rbbt-util 5.32.24 → 5.32.28

data/lib/rbbt/workflow/examples.rb

@@ -25,71 +25,6 @@ module Workflow
     end.compact
   end
 
-  def self.load_inputs(dir, input_names, input_types)
-    inputs = {}
-    if File.exists?(dir) && ! File.directory?(dir)
-      Log.debug "Loading inputs from #{dir}, not a directory trying as tar.gz"
-      tarfile = dir
-      digest = CMD.cmd("md5sum '#{tarfile}'").read.split(" ").first
-      tmpdir = Rbbt.tmp.input_bundle[digest].find
-      Misc.untar(tarfile, tmpdir) unless File.exists? tmpdir
-      files = tmpdir.glob("*")
-      if files.length == 1 && File.directory?(files.first)
-        tmpdir = files.first
-      end
-      load_inputs(tmpdir, input_names, input_types)
-    else
-      dir = Path.setup(dir.dup)
-      input_names.each do |input|
-        file = dir[input].find
-        file = dir.glob(input.to_s + ".*").reject{|f| f =~ /\.md5$/}.first if file.nil? or not file.exists?
-        Log.debug "Trying #{ input }: #{file}"
-        next unless file and file.exists?
-
-
-        case input_types[input]
-        when :file, :binary
-          Log.debug "Pointing #{ input } to #{file}"
-          if file =~ /\.yaml/
-            inputs[input.to_sym]  = YAML.load(Open.read(file))
-          else
-            if File.symlink?(file)
-              link_target = File.expand_path(File.readlink(file), File.dirname(file))
-              inputs[input.to_sym]  = link_target
-            else
-              inputs[input.to_sym]  = Open.realpath(file)
-            end
-          end
-        when :text
-          Log.debug "Reading #{ input } from #{file}"
-          inputs[input.to_sym]  = Open.read(file)
-        when :array
-          Log.debug "Reading array #{ input } from #{file}"
-          inputs[input.to_sym]  = Open.read(file).split("\n")
-        when :tsv
-          Log.debug "Opening tsv #{ input } from #{file}"
-          inputs[input.to_sym]  = TSV.open(file)
-        when :boolean
-          inputs[input.to_sym]  = (file.read.strip == 'true')
-        else
-          Log.debug "Loading #{ input } from #{file}"
-          inputs[input.to_sym]  = file.read.strip
-        end
-
-      end
-      inputs = IndiferentHash.setup(inputs)
-
-      dir.glob("*#*").each do |od|
-        name = File.basename(od)
-        value = Open.read(od)
-        Log.debug "Loading override dependency #{ name } as #{value}"
-        inputs[name] = value.chomp
-      end
-
-      inputs
-    end
-  end
-
   def example_inputs(task_name, example)
     inputs = {}
     IndiferentHash.setup(inputs)

data/lib/rbbt/workflow/integration/nextflow.rb

@@ -1,37 +1,97 @@
 module Workflow
-  def nextflow_file(file, name = nil)
+  def self.nextflow_file_params(file)
+    Open.read(file).scan(/params\.\w+/).collect{|p| p.split(".").last}.uniq
+  end
+
+  def self.nextflow_includes(file)
+    Open.read(file).scan(/^include\s*{\s*(.*?)(?:\s*as.*?)?}\s*from\s+"(.*?)"(?:\s*params.*)?/).collect{|p| p}.uniq
+  end
+
+  def self.nextflow_recursive_params(file)
+    params = nextflow_file_params(file)
+    dir = File.dirname(file)
+    nextflow_includes(file).inject(params) do |params,info|
+      name_str, included_file = info
+      included_file = File.join(dir, included_file)
+      included_file += '.nf' unless File.exists?(included_file) || ! File.exists?(included_file + '.nf')
+      name_str.split(";").each do |name|
+        name = name.strip
+        include_params = nextflow_recursive_params(included_file).collect{|p| [p,name] * "-"}
+        params += include_params
+      end
+      params
+    end
+  end
+
+  def nextflow_file(file, name = nil, output = nil)
+    name, output = nil, name if Hash === name
+
+    if Hash === output
+      result, output = output.collect.first
+    else
+      result = :text
+    end
+
     file = file + '.nf' unless File.exists?(file) || ! File.exists?(file + '.nf')
     file = File.expand_path(file)
-    name ||= File.basename(file).sub(/\.nf$/,'')
-    params = Open.read(file).scan(/params\.\w+/).collect{|p| p.split(".").last}.uniq
+    name ||= File.basename(file).sub(/\.nf$/,'').gsub(/\s/,'_')
+    params = Workflow.nextflow_recursive_params(file)
 
