rbbt-util 5.6.3 → 5.6.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: a2ebf3798cb4ee454a3050307816b5d6ad46747d
+  metadata.gz: c71dfbcf2b547eae0ab59b0fcf3b590d08668244
+  data.tar.gz: 27f56badaca1455685f00466bce558785ed357a8
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+  data.tar.gz: 44dcbc2f220861724f3de420d7e6f6c65676893365b3d4c99391d0928b0ae12816db168b181af0e1349d35dc4441237687331f2f55febb459503ea928d8dfe95

data/bin/rbbt

@@ -25,10 +25,9 @@ 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)}.
+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 commands(prev)
@@ -43,6 +42,38 @@ def commands(prev)
     command_files.collect{|p| File.basename(p) }.uniq.reject{|p| p =~ /\.desc$/}.sort
 end
 
+def rbbt_usage(prev = nil)
+  puts SOPT.doc
+
+  if prev
+    puts "## COMMANDS"
+    puts
+    puts "Command:"
+    puts 
+    puts "  #{File.basename($0)} #{prev * " "}"
+    puts 
+    puts "Subcommands:"
+    puts 
+    commands(prev).each do |command|
+      puts "  " << command
+    end
+  end
+end
+
+def print_error(error, backtrace = nil)
+  puts
+  puts Term::ANSIColor.red("Error:")
+  puts
+  puts error
+  if backtrace
+    puts
+    puts Term::ANSIColor.red("Backtrace:")
+    puts
+    puts backtrace * "\n"
+  end
+  puts
+end
+    
 dir = $rbbt_command_dir
 prev = []
 
@@ -58,12 +89,15 @@ begin
       exit 0
     else
       error = "Command '#{command }' not understood"
-      break
+      rbbt_usage(prev)
+      print_error(error)
+      exit -1
     end
   end
 rescue ParameterException
-  error = $!.message
-  backtrace = $!.backtrace
+  rbbt_usage
+  print_error($!.message, $!.backtrace)
+  exit -1
 ensure
   if options[:profile]
     result = RubyProf.stop
@@ -72,31 +106,3 @@ ensure
   end
 end
 
-puts SOPT.doc
-
-puts "## COMMANDS"
-puts
-puts "Command:"
-puts 
-puts "  #{File.basename($0)} #{prev * " "}"
-puts 
-puts "Subcommands:"
-puts 
-commands(prev).each do |command|
-    puts "  " << command
-end
-
-if error
-  puts
-  puts Term::ANSIColor.red("Error executing '#{ [File.basename($0), prev, command].compact.flatten * " " }':")
-  puts
-  puts error
-  if backtrace
-    puts
-    puts Term::ANSIColor.red("Backtrace:")
-    puts
-    puts backtrace * "\n"
-  end
-  puts
-end
-    

data/lib/rbbt/util/misc.rb

@@ -17,6 +17,9 @@ class Hash
   end
 end
 
+class ParameterException < Exception; end
+class FieldNotFoundError < StandardError;end
+
 module LaterString
   def to_s
     yield
@@ -24,7 +27,6 @@ module LaterString
 end
 
 module Misc
-  class FieldNotFoundError < StandardError;end
 
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str

data/lib/rbbt/workflow/step.rb

@@ -4,7 +4,6 @@ require 'rbbt/util/log'
 require 'rbbt/util/semaphore'
 require 'rbbt/workflow/accessor'
 
-class ParameterException < Exception; end
 
 class Step
   attr_accessor :path, :task, :inputs, :dependencies, :bindings

data/share/rbbt_commands/workflow/task

@@ -6,7 +6,7 @@ require 'rbbt/workflow/usage'
 
 YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
 
-def usage(workflow = nil, task = nil, error = nil, backtrace = nil)
+def usage(workflow = nil, task = nil, exception=nil)
   puts SOPT.doc
   puts "## WORKFLOW"
   puts
@@ -25,13 +25,9 @@ def usage(workflow = nil, task = nil, error = nil, backtrace = nil)
     puts workflow.workflow_description
     puts
     workflow.doc(task)
-    if error
-        puts
-        puts Term::ANSIColor.red("Error: ") << error
-        puts Term::ANSIColor.red("Backtrace: ") << backtrace * "\n"
-    end
   end
 
+  raise exception if exception
   exit 0
 end
 
@@ -249,7 +245,7 @@ begin
   end
 rescue ParameterException
   SOPT.delete_inputs(workflow.rec_inputs(task.name))
-  usage(workflow, task, $!.message, $!.backtrace)
+  usage(workflow, task, $!)
 end
 
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.3
+  version: 5.6.4
 platform: ruby
 authors:
 - Miguel Vazquez