rbbt-util 5.6.5 → 5.6.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6a46ea266ad3643e792d4ada78b8fc6481cb0402
-  data.tar.gz: f0d162717d49d90ed84fcf3a470970463210db11
+  metadata.gz: dfcdf5fe55d3a3ddb6a46648fd5a7d378b2eb692
+  data.tar.gz: f7a1a8275c767cb3347e3ac8856be2353014f4f3
 SHA512:
-  metadata.gz: 3f94543a04e6919ced4606fe6d58a5211c6f4f84803d6320e99c87fc9a0d28802e8b7ee76011fbe2f5bcbf9bc993fb788ea5cd01f5edc178bddf823de47dc32f
-  data.tar.gz: cca962588cea1323d696ca06d8e4a81e936393cd7f217fc21d3879731276ca080144e21e42b3f1ae8469be61825e4accbd3f94b2baee19d7467583f6fdffb801
+  metadata.gz: 2caa0e4bb980ef419ba0390c2d2b34eec883e88f71e24979e837b3e2720198f5ea7a1dc053583fa0941a8e3071d3a31e7db897fd0fec03cf8f64664d3e119924
+  data.tar.gz: c51c7c567113673fca18fa95dae7bf2722e6a0d0bdd75f5236fa4fd2a89109bfa72a3fc648d212540ebf4c2d89e4f5435afdd01a66ca9b060e44a386aa82afce

data/bin/rbbt

@@ -3,7 +3,7 @@
 require 'rbbt'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):--command_dir* Directory from where to load commands:--profile Profile execution")
+options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):-cd--command_dir* Directory from where to load commands:--profile Profile execution")
 
 if options[:log]
   Log.severity = options[:log].to_i

data/lib/rbbt/tsv.rb

@@ -96,7 +96,7 @@ module TSV
       stream.open do |f|
         Parser.new f, options
       end
-    when (String === stream and stream.length < 300 and Open.exists? stream or Open.remote? stream)
+    when (String === stream and stream.length < 300 and (Open.exists? stream or Open.remote? stream))
       Open.open(stream) do |f|
         Parser.new f, options
       end

data/lib/rbbt/util/misc.rb

@@ -1366,6 +1366,19 @@ end
     array[0].zip(*array[1..-1])
   end
 
+  def self.camel_case(string)
+    return string if string !~ /_/ && string =~ /[A-Z]+.*/
+      string.split(/_|(\d+)/).map{|e| 
+        (e =~ /^[A-Z]{2,}$/ ? e : e.capitalize) 
+      }.join
+  end
+
+  def self.camel_case_lower(string)
+      string.split('_').inject([]){ |buffer,e| 
+        buffer.push(buffer.empty? ? e.downcase : (e =~ /^[A-Z]{2,}$/ ? e : e.capitalize)) 
+      }.join
+  end
+
   def self.snake_case(string)
     return nil if string.nil?
     string = string.to_s if Symbol === string

data/lib/rbbt/workflow.rb

@@ -37,6 +37,19 @@ module Workflow
     end
   end
 
+  def self.workflow_dir
+    case
+    when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
+      dir = Rbbt.etc.workflow_dir.read.strip
+      Path.setup(dir)
+    when defined?(Rbbt)
+      Rbbt.workflows
+    else
+      dir = File.join(ENV['HOME'], '.workflows')
+      Path.setup(dir)
+    end
+  end
+
   def self.require_local_workflow(wf_name)
     filename = nil
 
@@ -52,21 +65,27 @@ module Workflow
       end
 
     else
-      case
-        # Points to workflow file
-      when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb'))
+      if ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb'))
         filename = (wf_name =~ /\.?\//) ? wf_name : "./" << wf_name 
-      when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
-        dir = Rbbt.etc.workflow_dir.read.strip
-        dir = File.join(dir, wf_name)
-        filename = File.join(dir, 'workflow.rb')
-      when defined?(Rbbt)
-        path = Rbbt.workflows[wf_name].find
-        filename = File.join(path, 'workflow.rb')
       else
-        path = File.join(ENV['HOME'], '.workflows', wf_name)
-        filename = File.join(dir, 'workflow.rb')
+        filename = workflow_dir[wf_name]['workflow.rb'].find
       end
+
+      #case
+      #  # Points to workflow file
+      #when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb'))
+      #  filename = (wf_name =~ /\.?\//) ? wf_name : "./" << wf_name 
+      #when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
+      #  dir = Rbbt.etc.workflow_dir.read.strip
+      #  dir = File.join(dir, wf_name)
+      #  filename = File.join(dir, 'workflow.rb')
+      #when defined?(Rbbt)
+      #  path = Rbbt.workflows[wf_name].find
+      #  filename = File.join(path, 'workflow.rb')
+      #else
+      #  path = File.join(ENV['HOME'], '.workflows', wf_name)
+      #  filename = File.join(dir, 'workflow.rb')
+      #end
     end
 
     if filename and File.exists? filename
@@ -119,6 +138,11 @@ module Workflow
   attr_accessor :asynchronous_exports, :synchronous_exports, :exec_exports
 
