rbbt-util 5.6.12 → 5.6.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f7078269d0f470647e84541e1db1cb8a088e804c
-  data.tar.gz: ae9b295bb59220995ba1d8b81d833e809a4ddf0b
+  metadata.gz: b656db59e4d0eca0665f2f66988894887643c65a
+  data.tar.gz: ad90d4cf34155c405e418306f9376716c514db4e
 SHA512:
-  metadata.gz: c6c0e5e5b36bc9b9606ebcc45b9f2ab6d00ef4c86f1ca1ee16740e3674a8c594f71c93cef42330f7b85c7c168934b9b4973ca73eb9cde3e4b8c92f0b7fe976f4
-  data.tar.gz: 99e0a39b90f299e839136bbe618189ee37d5b48089a82209d58eca81481f5d5a1a3bedaef3d332b73bc34aaac6cc2439273756a1629d789dcb71c468129b733f
+  metadata.gz: bd6c1cf896bcbd16e00f35064b764789a0d35e6e5ef3db98d93bbe86ab55a1de92a5a72fe2c5559cfeba9cd06c645d20ec5f1a62cd4dca482a3f8f2aa9ff8678
+  data.tar.gz: 2909d49e91db24d697b445256475b6066bf807018394eb1560f1161fd8fd1966483db16f7c222bde72cfc54b90869a1bdf794e662bd4dd73f29ecafd3516d793

data/bin/rbbt

@@ -78,10 +78,22 @@ def print_error(error, backtrace = nil)
   end
   puts
 end
+
+def aliases
+  @aliases ||= Rbbt.etc.cmd_alias.exists? ? Rbbt.etc.cmd_alias.yaml : {}
+end
+
+def cmd_alias
+  while aliases.include? ARGV[0]
+    ARGV.replace Misc.parse_cmd_params(aliases[ARGV[0]]) + ARGV[1..-1]
+  end
+end
     
 dir = $rbbt_command_dir
 prev = []
 
+cmd_alias
+
 begin
   while ARGV.any?
     command = ARGV.shift

data/lib/rbbt/persist/tsv.rb

@@ -81,15 +81,15 @@ module Persist
 
     lock_filename = Persist.persistence_path(path, {:dir => TSV.lock_dir})
 
-    if is_persisted? path and not persist_options[:update]
+    if is_persisted?(path) and not persist_options[:update]
       Log.debug "TSV persistence up-to-date: #{ path }"
       return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB) 
     end
 
     Misc.lock lock_filename do
       begin
-        if is_persisted? path 
-          Log.debug "TSV persistence up-to-date: #{ path }"
+        if is_persisted?(path) and not persist_options[:update]
+          Log.debug "TSV persistence (suddenly) up-to-date: #{ path }"
           return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB) 
         end
 

data/lib/rbbt/tsv/accessor.rb

@@ -193,6 +193,18 @@ module TSV
     end
   end
 
+  def zip_new(key, values)
+    if self.include? key
+      new = []
+      self[key, true].each_with_index do |v,i|
+        new << (v << values[i])
+      end
+      self[key] == new
+    else
+      self[key] = values.collect{|v| [v] }
+    end
+  end
+
   def keys
     keys = super - ENTRY_KEYS.to_a
     return keys if @unnamed or key_field.nil?

data/lib/rbbt/util/misc.rb

@@ -29,6 +29,14 @@ end
 Lockfile.refresh = false if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
 module Misc
 
+  def self.parse_cmd_params(str)
+    return str if Array === str
+    str.scan(/
+      (?:["']([^"']*?)["']) |
+      ([^"'\s]+)
+    /x).flatten.compact
+  end
+
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str
     mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/

data/share/rbbt_commands/alias

@@ -0,0 +1,23 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+
+
+cmd, *rest = ARGV
+
+aliases ||= Rbbt.etc.cmd_alias.exists? ? Rbbt.etc.cmd_alias.yaml : {}
+
+if cmd.nil?
+  require 'pp'
+  pp aliases
+  exit 0
+end
+
+if rest.empty?
+  aliases.delete cmd
+else
+  aliases[cmd] = rest
+end
+
+Open.write(Rbbt.etc.cmd_alias.find,(aliases.to_yaml))
+

data/share/rbbt_commands/workflow/example

@@ -0,0 +1,55 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/util/simpleopt'
+require 'rbbt/workflow'
+require 'rbbt/workflow/usage'
+
+def run_task(workflow, task, name)
+  Log.info "Running example #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
+
+  example_dir = workflow.libdir.examples[task][name].find
+  Log.debug "Using #{example_dir}"
+
+  ARGV.replace([workflow.to_s, task, '--load_inputs', example_dir, '--jobname', name,'--O','/dev/null'] + $saved_args)
+
+  @pid = Process.fork{
+    load Rbbt.share.rbbt_commands.workflow.task.find
+  }
+  Signal.trap(:INT) do
+    begin
+      Process.kill "INT", @pid
+    ensure
+      exit -1
+    end
+  end
+  Process.wait @pid
+
+  if $?.success?
+    Log.info "#{Log.color :green, "SUCCESS"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
+  else
+    Log.info "#{Log.color :red, "ERROR"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
+  end
+end
+
+workflow = ARGV.shift
+raise ParameterException if workflow.nil?
+
+task = ARGV.shift
+task = nil if task == '--'
+
+name = ARGV.shift if task
+name = nil if name == '--'
+
+$saved_args = ARGV.dup
+
+
+workflow = Workflow.require_workflow workflow
+
+tasks = task ? [task] : workflow.libdir.examples.glob('*').collect{|file| File.basename file }
+
+tasks.each do |task|
+  names = name ? [name] : workflow.libdir.examples[task].glob('*').collect{|file| File.basename file }
+  names.each do |name|
+    run_task workflow, task, name
+  end
+end