     params.each do |param|
-      input param, :string
+      p,_sep, section = param.partition("-")
+      if section.nil? || section.empty?
+        input param, :string, "Nextflow param #{p}", nil, :nofile => true
+      else
+        input param, :string, "Nextflow param #{p} from import #{section}", nil, :nofile => true
+      end
     end
-    task name => :text do 
+    task name => result do 
       work = file('work')
-      output = file('output')
       profile = config :profile, :nextflow
-      Misc.in_dir output do
+
+      new_inputs = inputs.zip(inputs.fields).collect do |v,f|
+        if String === v && m = v.match(/^JOB_FILE:(.*)/)
+          file(m[1]) 
+        elsif v.nil?
+          Rbbt::Config.get(['nextflow', f] * "_", 'default', f)
+        else
+          v
+        end
+      end
+      
+      inputs.replace new_inputs
+
+      Misc.in_dir file('stage') do
         if profile
-          cmd("nextflow run -work-dir #{work} -name #{clean_name} -ansi-log false  -profile #{profile} #{file}", inputs.to_hash.merge('add_option_dashes' => true))
+          cmd("nextflow run -work-dir #{work} -ansi-log false  -profile #{profile} #{file}", inputs.to_hash.merge('add_option_dashes' => true))
         else
-          cmd("nextflow run -work-dir #{work} -name #{clean_name} -ansi-log false #{file}", inputs.to_hash.merge('add_option_dashes' => true))
+          cmd("nextflow run -work-dir #{work} -ansi-log false #{file}", inputs.to_hash.merge('add_option_dashes' => true))
         end
       end
+
+      output_file = file(output).glob.first if output
+      output_file = work[File.join('*', '*', output)].glob.first if output && output_file.nil?
+
+      if output_file.nil?
+        work[File.join("*", "*", "*")].glob * "\n"
+      else
+        Open.link output_file, self.tmp_path
+        #Open.rm_rf file('work')
+        nil
+      end
     end
   end
 
-  def nextflow_dir(path)
+  def nextflow_dir(path, output = nil)
     main = File.join(path, 'main.nf')
-    nextflow_file main, File.basename(path)
+    nextflow_file main, File.basename(path), output
   end
 
-  def nextflow(path)
+  def nextflow(path, *args)
     if File.directory?(path)
-      nextflow_dir path
+      nextflow_dir path, *args
     else
-      nextflow_file path
+      nextflow_file path, *args
     end
   end
 end