   #{{{ ATTR DEFAULTS
+  
+  def workdir=(path)
+    path = Path.setup path.dup unless Path === path
+    @workdir = path
+  end
 
   def workdir
     @workdir ||= if defined? Rbbt
@@ -239,16 +263,19 @@ module Workflow
     step
   end
 
-  def jobs(task, query = nil)
-    task_dir = File.join(workdir.find, task.to_s)
-    if query.nil?
-      path = File.join(task_dir, "**/*.info")
-    else
-      path = File.join(task_dir, query + "*.info")
-    end
+  def load_name(task, name)
+    task = tasks[task.to_sym] if String === task or Symbol === task
+    path = step_path task.name, name, [], [], task.extension
+    Step.new path, task
+  end
 
-    Dir.glob(path).collect{|f|
-      Misc.path_relative_to(task_dir, f).sub(".info",'')
+  def jobs(taskname, query = nil)
+    task_dir = File.join(workdir.find, taskname.to_s)
+    pattern = File.join(task_dir, '**/*')
+    job_info_files = Dir.glob(Step.info_file(pattern)).collect{|f| Misc.path_relative_to task_dir, f }
+    job_info_files = job_info_files.select{|f| f.index(query) == 0 } if query
+    job_info_files.collect{|f|
+      job_name = Step.job_name_for_info_file(f, tasks[taskname].extension)
     }
   end
 

data/lib/rbbt/workflow/accessor.rb

@@ -5,6 +5,22 @@ class Step
    
   INFO_SERIALIAZER = Marshal
 
+  def self.files_dir(path)
+    path.nil? ? nil : path + '.files'
+  end
+
+  def self.info_file(path)
+    path.nil? ? nil : path + '.info'
+  end
+
+  def self.job_name_for_info_file(info_file, extension = nil)
+    if extension and not extension.empty?
+      info_file.sub(/\.#{extension}\.info$/,'')
+    else
+      info_file.sub(/\.info$/,'')
+    end
+  end
+
   def name
     path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1')
   end
@@ -20,9 +36,7 @@ class Step
   # {{{ INFO
 
   def info_file
-    @info_file ||= begin
-                     path.nil? ? nil : path + '.info'
-                   end
+    @info_file ||= Step.info_file(path)
   end
 
   def info
@@ -117,7 +131,7 @@ class Step
   # {{{ INFO
 
   def files_dir
-    path + '.files'
+    @files_dir ||= Step.files_dir path
   end
 
   def files

data/lib/rbbt/workflow/step.rb

@@ -92,8 +92,7 @@ class Step
   end
 
   def checks
-    deps = rec_dependencies.collect{|dependency| dependency.path }.uniq
-    deps.select!{|p| p.exists? }
+    rec_dependencies.collect{|dependency| dependency.path }.uniq
   end
 
   def run(no_load = false)
@@ -276,7 +275,14 @@ class Step
   end
 
   def rec_dependencies
-    @dependencies.collect{|step| step.rec_dependencies}.flatten.concat  @dependencies
+
+    # A step result with no info_file means that it was manually
+    # placed. In that case, do not consider its dependencies
+    return [] if self.done? and not Open.exists? self.info_file
+
+    @dependencies.collect{|step| 
+      step.rec_dependencies 
+    }.flatten.concat  @dependencies
   end
 
   def recursive_clean

data/lib/rbbt/workflow/task.rb

@@ -72,5 +72,4 @@ module Task
       exec_in *args
     end
   end
-
 end

data/share/rbbt_commands/system/report

@@ -1,8 +1,13 @@
 #!/usr/bin/env ruby
 
-options = SOPT.get("-a--app*")
+options = SOPT.get("-a--app* Apps to add:-wd--workdir* Workflow workdir:-h--help Help")
 