data/share/rbbt_commands/workflow/task

@@ -9,17 +9,30 @@ def load_inputs(dir, task)
   dir = Path.setup(dir.dup)
   task.inputs.each do |input|
     file = dir[input].find
+    Log.debug "Trying #{ input }: #{file}"
     next unless file.exists?
     case task.input_types[input]
     when :tsv, :array, :text
+      Log.debug "Pointing #{ input } to #{file}"
       inputs[input.to_sym]  = file
     else
+      Log.debug "Loading #{ input } from #{file}"
       inputs[input.to_sym]  = file.read
     end
   end
   inputs
 end
 
+def report_options(options)
+  if options.nil? or options.empty?
+    puts "No options"
+  else
+    options.each do |key, value|
+      puts [Log.color(:cyan, key), Misc.fingerprint(value)] * ": "
+    end
+  end
+end
+
 def usage(workflow = nil, task = nil, exception=nil)
   puts SOPT.doc
   puts Log.color :magenta, "## WORKFLOW"
@@ -42,7 +55,8 @@ def usage(workflow = nil, task = nil, exception=nil)
   end
 
   print_error(exception.message, exception.backtrace) if exception
-  exit -1
+
+  true
 end
 
 def SOPT_options(workflow, task)
@@ -135,7 +149,7 @@ options = SOPT.get <<EOF
 EOF
 
 workflow = ARGV.shift
-usage if workflow.nil?
+usage and exit -1 if workflow.nil?
 
 task     = ARGV.shift
 
@@ -171,7 +185,7 @@ namespace = nil, nil
 
 case 
 when task.nil?
-  usage workflow
+  usage workflow and exit 0
   # Can not remember what this was
 #when (task =~ /\./)
 #  namespace, task = options.delete(:task).split('.')
@@ -182,7 +196,7 @@ else
   raise ParameterException, "Task not found: #{ task_name }" if task.nil?
 end
 
-usage workflow, task if help
+usage workflow, task and exit 0 if help
 
 name = options.delete(:jobname) || "Default"
 
@@ -194,6 +208,7 @@ else
   job_options = SOPT.get sopt_option_string
 end
 job_options = fix_options(workflow, task, job_options)
+saved_job_options = job_options
 
 workflow.workdir = Path.setup(File.expand_path(options.delete(:workdir))) if options[:workdir]
 
@@ -222,6 +237,7 @@ begin
     pp job.info
     exit 0
   end
+
   if do_exec
     res = job.exec
     case
@@ -265,6 +281,11 @@ begin
 rescue ParameterException
   SOPT.delete_inputs(workflow.rec_inputs(task.name))
   usage(workflow, task, $!)
+  puts Log.color :magenta, "Options:"
+  puts
+  report_options saved_job_options
+  puts
+  exit -1
 end
 
 

data/test/rbbt/tsv/test_accessor.rb

@@ -19,6 +19,18 @@ row2    A    B    Id3
     end
   end
 
+  def test_zip_new
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b|bb|bbb    Id1|Id2|Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      tsv.zip_new("row1", %w(aaaa bbbb Id4))
+      assert_equal %w(b bb bbb bbbb), tsv["row1"]["ValueB"]
+    end
+  end
 
   def test_tsv
     content =<<-EOF

data/test/rbbt/util/test_misc.rb

@@ -6,6 +6,10 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
+  def test_parse_cmd_params
+    ddd Misc.parse_cmd_params("workflow task Translation translate -f 'Associated Gene Name' -l -")
+  end
+
 
   def test_fixutf8
     string = "abc\xffdef"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.12
+  version: 5.6.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-26 00:00:00.000000000 Z
+date: 2014-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -201,6 +201,7 @@ files:
 - share/Rlib/util.R
 - share/config.ru
 - share/install/software/lib/install_helpers
+- share/rbbt_commands/alias
 - share/rbbt_commands/app/install
 - share/rbbt_commands/app/start
 - share/rbbt_commands/app/template
@@ -225,6 +226,7 @@ files:
 - share/rbbt_commands/tsv/unzip
 - share/rbbt_commands/tsv/values
 - share/rbbt_commands/workflow/cmd
+- share/rbbt_commands/workflow/example
 - share/rbbt_commands/workflow/install
 - share/rbbt_commands/workflow/list
 - share/rbbt_commands/workflow/monitor