data/lib/rbbt/workflow/step/accessor.rb

@@ -86,76 +86,6 @@ class Step
     end
   end
 
-  def self.save_inputs(inputs, input_types, dir)
-    inputs.each do |name,value|
-      type = input_types[name]
-      type = type.to_s if type
-      path = File.join(dir, name.to_s)
-
-      Log.debug "Saving job input #{name} (#{type}) into #{path}"
-      case
-      when Step === value
-        Open.ln_s(value.path, path)
-      when type.to_s == "file"
-        if String === value && File.exists?(value)
-          value = File.expand_path(value)
-          Open.ln_s(value, path)
-        else
-          value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value
-          value = "#{value}" if Path === value
-          Open.write(path + '.yaml', value.to_yaml)
-        end
-      when Array === value
-        Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
-      when IO === value
-        if value.filename && String === value.filename && File.exists?(value.filename)
-          Open.ln_s(value.filename, path)
-        else
-          Open.write(path, value)
-        end
-      else
-        Open.write(path, value.to_s)
-      end
-    end.any?
-  end
-
-  def self.save_job_inputs(job, dir, options = nil)
-    options = IndiferentHash.setup options.dup if options
-
-    task_name = Symbol === job.overriden ? job.overriden : job.task_name
-    workflow = job.workflow
-    workflow = Kernel.const_get workflow if String === workflow
-    if workflow
-      task_info = IndiferentHash.setup(workflow.task_info(task_name))
-      input_types = IndiferentHash.setup(task_info[:input_types])
-      task_inputs = IndiferentHash.setup(task_info[:inputs])
-      input_defaults = IndiferentHash.setup(task_info[:input_defaults])
-    else
-      task_info = IndiferentHash.setup({})
-      input_types = IndiferentHash.setup({})
-      task_inputs = IndiferentHash.setup({})
-      input_defaults = IndiferentHash.setup({})
-    end
-
-    inputs = IndiferentHash.setup({})
-    real_inputs = job.real_inputs || job.info[:real_inputs]
-    job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
-      next unless task_inputs.include? name.to_sym
-      next unless real_inputs.include? name.to_sym
-      next if options && ! options.include?(name)
-      next if value.nil?
-      next if input_defaults[name] == value
-      inputs[name] = value
-    end
-
-    if options && options.include?('override_dependencies')
-      inputs.merge!(:override_dependencies => open[:override_dependencies])
-      input_types = IndiferentHash.setup(input_types.merge(:override_dependencies => :array))
-    end
-    save_inputs(inputs, input_types, dir)
-
-    inputs.keys
-  end
 
   def name
     @name ||= path.sub(/.*\/#{Regexp.quote task_name.to_s}\/(.*)/, '\1')

data/lib/rbbt/workflow/step/dependencies.rb

@@ -254,7 +254,12 @@ class Step
     when :bootstrap
       cpus = rest.nil? ? nil : rest.first 
 
-      cpus = config('dep_cpus', 'bootstrap', :default => [5, list.length / 2].min) if cpus.nil? || cpus.to_i == 0
+      if cpus.nil? 
+        keys = ['bootstrap'] + list.collect{|d| [d.task_name, d.task_signature] }.flatten.uniq
+        cpus = config('dep_cpus', *keys, :default => [5, list.length / 2].min)
+      elsif Symbol === cpus
+        cpus = config('dep_cpus', cpus, :default => [5, list.length / 2].min)
+      end
 
       respawn = rest && rest.include?(:respawn)
       respawn = false if rest && rest.include?(:norespawn)
@@ -369,7 +374,8 @@ class Step
       next unless step.dependencies and step.dependencies.any?
       (step.dependencies + step.input_dependencies).each do |step_dep|
         next unless step.dependencies.include?(step_dep)
-        next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
+        next if step_dep.done? or step_dep.running? or 
+          (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
         dep_step[step_dep.path] ||= []
         dep_step[step_dep.path] << step
       end

data/lib/rbbt/workflow/step/run.rb

@@ -419,7 +419,7 @@ class Step
           set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
 
           config_keys = Rbbt::Config::GOT_KEYS[config_keys_pre.length..-1]
-          set_info :config_keys, config_keys
+          set_info :config_keys, config_keys.uniq
 
           if result.nil? && File.exists?(self.tmp_path) && ! File.exists?(self.path)
             Open.mv self.tmp_path, self.path