-workflow_dir = Rbbt.var.jobs.find
+if options[:help]
+  puts SOPT.doc
+  exit 0
+end
+
+workflow_dir = options[:workdir] || Rbbt.var.jobs.find
 
 def report_jobs(workflow_dir, title = "WORKFLOW")
   error = {}
@@ -50,7 +55,7 @@ end if options[:app]
 
 puts <<EOF
 
-#{ report_jobs Rbbt.var.jobs.find}
+#{ report_jobs workflow_dir}
 #{ app_dirs.collect{|d,report| report } * "\n" }
 
 # LOCKED TSV

data/share/rbbt_commands/tsv/attach

@@ -8,6 +8,7 @@ file = ARGV.shift
 identifiers = ARGV.shift
 format = ARGV.shift
 
+file = STDIN if file == '-'
 
 puts TSV.open(file).attach identifiers, :fields => [format]
 

data/share/rbbt_commands/tsv/info

@@ -3,7 +3,10 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd")
+options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd:-t--type*:-h--header_hash*:-k--key_field*:-f--fields*")
+
+options[:fields] = options[:fields].split(/,\|/) if options[:fields]
+options[:header_hash] = options["header_hash"]
 
 file = ARGV.shift
 
@@ -19,16 +22,19 @@ when options[:tokyocabinet_bd]
   tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
   puts tsv.summary
 else
-  header = TSV.parse_header(Open.open(file))
+  header = TSV.parse_header(Open.open(file), options)
 
   puts "File: #{ file }"
   puts "Type: #{header.type}"
   puts "Key: #{header.key_field}"
   puts "Fields: "
-  header.fields.each_with_index do |f,i|
-    puts "  - #{i + 1}: " << f
+  if header.fields.nil?
+  else
+    header.fields.each_with_index do |f,i|
+      puts "  - #{i + 1}: " << f
+    end
   end
-  puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}"
+  puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}" unless Open.remote? file
   puts "First line:"
   parts = []
   header.first_line.split(header.sep).each_with_index{|p,i| parts << "(#{i}) #{p}"}

data/share/rbbt_commands/workflow/list

@@ -0,0 +1,31 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/workflow'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.get('-wd--workflow_dir*:-d--describe')
+
+workflow_dir = options[:workflow_dir] || Workflow.workflow_dir
+
+Path.setup(workflow_dir) unless Path === workflow_dir
+
+files = workflow_dir.find_all.collect{|p| p.glob("*") }.flatten.select{|f| File.directory? f }
+
+puts defined? COSMIC
+if options[:describe]
+  files.each do |file|
+    workflow = File.basename(file)
+    Workflow.require_workflow workflow
+    ddd Workflow.workflows
+    workflow = Workflow.workflows.select{|w| Misc.camel_case(w.to_s) == Misc.camel_case(workflow)}.first
+    ddd workflow
+    puts [Misc.camel_case(workflow.to_s), workflow.description] * ":"
+    puts defined? COSMIC
+  end
+else
+  files.each do |file|
+    workflow = File.basename(file)
+    puts Misc.camel_case(workflow.to_s)
+  end
+end

data/test/rbbt/test_workflow.rb

@@ -106,6 +106,8 @@ class TestWorkflow < Test::Unit::TestCase
     assert TestWF.jobs(:repeat2).include?(job1.name)
     assert TestWF.jobs(:repeat2).include?(job2.name)
     assert TestWF.jobs(:repeat2).include?(job3.name)
+    assert TestWF.load_name(:repeat2, TestWF.jobs(:repeat2).first).done?
+    assert_equal "TEST\nTEST\nTEST\nTEST\nTEST\nTEST", TestWF.load_name(:repeat2, TestWF.jobs(:repeat2).first).load
   end
 
   def test_double_dep

data/test/rbbt/util/test_misc.rb

@@ -254,6 +254,14 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
+  def test_camel_case
+    assert_equal "DbSNP", Misc.camel_case("db_SNP")
+    assert_equal "D3Js", Misc.camel_case("D3Js")
+    assert_equal "Structure", Misc.camel_case("Structure")
+    assert_equal "MutEval", Misc.camel_case("mut_eval")
+    assert_equal "COSMIC", Misc.camel_case("COSMIC")
+  end
+
   def test_pipe
     t = 5
     stream = Misc.open_pipe do |sin|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.5
+  version: 5.6.6
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-18 00:00:00.000000000 Z
+date: 2014-02-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -239,6 +239,7 @@ files:
 - share/rbbt_commands/tsv/values
 - share/rbbt_commands/workflow/cmd
 - share/rbbt_commands/workflow/install
+- share/rbbt_commands/workflow/list
 - share/rbbt_commands/workflow/monitor
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list