout_command_dir}'. 
+Known locations are: #{([$scout_command_dir] + $scout_command_dir.find_all) * ", " }. 
+You can place your own commads at #{$scout_command_dir.find(:user)}.
 EOF
 
 if options[:profile]
@@ -145,25 +119,24 @@ end
 
 
 def prev_dir(prev)
-    rbbt_command_dir = $rbbt_command_dir
+    scout_command_dir = $scout_command_dir
 
     prev.each do |previous_command|
-        rbbt_command_dir = rbbt_command_dir[previous_command]
+        scout_command_dir = scout_command_dir[previous_command]
     end
 
-    rbbt_command_dir
+    scout_command_dir
 end
 
 def commands(prev)
-    rbbt_command_dir = prev_dir(prev)
+    scout_command_dir = prev_dir(prev)
 
-    command_file_dirs = rbbt_command_dir.find_all
+    command_file_dirs = scout_command_dir.find_all
     command_files = command_file_dirs.collect{|d| d.glob('*') }.flatten
     command_files.collect{|p| File.basename(p) }.uniq.reject{|p| p =~ /\.desc$/}.sort
 end
 
-def rbbt_usage(prev = nil)
-  puts
+def scout_usage(prev = nil)
   puts SOPT.doc
 
   if prev
@@ -190,7 +163,7 @@ def rbbt_usage(prev = nil)
   true
 end
 
-alias usage rbbt_usage 
+alias usage scout_usage 
 
 def print_error(error, backtrace = nil)
   puts Log.color :magenta, "## ERROR"
@@ -209,13 +182,21 @@ def aliases
   @aliases ||= Rbbt.etc.cmd_alias.exists? ? Rbbt.etc.cmd_alias.yaml : {}
 end
 
+def tokenize_cmd_params(str)
+ return str if Array === str
+ str.scan(/
+          (?:["']([^"']*?)["']) |
+          ([^"'\s]+)
+          /x).flatten.compact
+end
+
 def cmd_alias
-  while aliases.include? ARGV[0]
-    ARGV.replace Misc.parse_cmd_params(aliases[ARGV[0]]) + ARGV[1..-1]
+  while ARGV[0] && aliases.include?(ARGV[0])
+    ARGV.replace tokenize_cmd_params(aliases[ARGV[0]]) + ARGV[1..-1]
   end
 end
     
-dir = $rbbt_command_dir
+dir = $scout_command_dir
 $previous_commands = []
 
 cmd_alias
@@ -244,31 +225,27 @@ begin
       exit exit_status
     else
       error = "Command '#{$command }' not understood"
-      rbbt_usage($previous_commands)
+      scout_usage($previous_commands)
       print_error(error)
       exit_status = -1
       exit exit_status
     end
   end
 
-  rbbt_usage($previous_commands)
+  scout_usage($previous_commands)
   exit_status = 0
-  exit exit_status
 
 rescue ParameterException
   puts
-  rbbt_usage
+  scout_usage
   print_error($!.message, $!.backtrace)
   puts
   exit_status = -1
-  exit exit_status
 rescue SystemExit,CmdStop
   exit_status = $!.status
-  exit exit_status
 rescue Exception
   Log.exception $!
   exit_status = -1
-  exit exit_status
 ensure
   if options[:profile]
     result = RubyProf.stop

data/bin/rbbt_exec.rb

@@ -30,7 +30,7 @@ data = data * "\n" if Array === data
 
 case
 when (output.nil? or output == '-')
-  puts data
+  STDOUT.write data
 when output == "file"
   if Misc.filename? data
     tmpfile = data
@@ -39,7 +39,7 @@ when output == "file"
     Open.write(tmpfile, data.to_s)
   end
 
-  puts tmpfile
+  STDOUT.puts tmpfile
 else
   Open.write(output, data.to_s)
 end

data/etc/app.d/base.rb

@@ -22,8 +22,8 @@ use Rack::Session::Cookie, :key => 'rack.session',
   :secret => Misc.digest("#{self.to_s} secret!!") * 4
 
 #{{{ DIRECTORIES
-global_var = Rbbt.var.sinatra
-local_var = Rbbt.var.sinatra.app[$app_name]
+global_var = Rbbt.var.rbbt6_sinatra
+local_var = Rbbt.var.rbbt6_sinatra.app[$app_name]
 
 set :cache_dir           , local_var.cache
 set :persist_dir         , local_var.cache.persistence

data/etc/app.d/semaphores.rb

@@ -1,13 +1,13 @@
 # This is used by rbbt-rest when issuing a new job
 
 $rest_cache_semaphore = ENV["RBBT_REST_CACHE_SEMAPHORE"] || "/REST_SEMAPHORE"
-parallel_rest_jobs = Rbbt::Config.get('parallel_rest_jobs', :parallel_rest_jobs, :rest_jobs, :default => 2)
+parallel_rest_jobs = Rbbt::Config.get('parallel_rest_jobs', :parallel_rest_jobs, :rest_jobs, :default => 10)
 
 parallel_rest_jobs = parallel_rest_jobs.to_i if String === parallel_rest_jobs
 
 begin
-  RbbtSemaphore.delete_semaphore($rest_cache_semaphore)
+  ScoutSemaphore.delete_semaphore($rest_cache_semaphore)
 ensure
-  RbbtSemaphore.create_semaphore($rest_cache_semaphore, parallel_rest_jobs)
+  ScoutSemaphore.create_semaphore($rest_cache_semaphore, parallel_rest_jobs)
 end
 Log.debug("Created semaphore: #{$rest_cache_semaphore} with #{parallel_rest_jobs} size")