data/lib/rbbt/workflow/step/save_load_inputs.rb

@@ -0,0 +1,162 @@
+module Workflow
+  def self.load_inputs(dir, input_names, input_types)
+    inputs = {}
+    if File.exists?(dir) && ! File.directory?(dir)
+      Log.debug "Loading inputs from #{dir}, not a directory trying as tar.gz"
+      tarfile = dir
+      digest = CMD.cmd("md5sum '#{tarfile}'").read.split(" ").first
+      tmpdir = Rbbt.tmp.input_bundle[digest].find
+      Misc.untar(tarfile, tmpdir) unless File.exists? tmpdir
+      files = tmpdir.glob("*")
+      if files.length == 1 && File.directory?(files.first)
+        tmpdir = files.first
+      end
+      load_inputs(tmpdir, input_names, input_types)
+    else
+      dir = Path.setup(dir.dup)
+      input_names.each do |input|
+        file = dir[input].find
+        file = dir.glob(input.to_s + ".*").reject{|f| f =~ /\.md5$/}.first if file.nil? or not (File.symlink?(file) || file.exists?)
+        Log.debug "Trying #{ input }: #{file}"
+        next unless file and (File.symlink?(file) || file.exists?)
+
+        type = input_types[input]
+
+        type = :io if file.split(".").last == 'as_io'
+
+        case type
+        when :io
+          inputs[input.to_sym] = Open.open(Open.realpath(file))
+        when :file, :binary
+          Log.debug "Pointing #{ input } to #{file}"
+          if file =~ /\.yaml/
+            inputs[input.to_sym]  = YAML.load(Open.read(file))
+          else
+            if File.symlink?(file)
+              link_target = File.expand_path(File.readlink(file), File.dirname(file))
+              inputs[input.to_sym]  = link_target
+            else
+              inputs[input.to_sym]  = Open.realpath(file)
+            end
+          end
+        when :text
+          Log.debug "Reading #{ input } from #{file}"
+          inputs[input.to_sym]  = Open.read(file)
+        when :array
+          Log.debug "Reading array #{ input } from #{file}"
+          inputs[input.to_sym]  = Open.read(file).split("\n")
+        when :tsv
+          Log.debug "Opening tsv #{ input } from #{file}"
+          inputs[input.to_sym]  = TSV.open(file)
+        when :boolean
+          inputs[input.to_sym]  = (file.read.strip == 'true')
+        else
+          Log.debug "Loading #{ input } from #{file}"
+          inputs[input.to_sym]  = file.read.strip
+        end
+
+      end
+      inputs = IndiferentHash.setup(inputs)
+
+      dir.glob("*#*").each do |od|
+        name = File.basename(od)
+        value = Open.read(od)
+        Log.debug "Loading override dependency #{ name } as #{value}"
+        inputs[name] = value.chomp
+      end
+
+      inputs
+    end
+  end
+
+  def task_inputs_from_directory(task_name, directory)
+    task_info = self.task_info(task_name)
+    Workflow.load_inputs(directory, task_info[:inputs], task_info[:input_types])
+  end
+
+  def job_for_directory_inputs(task_name, directory, jobname = nil)
+    inputs = task_inputs_from_directory(task_name, directory)
+    job(task_name, jobname, inputs)
+  end
+
+end
+
+class Step
+  def self.save_inputs(inputs, input_types, input_options, dir)
+    inputs.each do |name,value|
+      type = input_types[name]
+      type = type.to_s if type
+      path = File.join(dir, name.to_s)
+
+      path = path + '.as_io' if (IO === value || Step === value) && ! (input_options[name] && input_options[name][:nofile])
+      Log.debug "Saving job input #{name} (#{type}) into #{path}"
+
+      case
+      when IO === value
+        Open.write(path, value.to_s)
+      when Step === value
+        Open.ln_s(value.path, path)
+      when type.to_s == "file"
+        if String === value && File.exists?(value)
+          value = File.expand_path(value)
+          Open.ln_s(value, path)
+        else
+          value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value
+          value = "#{value}" if Path === value
+          Open.write(path + '.yaml', value.to_yaml)
+        end
+      when Array === value
+        Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
+      when IO === value
+        if value.filename && String === value.filename && File.exists?(value.filename)
+          Open.ln_s(value.filename, path)
+        else
+          Open.write(path, value)
+        end
+      else
+        Open.write(path, value.to_s)
+      end
+    end.any?
+  end
+
+  def self.save_job_inputs(job, dir, options = nil)
+    options = IndiferentHash.setup options.dup if options
+
+    task_name = Symbol === job.overriden ? job.overriden : job.task_name
+    workflow = job.workflow
+    workflow = Kernel.const_get workflow if String === workflow
+    if workflow
+      task_info = IndiferentHash.setup(workflow.task_info(task_name))
+      input_types = IndiferentHash.setup(task_info[:input_types])
+      input_options = IndiferentHash.setup(task_info[:input_options])
+      task_inputs = IndiferentHash.setup(task_info[:inputs])
+      input_defaults = IndiferentHash.setup(task_info[:input_defaults])
+    else
+      task_info = IndiferentHash.setup({})
+      input_types = IndiferentHash.setup({})
+      task_inputs = IndiferentHash.setup({})
+      task_options = IndiferentHash.setup({})
+      input_defaults = IndiferentHash.setup({})
+    end
+
+    inputs = IndiferentHash.setup({})
+    real_inputs = job.real_inputs || job.info[:real_inputs]
+    job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
+      next unless task_inputs.include? name.to_sym
+      next unless real_inputs.include? name.to_sym
+      next if options && ! options.include?(name)
+      next if value.nil?
+      next if input_defaults[name] == value
+      inputs[name] = value
+    end
+
+    if options && options.include?('override_dependencies')
+      inputs.merge!(:override_dependencies => open[:override_dependencies])
+      input_types = IndiferentHash.setup(input_types.merge(:override_dependencies => :array))
+    end
+
+    save_inputs(inputs, input_types, input_options, dir)
+
+    inputs.keys
+  end
+end

data/lib/rbbt/workflow/step.rb

@@ -6,6 +6,7 @@ require 'rbbt/workflow/step/accessor'
 require 'rbbt/workflow/step/prepare'
 require 'rbbt/workflow/step/status'
 require 'rbbt/workflow/step/info'
+require 'rbbt/workflow/step/save_load_inputs'
 
 class Step
   attr_accessor :clean_name, :path, :task, :workflow, :inputs, :dependencies, :bindings
@@ -321,7 +322,7 @@ class Step
   def load
     res = begin
             @result = nil if IO === @result && @result.closed?
-            if @result && @path != @result
+            if @result && @path != @result &&  ! StreamArray === @result
               res = @result
             else
               join if not done?

data/lib/rbbt/workflow/task.rb

@@ -90,11 +90,11 @@ module Task
 
       maps = (Array === dep and Hash === dep.last) ? dep.last.keys : []
       raise "Dependency task not found: #{dep}" if task.nil?
-      next if seen.include? [wf, task.name]
+      next if seen.include? [wf, task.name, maps]
 
       task.workflow = wf if wf
 
-      seen << [wf, task.name]
+      seen << [wf, task.name, maps]
       new_inputs = task.inputs - maps
       next unless new_inputs.any?
       if task_inputs[task].nil?

data/lib/rbbt/workflow.rb

@@ -244,7 +244,7 @@ module Workflow
                        when :hash
                          clean_inputs = Annotated.purge(inputs)
                          clean_inputs = clean_inputs.collect{|i| Symbol === i ? i.to_s : i }
-                         deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep === Step)) ? "Step: " << (d.overriden? ? d.path : d.short_path) : d }
+                         deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep === Step)) ? "Step: " << (Symbol === d.overriden ? d.path : d.short_path) : d }
                          key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
                          key_str = Misc.obj2str(key_obj)
                          hash_str = Misc.digest(key_str)
@@ -465,7 +465,14 @@ module Workflow
       extension = nil
       if dependencies.any?
         dep_basename = File.basename(dependencies.last.path)
-        extension = dep_basename.split(".").last if dep_basename.include?('.')
+        if dep_basename.include? "."
+          parts = dep_basename.split(".")
+          extension = [parts.pop]
+          while parts.last.length <= 4
+            extension << parts.pop
+          end
+          extension = extension.reverse * "."
+        end
       end
     end
 

data/share/rbbt_commands/hpc/tail

@@ -13,19 +13,6 @@ Queue a job in Marenostrum
 $ rbbt slurm tail <directory> [options] 
 
 -h--help Print this help
--d--done Done jobs only
--e--error Error jobs only
--a--aborted SLURM aboted jobs
--r--running Running jobs only
--q--queued Queued jobs only
--j--job* Job ids
--s--search* Regular expression
--t--tail* Show the last lines of the STDERR
--p--progress Report progress of job and the dependencies
--SBP--sbatch_parameters show sbatch parameters
--PERF--procpath_performance show Procpath performance summary
--sacct--sacct_peformance show sacct performance summary
--bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 
 if options[:help]

data/share/rbbt_commands/lsf/tail

@@ -13,19 +13,6 @@ Queue a job in Marenostrum
 $ rbbt slurm tail <directory> [options] 
 
 -h--help Print this help
--d--done Done jobs only
--e--error Error jobs only
--a--aborted SLURM aboted jobs
--r--running Running jobs only
--q--queued Queued jobs only
--j--job* Job ids
--s--search* Regular expression
--t--tail* Show the last lines of the STDERR
--p--progress Report progress of job and the dependencies
--SBP--sbatch_parameters show sbatch parameters
--PERF--procpath_performance show Procpath performance summary
--sacct--sacct_peformance show sacct performance summary
--bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 
 if options[:help]

data/share/rbbt_commands/slurm/tail

@@ -13,19 +13,6 @@ Queue a job in Marenostrum
 $ rbbt slurm tail <directory> [options] 
 
 -h--help Print this help
--d--done Done jobs only
--e--error Error jobs only
--a--aborted SLURM aboted jobs
--r--running Running jobs only
--q--queued Queued jobs only
--j--job* Job ids
--s--search* Regular expression
--t--tail* Show the last lines of the STDERR
--p--progress Report progress of job and the dependencies
--SBP--sbatch_parameters show sbatch parameters
--PERF--procpath_performance show Procpath performance summary
--sacct--sacct_peformance show sacct performance summary
--bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 
 if options[:help]

data/share/rbbt_commands/tsv/keys

@@ -41,19 +41,18 @@ parser = TSV::Parser.new TSV.get_stream(file), options.merge(:fields => [])
 
 options[:merge] = false if options[:merge] == "false"
 
-Thread.new do
-  line = parser.first_line
-  bar = Log::ProgressBar.new
-  while line 
-    bar.tick
-
-    line = Misc.fixutf8(line)
-    line = parser.process line
-    raise SKIP_LINE if line.empty?
-    parts = parser.chop_line line
-    key, values = parser.get_values parts
-    values = parser.cast_values values if parser.cast?
-    
-    puts key
-  end
+line = parser.first_line
+bar = Log::ProgressBar.new
+while line 
+  bar.tick
+
+  line = Misc.fixutf8(line)
+  line = parser.process line
+  raise SKIP_LINE if line.empty?
+  parts = parser.chop_line line
+  key, values = parser.get_values parts
+  values = parser.cast_values values if parser.cast?
+
+  puts key
+  line = parser.stream.gets
 end

data/share/rbbt_commands/tsv/read_excel

@@ -22,7 +22,7 @@ Use - to read from STDIN
 -h--help Print this help
 -s--sheet* Sheet to extract
 -skip--skip_rows* Initial rows to skip
-
+-o--original Dump the rows without parsing them into TSV
 EOF
 if options[:help]
   if defined? rbbt_usage
@@ -39,5 +39,5 @@ raise ParameterException, "No excel file given" if excelfile.nil?
 
 options[:zipped] ||= true if options[:merge]
 require 'rbbt/tsv/excel'
-puts TSV.excel(excelfile, options).to_s
+puts TSV.excel(excelfile, options.merge(:text => options[:original]))
 

data/share/rbbt_commands/workflow/task

@@ -104,7 +104,7 @@ def fix_options(workflow, task, job_options)
               elsif input_options[name] and input_options[name][:stream] and value == "-"
                 STDIN
               else
-                if Array === value
+                if Array === value || IO === value
                   value
                 else
                   array_separator = $array_separator
@@ -137,6 +137,8 @@ def fix_options(workflow, task, job_options)
                   TSV.open(STDIN, :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
                 when (Misc.is_filename?(value) and String)
                   TSV.open(value, :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
+                when IO
+                  TSV.open(value, :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
                 else
                   TSV.open(StringIO.new(value), :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
                 end
@@ -571,10 +573,14 @@ when Step
   elsif detach
     exit! 0
   else
-    res.join
-    Open.open(res.path, :mode => 'rb') do |io|
-      Misc.consume_stream(io, false, out)
-    end if Open.exist?(res.path) || Open.remote?(res.path) || Open.ssh?(res.path)
+    if %w(float integer string boolean).include?(res.result_type.to_s)
+      out.puts res.load
+    else
+      res.join
+      Open.open(res.path, :mode => 'rb') do |io|
+        Misc.consume_stream(io, false, out)
+      end if Open.exist?(res.path) || Open.remote?(res.path) || Open.ssh?(res.path)
+    end
   end
 else
   if Array === res